From 003c8896824163ceba8f92449e95c82971333019 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 17 Aug 2020 17:54:37 -0400
Subject: [PATCH 1/6] FIX: Ensure templateflow Layout is re-indexed when
 updating

---
 templateflow/conf/__init__.py | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/templateflow/conf/__init__.py b/templateflow/conf/__init__.py
index f4b387b7..9d29cf2f 100644
--- a/templateflow/conf/__init__.py
+++ b/templateflow/conf/__init__.py
@@ -45,11 +45,19 @@
 def update(local=False, overwrite=True, silent=False):
     """Update an existing DataLad or S3 home."""
     if TF_USE_DATALAD and _update_datalad():
-        return True
-
-    from ._s3 import update as _update_s3
+        success = True
+    else:
+        from ._s3 import update as _update_s3
+        success = _update_s3(TF_HOME, local=local, overwrite=overwrite, silent=silent)
 
-    return _update_s3(TF_HOME, local=local, overwrite=overwrite, silent=silent)
+    # update Layout only if necessary
+    if success and TF_LAYOUT is not None:
+        init_layout()
+        # ensure the api uses the updated layout
+        import importlib
+        from .. import api
+        importlib.reload(api)
+    return success
 
 
 def setup_home(force=False):
@@ -76,9 +84,12 @@ def _update_datalad():
 
 
 TF_LAYOUT = None
-try:
+
+
+def init_layout():
     from .bids import Layout
 
+    global TF_LAYOUT
     TF_LAYOUT = Layout(
         TF_HOME,
         validate=False,
@@ -92,5 +103,9 @@ def _update_datalad():
             "scripts",
         ],
     )
+
+
+try:
+    init_layout()
 except ImportError:
     pass

From ab17865112b8d4364e7f907e358ca5594dcaf7e8 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 17 Aug 2020 22:45:51 -0400
Subject: [PATCH 2/6] FIX: Allow redirects in GET request

---
 templateflow/conf/_s3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templateflow/conf/_s3.py b/templateflow/conf/_s3.py
index 9e20cbeb..4051ce86 100644
--- a/templateflow/conf/_s3.py
+++ b/templateflow/conf/_s3.py
@@ -27,7 +27,7 @@ def _get_skeleton_file():
     import requests
 
     try:
-        r = requests.get(TF_SKEL_URL(release="master", ext="md5", allow_redirects=True))
+        r = requests.get(TF_SKEL_URL(release="master", ext="md5"), allow_redirects=True)
     except requests.exceptions.ConnectionError:
         return
 
@@ -35,7 +35,7 @@ def _get_skeleton_file():
         return
 
     if r.content.decode().split()[0] != TF_SKEL_MD5:
-        r = requests.get(TF_SKEL_URL(release="master", ext="zip", allow_redirects=True))
+        r = requests.get(TF_SKEL_URL(release="master", ext="zip"), allow_redirects=True)
         if r.ok:
             from os import close
 

From c13b367e36faeaf4a5204626d863d54dfb15747c Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 17 Aug 2020 22:46:13 -0400
Subject: [PATCH 3/6] ENH: Add test for skeleton update

---
 templateflow/tests/test_conf.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 templateflow/tests/test_conf.py

diff --git a/templateflow/tests/test_conf.py b/templateflow/tests/test_conf.py
new file mode 100644
index 00000000..0c537943
--- /dev/null
+++ b/templateflow/tests/test_conf.py
@@ -0,0 +1,25 @@
+from pathlib import Path
+from .. import conf, api
+
+
+def test_update_s3(tmp_path):
+    conf.TF_HOME = tmp_path / 'templateflow'
+    conf.TF_HOME.mkdir(exist_ok=True)
+
+    # replace TF_SKEL_URL with the path of a legacy skeleton
+    _skel_url = conf._s3.TF_SKEL_URL
+    conf._s3.TF_SKEL_URL = (
+        "https://github.com/templateflow/python-client/raw/0.5.0/"
+        "templateflow/conf/templateflow-skel.{ext}".format
+    )
+    # initialize templateflow home, making sure to pull the legacy skeleton
+    conf.update(local=False)
+    # ensure we can grab a file
+    assert Path(api.get('MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask')).exists()
+    # and ensure we can't fetch one that doesn't yet exist
+    assert not api.get('Fischer344', hemi='L', desc='brain', suffix='mask')
+
+    # refresh the skeleton using the most recent skeleton
+    conf._s3.TF_SKEL_URL = _skel_url
+    conf.update(local=True, overwrite=True)
+    assert Path(api.get('Fischer344', hemi='L', desc='brain', suffix='mask')).exists()

