From 94d293f719ee66a4c45cb8d01c69fc62f4456eb7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 10 Oct 2023 22:54:25 +0000
Subject: [PATCH 01/40] Bump mypy from 1.5.1 to 1.6.0

Bumps [mypy](https://github.com/python/mypy) from 1.5.1 to 1.6.0.
- [Commits](https://github.com/python/mypy/compare/v1.5.1...v1.6.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 70 ++++++++++++++++++++++++++++----------------------
 pyproject.toml |  2 +-
 2 files changed, 41 insertions(+), 31 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 370225b..cfa833a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -568,38 +568,38 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.5.1"
+version = "1.6.0"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.8"
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@@ -1245,4 +1255,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "519657b6949e12e6030c9818a2e94e9eac44d072a4f831777cd405b769a2d97d"
+content-hash = "bb12b5bf5b358442c6866c9b1a283d24edc9df645e973796b697e7cb027febc4"
diff --git a/pyproject.toml b/pyproject.toml
index b85d905..05458f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ harmony-service-lib = "^1.0.23"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"
-mypy = "^1.4.1"
+mypy = "^1.6.0"
 black = "^23.9.1"
 ruff = "^0.0.292"
 coverage = "^7.3.2"

From 46ede987bc003e264ffe2a269fcbb9224d8f0604 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Oct 2023 22:42:21 +0000
Subject: [PATCH 02/40] Bump dask from 2023.9.3 to 2023.10.0

Bumps [dask](https://github.com/dask/dask) from 2023.9.3 to 2023.10.0.
- [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md)
- [Commits](https://github.com/dask/dask/compare/2023.9.3...2023.10.0)

---
updated-dependencies:
- dependency-name: dask
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 10 +++++-----
 pyproject.toml |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index cfa833a..a54c81c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -393,13 +393,13 @@ toml = ["tomli"]
 
 [[package]]
 name = "dask"
-version = "2023.9.3"
+version = "2023.10.0"
 description = "Parallel PyData with Task Scheduling"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "dask-2023.9.3-py3-none-any.whl", hash = "sha256:2e6c5de0dfce114ca9c0bb2b79d72d3a9e1499bf25cfef477659179614df5692"},
-    {file = "dask-2023.9.3.tar.gz", hash = "sha256:712090788a7822d538cf8f43f5afc887eebe7471bc46cc331424e1cfa248764c"},
+    {file = "dask-2023.10.0-py3-none-any.whl", hash = "sha256:cb133919ff6f1fc021efe1eef24df0e4acecf33a7708e7b04d2dea6b45e166bb"},
+    {file = "dask-2023.10.0.tar.gz", hash = "sha256:3fdfdbdb5f9f3a556487bf37142e5a730dab2f2c8eca0b6c79d11199c30220e3"},
 ]
 
 [package.dependencies]
@@ -417,7 +417,7 @@ array = ["numpy (>=1.21)"]
 complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)"]
 dataframe = ["dask[array]", "pandas (>=1.3)"]
 diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2023.9.3)"]
+distributed = ["distributed (==2023.10.0)"]
 test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
 
 [[package]]
@@ -1255,4 +1255,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "bb12b5bf5b358442c6866c9b1a283d24edc9df645e973796b697e7cb027febc4"
+content-hash = "e97b028839a88e7f8a6925f8af4c0e83e54163873f33ea6ad2ff31af1daf7ea1"
diff --git a/pyproject.toml b/pyproject.toml
index 05458f8..734982c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ packages = [
 python = "^3.10"
 netcdf4 = "^1.6.4"
 xarray = "^2023.9.0"
-dask = "^2023.9.3"
+dask = "^2023.10.0"
 harmony-service-lib = "^1.0.23"
 
 [tool.poetry.group.dev.dependencies]

From 61fdc643d7f90c9299ccb2099dcc03ccabfbb02a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 18 Oct 2023 01:25:37 +0000
Subject: [PATCH 03/40] Bump urllib3 from 1.26.17 to 1.26.18

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.17 to 1.26.18.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/1.26.17...1.26.18)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 370225b..239925b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -1032,6 +1032,7 @@ files = [
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     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"},
+    {file = "PyYAML-6.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290"},
     {file = "PyYAML-6.0.1-cp310-cp310-win32.whl", hash = "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924"},
     {file = "PyYAML-6.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d"},
     {file = "PyYAML-6.0.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007"},
@@ -1039,8 +1040,15 @@ files = [
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     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673"},
+    {file = "PyYAML-6.0.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b"},
     {file = "PyYAML-6.0.1-cp311-cp311-win32.whl", hash = "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741"},
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"},
+    {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"},
+    {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df"},
     {file = "PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
@@ -1057,6 +1065,7 @@ files = [
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
+    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
     {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
     {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
     {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -1064,6 +1073,7 @@ files = [
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
     {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
     {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -1190,13 +1200,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.17"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"},
-    {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"},
+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
 ]
 
 [package.extras]

From 10ea2fffb7d44b32e50834603cb025889cee2b00 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 24 Oct 2023 16:14:47 +0000
Subject: [PATCH 04/40] Bump mypy from 1.6.0 to 1.6.1

Bumps [mypy](https://github.com/python/mypy) from 1.6.0 to 1.6.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.6.0...v1.6.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 58 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 2d3bdfa..5154a75 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -568,38 +568,38 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.6.0"
+version = "1.6.1"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mypy-1.6.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:091f53ff88cb093dcc33c29eee522c087a438df65eb92acd371161c1f4380ff0"},
-    {file = "mypy-1.6.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:eb7ff4007865833c470a601498ba30462b7374342580e2346bf7884557e40531"},
-    {file = "mypy-1.6.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:49499cf1e464f533fc45be54d20a6351a312f96ae7892d8e9f1708140e27ce41"},
-    {file = "mypy-1.6.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:4c192445899c69f07874dabda7e931b0cc811ea055bf82c1ababf358b9b2a72c"},
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-    {file = "mypy-1.6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:856bad61ebc7d21dbc019b719e98303dc6256cec6dcc9ebb0b214b81d6901bd8"},
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-    {file = "mypy-1.6.0-cp39-cp39-win_amd64.whl", hash = "sha256:c69051274762cccd13498b568ed2430f8d22baa4b179911ad0c1577d336ed849"},
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+    {file = "mypy-1.6.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:21a1ad938fee7d2d96ca666c77b7c494c3c5bd88dff792220e1afbebb2925b5e"},
+    {file = "mypy-1.6.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:b96ae2c1279d1065413965c607712006205a9ac541895004a1e0d4f281f2ff9f"},
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+    {file = "mypy-1.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a8032e00ce71c3ceb93eeba63963b864bf635a18f6c0c12da6c13c450eedb183"},
+    {file = "mypy-1.6.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:4c46b51de523817a0045b150ed11b56f9fff55f12b9edd0f3ed35b15a2809de0"},
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+    {file = "mypy-1.6.1-cp312-cp312-win_amd64.whl", hash = "sha256:eb4f18589d196a4cbe5290b435d135dee96567e07c2b2d43b5c4621b6501531a"},
+    {file = "mypy-1.6.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:41697773aa0bf53ff917aa077e2cde7aa50254f28750f9b88884acea38a16169"},
+    {file = "mypy-1.6.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:7274b0c57737bd3476d2229c6389b2ec9eefeb090bbaf77777e9d6b1b5a9d143"},
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+    {file = "mypy-1.6.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:bb8ccb4724f7d8601938571bf3f24da0da791fe2db7be3d9e79849cb64e0ae85"},
+    {file = "mypy-1.6.1-cp38-cp38-win_amd64.whl", hash = "sha256:68351911e85145f582b5aa6cd9ad666c8958bcae897a1bfda8f4940472463c45"},
+    {file = "mypy-1.6.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:49ae115da099dcc0922a7a895c1eec82c1518109ea5c162ed50e3b3594c71208"},
+    {file = "mypy-1.6.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:8b27958f8c76bed8edaa63da0739d76e4e9ad4ed325c814f9b3851425582a3cd"},
+    {file = "mypy-1.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:925cd6a3b7b55dfba252b7c4561892311c5358c6b5a601847015a1ad4eb7d332"},
+    {file = "mypy-1.6.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:8f57e6b6927a49550da3d122f0cb983d400f843a8a82e65b3b380d3d7259468f"},
+    {file = "mypy-1.6.1-cp39-cp39-win_amd64.whl", hash = "sha256:a43ef1c8ddfdb9575691720b6352761f3f53d85f1b57d7745701041053deff30"},
+    {file = "mypy-1.6.1-py3-none-any.whl", hash = "sha256:4cbe68ef919c28ea561165206a2dcb68591c50f3bcf777932323bc208d949cf1"},
+    {file = "mypy-1.6.1.tar.gz", hash = "sha256:4d01c00d09a0be62a4ca3f933e315455bde83f37f892ba4b08ce92f3cf44bcc1"},
 ]
 
 [package.dependencies]
@@ -1255,4 +1255,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "e97b028839a88e7f8a6925f8af4c0e83e54163873f33ea6ad2ff31af1daf7ea1"
+content-hash = "01bcd79c242190051fcd6b794a1c6e189326d884b407048a1a258db05c3386dd"
diff --git a/pyproject.toml b/pyproject.toml
index 734982c..a420dc7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ harmony-service-lib = "^1.0.23"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"
-mypy = "^1.6.0"
+mypy = "^1.6.1"
 black = "^23.9.1"
 ruff = "^0.0.292"
 coverage = "^7.3.2"

From 7ef9537b6f9494043774f25cb1fc7c40551d35db Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 24 Oct 2023 16:33:26 +0000
Subject: [PATCH 05/40] Bump black from 23.9.1 to 23.10.1

Bumps [black](https://github.com/psf/black) from 23.9.1 to 23.10.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.9.1...23.10.1)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 44 ++++++++++++++++++++------------------------
 pyproject.toml |  2 +-
 2 files changed, 21 insertions(+), 25 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 5154a75..10ed551 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,33 +2,29 @@
 
 [[package]]
 name = "black"
-version = "23.9.1"
+version = "23.10.1"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "black-23.9.1-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:13ef033794029b85dfea8032c9d3b92b42b526f1ff4bf13b2182ce4e917f5100"},
-    {file = "black-23.9.1-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:75a2dc41b183d4872d3a500d2b9c9016e67ed95738a3624f4751a0cb4818fe71"},
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-    {file = "black-23.9.1-cp38-cp38-macosx_10_16_universal2.whl", hash = "sha256:a732b82747235e0542c03bf352c126052c0fbc458d8a239a94701175b17d4855"},
-    {file = "black-23.9.1-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:cf3a4d00e4cdb6734b64bf23cd4341421e8953615cba6b3670453737a72ec204"},
-    {file = "black-23.9.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cf99f3de8b3273a8317681d8194ea222f10e0133a24a7548c73ce44ea1679377"},
-    {file = "black-23.9.1-cp38-cp38-win_amd64.whl", hash = "sha256:14f04c990259576acd093871e7e9b14918eb28f1866f91968ff5524293f9c573"},
-    {file = "black-23.9.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:c619f063c2d68f19b2d7270f4cf3192cb81c9ec5bc5ba02df91471d0b88c4c5c"},
-    {file = "black-23.9.1-cp39-cp39-macosx_10_16_universal2.whl", hash = "sha256:6a3b50e4b93f43b34a9d3ef00d9b6728b4a722c997c99ab09102fd5efdb88325"},
-    {file = "black-23.9.1-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:c46767e8df1b7beefb0899c4a95fb43058fa8500b6db144f4ff3ca38eb2f6393"},
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-    {file = "black-23.9.1-cp39-cp39-win_amd64.whl", hash = "sha256:403397c033adbc45c2bd41747da1f7fc7eaa44efbee256b53842470d4ac5a70f"},
-    {file = "black-23.9.1-py3-none-any.whl", hash = "sha256:6ccd59584cc834b6d127628713e4b6b968e5f79572da66284532525a042549f9"},
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+    {file = "black-23.10.1-cp311-cp311-macosx_10_16_x86_64.whl", hash = "sha256:e293e4c2f4a992b980032bbd62df07c1bcff82d6964d6c9496f2cd726e246ace"},
+    {file = "black-23.10.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7d56124b7a61d092cb52cce34182a5280e160e6aff3137172a68c2c2c4b76bcb"},
+    {file = "black-23.10.1-cp311-cp311-win_amd64.whl", hash = "sha256:3f157a8945a7b2d424da3335f7ace89c14a3b0625e6593d21139c2d8214d55ce"},
+    {file = "black-23.10.1-cp38-cp38-macosx_10_16_arm64.whl", hash = "sha256:cfcce6f0a384d0da692119f2d72d79ed07c7159879d0bb1bb32d2e443382bf3a"},
+    {file = "black-23.10.1-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:33d40f5b06be80c1bbce17b173cda17994fbad096ce60eb22054da021bf933d1"},
+    {file = "black-23.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:840015166dbdfbc47992871325799fd2dc0dcf9395e401ada6d88fe11498abad"},
+    {file = "black-23.10.1-cp38-cp38-win_amd64.whl", hash = "sha256:037e9b4664cafda5f025a1728c50a9e9aedb99a759c89f760bd83730e76ba884"},
+    {file = "black-23.10.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:7cb5936e686e782fddb1c73f8aa6f459e1ad38a6a7b0e54b403f1f05a1507ee9"},
+    {file = "black-23.10.1-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:7670242e90dc129c539e9ca17665e39a146a761e681805c54fbd86015c7c84f7"},
+    {file = "black-23.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ed45ac9a613fb52dad3b61c8dea2ec9510bf3108d4db88422bacc7d1ba1243d"},
+    {file = "black-23.10.1-cp39-cp39-win_amd64.whl", hash = "sha256:6d23d7822140e3fef190734216cefb262521789367fbdc0b3f22af6744058982"},
+    {file = "black-23.10.1-py3-none-any.whl", hash = "sha256:d431e6739f727bb2e0495df64a6c7a5310758e87505f5f8cde9ff6c0f2d7e4fe"},
+    {file = "black-23.10.1.tar.gz", hash = "sha256:1f8ce316753428ff68749c65a5f7844631aa18c8679dfd3ca9dc1a289979c258"},
 ]
 
 [package.dependencies]
@@ -1255,4 +1251,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "01bcd79c242190051fcd6b794a1c6e189326d884b407048a1a258db05c3386dd"
+content-hash = "e793c7ff39732a92f9cf2a091227db589262e63550c52d85228571cfd9c7837e"
diff --git a/pyproject.toml b/pyproject.toml
index a420dc7..d8f1b69 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ harmony-service-lib = "^1.0.23"
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"
 mypy = "^1.6.1"
-black = "^23.9.1"
+black = "^23.10.1"
 ruff = "^0.0.292"
 coverage = "^7.3.2"
 

From 78924e75f17f822774204eda9b80aa3257a520de Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 26 Oct 2023 20:30:53 +0000
Subject: [PATCH 06/40] Bump urllib3 from 1.26.17 to 1.26.18

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.17 to 1.26.18.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/1.26.17...1.26.18)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 370225b..239925b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -1032,6 +1032,7 @@ files = [
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"},
+    {file = "PyYAML-6.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290"},
     {file = "PyYAML-6.0.1-cp310-cp310-win32.whl", hash = "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924"},
     {file = "PyYAML-6.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d"},
     {file = "PyYAML-6.0.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007"},
@@ -1039,8 +1040,15 @@ files = [
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673"},
+    {file = "PyYAML-6.0.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b"},
     {file = "PyYAML-6.0.1-cp311-cp311-win32.whl", hash = "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741"},
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"},
+    {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"},
+    {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df"},
     {file = "PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
@@ -1057,6 +1065,7 @@ files = [
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
+    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
     {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
     {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
     {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -1064,6 +1073,7 @@ files = [
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
     {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
     {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -1190,13 +1200,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.17"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"},
-    {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"},
+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
 ]
 
 [package.extras]

From 642b4679146c9f16f9a598692cc880be833457f2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Oct 2023 13:58:38 +0000
Subject: [PATCH 07/40] Bump ruff from 0.0.292 to 0.1.3

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.0.292 to 0.1.3.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/v0.0.292...v0.1.3)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 38 +++++++++++++++++++-------------------
 pyproject.toml |  2 +-
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 10ed551..b40be10 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1098,28 +1098,28 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "ruff"
-version = "0.0.292"
+version = "0.1.3"
 description = "An extremely fast Python linter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ruff-0.0.292-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:02f29db018c9d474270c704e6c6b13b18ed0ecac82761e4fcf0faa3728430c96"},
-    {file = "ruff-0.0.292-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:69654e564342f507edfa09ee6897883ca76e331d4bbc3676d8a8403838e9fade"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6c3c91859a9b845c33778f11902e7b26440d64b9d5110edd4e4fa1726c41e0a4"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:f4476f1243af2d8c29da5f235c13dca52177117935e1f9393f9d90f9833f69e4"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:be8eb50eaf8648070b8e58ece8e69c9322d34afe367eec4210fdee9a555e4ca7"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:9889bac18a0c07018aac75ef6c1e6511d8411724d67cb879103b01758e110a81"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:6bdfabd4334684a4418b99b3118793f2c13bb67bf1540a769d7816410402a205"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:aa7c77c53bfcd75dbcd4d1f42d6cabf2485d2e1ee0678da850f08e1ab13081a8"},
-    {file = "ruff-0.0.292-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8e087b24d0d849c5c81516ec740bf4fd48bf363cfb104545464e0fca749b6af9"},
-    {file = "ruff-0.0.292-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:f160b5ec26be32362d0774964e218f3fcf0a7da299f7e220ef45ae9e3e67101a"},
-    {file = "ruff-0.0.292-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:ac153eee6dd4444501c4bb92bff866491d4bfb01ce26dd2fff7ca472c8df9ad0"},
-    {file = "ruff-0.0.292-py3-none-musllinux_1_2_i686.whl", hash = "sha256:87616771e72820800b8faea82edd858324b29bb99a920d6aa3d3949dd3f88fb0"},
-    {file = "ruff-0.0.292-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:b76deb3bdbea2ef97db286cf953488745dd6424c122d275f05836c53f62d4016"},
-    {file = "ruff-0.0.292-py3-none-win32.whl", hash = "sha256:e854b05408f7a8033a027e4b1c7f9889563dd2aca545d13d06711e5c39c3d003"},
-    {file = "ruff-0.0.292-py3-none-win_amd64.whl", hash = "sha256:f27282bedfd04d4c3492e5c3398360c9d86a295be00eccc63914438b4ac8a83c"},
-    {file = "ruff-0.0.292-py3-none-win_arm64.whl", hash = "sha256:7f67a69c8f12fbc8daf6ae6d36705037bde315abf8b82b6e1f4c9e74eb750f68"},
-    {file = "ruff-0.0.292.tar.gz", hash = "sha256:1093449e37dd1e9b813798f6ad70932b57cf614e5c2b5c51005bf67d55db33ac"},
+    {file = "ruff-0.1.3-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:b46d43d51f7061652eeadb426a9e3caa1e0002470229ab2fc19de8a7b0766901"},
+    {file = "ruff-0.1.3-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:b8afeb9abd26b4029c72adc9921b8363374f4e7edb78385ffaa80278313a15f9"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ca3cf365bf32e9ba7e6db3f48a4d3e2c446cd19ebee04f05338bc3910114528b"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:4874c165f96c14a00590dcc727a04dca0cfd110334c24b039458c06cf78a672e"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:eec2dd31eed114e48ea42dbffc443e9b7221976554a504767ceaee3dd38edeb8"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:dc3ec4edb3b73f21b4aa51337e16674c752f1d76a4a543af56d7d04e97769613"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:2e3de9ed2e39160800281848ff4670e1698037ca039bda7b9274f849258d26ce"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:1c595193881922cc0556a90f3af99b1c5681f0c552e7a2a189956141d8666fe8"},
+    {file = "ruff-0.1.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0f75e670d529aa2288cd00fc0e9b9287603d95e1536d7a7e0cafe00f75e0dd9d"},
+    {file = "ruff-0.1.3-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:76dd49f6cd945d82d9d4a9a6622c54a994689d8d7b22fa1322983389b4892e20"},
+    {file = "ruff-0.1.3-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:918b454bc4f8874a616f0d725590277c42949431ceb303950e87fef7a7d94cb3"},
+    {file = "ruff-0.1.3-py3-none-musllinux_1_2_i686.whl", hash = "sha256:d8859605e729cd5e53aa38275568dbbdb4fe882d2ea2714c5453b678dca83784"},
+    {file = "ruff-0.1.3-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:0b6c55f5ef8d9dd05b230bb6ab80bc4381ecb60ae56db0330f660ea240cb0d4a"},
+    {file = "ruff-0.1.3-py3-none-win32.whl", hash = "sha256:3e7afcbdcfbe3399c34e0f6370c30f6e529193c731b885316c5a09c9e4317eef"},
+    {file = "ruff-0.1.3-py3-none-win_amd64.whl", hash = "sha256:7a18df6638cec4a5bd75350639b2bb2a2366e01222825562c7346674bdceb7ea"},
+    {file = "ruff-0.1.3-py3-none-win_arm64.whl", hash = "sha256:12fd53696c83a194a2db7f9a46337ce06445fb9aa7d25ea6f293cf75b21aca9f"},
+    {file = "ruff-0.1.3.tar.gz", hash = "sha256:3ba6145369a151401d5db79f0a47d50e470384d0d89d0d6f7fab0b589ad07c34"},
 ]
 
 [[package]]
@@ -1251,4 +1251,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "e793c7ff39732a92f9cf2a091227db589262e63550c52d85228571cfd9c7837e"
+content-hash = "0aeffc9e8bbf891cb8c488eb712db47b7a98b0e4ea782ce58020ff04fadae19e"
diff --git a/pyproject.toml b/pyproject.toml
index d8f1b69..134977b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,7 @@ harmony-service-lib = "^1.0.23"
 pytest = "^7.3.1"
 mypy = "^1.6.1"
 black = "^23.10.1"
-ruff = "^0.0.292"
+ruff = "^0.1.3"
 coverage = "^7.3.2"
 
 [tool.poetry.group.extras.dependencies]

From b098c20d0abc690bc9d19d736357ac705d809f52 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Oct 2023 14:03:02 +0000
Subject: [PATCH 08/40] Bump xarray from 2023.9.0 to 2023.10.1

Bumps [xarray](https://github.com/pydata/xarray) from 2023.9.0 to 2023.10.1.
- [Release notes](https://github.com/pydata/xarray/releases)
- [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md)
- [Commits](https://github.com/pydata/xarray/compare/v2023.09.0...v2023.10.1)

---
updated-dependencies:
- dependency-name: xarray
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 10 +++++-----
 pyproject.toml |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index b40be10..f51dda4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1212,17 +1212,17 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "xarray"
-version = "2023.9.0"
+version = "2023.10.1"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "xarray-2023.9.0-py3-none-any.whl", hash = "sha256:3fc4a558bd70968040a4e1cefc6ddb3f9a7a86ef6a48e67857156ffe655d3a66"},
-    {file = "xarray-2023.9.0.tar.gz", hash = "sha256:271955c05dc626dad37791a7807d920aaf9c64cac71d03b45ec7e402cc646603"},
+    {file = "xarray-2023.10.1-py3-none-any.whl", hash = "sha256:71ea549e9be6dfeab19c2736acf659967b861aad2397691a80e5fad0c61db2ad"},
+    {file = "xarray-2023.10.1.tar.gz", hash = "sha256:9eeee170c3fc2f3321eb6ba40c17ffe4d8c98d49d55e4a3fba66a75bdc7dd9e5"},
 ]
 
 [package.dependencies]
-numpy = ">=1.21"
+numpy = ">=1.22"
 packaging = ">=21.3"
 pandas = ">=1.4"
 
@@ -1251,4 +1251,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "0aeffc9e8bbf891cb8c488eb712db47b7a98b0e4ea782ce58020ff04fadae19e"
+content-hash = "6ed35a9d889e824c89055341c74d784f61bcf7883f58762820fa00d3bb1692e8"
diff --git a/pyproject.toml b/pyproject.toml
index 134977b..20fb12e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,7 +14,7 @@ packages = [
 [tool.poetry.dependencies]
 python = "^3.10"
 netcdf4 = "^1.6.4"
-xarray = "^2023.9.0"
+xarray = "^2023.10.1"
 dask = "^2023.10.0"
 harmony-service-lib = "^1.0.23"
 

From ac629ccfd30d0d00cf20ef64ab99dc695b31237b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Oct 2023 14:05:08 +0000
Subject: [PATCH 09/40] Bump pytest from 7.4.2 to 7.4.3

Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.2 to 7.4.3.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.4.2...7.4.3)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 8 ++++----
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f51dda4..345f299 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -960,13 +960,13 @@ validation = ["jsonschema (==3.2.0)"]
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
-    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
+    {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
+    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
 ]
 
 [package.dependencies]
@@ -1251,4 +1251,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "6ed35a9d889e824c89055341c74d784f61bcf7883f58762820fa00d3bb1692e8"
+content-hash = "fae5fd0bf0df0dedad5db17728cdd7c091d902a2b4a4f5ad306d408e8fb3e65d"
diff --git a/pyproject.toml b/pyproject.toml
index 20fb12e..d5c1ffb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ dask = "^2023.10.0"
 harmony-service-lib = "^1.0.23"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.3.1"
+pytest = "^7.4.3"
 mypy = "^1.6.1"
 black = "^23.10.1"
 ruff = "^0.1.3"

From f85afe3d5712794f6432474d38dda08ba0ce2c84 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 27 Oct 2023 10:06:29 -0400
Subject: [PATCH 10/40] update dependabot.yml schedules to weekly

---
 .github/dependabot.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 5a488df..c2c98d6 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -3,15 +3,12 @@ updates:
   - package-ecosystem: pip
     directory: "/"
     schedule:
-      interval: daily
+      interval: "weekly"
     # Raise pull requests for version updates
     # to pip against the `develop` branch
     target-branch: "develop"
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      # Check for updates to GitHub Actions every weekday
-      interval: "daily"
-    # Raise pull requests for version updates
-    # to pip against the `develop` branch
+      interval: "weekly"
     target-branch: "develop"

From 6a10ecd97c20db252f177c483cfc157b6739afd7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Oct 2023 14:09:03 +0000
Subject: [PATCH 11/40] Bump netcdf4 from 1.6.4 to 1.6.5

Bumps [netcdf4](https://github.com/Unidata/netcdf4-python) from 1.6.4 to 1.6.5.
- [Release notes](https://github.com/Unidata/netcdf4-python/releases)
- [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog)
- [Commits](https://github.com/Unidata/netcdf4-python/commits)

---
updated-dependencies:
- dependency-name: netcdf4
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 61 ++++++++++++++++++++++++++------------------------
 pyproject.toml |  2 +-
 2 files changed, 33 insertions(+), 30 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 345f299..4bcc661 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -636,38 +636,38 @@ packaging = "*"
 