From f8e38b473b1466612ed85b04dffa5a7cb5210acb Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 17 Aug 2020 22:54:27 -0400
Subject: [PATCH 4/6] FIX: failing doi test

---
 setup.cfg                      | 2 +-
 templateflow/tests/test_api.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 16b5cc95..ec60d3a5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,7 +49,7 @@ exclude =
 
 [options.extras_require]
 citations =
-    doi2bib
+    doi2bib >= 0.4.0
 datalad =
     datalad ~= 0.12.0
 doc =
diff --git a/templateflow/tests/test_api.py b/templateflow/tests/test_api.py
index ba98fc22..874c39b9 100644
--- a/templateflow/tests/test_api.py
+++ b/templateflow/tests/test_api.py
@@ -24,7 +24,7 @@
     "\tauthor = {Vladimir Fonov and Alan C. Evans and Kelly Botteron and C. "
     "Robert Almli and Robert C. McKinstry and D. Louis Collins},\n"
     "\ttitle = {Unbiased average age-appropriate atlases for pediatric studies},\n"
-    "\tjournal = {{NeuroImage}}\n}"
+    "\tjournal = {NeuroImage}}\n}"
 )
 
 mni2009_lbib = (

From c9fe6cd76413f9b5a31fbed0d0c74b5f95b3868f Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 17 Aug 2020 23:23:02 -0400
Subject: [PATCH 5/6] FIX: skip test if using datalad

---
 templateflow/tests/test_conf.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/templateflow/tests/test_conf.py b/templateflow/tests/test_conf.py
index 0c537943..c2d95f22 100644
--- a/templateflow/tests/test_conf.py
+++ b/templateflow/tests/test_conf.py
@@ -1,7 +1,9 @@
 from pathlib import Path
+import pytest
 from .. import conf, api
 
 
+@pytest.mark.skipif(conf.TF_USE_DATALAD, reason="S3 only")
 def test_update_s3(tmp_path):
     conf.TF_HOME = tmp_path / 'templateflow'
     conf.TF_HOME.mkdir(exist_ok=True)

From 72811b802a1ef68d4fbe286d56dc9904ec748d17 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Sun, 13 Sep 2020 11:33:15 -0400
Subject: [PATCH 6/6] PIN: doi2bib to older versions until bibcure/doi2bib#6 is
 resolved

---
 .circleci/config.yml           | 2 +-
 setup.cfg                      | 2 +-
 templateflow/tests/test_api.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 115902f4..f9399f75 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -45,7 +45,7 @@ jobs:
             source /tmp/venv/bin/activate
             pip install -U pip
             pip install -r /tmp/src/templateflow/requirements.txt
-            pip install "datalad ~= 0.11.8" doi2bib
+            pip install "datalad ~= 0.11.8" "doi2bib < 0.4"
             pip install "setuptools>=42.0" "setuptools_scm[toml] >= 3.4" twine codecov
 
       - run:
diff --git a/setup.cfg b/setup.cfg
index ec60d3a5..10123688 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,7 +49,7 @@ exclude =
 
 [options.extras_require]
 citations =
-    doi2bib >= 0.4.0
+    doi2bib < 0.4.0
 datalad =
     datalad ~= 0.12.0
 doc =
diff --git a/templateflow/tests/test_api.py b/templateflow/tests/test_api.py
index 874c39b9..ba98fc22 100644
--- a/templateflow/tests/test_api.py
+++ b/templateflow/tests/test_api.py
@@ -24,7 +24,7 @@
     "\tauthor = {Vladimir Fonov and Alan C. Evans and Kelly Botteron and C. "
     "Robert Almli and Robert C. McKinstry and D. Louis Collins},\n"
     "\ttitle = {Unbiased average age-appropriate atlases for pediatric studies},\n"
-    "\tjournal = {NeuroImage}}\n}"
+    "\tjournal = {{NeuroImage}}\n}"
 )
 
 mni2009_lbib = (