 [[package]]
 name = "netcdf4"
-version = "1.6.4"
+version = "1.6.5"
 description = "Provides an object-oriented python interface to the netCDF version 4 library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "netCDF4-1.6.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:59eba11eac34f9c7bd209121b26954c71ff69a2eb2838d2ac339b39ea60a95c0"},
-    {file = "netCDF4-1.6.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:541286ce7318033b326da2e4325f08037b561887d5fd25d12c2b0cad74eb1edc"},
-    {file = "netCDF4-1.6.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6620f7962daff02df2fbcbc8f7af53edf21512bc7f5697d846d424a094f96345"},
-    {file = "netCDF4-1.6.4-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:2dcf74f7b15ae6105c09df93af22ad61366a288fbb329fdbe3b9606c56c788f5"},
-    {file = "netCDF4-1.6.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b368fc185cac7d8890a8cf1016488cd252a144008144d06a615925b09bf8d67e"},
-    {file = "netCDF4-1.6.4-cp310-cp310-win_amd64.whl", hash = "sha256:eb19c51fa090b562be4f87ff736b629ffafc03d7bf1fa10f623f957d49417b4f"},
-    {file = "netCDF4-1.6.4-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:08a7efab50d5a4da6227244e544a74f676b732ccdff2b8a4678174c15a3f8dff"},
-    {file = "netCDF4-1.6.4-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:f9b7ad3f66d50970fa1bd5509c52bb8a99740c8a79fafa83bfd0bc7348b6ab5a"},
-    {file = "netCDF4-1.6.4-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:2c5cad50d4e6e5a3b35c76862c58393ddf93baa44de98b6e040ac21896145881"},
-    {file = "netCDF4-1.6.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1c2395c53a37717b1047650e1c9de68a3d69542bb25df5c594e1e14e9480bb18"},
-    {file = "netCDF4-1.6.4-cp311-cp311-win_amd64.whl", hash = "sha256:c85f77599c61a88d512d6536e181ff1c01fd16f4740367e4f8e5cacb36500293"},
-    {file = "netCDF4-1.6.4-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:3e3efefdb9fc936503e89ff5b40b33f2c96527bae1e9672a2d369c5f7cb30bbd"},
-    {file = "netCDF4-1.6.4-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:74a3e720a9764d13d669763c1f3c73f3f719ef181dccecad062440eea03f069e"},
-    {file = "netCDF4-1.6.4-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c67bc7fafced3f9370fdef6ce7abe235a771bed7ebe534f4ba3c84d9689dae23"},
-    {file = "netCDF4-1.6.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b599a3b5c0d0e3affa70d7954c2b0c4ab7d7bdb52b0e413c811da9725982de33"},
-    {file = "netCDF4-1.6.4-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:b21d47c23edd02ff83160c8ccc1e4d4946a91d454b246e7f63d7a6d63901707c"},
-    {file = "netCDF4-1.6.4-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:8eff69acdf250ebaf817cc9bbfb457d241f92f989c7f9cca33eb29985c0f9797"},
-    {file = "netCDF4-1.6.4-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4d6bcdf27fd611eaec891f4281caf5c56bbad6f5fc245ce3e6dd2dc4fc3fad56"},
-    {file = "netCDF4-1.6.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c99a3d476242d489da26f71e318ddd314723ca766f4db11270863a764b107bc3"},
-    {file = "netCDF4-1.6.4-cp38-cp38-win_amd64.whl", hash = "sha256:422077c7303cb17cbe8b9ace965cafda1f9d4c9b035809fc5c87091e7ff4d606"},
-    {file = "netCDF4-1.6.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:0050e49889c357ae0a73f96e2b9988f250396689b78142de88a39ac8b1e702aa"},
-    {file = "netCDF4-1.6.4-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:0a2cd2e2a9da98f1838e1edfeb011b840a434e04d156052b936ffe49f5298126"},
-    {file = "netCDF4-1.6.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:695cd0a40df49b4218350686c44e13b3a4671e53ee33faf7439a89940cbccc68"},
-    {file = "netCDF4-1.6.4-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e582e6e41b27fc3a3296239afe065941bda60118d585df0ad41603f6f962888e"},
-    {file = "netCDF4-1.6.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f7b4ab3f0cd28a6685031e8b9be00c3047b4256da576c9de540440d013a31cea"},
-    {file = "netCDF4-1.6.4-cp39-cp39-win_amd64.whl", hash = "sha256:1a950b3d8fcffca05e371a4cb64dc76580375588d1fca43b788192f409108ebe"},
-    {file = "netCDF4-1.6.4.tar.gz", hash = "sha256:66da6542cbc7a6045cd1d979397dfd5a3f6c880c76d52b8f98bb108c82ee8c6e"},
+    {file = "netCDF4-1.6.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d23b97cbde2bf413fadc4697c5c255a0436511c02f811e127e0fb12f5b882a4c"},
+    {file = "netCDF4-1.6.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9e5edfed673005f47f8d2fbea9c72c382b085dd358ac3c20ca743a563ed7b90e"},
+    {file = "netCDF4-1.6.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:10d2ac9ae1308ca837d86c6dc304ec455a85bdba0f2175e222844a54589168dc"},
+    {file = "netCDF4-1.6.5-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9a63a2be2f80977ac23bb0aa736c565011fd4639097ce0922e01b0dc38015df2"},
+    {file = "netCDF4-1.6.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3aaceea2097d292bad398d9f9b4fe403efa7b1568fcfa6faba9b67b1630027f9"},
+    {file = "netCDF4-1.6.5-cp310-cp310-win_amd64.whl", hash = "sha256:111357d9e12eb79e8d58bfd91bc6b230d35b17a0ebd8c546d17416e8ceebea49"},
+    {file = "netCDF4-1.6.5-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:1c5fede0b34c0a02a1b9e84116bfb3fcd2f80124a651d4836e72b785d10e2f15"},
+    {file = "netCDF4-1.6.5-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:3de5512b9270aa6472e4f3aa2bf895a7364c1d4f8667ce3b82e8232197d4fec8"},
+    {file = "netCDF4-1.6.5-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b20971a164431f6eca1d24df8aa153db15c2c1b9630e83ccc5cf004e8ac8151d"},
+    {file = "netCDF4-1.6.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ad1101d538077152b866782e44458356981526bf2ea9cc07930bf28b589c82a7"},
+    {file = "netCDF4-1.6.5-cp311-cp311-win_amd64.whl", hash = "sha256:de4dc973fae9e2bbdf42e094125e423a4c25393172a61958314969b055a38889"},
+    {file = "netCDF4-1.6.5-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:19e16c63cdd7c0dbffe284a4a65f226ba1026f476f35cbedd099b4792b395f69"},
+    {file = "netCDF4-1.6.5-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:b994afce2ca4073f6b757385a6c0ffec25ecaae2b8821535b303c7cdbf6de42b"},
+    {file = "netCDF4-1.6.5-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0187646e3348e7a8cd654617dda65517df138042c94c2fcc6682ff7c8c6654dc"},
+    {file = "netCDF4-1.6.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a1ab5dabac27d25fcc82c52dc29a74a6585e865208cce35f4e285df83d3df0b2"},
+    {file = "netCDF4-1.6.5-cp312-cp312-win_amd64.whl", hash = "sha256:081e9043ac6160989f60570928eabe803c88ce7df1d3f79f2345dc48f68ef752"},
+    {file = "netCDF4-1.6.5-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:9b47b22dda5b25ba6291f97634d7ac67b0a843f8ae5c9d9d5813c15364f66d0a"},
+    {file = "netCDF4-1.6.5-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4609dd62d14798c9524327287091875449d68588c128abb768fc0c76c4a28165"},
+    {file = "netCDF4-1.6.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2455e9d35fde067e6a6bdc24aa9d44962235a071cec49904d1589e298c23dcd3"},
+    {file = "netCDF4-1.6.5-cp38-cp38-win_amd64.whl", hash = "sha256:2c210794d96431d92b5992e46ad8a9f97237bf6d6956f8816978a03dc0fa18c3"},
+    {file = "netCDF4-1.6.5-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:18255b8b283d32d3900092f29c67e53aa25bd8f0dfe7adde59fe782d865a381c"},
+    {file = "netCDF4-1.6.5-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:53050562bac84738bbd121fbbee9593d074579f5d6fdaafcb981abeb5c964225"},
+    {file = "netCDF4-1.6.5-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:938c062382406bca9198b16adddd87c09b00521766b138cdfd11c95546eefeb8"},
+    {file = "netCDF4-1.6.5-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4a8300451d7542d3c4ff1dcccf5fb1c7d44bdd1dc08ec77dab04416caf13cb1f"},
+    {file = "netCDF4-1.6.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a27db2701feef31201c9b20b04a9579196edc20dfc339ca423c7b81e462d6e14"},
+    {file = "netCDF4-1.6.5-cp39-cp39-win_amd64.whl", hash = "sha256:574d7742ab321e5f9f33b5b1296c4ad4e5c469152c17d4fc453d5070e413e596"},
+    {file = "netCDF4-1.6.5.tar.gz", hash = "sha256:824881d0aacfde5bd982d6adedd8574259c85553781e7b83e0ce82b890bfa0ef"},
 ]
 
 [package.dependencies]
@@ -675,6 +675,9 @@ certifi = "*"
 cftime = "*"
 numpy = "*"
 
+[package.extras]
+tests = ["Cython", "packaging", "pytest"]
+
 [[package]]
 name = "numpy"
 version = "1.25.2"
@@ -1251,4 +1254,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "fae5fd0bf0df0dedad5db17728cdd7c091d902a2b4a4f5ad306d408e8fb3e65d"
+content-hash = "a471c7db74fd63365bcfd3cd10aee5a06f258fdabcc1c0b5eba27679930c471e"
diff --git a/pyproject.toml b/pyproject.toml
index d5c1ffb..a06d8b0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.10"
-netcdf4 = "^1.6.4"
+netcdf4 = "^1.6.5"
 xarray = "^2023.10.1"
 dask = "^2023.10.0"
 harmony-service-lib = "^1.0.23"

From da4aa0de1a72e85dea96d9d4b00d084f55a106b7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 27 Oct 2023 22:33:54 +0000
Subject: [PATCH 12/40] Bump dask from 2023.10.0 to 2023.10.1

Bumps [dask](https://github.com/dask/dask) from 2023.10.0 to 2023.10.1.
- [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md)
- [Commits](https://github.com/dask/dask/compare/2023.10.0...2023.10.1)

---
updated-dependencies:
- dependency-name: dask
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 10 +++++-----
 pyproject.toml |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 4bcc661..b306a7c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -389,13 +389,13 @@ toml = ["tomli"]
 
 [[package]]
 name = "dask"
-version = "2023.10.0"
+version = "2023.10.1"
 description = "Parallel PyData with Task Scheduling"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "dask-2023.10.0-py3-none-any.whl", hash = "sha256:cb133919ff6f1fc021efe1eef24df0e4acecf33a7708e7b04d2dea6b45e166bb"},
-    {file = "dask-2023.10.0.tar.gz", hash = "sha256:3fdfdbdb5f9f3a556487bf37142e5a730dab2f2c8eca0b6c79d11199c30220e3"},
+    {file = "dask-2023.10.1-py3-none-any.whl", hash = "sha256:1fb0ee4d79e3c7c8f2e7c9f2680fd0ef0668801a10eaa290b970982b26a714da"},
+    {file = "dask-2023.10.1.tar.gz", hash = "sha256:da3ef0526992845408df491fcd0b3a49c7207aa908a1675cea12ab2ea10c7940"},
 ]
 
 [package.dependencies]
@@ -413,7 +413,7 @@ array = ["numpy (>=1.21)"]
 complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)"]
 dataframe = ["dask[array]", "pandas (>=1.3)"]
 diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2023.10.0)"]
+distributed = ["distributed (==2023.10.1)"]
 test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
 
 [[package]]
@@ -1254,4 +1254,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "a471c7db74fd63365bcfd3cd10aee5a06f258fdabcc1c0b5eba27679930c471e"
+content-hash = "ddc5152441a76d77232416c3125f8e9b02e9b727f7a84a246f268f3bef6c6ced"
diff --git a/pyproject.toml b/pyproject.toml
index a06d8b0..46fc7d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ packages = [
 python = "^3.10"
 netcdf4 = "^1.6.5"
 xarray = "^2023.10.1"
-dask = "^2023.10.0"
+dask = "^2023.10.1"
 harmony-service-lib = "^1.0.23"
 
 [tool.poetry.group.dev.dependencies]

From 58b1553573d9d918ca89c601ddf7542862d7c7c5 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 15:17:44 -0400
Subject: [PATCH 13/40] initial commit of Harmony service code (cli, adapter,
 downloader,utils)

---
 concatenator/harmony/__init__.py        |   0
 concatenator/harmony/cli.py             |  33 ++++++
 concatenator/harmony/download_worker.py | 113 +++++++++++++++++++++
 concatenator/harmony/service_adapter.py | 128 ++++++++++++++++++++++++
 concatenator/harmony/util.py            |  98 ++++++++++++++++++
 5 files changed, 372 insertions(+)
 create mode 100644 concatenator/harmony/__init__.py
 create mode 100644 concatenator/harmony/cli.py
 create mode 100644 concatenator/harmony/download_worker.py
 create mode 100644 concatenator/harmony/service_adapter.py
 create mode 100644 concatenator/harmony/util.py

diff --git a/concatenator/harmony/__init__.py b/concatenator/harmony/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/concatenator/harmony/cli.py b/concatenator/harmony/cli.py
new file mode 100644
index 0000000..3329095
--- /dev/null
+++ b/concatenator/harmony/cli.py
@@ -0,0 +1,33 @@
+"""A Harmony CLI wrapper around the concatenate-batcher"""
+from argparse import ArgumentParser
+
+import harmony
+
+from concatenator.harmony.service_adapter import StitcheeAdapter as HarmonyAdapter
+
+
+def main(config: harmony.util.Config = None) -> None:
+    """Parse command line arguments and invoke the service to respond to them.
+
+    Parameters
+    ----------
+    config : harmony.util.Config
+        harmony.util.Config is injectable for tests
+
+    Returns
+    -------
+    None
+    """
+    parser = ArgumentParser(
+        prog="Stitchee", description="Run the STITCH by Extending a dimEnsion service"
+    )
+    harmony.setup_cli(parser)
+    args = parser.parse_args()
+    if harmony.is_harmony_cli(args):
+        harmony.run_cli(parser, args, HarmonyAdapter, cfg=config)
+    else:
+        parser.error("Only --harmony CLIs are supported")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/concatenator/harmony/download_worker.py b/concatenator/harmony/download_worker.py
new file mode 100644
index 0000000..0c177af
--- /dev/null
+++ b/concatenator/harmony/download_worker.py
@@ -0,0 +1,113 @@
+"""A utility for downloading multiple granules simultaneously"""
+
+import queue
+import re
+from copy import deepcopy
+from multiprocessing import Manager, Process
+from os import cpu_count
+from pathlib import Path
+from urllib.parse import urlparse
+
+from harmony.logging import build_logger
+from harmony.util import download
+
+
+def multi_core_download(urls, destination_dir, access_token, cfg, process_count=None):
+    """
+    A method which automagically scales downloads to the number of CPU
+    cores. For further explaination, see documentation on "multi-track
+    drifting"
+
+    Parameters
+    ----------
+    urls : list
+        list of urls to download
+    destination_dir : str
+        output path for downloaded files
+    access_token : str
+        access token as provided in Harmony input
+    cfg : dict
+        Harmony configuration information
+    process_count : int
+        Number of worker processes to run (expected >= 1)
+
+    Returns
+    -------
+    list
+        list of downloaded files as pathlib.Path objects
+    """
+
+    if process_count is None:
+        process_count = cpu_count()
+
+    with Manager() as manager:
+        url_queue = manager.Queue(len(urls))
+        path_list = manager.list()
+
+        for url in urls:
+            url_queue.put(url)
+
+        # Spawn worker processes
+        processes = []
+        for _ in range(process_count):
+            download_process = Process(
+                target=_download_worker,
+                args=(url_queue, path_list, destination_dir, access_token, cfg),
+            )
+            processes.append(download_process)
+            download_process.start()
+
+        # Ensure worker processes exit successfully
+        for process in processes:
+            process.join()
+            if process.exitcode != 0:
+                raise RuntimeError(f"Download failed - exit code: {process.exitcode}")
+
+            process.close()
+
+        path_list = deepcopy(path_list)  # ensure GC can cleanup multiprocessing
+
+    return [Path(path) for path in path_list]
+
+
+def _download_worker(url_queue, path_list, destination_dir, access_token, cfg):
+    """
+    A method to be executed in a separate process which processes the url_queue
+    and places paths to completed downloads into the path_list. Downloads are
+    handled by harmony.util.download
+
+    Parameters
+    ----------
+    url_queue : queue.Queue
+        URLs to process - should be filled from start and only decreases
+    path_list : list
+        paths to completed file downloads
+    destination_dir : str
+        output path for downloaded files
+    access_token : str
+        access token as provided in Harmony input
+    cfg : dict
+        Harmony configuration information
+    """
+
+    logger = build_logger(cfg)
+
+    while not url_queue.empty():
+        try:
+            url = url_queue.get_nowait()
+        except queue.Empty:
+            break
+
+        path = Path(
+            download(url, destination_dir, logger=logger, access_token=access_token, cfg=cfg)
+        )
+        filename_match = re.match(r".*\/(.+\..+)", urlparse(url).path)
+
+        if filename_match is not None:
+            filename = filename_match.group(1)
+            dest_path = path.parent.joinpath(filename)
+            path = path.rename(dest_path)
+        else:
+            logger.warning("Origin filename could not be assertained - %s", url)
+
+        path_list.append(str(path))
diff --git a/concatenator/harmony/service_adapter.py b/concatenator/harmony/service_adapter.py
new file mode 100644
index 0000000..5905229
--- /dev/null
+++ b/concatenator/harmony/service_adapter.py
@@ -0,0 +1,128 @@
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from uuid import uuid4
+
+import pystac
+from harmony.adapter import BaseHarmonyAdapter
+from harmony.util import bbox_to_geometry
+from pystac import Item
+from pystac.item import Asset
+
+from concatenator.harmony.download_worker import multi_core_download
+from concatenator.harmony.util import (
+    _get_netcdf_urls,
+    _get_output_bounding_box,
+    _get_output_date_range,
+)
+from concatenator.stitchee import stitchee
+
+
+class StitcheeAdapter(BaseHarmonyAdapter):
+    """
+    A harmony-service-lib wrapper around the concatenate-batcher module.
+    This wrapper does not support Harmony calls that do not have STAC catalogs
+    as support for this behavior is being depreciated in harmony-service-lib
+    """
+
+    def __init__(self, message, catalog=None, config=None):
+        """
+        Constructs the adapter
+
+        Parameters
+        ----------
+        message : harmony.Message
+            The Harmony input which needs acting upon
+        catalog : pystac.Catalog
+            A STAC catalog containing the files on which to act
+        config : harmony.util.Config
+            The configuration values for this runtime environment.
+        """
+        super().__init__(message, catalog=catalog, config=config)
+
+    def invoke(self):
+        """
+        Primary entrypoint into the service wrapper. Overrides BaseHarmonyAdapter.invoke
+        """
+        if not self.catalog:
+            # Message-only support is being depreciated in Harmony, so we should expect to
+            # only see requests with catalogs when invoked with a newer Harmony instance
+            # https://github.com/nasa/harmony-service-lib-py/blob/21bcfbda17caf626fb14d2ac4f8673be9726b549/harmony/adapter.py#L71
+            raise RuntimeError("Invoking Batchee without a STAC catalog is not supported")
+
+        return self.message, self.process_catalog(self.catalog)
+
+    def process_catalog(self, catalog: pystac.Catalog):
+        """Converts a list of STAC catalogs into a list of lists of STAC catalogs."""
+        self.logger.info("process_catalog() started.")
+        try:
+            result = catalog.clone()
+            result.id = str(uuid4())
+            result.clear_children()
+
+            # Get all the items from the catalog, including from child or linked catalogs
+            items = list(self.get_all_catalog_items(catalog))
+
+            self.logger.info(f"length of items==={len(items)}.")
+
+            # Quick return if catalog contains no items
+            if len(items) == 0:
+                return result
+
+            # # --- Get granule filepaths (urls) ---
+            netcdf_urls: list[str] = _get_netcdf_urls(items)
+            self.logger.info(f"netcdf_urls==={netcdf_urls}.")
+
+            # -- Process metadata --
+            bounding_box: list | None = _get_output_bounding_box(items)
+            datetimes = _get_output_date_range(items)
+
+            # Items did not have a bbox; valid under spec
+            if bounding_box and len(bounding_box) == 0:
+                bounding_box = None
+
+            # -- Perform merging --
+            collection = self._get_item_source(items[0]).collection
+            filename = f"{collection}_merged.nc4"
+
+            with TemporaryDirectory() as temp_dir:
+                self.logger.info("Starting granule downloads")
+                input_files = multi_core_download(
+                    netcdf_urls, temp_dir, self.message.accessToken, self.config
+                )
+                self.logger.info("Finished granule downloads")
+
+                output_path = str(Path(temp_dir).joinpath(filename).resolve())
+
+                # # --- Run STITCHEE ---
+                stitchee(
+                    input_files,
+                    output_path,
+                    write_tmp_flat_concatenated=False,
+                    keep_tmp_files=False,
+                    concat_dim="mirror_step",  # This is currently set only for TEMPO
+                    logger=self.logger,
+                )
+                staged_url = self._stage(output_path, filename, "application/x-netcdf4")
+
+            # -- Output to STAC catalog --
+            result.clear_items()
+            properties = dict(
+                start_datetime=datetimes["start_datetime"], end_datetime=datetimes["end_datetime"]
+            )
+
+            item = Item(
+                str(uuid4()), bbox_to_geometry(bounding_box), bounding_box, None, properties
+            )
+            asset = Asset(
+                staged_url, title=filename, media_type="application/x-netcdf4", roles=["data"]
+            )
+            item.add_asset("data", asset)
+            result.add_item(item)
+
+            self.logger.info("STAC catalog creation complete.")
+
+            return result
+
+        except Exception as service_exception:
+            self.logger.error(service_exception, exc_info=1)
+            raise service_exception
diff --git a/concatenator/harmony/util.py b/concatenator/harmony/util.py
new file mode 100644
index 0000000..f77aeb9
--- /dev/null
+++ b/concatenator/harmony/util.py
@@ -0,0 +1,98 @@
+"""Misc utility functions"""
+from datetime import datetime
+
+from pystac import Asset, Item
+
+VALID_EXTENSIONS = (".nc4", ".nc")
+VALID_MEDIA_TYPES = ["application/x-netcdf", "application/x-netcdf4"]
+
+
+def _is_netcdf_asset(asset: Asset) -> bool:
+    """Check that a `pystac.Asset` is a valid NetCDF-4 granule. This can be
+    ascertained via either the media type or by checking the extension of
+    granule itself if that media type is absent.
+
+    """
+    return asset.media_type in VALID_MEDIA_TYPES or (
+        asset.media_type is None and asset.href.lower().endswith(VALID_EXTENSIONS)
+    )
+
+
+def _get_item_url(item: Item) -> str | None:
+    """Check the `pystac.Item` for the first asset with the `data` role and a
+    valid input format. If there are no matching assets, return None
+
+    """
+    return next(
+        (
+            asset.href
+            for asset in item.assets.values()
+            if "data" in (asset.roles or []) and _is_netcdf_asset(asset)
+        ),
+        None,
+    )
+
+
+def _get_netcdf_urls(items: list[Item]) -> list[str]:
+    """Iterate through a list of `pystac.Item` instances, from the input
+    `pystac.Catalog`. Extract the `pystac.Asset.href` for the first asset
+    of each item that has a role of "data". If there are any items that do
+    not have a data asset, then raise an exception.
+
+    """
+    catalog_urls = [_get_item_url(item) for item in items]
+
+    if None in catalog_urls:
+        raise RuntimeError("Some input granules do not have NetCDF-4 assets.")
+
+    return catalog_urls  # type: ignore[return-value]
+
+
+def _get_output_bounding_box(input_items: list[Item]) -> list[float]:
+    """Create a bounding box that is the maximum combined extent of all input
+    `pystac.Item` bounding box extents.
+
+    """
+    bounding_box = input_items[0].bbox
+
+    for item in input_items:
+        bounding_box[0] = min(bounding_box[0], item.bbox[0])
+        bounding_box[1] = min(bounding_box[1], item.bbox[1])
+        bounding_box[2] = max(bounding_box[2], item.bbox[2])
+        bounding_box[3] = max(bounding_box[3], item.bbox[3])
+
+    return bounding_box
+
+
+def _get_output_date_range(input_items: list[Item]) -> dict[str, str]:
+    """Create a dictionary of start and end datetime, which encompasses the
+    full temporal range of all input `pystac.Item` instances. This output
+    dictionary will be used for the `properties` of the output Zarr store
+    `pystac.Item`.
+
+    """
+    start_datetime, end_datetime = _get_item_date_range(input_items[0])
+
+    for item in input_items:
+        new_start_datetime, new_end_datetime = _get_item_date_range(item)
+        start_datetime = min(start_datetime, new_start_datetime)
+        end_datetime = max(end_datetime, new_end_datetime)
+
+    return {"start_datetime": start_datetime.isoformat(), "end_datetime": end_datetime.isoformat()}
+
+
+def _get_item_date_range(item: Item) -> tuple[datetime, datetime]:
+    """A helper function to retrieve the temporal range from a `pystac.Item`
+    instance. If the `pystac.Item.datetime` property exists, there is a
+    single datetime associated with the granule, otherwise there will be a
+    start and end time contained within the `pystac.Item` metadata.
+
+    """
+    if item.datetime is None:
+        start_datetime = item.common_metadata.start_datetime
+        end_datetime = item.common_metadata.end_datetime
+    else:
+        start_datetime = item.datetime
+        end_datetime = item.datetime
+
+    return start_datetime, end_datetime

From db16b9f70332238ecc0cd6b9ceacc194e5bae763 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 15:18:23 -0400
Subject: [PATCH 14/40] update poetry lock

---
 poetry.lock | 315 ++++++++++++++++++++++++++++------------------------
 1 file changed, 168 insertions(+), 147 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index b306a7c..705cafe 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -20,7 +20,6 @@ files = [
     {file = "black-23.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:840015166dbdfbc47992871325799fd2dc0dcf9395e401ada6d88fe11498abad"},
     {file = "black-23.10.1-cp38-cp38-win_amd64.whl", hash = "sha256:037e9b4664cafda5f025a1728c50a9e9aedb99a759c89f760bd83730e76ba884"},
     {file = "black-23.10.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:7cb5936e686e782fddb1c73f8aa6f459e1ad38a6a7b0e54b403f1f05a1507ee9"},
-    {file = "black-23.10.1-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:7670242e90dc129c539e9ca17665e39a146a761e681805c54fbd86015c7c84f7"},
     {file = "black-23.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ed45ac9a613fb52dad3b61c8dea2ec9510bf3108d4db88422bacc7d1ba1243d"},
     {file = "black-23.10.1-cp39-cp39-win_amd64.whl", hash = "sha256:6d23d7822140e3fef190734216cefb262521789367fbdc0b3f22af6744058982"},
     {file = "black-23.10.1-py3-none-any.whl", hash = "sha256:d431e6739f727bb2e0495df64a6c7a5310758e87505f5f8cde9ff6c0f2d7e4fe"},
@@ -44,17 +43,17 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "boto3"
-version = "1.28.60"
+version = "1.28.74"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.60-py3-none-any.whl", hash = "sha256:d5f270c2c9a051f78c308cbba4268458e8df441057b73ba140742707ac1bc7ea"},
-    {file = "boto3-1.28.60.tar.gz", hash = "sha256:dccb49cc10b31314b8553c6c9614c44b2249e0d0285d73f608a5d2010f6e1d82"},
+    {file = "boto3-1.28.74-py3-none-any.whl", hash = "sha256:a12619d23d50523bdfa6bd2d0c124a9567a5434ec63e47df71c3e88fc9d482f6"},
+    {file = "boto3-1.28.74.tar.gz", hash = "sha256:c4d89ff98cf53e1e74ed8c1c1bb13a7bd7d909e1c0d9ad25792ccfe2cb1575bc"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.60,<1.32.0"
+botocore = ">=1.31.74,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.7.0,<0.8.0"
 
@@ -63,19 +62,19 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.60"
+version = "1.31.74"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.60-py3-none-any.whl", hash = "sha256:b6de7a6a03ca3da18b78615a2cb5221c9fdb9483d3f50cb4281ae038b3f22d9f"},
-    {file = "botocore-1.31.60.tar.gz", hash = "sha256:578470a15a5bd64f67437a81f23feccba85084167acf63c56acada2c1c1d95d8"},
+    {file = "botocore-1.31.74-py3-none-any.whl", hash = "sha256:3eef070a8d8c4240aad07e5c89395002b140af213bcfc4dcd1d441e3ee4b3bee"},
+    {file = "botocore-1.31.74.tar.gz", hash = "sha256:2549ca7dc0f9227d8692a56a133c1346642efb38736c7c3f1330724d937ad6ec"},
 ]
 
 [package.dependencies]
 jmespath = ">=0.7.1,<2.0.0"
 python-dateutil = ">=2.1,<3.0.0"
-urllib3 = ">=1.25.4,<1.27"
+urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
 
 [package.extras]
 crt = ["awscrt (==0.16.26)"]
@@ -188,103 +187,135 @@ files = [
 [package.dependencies]
 numpy = ">1.13.3"
 
+[[package]]
+name = "cftime"
+version = "1.6.3"
+description = "Time-handling functionality from netcdf4-python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "cftime-1.6.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b62d42546fa5c914dfea5b15a9aaed2087ea1211cc36d08c374502ef95892038"},
+    {file = "cftime-1.6.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:eb6dd70b2ccabfe1a14b7fbb0bbdce0418e71697094373c0d573c880790fa291"},
+    {file = "cftime-1.6.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f9878bfd8c1c3f24184ecbd528f739ba46ebaceaf1c8a24d348d7befb117a285"},
+    {file = "cftime-1.6.3-cp310-cp310-win_amd64.whl", hash = "sha256:3cf6e216a4c06f9a628cdf8e9c9d5e8097fb3eb02dd087dd14ab3b18478a7271"},
+    {file = "cftime-1.6.3-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:8d2c01456d9d7b46aa710a41d1c711a50d5ea259aff4a987d0e973d1093bc922"},
+    {file = "cftime-1.6.3-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:80eb1170ce1639016f55760847f4aadd04b0312496c5bac2797e930914bba48d"},
+    {file = "cftime-1.6.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d87dadd0824262bdd7493babd2a44447da0a22175ded8ae9e060a3aebec7c5d7"},
+    {file = "cftime-1.6.3-cp311-cp311-win_amd64.whl", hash = "sha256:0a38eb9f5c733a23e1714bd3ef2762ed5acee34f127670f8fb4ad6464946f6b3"},
+    {file = "cftime-1.6.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:2d113a01ab924445e61d65c26bbd95bc08e4a22878d3b947064bba056c884c4a"},
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 [[package]]
@@ -303,13 +334,13 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "cloudpickle"
-version = "2.2.1"
-description = "Extended pickling support for Python objects"
+version = "3.0.0"
+description = "Pickler class to extend the standard pickle.Pickler functionality"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 [[package]]
@@ -446,13 +477,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "fsspec"
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+version = "2023.10.0"
 description = "File-system specification"
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 [package.extras]
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 [package.dependencies]
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
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-    {file = "PyYAML-6.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df"},
     {file = "PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
@@ -1064,7 +1087,6 @@ files = [
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
-    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
     {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
     {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
     {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -1072,7 +1094,6 @@ files = [
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
-    {file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
     {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
     {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},

From 883bfdfdb6603a8998b5135c1be12cb8b8b0bb2d Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 16:50:41 -0400
Subject: [PATCH 15/40] remove dockerfilelint

---
 .pre-commit-config.yaml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2aa0f30..ba7dee6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -38,9 +38,3 @@ repos:
       - id: yamllint
         args: ["-d {extends: relaxed, rules: {line-length: {max: 120}}}"]
         stages: [commit, push]
-
-  - repo: https://github.com/pryorda/dockerfilelint-precommit-hooks
-    rev: v0.1.0
-    hooks:
-      - id: dockerfilelint
-        stages: [commit, push]

From 7b3ed1d7db65c0af1929c40f941f73caa9447099 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 16:51:06 -0400
Subject: [PATCH 16/40] initial commit of Docker files

---
 .dockerignore        | 103 +++++++++++++++++++++++++++++++++++++++++++
 Dockerfile           |  53 ++++++++++++++++++++++
 build-service        |   3 ++
 docker-entrypoint.sh |  10 +++++
 4 files changed, 169 insertions(+)
 create mode 100644 .dockerignore
 create mode 100644 Dockerfile
 create mode 100755 build-service
 create mode 100644 docker-entrypoint.sh

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..a38a8b4
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,103 @@
+.travis.yaml
+.swagger-codegen-ignore
+README.md
+tox.ini
+git_push.sh
+test-requirements.txt
+setup.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+venv/
+.python-version
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+# Intellij project settings
+.idea
+
+# VSCode project settings
+.vscode
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache/
+# pytest
+.pytest_cache/
+
+# Pyre type checker
+.pyre/
+
+# Github integration settings
+.github
+
+# .dockerignore, Dockerfile and builder script themselves are not needed by
+# docker build.
+.dockerignore
+Dockerfile*
+build-service
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..ee4a61c
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,53 @@
+
+FROM python:3.10-slim
+
+RUN apt-get update \
+     && DEBIAN_FRONTEND=noninteractive apt-get upgrade -y \
+    gcc \
+    libnetcdf-dev \
+    #libhdf5-dev \
+    #hdf5-helpers \
+    && pip3 install --upgrade pip \
+    && pip3 install cython \
+    && pip3 install poetry \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+
+# Create a new user
+RUN adduser --quiet --disabled-password --shell /bin/sh --home /home/dockeruser --gecos "" --uid 1000 dockeruser
+USER dockeruser
+ENV HOME /home/dockeruser
+ENV PYTHONPATH "${PYTHONPATH}:/home/dockeruser/.local/bin"
+ENV PATH="/home/dockeruser/.local/bin:${PATH}"
+
+# The 'SOURCE' argument is what will be used in 'pip install'.
+ARG SOURCE
+
+# Set this argument if running the pip install on a local directory, so
+# the local dist files are copied into the container.
+ARG DIST_PATH
+
+USER root
+RUN mkdir -p /worker && chown dockeruser /worker
+COPY pyproject.toml /worker
+# COPY ../pyproject.toml /worker
+USER dockeruser
+
+WORKDIR /worker
+
+# ENV PYTHONPATH=${PYTHONPATH}:${PWD}
+
+COPY --chown=dockeruser $DIST_PATH $DIST_PATH
+USER dockeruser
+#RUN pip3 install --no-cache-dir --force --user --index-url https://pypi.org/simple/ --extra-index-url https://test.pypi.org/simple/ $SOURCE \
+#    && rm -rf $DIST_PATH
+
+#install poetry as root
+USER root
+RUN poetry config virtualenvs.create false
+RUN poetry install --no-dev
+
+USER dockeruser
+COPY --chown=dockeruser ./docker-entrypoint.sh docker-entrypoint.sh
+# Run the service
+ENTRYPOINT ["./docker-entrypoint.sh"]
diff --git a/build-service b/build-service
new file mode 100755
index 0000000..1026e26
--- /dev/null
+++ b/build-service
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker build -t "asdc-trade/stitchee:${VERSION-latest}" .
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
new file mode 100644
index 0000000..000ebbe
--- /dev/null
+++ b/docker-entrypoint.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+set -e
+
+if [ "$1" = 'stitchee' ]; then
+  exec stitchee "$@"
+elif [ "$1" = 'stitchee_harmony' ]; then
+  exec stitchee_harmony "$@"
+else
+  exec stitchee_harmony "$@"
+fi

From d062a4a53aa1e34092aa1966c6843efb2828b26a Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 17:16:15 -0400
Subject: [PATCH 17/40] update .dockerignore

---
 .dockerignore | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index a38a8b4..3207eef 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,10 +1,10 @@
+TEMPO_*.nc
+tests/*data*/
+.git
+.gitignore
 .travis.yaml
 .swagger-codegen-ignore
-README.md
 tox.ini
-git_push.sh
-test-requirements.txt
-setup.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -96,8 +96,7 @@ dmypy.json
 # Github integration settings
 .github
 
-# .dockerignore, Dockerfile and builder script themselves are not needed by
+# .dockerignore and builder script themselves are not needed by
 # docker build.
 .dockerignore
-Dockerfile*
 build-service

From f8585822476f8e6b1bb8f26179bb2c818230ad2e Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 17:16:26 -0400
Subject: [PATCH 18/40] update Dockerfile

---
 Dockerfile | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ee4a61c..b2a3501 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -31,21 +31,16 @@ USER root
 RUN mkdir -p /worker && chown dockeruser /worker
 COPY pyproject.toml /worker
 # COPY ../pyproject.toml /worker
-USER dockeruser
 
 WORKDIR /worker
-
 # ENV PYTHONPATH=${PYTHONPATH}:${PWD}
-
 COPY --chown=dockeruser $DIST_PATH $DIST_PATH
-USER dockeruser
 #RUN pip3 install --no-cache-dir --force --user --index-url https://pypi.org/simple/ --extra-index-url https://test.pypi.org/simple/ $SOURCE \
 #    && rm -rf $DIST_PATH
 
 #install poetry as root
-USER root
 RUN poetry config virtualenvs.create false
-RUN poetry install --no-dev
+RUN poetry install --only main
 
 USER dockeruser
 COPY --chown=dockeruser ./docker-entrypoint.sh docker-entrypoint.sh

From ae72c7db47f1ce0f3b69bbb91703519d677dfcfe Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 17:16:44 -0400
Subject: [PATCH 19/40] add stitchee_harmony poetry script entry

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 46fc7d5..82535b2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,6 +29,7 @@ coverage = "^7.3.2"
 nco = "^1.1.0"
 
 [tool.poetry.scripts]
+stitchee_harmony = 'concatenator.harmony.cli:main'
 stitchee = 'concatenator.run_stitchee:main'
 
 [build-system]

From 54348c2c3206417770229813b9a96f662c38d5b1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 31 Oct 2023 21:18:06 +0000
Subject: [PATCH 20/40] Bump urllib3 from 1.26.17 to 1.26.18

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.17 to 1.26.18.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/1.26.17...1.26.18)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 370225b..239925b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -1032,6 +1032,7 @@ files = [
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"},
+    {file = "PyYAML-6.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290"},
     {file = "PyYAML-6.0.1-cp310-cp310-win32.whl", hash = "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924"},
     {file = "PyYAML-6.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d"},
     {file = "PyYAML-6.0.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007"},
@@ -1039,8 +1040,15 @@ files = [
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673"},
+    {file = "PyYAML-6.0.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b"},
     {file = "PyYAML-6.0.1-cp311-cp311-win32.whl", hash = "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741"},
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"},
+    {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"},
+    {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df"},
     {file = "PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
@@ -1057,6 +1065,7 @@ files = [
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
+    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
     {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
     {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
     {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -1064,6 +1073,7 @@ files = [
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
     {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
     {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -1190,13 +1200,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.17"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"},
-    {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"},
+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
 ]
 
 [package.extras]

From 7e6a7646eee8678693af1780fee06f403009bb09 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 17:21:14 -0400
Subject: [PATCH 21/40] update permissions on docker-entrypoint.sh

---
 docker-entrypoint.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 docker-entrypoint.sh

diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
old mode 100644
new mode 100755

From b9d8a8a259b08a7cedac54bdca2b1b627dedd408 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 1 Nov 2023 11:05:08 -0400
Subject: [PATCH 22/40] remove comment

---
 Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index b2a3501..eedcd8a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,7 +30,6 @@ ARG DIST_PATH
 USER root
 RUN mkdir -p /worker && chown dockeruser /worker
 COPY pyproject.toml /worker
-# COPY ../pyproject.toml /worker
 
 WORKDIR /worker
 # ENV PYTHONPATH=${PYTHONPATH}:${PWD}

From aa3baaed4413640a6337e53df1cb412505cf1a2b Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 1 Nov 2023 12:01:15 -0400
Subject: [PATCH 23/40] exclude all tests and pytest config from docker build

---
 .dockerignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.dockerignore b/.dockerignore
index 3207eef..3c94215 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,5 +1,6 @@
 TEMPO_*.nc
-tests/*data*/
+tests/
+pytest.ini
 .git
 .gitignore
 .travis.yaml

From 439cd5bf54d616cd5de30fe199921e132a557640 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 3 Nov 2023 12:45:38 -0400
Subject: [PATCH 24/40] add missing file staging method, and improve logging

---
 concatenator/harmony/service_adapter.py | 57 +++++++++++++++++++++++--
 concatenator/harmony/util.py            | 12 ++++++
 2 files changed, 66 insertions(+), 3 deletions(-)

diff --git a/concatenator/harmony/service_adapter.py b/concatenator/harmony/service_adapter.py
index 5905229..f3eb3ec 100644
--- a/concatenator/harmony/service_adapter.py
+++ b/concatenator/harmony/service_adapter.py
@@ -1,10 +1,12 @@
 from pathlib import Path
+from shutil import copyfile
 from tempfile import TemporaryDirectory
+from urllib.parse import urlsplit
 from uuid import uuid4
 
 import pystac
 from harmony.adapter import BaseHarmonyAdapter
-from harmony.util import bbox_to_geometry
+from harmony.util import bbox_to_geometry, stage
 from pystac import Item
 from pystac.item import Asset
 
@@ -13,6 +15,7 @@
     _get_netcdf_urls,
     _get_output_bounding_box,
     _get_output_date_range,
+    sizeof_fmt,
 )
 from concatenator.stitchee import stitchee
 
@@ -51,7 +54,7 @@ def invoke(self):
 
         return self.message, self.process_catalog(self.catalog)
 
-    def process_catalog(self, catalog: pystac.Catalog):
+    def process_catalog(self, catalog: pystac.Catalog) -> pystac.Catalog:
         """Converts a list of STAC catalogs into a list of lists of STAC catalogs."""
         self.logger.info("process_catalog() started.")
         try:
@@ -83,14 +86,20 @@ def process_catalog(self, catalog: pystac.Catalog):
             # -- Perform merging --
             collection = self._get_item_source(items[0]).collection
             filename = f"{collection}_merged.nc4"
+            self.logger.info(f"Merged filename will be === {filename}.")
 
             with TemporaryDirectory() as temp_dir:
                 self.logger.info("Starting granule downloads")
                 input_files = multi_core_download(
                     netcdf_urls, temp_dir, self.message.accessToken, self.config
                 )
-                self.logger.info("Finished granule downloads")
+                self.logger.info("Finished granule downloads.")
 
+                for file_count, file in enumerate(input_files):
+                    file_size = sizeof_fmt(file.stat().st_size)
+                    self.logger.info(f"File {file_count} is size <{file_size}>. Path={file}")
+
+                self.logger.info("Running Stitchee..")
                 output_path = str(Path(temp_dir).joinpath(filename).resolve())
 
                 # # --- Run STITCHEE ---
@@ -102,7 +111,9 @@ def process_catalog(self, catalog: pystac.Catalog):
                     concat_dim="mirror_step",  # This is currently set only for TEMPO
                     logger=self.logger,
                 )
+                self.logger.info("Stitchee completed.")
                 staged_url = self._stage(output_path, filename, "application/x-netcdf4")
+                self.logger.info("Staging completed.")
 
             # -- Output to STAC catalog --
             result.clear_items()
@@ -126,3 +137,43 @@ def process_catalog(self, catalog: pystac.Catalog):
         except Exception as service_exception:
             self.logger.error(service_exception, exc_info=1)
             raise service_exception
+
+    def _stage(self, local_filename: str, remote_filename: str, mime: str) -> str:
+        """
+        Stages a local file to either to S3 (utilizing harmony.util.stage) or to
+        the local filesystem by performing a file copy. Staging location is
+        determined by message.stagingLocation or the --harmony-data-location
+        CLI argument override
+
+        Parameters
+        ----------
+        local_filename : string
+            A path and filename to the local file that should be staged
+        remote_filename : string
+            The basename to give to the remote file
+        mime : string
+            The mime type to apply to the staged file for use when it is served, e.g. "application/x-netcdf4"
+
+        Returns
+        -------
+        url : string
+            A URL to the staged file
+        """
+        url_components = urlsplit(self.message.stagingLocation)
+        scheme = url_components.scheme
+
+        if scheme == "file":
+            dest_path = Path(url_components.path).joinpath(remote_filename)
+            self.logger.info("Staging to local filesystem: '%s'", str(dest_path))
+
+            copyfile(local_filename, dest_path)
+            return dest_path.as_uri()
+
+        return stage(
+            local_filename,
+            remote_filename,
+            mime,
+            logger=self.logger,
+            location=self.message.stagingLocation,
+            cfg=self.config,
+        )
diff --git a/concatenator/harmony/util.py b/concatenator/harmony/util.py
index f77aeb9..a972aaf 100644
--- a/concatenator/harmony/util.py
+++ b/concatenator/harmony/util.py
@@ -96,3 +96,15 @@ def _get_item_date_range(item: Item) -> tuple[datetime, datetime]:
         end_datetime = item.datetime
 
     return start_datetime, end_datetime
+
+
+def sizeof_fmt(num: float, suffix="B") -> str:
+    """Get a human-readable version of file size
+
+    From: https://stackoverflow.com/a/1094933
+    """
+    for unit in ("", "Ki", "Mi", "Gi", "Ti", "Pi", "Ei", "Zi"):
+        if abs(num) < 1024.0:
+            return f"{num:3.1f}{unit}{suffix}"
+        num /= 1024.0
+    return f"{num:.1f}Yi{suffix}"

From c6a9b546ffa5c3883517caca597bb57f587baab5 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 3 Nov 2023 12:47:18 -0400
Subject: [PATCH 25/40] put concatenation in a try except block

---
 concatenator/stitchee.py | 153 +++++++++++++++++++++------------------
 1 file changed, 81 insertions(+), 72 deletions(-)

diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index 103e3b6..3e2f061 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -52,84 +52,93 @@ def stitchee(
         logger.info("No non-empty netCDF files found. Exiting.")
         return ""
 
-    logger.debug("Flattening all input files...")
+    logger.info("Flattening all input files...")
     xrdataset_list = []
-    for i, filepath in enumerate(input_files):
-        # The group structure is flattened.
+
+    try:
+        for i, filepath in enumerate(input_files):
+            # The group structure is flattened.
+            start_time = time.time()
+            logger.info("    ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath)
+            flat_dataset, coord_vars, _ = flatten_grouped_dataset(
+                nc.Dataset(filepath, "r"), filepath, ensure_all_dims_are_coords=True
+            )
+
+            logger.info("Removing duplicate dimensions")
+            flat_dataset = remove_duplicate_dims(flat_dataset)
+
+            logger.info("Opening flattened file with xarray.")
+            xrds = xr.open_dataset(
+                xr.backends.NetCDF4DataStore(flat_dataset),
+                decode_times=False,
+                decode_coords=False,
+                drop_variables=coord_vars,
+            )
+
+            benchmark_log["flattening"] = time.time() - start_time
+
+            # The flattened file is written to disk.
+            # flat_file_path = add_label_to_path(filepath, label="_flat_intermediate")
+            # xrds.to_netcdf(flat_file_path, encoding={v_name: {'dtype': 'str'} for v_name in string_vars})
+            # intermediate_flat_filepaths.append(flat_file_path)
+            # xrdataset_list.append(xr.open_dataset(flat_file_path))
+            xrdataset_list.append(xrds)
+
+        # Flattened files are concatenated together (Using XARRAY).
         start_time = time.time()
-        logger.debug("    ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath)
-        flat_dataset, coord_vars, _ = flatten_grouped_dataset(
-            nc.Dataset(filepath, "r"), filepath, ensure_all_dims_are_coords=True
+        logger.info("Concatenating flattened files...")
+        # combined_ds = xr.open_mfdataset(intermediate_flat_filepaths,
+        #                                 decode_times=False,
+        #                                 decode_coords=False,
+        #                                 data_vars='minimal',
+        #                                 coords='minimal',
+        #                                 compat='override')
+
+        if concat_kwargs is None:
+            concat_kwargs = {}
+
+        combined_ds = xr.concat(
+            xrdataset_list,
+            dim=GROUP_DELIM + concat_dim,
+            data_vars="minimal",
+            coords="minimal",
+            **concat_kwargs,
         )
 
-        flat_dataset = remove_duplicate_dims(flat_dataset)
+        benchmark_log["concatenating"] = time.time() - start_time
 
-        xrds = xr.open_dataset(
-            xr.backends.NetCDF4DataStore(flat_dataset),
-            decode_times=False,
-            decode_coords=False,
-            drop_variables=coord_vars,
-        )
+        if write_tmp_flat_concatenated:
+            logger.info("Writing concatenated flattened temporary file to disk...")
+            # Concatenated, yet still flat, file is written to disk for debugging.
+            tmp_flat_concatenated_path = add_label_to_path(output_file, label="_flat_intermediate")
+            combined_ds.to_netcdf(tmp_flat_concatenated_path, format="NETCDF4")
+        else:
+            tmp_flat_concatenated_path = None
 
-        benchmark_log["flattening"] = time.time() - start_time
-
-        # The flattened file is written to disk.
-        # flat_file_path = add_label_to_path(filepath, label="_flat_intermediate")
-        # xrds.to_netcdf(flat_file_path, encoding={v_name: {'dtype': 'str'} for v_name in string_vars})
-        # intermediate_flat_filepaths.append(flat_file_path)
-        # xrdataset_list.append(xr.open_dataset(flat_file_path))
-        xrdataset_list.append(xrds)
-
-    # Flattened files are concatenated together (Using XARRAY).
-    start_time = time.time()
-    logger.debug("Concatenating flattened files...")
-    # combined_ds = xr.open_mfdataset(intermediate_flat_filepaths,
-    #                                 decode_times=False,
-    #                                 decode_coords=False,
-    #                                 data_vars='minimal',
-    #                                 coords='minimal',
-    #                                 compat='override')
-
-    if concat_kwargs is None:
-        concat_kwargs = {}
-
-    combined_ds = xr.concat(
-        xrdataset_list,
-        dim=GROUP_DELIM + concat_dim,
-        data_vars="minimal",
-        coords="minimal",
-        **concat_kwargs,
-    )
-
-    benchmark_log["concatenating"] = time.time() - start_time
-
-    if write_tmp_flat_concatenated:
-        logger.debug("Writing concatenated flattened temporary file to disk...")
-        # Concatenated, yet still flat, file is written to disk for debugging.
-        tmp_flat_concatenated_path = add_label_to_path(output_file, label="_flat_intermediate")
-        combined_ds.to_netcdf(tmp_flat_concatenated_path, format="NETCDF4")
-    else:
-        tmp_flat_concatenated_path = None
-
-    # The group hierarchy of the concatenated file is reconstructed (using XARRAY).
-    start_time = time.time()
-    logger.debug("Reconstructing groups within concatenated file...")
-    regroup_flattened_dataset(combined_ds, output_file)
-    benchmark_log["reconstructing_groups"] = time.time() - start_time
-
-    logger.info("--- Benchmark results ---")
-    total_time = 0.0
-    for k, v in benchmark_log.items():
-        logger.info("%s: %f", k, v)
-        total_time += v
-    logger.info("-- total processing time: %f", total_time)
-
-    # If requested, remove temporary intermediate files.
-    if not keep_tmp_files:
-        for file in intermediate_flat_filepaths:
-            os.remove(file)
-        if tmp_flat_concatenated_path:
-            os.remove(tmp_flat_concatenated_path)
+        # The group hierarchy of the concatenated file is reconstructed (using XARRAY).
+        start_time = time.time()
+        logger.info("Reconstructing groups within concatenated file...")
+        regroup_flattened_dataset(combined_ds, output_file)
+        benchmark_log["reconstructing_groups"] = time.time() - start_time
+
+        logger.info("--- Benchmark results ---")
+        total_time = 0.0
+        for k, v in benchmark_log.items():
+            logger.info("%s: %f", k, v)
+            total_time += v
+        logger.info("-- total processing time: %f", total_time)
+
+        # If requested, remove temporary intermediate files.
+        if not keep_tmp_files:
+            for file in intermediate_flat_filepaths:
+                os.remove(file)
+            if tmp_flat_concatenated_path:
+                os.remove(tmp_flat_concatenated_path)
+
+    except Exception as err:
+        logger.info("Stitchee encountered an error!")
+        logger.error(err)
+        raise err
 
     return output_file
 

From 4ce3bd7a94cec406addb0e867bfb98f77feee90a Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Fri, 3 Nov 2023 12:53:36 -0400
Subject: [PATCH 26/40] add type annotations

---
 concatenator/harmony/download_worker.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/concatenator/harmony/download_worker.py b/concatenator/harmony/download_worker.py
index 0c177af..3f502e3 100644
--- a/concatenator/harmony/download_worker.py
+++ b/concatenator/harmony/download_worker.py
@@ -12,7 +12,9 @@
 from harmony.util import download
 
 
-def multi_core_download(urls, destination_dir, access_token, cfg, process_count=None):
+def multi_core_download(
+    urls: list, destination_dir: str, access_token: str, cfg: dict, process_count: int | None = None
+) -> list[Path]:
     """
     A method which automagically scales downloads to the number of CPU
     cores. For further explaination, see documentation on "multi-track
@@ -28,7 +30,7 @@ def multi_core_download(urls, destination_dir, access_token, cfg, process_count=
         access token as provided in Harmony input
     cfg : dict
         Harmony configuration information
-    process_count : int
+    process_count : int, optional
         Number of worker processes to run (expected >= 1)
 
     Returns
@@ -39,6 +41,8 @@ def multi_core_download(urls, destination_dir, access_token, cfg, process_count=
 
     if process_count is None:
         process_count = cpu_count()
+    if process_count is None:
+        raise RuntimeError("cannot determine number of cpus")
 
     with Manager() as manager:
         url_queue = manager.Queue(len(urls))
@@ -70,7 +74,9 @@ def multi_core_download(urls, destination_dir, access_token, cfg, process_count=
     return [Path(path) for path in path_list]
 
 
-def _download_worker(url_queue, path_list, destination_dir, access_token, cfg):
+def _download_worker(
+    url_queue: queue.Queue, path_list: list, destination_dir: str, access_token: str, cfg: dict
+) -> None:
     """
     A method to be executed in a separate process which processes the url_queue
     and places paths to completed downloads into the path_list. Downloads are

From cfceb88123cba3c8d20231741d1494ac98377be4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 3 Nov 2023 22:51:06 +0000
Subject: [PATCH 27/40] Bump ruff from 0.1.3 to 0.1.4

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.3 to 0.1.4.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/v0.1.3...v0.1.4)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 40 ++++++++++++++++++++--------------------
 pyproject.toml |  2 +-
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index b306a7c..dbc63c1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1101,28 +1101,28 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "ruff"
-version = "0.1.3"
-description = "An extremely fast Python linter, written in Rust."
+version = "0.1.4"
+description = "An extremely fast Python linter and code formatter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ruff-0.1.3-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:b46d43d51f7061652eeadb426a9e3caa1e0002470229ab2fc19de8a7b0766901"},
-    {file = "ruff-0.1.3-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:b8afeb9abd26b4029c72adc9921b8363374f4e7edb78385ffaa80278313a15f9"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ca3cf365bf32e9ba7e6db3f48a4d3e2c446cd19ebee04f05338bc3910114528b"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:4874c165f96c14a00590dcc727a04dca0cfd110334c24b039458c06cf78a672e"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:eec2dd31eed114e48ea42dbffc443e9b7221976554a504767ceaee3dd38edeb8"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:dc3ec4edb3b73f21b4aa51337e16674c752f1d76a4a543af56d7d04e97769613"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:2e3de9ed2e39160800281848ff4670e1698037ca039bda7b9274f849258d26ce"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:1c595193881922cc0556a90f3af99b1c5681f0c552e7a2a189956141d8666fe8"},
-    {file = "ruff-0.1.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0f75e670d529aa2288cd00fc0e9b9287603d95e1536d7a7e0cafe00f75e0dd9d"},
-    {file = "ruff-0.1.3-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:76dd49f6cd945d82d9d4a9a6622c54a994689d8d7b22fa1322983389b4892e20"},
-    {file = "ruff-0.1.3-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:918b454bc4f8874a616f0d725590277c42949431ceb303950e87fef7a7d94cb3"},
-    {file = "ruff-0.1.3-py3-none-musllinux_1_2_i686.whl", hash = "sha256:d8859605e729cd5e53aa38275568dbbdb4fe882d2ea2714c5453b678dca83784"},
-    {file = "ruff-0.1.3-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:0b6c55f5ef8d9dd05b230bb6ab80bc4381ecb60ae56db0330f660ea240cb0d4a"},
-    {file = "ruff-0.1.3-py3-none-win32.whl", hash = "sha256:3e7afcbdcfbe3399c34e0f6370c30f6e529193c731b885316c5a09c9e4317eef"},
-    {file = "ruff-0.1.3-py3-none-win_amd64.whl", hash = "sha256:7a18df6638cec4a5bd75350639b2bb2a2366e01222825562c7346674bdceb7ea"},
-    {file = "ruff-0.1.3-py3-none-win_arm64.whl", hash = "sha256:12fd53696c83a194a2db7f9a46337ce06445fb9aa7d25ea6f293cf75b21aca9f"},
-    {file = "ruff-0.1.3.tar.gz", hash = "sha256:3ba6145369a151401d5db79f0a47d50e470384d0d89d0d6f7fab0b589ad07c34"},
+    {file = "ruff-0.1.4-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:864958706b669cce31d629902175138ad8a069d99ca53514611521f532d91495"},
+    {file = "ruff-0.1.4-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:9fdd61883bb34317c788af87f4cd75dfee3a73f5ded714b77ba928e418d6e39e"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b4eaca8c9cc39aa7f0f0d7b8fe24ecb51232d1bb620fc4441a61161be4a17539"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:a9a1301dc43cbf633fb603242bccd0aaa34834750a14a4c1817e2e5c8d60de17"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:78e8db8ab6f100f02e28b3d713270c857d370b8d61871d5c7d1702ae411df683"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:80fea754eaae06335784b8ea053d6eb8e9aac75359ebddd6fee0858e87c8d510"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:6bc02a480d4bfffd163a723698da15d1a9aec2fced4c06f2a753f87f4ce6969c"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:9862811b403063765b03e716dac0fda8fdbe78b675cd947ed5873506448acea4"},
+    {file = "ruff-0.1.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:58826efb8b3efbb59bb306f4b19640b7e366967a31c049d49311d9eb3a4c60cb"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:fdfd453fc91d9d86d6aaa33b1bafa69d114cf7421057868f0b79104079d3e66e"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:e8791482d508bd0b36c76481ad3117987301b86072158bdb69d796503e1c84a8"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_i686.whl", hash = "sha256:01206e361021426e3c1b7fba06ddcb20dbc5037d64f6841e5f2b21084dc51800"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:645591a613a42cb7e5c2b667cbefd3877b21e0252b59272ba7212c3d35a5819f"},
+    {file = "ruff-0.1.4-py3-none-win32.whl", hash = "sha256:99908ca2b3b85bffe7e1414275d004917d1e0dfc99d497ccd2ecd19ad115fd0d"},
+    {file = "ruff-0.1.4-py3-none-win_amd64.whl", hash = "sha256:1dfd6bf8f6ad0a4ac99333f437e0ec168989adc5d837ecd38ddb2cc4a2e3db8a"},
+    {file = "ruff-0.1.4-py3-none-win_arm64.whl", hash = "sha256:d98ae9ebf56444e18a3e3652b3383204748f73e247dea6caaf8b52d37e6b32da"},
+    {file = "ruff-0.1.4.tar.gz", hash = "sha256:21520ecca4cc555162068d87c747b8f95e1e95f8ecfcbbe59e8dd00710586315"},
 ]
 
 [[package]]
@@ -1254,4 +1254,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "ddc5152441a76d77232416c3125f8e9b02e9b727f7a84a246f268f3bef6c6ced"
+content-hash = "69a415b143a1727dba7eb712ce7ae20ede1afbb208f336120e64352186f1e9b9"
diff --git a/pyproject.toml b/pyproject.toml
index 46fc7d5..90d511b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,7 @@ harmony-service-lib = "^1.0.23"
 pytest = "^7.4.3"
 mypy = "^1.6.1"
 black = "^23.10.1"
-ruff = "^0.1.3"
+ruff = "^0.1.4"
 coverage = "^7.3.2"
 
 [tool.poetry.group.extras.dependencies]

From a833be28200dbe1564cecac12f6a0a4f8d5717c5 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 7 Nov 2023 11:25:05 -0500
Subject: [PATCH 28/40] update CHANGELOG.md

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a69d564..59e7003 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
   - [PR #1](https://github.com/danielfromearth/stitchee/pull/1): An initial GitHub Actions workflow
+  - [Issue #8](https://github.com/danielfromearth/stitchee/issues/8): Create working Docker image
+  - [Issue #10](https://github.com/danielfromearth/stitchee/issues/10): Add code necessary to communicate with Harmony
 ### Changed
   - [PR #12](https://github.com/danielfromearth/stitchee/pull/12): Changed name to "stitchee"
   - [PR #15](https://github.com/danielfromearth/stitchee/pull/15): Use ruff+black chain for pre-commit lint & format

From dca81764f80dc98a56fe192c0429efe1e4613aad Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 7 Nov 2023 22:29:09 +0000
Subject: [PATCH 29/40] Bump harmony-service-lib from 1.0.23 to 1.0.24

Bumps [harmony-service-lib](https://github.com/nasa/harmony-service-lib-py) from 1.0.23 to 1.0.24.
- [Release notes](https://github.com/nasa/harmony-service-lib-py/releases)
- [Commits](https://github.com/nasa/harmony-service-lib-py/compare/v1.0.23...v1.0.24)

---
updated-dependencies:
- dependency-name: harmony-service-lib
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock    | 22 +++++++++++++++++-----
 pyproject.toml |  2 +-
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index aad48b6..170ea00 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -20,6 +20,7 @@ files = [
     {file = "black-23.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:840015166dbdfbc47992871325799fd2dc0dcf9395e401ada6d88fe11498abad"},
     {file = "black-23.10.1-cp38-cp38-win_amd64.whl", hash = "sha256:037e9b4664cafda5f025a1728c50a9e9aedb99a759c89f760bd83730e76ba884"},
     {file = "black-23.10.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:7cb5936e686e782fddb1c73f8aa6f459e1ad38a6a7b0e54b403f1f05a1507ee9"},
+    {file = "black-23.10.1-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:7670242e90dc129c539e9ca17665e39a146a761e681805c54fbd86015c7c84f7"},
     {file = "black-23.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ed45ac9a613fb52dad3b61c8dea2ec9510bf3108d4db88422bacc7d1ba1243d"},
     {file = "black-23.10.1-cp39-cp39-win_amd64.whl", hash = "sha256:6d23d7822140e3fef190734216cefb262521789367fbdc0b3f22af6744058982"},
     {file = "black-23.10.1-py3-none-any.whl", hash = "sha256:d431e6739f727bb2e0495df64a6c7a5310758e87505f5f8cde9ff6c0f2d7e4fe"},
@@ -214,6 +215,7 @@ files = [
     {file = "cftime-1.6.3-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:523b9a6bf03f5e36407979e248381d0fcab2d225b915bbde77d00c6dde192b90"},
     {file = "cftime-1.6.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8a14d2c7d22fd2a6dfa6ad563283b6d6679f1df95e0ed8d14b8f284dad402887"},
     {file = "cftime-1.6.3-cp39-cp39-win_amd64.whl", hash = "sha256:d9b00c2844c7a1701d8ede5336b6321dfee256ceab81a34a1aff0483d56891a6"},
+    {file = "cftime-1.6.3.tar.gz", hash = "sha256:d0a6b29f72a13f08e008b9becff247cc75c84acb213332ede18879c5b6aa4dfd"},
 ]
 
 [package.dependencies]
@@ -512,13 +514,13 @@ tqdm = ["tqdm"]
 
 [[package]]
 name = "harmony-service-lib"
-version = "1.0.23"
+version = "1.0.24"
 description = "A library for Python-based Harmony services to parse incoming messages, fetch data, stage data, and call back to Harmony"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "harmony-service-lib-1.0.23.tar.gz", hash = "sha256:f3c3887a02218f8e2c6cf45d2d730d2a6bf65ea1b7b2ca10533b1562bd74cb17"},
-    {file = "harmony_service_lib-1.0.23-py3-none-any.whl", hash = "sha256:4ec97200dd0a03851d17278df73c39b655b273ba5a5da6dbeb267daaa617dd33"},
+    {file = "harmony-service-lib-1.0.24.tar.gz", hash = "sha256:5b12456c14b530aaa9b878714bb9754f7403e2f536e98c8649f4379465c8f1e9"},
+    {file = "harmony_service_lib-1.0.24-py3-none-any.whl", hash = "sha256:af7ea2ea83e5f1a629940682ffee13249615298c0bade2f2c328bb56c28bb926"},
 ]
 
 [package.dependencies]
@@ -1062,6 +1064,7 @@ files = [
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"},
     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"},
+    {file = "PyYAML-6.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290"},
     {file = "PyYAML-6.0.1-cp310-cp310-win32.whl", hash = "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924"},
     {file = "PyYAML-6.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d"},
     {file = "PyYAML-6.0.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007"},
@@ -1069,8 +1072,15 @@ files = [
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc"},
     {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673"},
+    {file = "PyYAML-6.0.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b"},
     {file = "PyYAML-6.0.1-cp311-cp311-win32.whl", hash = "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741"},
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"},
+    {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"},
+    {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df"},
     {file = "PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
@@ -1087,6 +1097,7 @@ files = [
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
+    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
     {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
     {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
     {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -1094,6 +1105,7 @@ files = [
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
     {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
     {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -1275,4 +1287,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "69a415b143a1727dba7eb712ce7ae20ede1afbb208f336120e64352186f1e9b9"
+content-hash = "172a34428efd32287335f604c729a3cb6a0985f9600caff28310e9549c803c63"
diff --git a/pyproject.toml b/pyproject.toml
index 2b0e455..b151b27 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ python = "^3.10"
 netcdf4 = "^1.6.5"
 xarray = "^2023.10.1"
 dask = "^2023.10.1"
-harmony-service-lib = "^1.0.23"
+harmony-service-lib = "^1.0.24"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"

From b26a2d10535c42f1d12af83a304fb2f862a0c301 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 09:56:30 -0500
Subject: [PATCH 30/40] rename CLI argument to clarify copy behavior

---
 concatenator/run_stitchee.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py
index 580df22..c5a45ca 100644
--- a/concatenator/run_stitchee.py
+++ b/concatenator/run_stitchee.py
@@ -50,10 +50,10 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
         help="Dimension to concatenate along, if possible.",
     )
     parser.add_argument(
-        "--make_dir_copy",
+        "--copy_input_files_to_temp_dir",
         action="store_true",
-        help="Make a duplicate of the input directory to avoid modification of input files. "
-        "This is useful for testing, but uses more disk space.",
+        help="Make a duplicate of the input files in a temporary directory to avoid modification "
+        "of input files. This is useful for testing, but uses more disk space.",
     )
     parser.add_argument(
         "--keep_tmp_files",

From 37286d58def8586ceb106298cd455f781ef5491e Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 09:56:42 -0500
Subject: [PATCH 31/40] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 59e7003..6fa3a74 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
   - [PR #12](https://github.com/danielfromearth/stitchee/pull/12): Changed name to "stitchee"
   - [PR #15](https://github.com/danielfromearth/stitchee/pull/15): Use ruff+black chain for pre-commit lint & format
+  - [Issue #45](https://github.com/danielfromearth/stitchee/issues/45): Rename CLI argument to clarify temporary copying behavior
 ### Deprecated
 ### Removed
 ### Fixed

From 9d19fb62a235d853b4f0001d7abfdcd51662cb11 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 10:04:11 -0500
Subject: [PATCH 32/40] reversed default behavior, so that input files are
 copied *unless* cli arg is specified.

---
 concatenator/run_stitchee.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py
index c5a45ca..8afada0 100644
--- a/concatenator/run_stitchee.py
+++ b/concatenator/run_stitchee.py
@@ -50,10 +50,11 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
         help="Dimension to concatenate along, if possible.",
     )
     parser.add_argument(
-        "--copy_input_files_to_temp_dir",
+        "--no_input_file_copies",
         action="store_true",
-        help="Make a duplicate of the input files in a temporary directory to avoid modification "
-        "of input files. This is useful for testing, but uses more disk space.",
+        help="By default, input files are copied into a temporary directory to avoid modification "
+        "of input files. This is useful for testing, but uses more disk space.  "
+        "By specifying this argument, no copying is performed.",
     )
     parser.add_argument(
         "--keep_tmp_files",
@@ -107,7 +108,7 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
 
     # If requested, make a temporary directory with copies of the original input files
     temporary_dir_to_remove = None
-    if parsed.make_dir_copy:
+    if not parsed.no_input_file_copies:
         new_data_dir = Path(
             add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4()))
         ).resolve()

From 0806466f3dfd95c6fa34115e89829e73fa98e0df Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 10:17:46 -0500
Subject: [PATCH 33/40] change concat_dim argument from optional to required

---
 concatenator/run_stitchee.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py
index 8afada0..f8487ac 100644
--- a/concatenator/run_stitchee.py
+++ b/concatenator/run_stitchee.py
@@ -37,18 +37,17 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
     req_grp.add_argument(
         "-o",
         "--output_path",
-        metavar="output_path",
         required=True,
         help="The output filename for the merged output.",
     )
-
-    # Optional arguments
-    parser.add_argument(
+    req_grp.add_argument(
         "--concat_dim",
-        metavar="concat_dim",
         nargs=1,
+        required=True,
         help="Dimension to concatenate along, if possible.",
     )
+
+    # Optional arguments
     parser.add_argument(
         "--no_input_file_copies",
         action="store_true",

From 67e0c20153f683473e9adac56939342ab5c22226 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 10:18:04 -0500
Subject: [PATCH 34/40] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6fa3a74..b9b6ce5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - [PR #12](https://github.com/danielfromearth/stitchee/pull/12): Changed name to "stitchee"
   - [PR #15](https://github.com/danielfromearth/stitchee/pull/15): Use ruff+black chain for pre-commit lint & format
   - [Issue #45](https://github.com/danielfromearth/stitchee/issues/45): Rename CLI argument to clarify temporary copying behavior
+  - [Issue #44](https://github.com/danielfromearth/stitchee/issues/44): Concatenation dimension CLI argument is required but isn't listed as such in the help message
 ### Deprecated
 ### Removed
 ### Fixed

From 5ee77ca927f4199584e01593b9ef8a4991e19757 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 11:36:46 -0500
Subject: [PATCH 35/40] add finer CLI control of concatenation method and args
 passed to xarray

---
 concatenator/group_handling.py |   1 -
 concatenator/run_stitchee.py   | 145 ++++++++++++++++++++++++---------
 concatenator/stitchee.py       |  25 ++++--
 3 files changed, 126 insertions(+), 45 deletions(-)

diff --git a/concatenator/group_handling.py b/concatenator/group_handling.py
index 2cc3193..277011c 100644
--- a/concatenator/group_handling.py
+++ b/concatenator/group_handling.py
@@ -174,7 +174,6 @@ def regroup_flattened_dataset(
     output_file : str
         Name of the output file to write the resulting NetCDF file to.
     """
-
     with nc.Dataset(output_file, mode="w", format="NETCDF4") as base_dataset:
         # Copy global attributes
         base_dataset.setncatts(dataset.attrs)
diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py
index f8487ac..6da6c84 100644
--- a/concatenator/run_stitchee.py
+++ b/concatenator/run_stitchee.py
@@ -11,7 +11,7 @@
 from concatenator.stitchee import stitchee
 
 
-def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
+def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None, str, dict]:
     """
     Parse args for this script.
 
@@ -40,12 +40,6 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
         required=True,
         help="The output filename for the merged output.",
     )
-    req_grp.add_argument(
-        "--concat_dim",
-        nargs=1,
-        required=True,
-        help="Dimension to concatenate along, if possible.",
-    )
 
     # Optional arguments
     parser.add_argument(
@@ -62,6 +56,29 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
         "(1) the flattened concatenated file and "
         "(2) the input directory copy  if created by '--make_dir_copy'.",
     )
+    parser.add_argument(
+        "--concat_method",
+        choices=["xarray-concat", "xarray-combine"],
+        default="xarray-concat",
+        help="Whether to use the xarray concat method or the combine-by-coords method.",
+    )
+    parser.add_argument(
+        "--concat_dim",
+        help="Dimension to concatenate along, if possible.  "
+        "This is required if using the 'xarray-concat' method",
+    )
+    parser.add_argument(
+        "--concat_arg_compat",
+        help="'compat' argument passed to xarray.concat.",
+    )
+    parser.add_argument(
+        "--concat_arg_combine_attrs",
+        help="'combine_attrs' argument passed to xarray.concat.",
+    )
+    parser.add_argument(
+        "--concat_arg_join",
+        help="'join' argument passed to xarray.concat.",
+    )
     parser.add_argument(
         "-O", "--overwrite", action="store_true", help="Overwrite output file if it already exists."
     )
@@ -77,6 +94,71 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
     if parsed.verbose:
         logging.basicConfig(level=logging.DEBUG)
 
+    # Validate the input and output paths
+    output_path = _validate_output_path(parsed)
+    input_files = _validate_input_path(parsed)
+
+    print(f"CONCAT METHOD === {parsed.concat_method}")
+    print(f"CONCAT DIM === {parsed.concat_dim}")
+    if parsed.concat_method == "xarray-concat":
+        if not parsed.concat_dim:
+            raise ValueError(
+                "If using the xarray-concat method, then 'concat_dim' must be specified."
+            )
+    elif parsed.concat_method == "xarray-combine":
+        if parsed.concat_dim:
+            raise ValueError(
+                "If using the xarray-combine method, then 'concat_dim' cannot be specified."
+            )
+
+    # Gather the concatenation arguments that will be passed to xarray.
+    concat_kwargs = {}
+    if parsed.concat_arg_compat:
+        concat_kwargs["compat"] = parsed.concat_arg_compat
+    if parsed.concat_arg_combine_attrs:
+        concat_kwargs["combine_attrs"] = parsed.concat_arg_combine_attrs
+    if parsed.concat_arg_join:
+        concat_kwargs["join"] = parsed.concat_arg_join
+
+    # If requested, make a temporary directory with new copies of the original input files
+    temporary_dir_to_remove = None
+    if not parsed.no_input_file_copies:
+        input_files, temporary_dir_to_remove = _make_temp_dir_with_input_file_copies(
+            input_files, output_path
+        )
+
+    return (
+        input_files,
+        str(output_path),
+        parsed.concat_dim,
+        bool(parsed.keep_tmp_files),
+        temporary_dir_to_remove,
+        parsed.concat_method,
+        concat_kwargs,
+    )
+
+
+def _make_temp_dir_with_input_file_copies(input_files, output_path):
+    new_data_dir = Path(
+        add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4()))
+    ).resolve()
+    os.makedirs(new_data_dir, exist_ok=True)
+    print("Created temporary directory: %s", str(new_data_dir))
+
+    new_input_files = []
+    for file in input_files:
+        new_path = new_data_dir / Path(file).name
+        shutil.copyfile(file, new_path)
+        new_input_files.append(str(new_path))
+
+    input_files = new_input_files
+    print("Copied files to temporary directory: %s", new_data_dir)
+    temporary_dir_to_remove = str(new_data_dir)
+
+    return input_files, temporary_dir_to_remove
+
+
+def _validate_output_path(parsed):
     # The output file path is validated.
     output_path = Path(parsed.output_path).resolve()
     if output_path.is_file():  # the file already exists
@@ -86,7 +168,12 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
             raise FileExistsError(
                 f"File already exists at <{output_path}>. Run again with option '-O' to overwrite."
             )
+    if output_path.is_dir():  # the specified path is an existing directory
+        raise TypeError("Output path cannot be a directory. Please specify a new filepath.")
+    return output_path
 
+
+def _validate_input_path(parsed):
     # The input directory or file is validated.
     print(f"parsed_input === {parsed.input}")
     if len(parsed.input) > 1:
@@ -99,38 +186,12 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]:
             input_files = _get_list_of_filepaths_from_file(directory_or_path)
         else:
             raise TypeError(
-                "if one path is provided for 'data_dir_or_file_or_filepaths', "
+                "If one path is provided for 'data_dir_or_file_or_filepaths', "
                 "then it must be an existing directory or file."
             )
     else:
         raise TypeError("input argument must be one path/directory or a list of paths.")
-
-    # If requested, make a temporary directory with copies of the original input files
-    temporary_dir_to_remove = None
-    if not parsed.no_input_file_copies:
-        new_data_dir = Path(
-            add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4()))
-        ).resolve()
-        os.makedirs(new_data_dir, exist_ok=True)
-        print("Created temporary directory: %s", str(new_data_dir))
-
-        new_input_files = []
-        for file in input_files:
-            new_path = new_data_dir / Path(file).name
-            shutil.copyfile(file, new_path)
-            new_input_files.append(str(new_path))
-
-        input_files = new_input_files
-        print("Copied files to temporary directory: %s", new_data_dir)
-        temporary_dir_to_remove = str(new_data_dir)
-
-    return (
-        input_files,
-        str(output_path),
-        parsed.concat_dim[0],
-        bool(parsed.keep_tmp_files),
-        temporary_dir_to_remove,
-    )
+    return input_files
 
 
 def _get_list_of_filepaths_from_file(file_with_paths: Path):
@@ -144,7 +205,7 @@ def _get_list_of_filepaths_from_file(file_with_paths: Path):
 
 
 def _get_list_of_filepaths_from_dir(data_dir: Path):
-    # Get list of files (ignoring hidden files) in directory.
+    # Get a list of files (ignoring hidden files) in directory.
     input_files = [str(f) for f in data_dir.iterdir() if not f.name.startswith(".")]
     return input_files
 
@@ -153,7 +214,15 @@ def run_stitchee(args: list) -> None:
     """
     Parse arguments and run subsetter on the specified input file
     """
-    input_files, output_path, concat_dim, keep_tmp_files, temporary_dir_to_remove = parse_args(args)
+    (
+        input_files,
+        output_path,
+        concat_dim,
+        keep_tmp_files,
+        temporary_dir_to_remove,
+        concat_method,
+        concat_kwargs,
+    ) = parse_args(args)
     num_inputs = len(input_files)
 
     logging.info("Executing stitchee concatenation on %d files...", num_inputs)
@@ -162,7 +231,9 @@ def run_stitchee(args: list) -> None:
         output_path,
         write_tmp_flat_concatenated=keep_tmp_files,
         keep_tmp_files=keep_tmp_files,
+        concat_method=concat_method,
         concat_dim=concat_dim,
+        concat_kwargs=concat_kwargs,
     )
     logging.info("STITCHEE complete. Result in %s", output_path)
 
diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index 3e2f061..5976fc6 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -23,6 +23,7 @@ def stitchee(
     output_file: str,
     write_tmp_flat_concatenated: bool = False,
     keep_tmp_files: bool = True,
+    concat_method: str = "xarray-concat",
     concat_dim: str = "",
     concat_kwargs: dict | None = None,
     logger: Logger = default_logger,
@@ -97,13 +98,23 @@ def stitchee(
         if concat_kwargs is None:
             concat_kwargs = {}
 
-        combined_ds = xr.concat(
-            xrdataset_list,
-            dim=GROUP_DELIM + concat_dim,
-            data_vars="minimal",
-            coords="minimal",
-            **concat_kwargs,
-        )
+        if concat_method == "xarray-concat":
+            combined_ds = xr.concat(
+                xrdataset_list,
+                dim=GROUP_DELIM + concat_dim,
+                data_vars="minimal",
+                coords="minimal",
+                **concat_kwargs,
+            )
+        elif concat_method == "xarray-combine":
+            combined_ds = xr.combine_by_coords(
+                xrdataset_list,
+                data_vars="minimal",
+                coords="minimal",
+                **concat_kwargs,
+            )
+        else:
+            raise ValueError("Unexpected concatenation method, <%s>." % concat_method)
 
         benchmark_log["concatenating"] = time.time() - start_time
 

From 5ede24d80422336e8be3141633b5bc1fb32a86df Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 13:59:27 -0500
Subject: [PATCH 36/40] rename cli args

---
 concatenator/run_stitchee.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py
index 6da6c84..5b1ef79 100644
--- a/concatenator/run_stitchee.py
+++ b/concatenator/run_stitchee.py
@@ -68,16 +68,16 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None, str,
         "This is required if using the 'xarray-concat' method",
     )
     parser.add_argument(
-        "--concat_arg_compat",
-        help="'compat' argument passed to xarray.concat.",
+        "--xarray_arg_compat",
+        help="'compat' argument passed to xarray.concat() or xarray.combine_by_coords().",
     )
     parser.add_argument(
-        "--concat_arg_combine_attrs",
-        help="'combine_attrs' argument passed to xarray.concat.",
+        "--xarray_arg_combine_attrs",
+        help="'combine_attrs' argument passed to xarray.concat() or xarray.combine_by_coords().",
     )
     parser.add_argument(
-        "--concat_arg_join",
-        help="'join' argument passed to xarray.concat.",
+        "--xarray_arg_join",
+        help="'join' argument passed to xarray.concat() or xarray.combine_by_coords().",
     )
     parser.add_argument(
         "-O", "--overwrite", action="store_true", help="Overwrite output file if it already exists."
@@ -113,12 +113,12 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None, str,
 
     # Gather the concatenation arguments that will be passed to xarray.
     concat_kwargs = {}
-    if parsed.concat_arg_compat:
-        concat_kwargs["compat"] = parsed.concat_arg_compat
-    if parsed.concat_arg_combine_attrs:
-        concat_kwargs["combine_attrs"] = parsed.concat_arg_combine_attrs
-    if parsed.concat_arg_join:
-        concat_kwargs["join"] = parsed.concat_arg_join
+    if parsed.xarray_arg_compat:
+        concat_kwargs["compat"] = parsed.xarray_arg_compat
+    if parsed.xarray_arg_combine_attrs:
+        concat_kwargs["combine_attrs"] = parsed.xarray_arg_combine_attrs
+    if parsed.xarray_arg_join:
+        concat_kwargs["join"] = parsed.xarray_arg_join
 
     # If requested, make a temporary directory with new copies of the original input files
     temporary_dir_to_remove = None

From e28021633522b4dccb7db08ab064c2a1a5cf432d Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 14:05:07 -0500
Subject: [PATCH 37/40] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b9b6ce5..9fde59f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - [PR #1](https://github.com/danielfromearth/stitchee/pull/1): An initial GitHub Actions workflow
   - [Issue #8](https://github.com/danielfromearth/stitchee/issues/8): Create working Docker image
   - [Issue #10](https://github.com/danielfromearth/stitchee/issues/10): Add code necessary to communicate with Harmony
+  - [Issue #49](https://github.com/danielfromearth/stitchee/issues/49): More CLI arguments for finer control of concatenation method
 ### Changed
   - [PR #12](https://github.com/danielfromearth/stitchee/pull/12): Changed name to "stitchee"
   - [PR #15](https://github.com/danielfromearth/stitchee/pull/15): Use ruff+black chain for pre-commit lint & format

From e3b1b529bbd4e00c3b55daa66d766c07b06a2dfd Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 14:34:55 -0500
Subject: [PATCH 38/40] add warning if concat-dim argument is supplied when not
 being used

---
 concatenator/stitchee.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py
index 5976fc6..d1f2c8d 100644
--- a/concatenator/stitchee.py
+++ b/concatenator/stitchee.py
@@ -3,6 +3,7 @@
 import os
 import time
 from logging import Logger
+from warnings import warn
 
 import netCDF4 as nc
 import xarray as xr
@@ -53,6 +54,11 @@ def stitchee(
         logger.info("No non-empty netCDF files found. Exiting.")
         return ""
 
+    if concat_dim and (concat_method == "xarray-combine"):
+        warn(
+            "'concat_dim' was specified, but will not be used because xarray-combine method was selected."
+        )
+
     logger.info("Flattening all input files...")
     xrdataset_list = []
 

From b29edb4ff837bf52859816c3ad1bb275e087242f Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 14:40:58 -0500
Subject: [PATCH 39/40] update concat tests to use new arguments

---
 tests/test_concat.py | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/tests/test_concat.py b/tests/test_concat.py
index 24511f1..2ec0f82 100644
--- a/tests/test_concat.py
+++ b/tests/test_concat.py
@@ -34,6 +34,7 @@ def run_verification_with_stitchee(
         self,
         data_dir,
         output_name,
+        concat_method: str = "xarray-concat",
         record_dim_name: str = "mirror_step",
         concat_kwargs: dict | None = None,
     ):
@@ -55,6 +56,7 @@ def run_verification_with_stitchee(
             output_file=output_path,
             write_tmp_flat_concatenated=True,
             keep_tmp_files=True,
+            concat_method=concat_method,
             concat_dim=record_dim_name,
             concat_kwargs=concat_kwargs,
         )
@@ -93,16 +95,24 @@ def run_verification_with_nco(self, data_dir, output_name, record_dim_name="mirr
         assert length_sum == len(merged_dataset.variables[record_dim_name])
 
     def test_tempo_no2_concat_with_stitchee(self):
-        self.run_verification_with_stitchee("tempo/no2", "tempo_no2_bee_concatenated.nc")
+        self.run_verification_with_stitchee(
+            "tempo/no2", "tempo_no2_bee_concatenated.nc", concat_method="xarray-concat"
+        )
 
     def test_tempo_hcho_concat_with_stitchee(self):
-        self.run_verification_with_stitchee("tempo/hcho", "tempo_hcho_bee_concatenated.nc")
+        self.run_verification_with_stitchee(
+            "tempo/hcho", "tempo_hcho_bee_concatenated.nc", concat_method="xarray-concat"
+        )
 
     def test_tempo_cld04_concat_with_stitchee(self):
-        self.run_verification_with_stitchee("tempo/cld04", "tempo_cld04_bee_concatenated.nc")
+        self.run_verification_with_stitchee(
+            "tempo/cld04", "tempo_cld04_bee_concatenated.nc", concat_method="xarray-concat"
+        )
 
     def test_tempo_o3prof_concat_with_stitchee(self):
-        self.run_verification_with_stitchee("tempo/o3prof", "tempo_o3prof_bee_concatenated.nc")
+        self.run_verification_with_stitchee(
+            "tempo/o3prof", "tempo_o3prof_bee_concatenated.nc", concat_method="xarray-concat"
+        )
 
     # def test_icesat_concat_with_stitchee(self):
     #     self.run_verification_with_stitchee('icesat', 'icesat_concat_with_stitchee.nc')
@@ -111,15 +121,18 @@ def test_ceres_concat_with_stitchee(self):
         self.run_verification_with_stitchee(
             "ceres-subsetter-output",
             "ceres_bee_concatenated.nc",
+            concat_method="xarray-combine",
             record_dim_name="time",
-            concat_kwargs={"compat": "override"},
+            concat_kwargs={"compat": "override", "combine_attrs": "override"},
         )
 
     def test_ceres_flash_concat_with_stitchee(self):
         self.run_verification_with_stitchee(
             "ceres_flash-subsetter-output",
             "ceres_flash_bee_concatenated.nc",
+            concat_method="xarray-combine",
             record_dim_name="time",
+            concat_kwargs={"compat": "override", "combine_attrs": "override"},
         )
 
     # def test_ceres_flash_concat_with_stitchee(self):

From 1e9505134440927af4914006249ee106d87938c9 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Wed, 8 Nov 2023 14:49:07 -0500
Subject: [PATCH 40/40] update README.md with new CLI args

---
 README.md | 34 ++++++++++++++++++++++------------
 1 file changed, 22 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 6b87d96..1e823d9 100644
--- a/README.md
+++ b/README.md
@@ -25,35 +25,45 @@ poetry run pytest tests/
 
 ```shell
 $ poetry run stitchee --help
-usage: stitchee [-h] -o output_path [--concat_dim concat_dim] [--make_dir_copy] [--keep_tmp_files] [-O] [-v]
+usage: stitchee [-h] -o OUTPUT_PATH [--no_input_file_copies] [--keep_tmp_files] [--concat_method {xarray-concat,xarray-combine}] [--concat_dim CONCAT_DIM]
+                [--xarray_arg_compat XARRAY_ARG_COMPAT] [--xarray_arg_combine_attrs XARRAY_ARG_COMBINE_ATTRS] [--xarray_arg_join XARRAY_ARG_JOIN] [-O]
+                [-v]
                 path/directory or path list [path/directory or path list ...]
 
 Run the along-existing-dimension concatenator.
 
 options:
   -h, --help            show this help message and exit
-  --concat_dim concat_dim
-                        Dimension to concatenate along, if possible.
-  --make_dir_copy       Make a duplicate of the input directory to avoid modification of input files. This is useful for testing, but
-                        uses more disk space.
-  --keep_tmp_files      Prevents removal, after successful execution, of (1) the flattened concatenated file and (2) the input
-                        directory copy if created by '--make_dir_copy'.
+  --no_input_file_copies
+                        By default, input files are copied into a temporary directory to avoid modification of input files. This is useful for testing,
+                        but uses more disk space. By specifying this argument, no copying is performed.
+  --keep_tmp_files      Prevents removal, after successful execution, of (1) the flattened concatenated file and (2) the input directory copy if created
+                        by '--make_dir_copy'.
+  --concat_method {xarray-concat,xarray-combine}
+                        Whether to use the xarray concat method or the combine-by-coords method.
+  --concat_dim CONCAT_DIM
+                        Dimension to concatenate along, if possible. This is required if using the 'xarray-concat' method
+  --xarray_arg_compat XARRAY_ARG_COMPAT
+                        'compat' argument passed to xarray.concat() or xarray.combine_by_coords().
+  --xarray_arg_combine_attrs XARRAY_ARG_COMBINE_ATTRS
+                        'combine_attrs' argument passed to xarray.concat() or xarray.combine_by_coords().
+  --xarray_arg_join XARRAY_ARG_JOIN
+                        'join' argument passed to xarray.concat() or xarray.combine_by_coords().
   -O, --overwrite       Overwrite output file if it already exists.
   -v, --verbose         Enable verbose output to stdout; useful for debugging
 
 Required:
   path/directory or path list
-                        Files to be concatenated, specified via a (1) single directory containing the files to be concatenated, (2)
-                        single text file containing linebreak-separated paths of the files to be concatenated, or (3) multiple
-                        filepaths of the files to be concatenated.
-  -o output_path, --output_path output_path
+                        Files to be concatenated, specified via a (1) single directory containing the files to be concatenated, (2) single text file
+                        containing linebreak-separated paths of the files to be concatenated, or (3) multiple filepaths of the files to be concatenated.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
                         The output filename for the merged output.
 ```
 
 For example:
 
 ```shell
-poetry run stitchee /path/to/netcdf/directory/ /path/to/output.nc
+poetry run stitchee /path/to/netcdf/directory/ -o /path/to/output.nc
 ```
 
 ## Roadmap