Merge branch 'main' of github.com:SciTools/python-stratify into auto_…

…pr_labels

* 'main' of github.com:SciTools/python-stratify:
  Updated environment lockfiles (SciTools#129)
  adopting sort-all pre-commit git hook (SciTools#128)
  Updated environment lockfiles (SciTools#127)
  Bump scitools/workflows from 2023.05.0 to 2023.06.0 (SciTools#126)
  Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 (SciTools#125)
  Updated environment lockfiles (SciTools#124)
  adding a CITATION.cff and a GHA to check it (SciTools#123)
  Updated environment lockfiles (SciTools#122)
  Adding a GHA to check for stale issues and pull-requests (SciTools#120)

Rebase to upstream

.github/workflows/ci-citation.yml

@@ -0,0 +1,30 @@
+name: ci-citation
+
+on:
+  pull_request:
+    paths:
+      - "CITATION.cff"
+
+  push:
+    paths:
+      - "CITATION.cff"
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: "check CITATION.cff"
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"

.github/workflows/ci-locks.yml

@@ -18,5 +18,5 @@ concurrency:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.05.0
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.06.0
     secrets: inherit

.github/workflows/ci-manifest.yml

@@ -25,4 +25,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.05.0
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.06.0

.github/workflows/ci-wheels.yml

@@ -48,7 +48,7 @@ jobs:
         fetch-depth: 0
 
     - name: "build ${{ matrix.os }} (${{ matrix.arch }}) wheels"
-      uses: pypa/[email protected].0
+      uses: pypa/[email protected].1
       env:
         CIBW_SKIP: "cp36-* cp37-* pp* *-musllinux*"
         CIBW_ARCHS: ${{ matrix.arch }}

.github/workflows/stale.yml

@@ -0,0 +1,88 @@
+# See https://github.com/actions/stale
+
+name: Stale issues and pull-requests
+
+on:
+  schedule:
+    # Run once a day
+    # N.B. "should" be quoted, according to
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#onschedule
+    - cron: "0 0 * * *"
+
+jobs:
+  stale:
+    if: "github.repository == 'SciTools/python-stratify'"
+    runs-on: ubuntu-latest
+
+    env:
+      DAYS_BEFORE_STALE: 500
+      DAYS_BEFORE_CLOSE: 28
+
+    steps:
+      - uses: actions/stale@v8
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+          # Idle number of days before marking issues/prs stale.
+          days-before-stale: ${{ env.DAYS_BEFORE_STALE }}
+
+          # Idle number of days before closing stale issues/prs.
+          days-before-close: ${{ env.DAYS_BEFORE_CLOSE }}
+
+          # Comment on the staled issues.
+          stale-issue-message: |
+            In order to maintain a backlog of relevant issues, we automatically label them as stale after ${{ env.DAYS_BEFORE_STALE }} days of inactivity.
+
+            If this issue is still important to you, then please comment on this issue and the stale label will be removed.
+
+            Otherwise this issue will be automatically closed in ${{ env.DAYS_BEFORE_CLOSE }} days time.
+
+          # Comment on the staled prs.
+          stale-pr-message: | 
+            In order to maintain a backlog of relevant PRs, we automatically label them as stale after ${{ env.DAYS_BEFORE_STALE }} days of inactivity.
+
+            If this PR is still important to you, then please comment on this PR and the stale label will be removed.
+
+            Otherwise this PR will be automatically closed in ${{ env.DAYS_BEFORE_CLOSE }} days time.
+
+          # Comment on the staled issues while closed.
+          close-issue-message: |
+            This stale issue has been automatically closed due to a lack of community activity.
+            
+            If you still care about this issue, then please either:
+              * Re-open this issue, if you have sufficient permissions, or
+              * Add a comment pinging `@SciTools/stratify-maintainers` who will re-open on your behalf.
+
+          # Comment on the staled prs while closed.
+          close-pr-message: |
+            This stale PR has been automatically closed due to a lack of community activity.
+            
+            If you still care about this PR, then please either:
+              * Re-open this PR, if you have sufficient permissions, or
+              * Add a comment pinging `@SciTools/stratify-maintainers` who will re-open on your behalf.
+
+          # Label to apply on staled issues.
+          stale-issue-label: Stale
+
+          # Label to apply on staled prs.
+          stale-pr-label: Stale
+
+          # Labels on issues exempted from stale.
+          exempt-issue-labels:
+            "Status: Blocked,Status: Decision Required"
+
+          # Labels on prs exempted from stale.
+          exempt-pr-labels:
+            "Status: Blocked,Status: Decision Required"
+
+          # Max number of operations per run.
+          operations-per-run: 300
+
+          # Remove stale label from issues/prs on updates/comments.
+          remove-stale-when-updated: true
+
+          # Order to get issues/PRs.
+          ascending: true
+
+          # Exempt all issues/prs with milestones from stale.
+          exempt-all-milestones: true

.pre-commit-config.yaml

@@ -39,3 +39,9 @@ repos:
         name: isort (cython)
         types: [file, cython]
         args: [--filter-files]
+
+-   repo: https://github.com/aio-libs/sort-all
+    rev: "v1.2.0"
+    hooks:
+    - id: sort-all
+      types: [file, python]

CITATION.cff

@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+message: "If Python-Stratify played an important part in your research then please add us to your reference list by using the references below."
+authors:
+- family-names: "Elson"
+  given-names: "Phil"
+  orcid: "https://orcid.org/0000-0001-6360-749X"
+- family-names: "Little"
+  given-names: "Bill"
+  orcid: "https://orcid.org/0000-0002-1345-9465"
+- family-names: "Andela"
+  given-names: "Bouwe"
+  orcid: "https://orcid.org/0000-0001-9005-8940"
+- family-names: "Dreyer"
+  given-names: "Laura"
+  orcid: "https://orcid.org/0009-0006-6310-3658"
+- family-names: "Fernandes"
+  given-names: "Filipe"
+  orcid: "https://orcid.org/0000-0003-4165-2913"
+- family-names: "Rol"
+  given-names: "Evert"
+  orcid: "https://orcid.org/0000-0001-8357-4453"
+- family-names: "Wright"
+  given-names: "Henry"
+  orcid: "https://orcid.org/0009-0005-1489-760X"
+- family-names: "Yeo"
+  given-names: "Martin"
+  orcid: "https://orcid.org/0009-0000-6857-560X"
+title: "python-stratify"
+abstract: "Interpolation for restratification, particularly useful for Nd vertical interpolation of atmospheric and oceanographic datasets"
+license: "BSD-3-Clause"
+license-url: "https://spdx.org/licenses/BSD-3-Clause.html"
+date-released: "2018-06-01"
+doi: "10.5281/zenodo.7863857"
+repository-code: "https://github.com/SciTools/python-stratify"
+type: "software"

MANIFEST.in

@@ -2,6 +2,7 @@ prune .github
 prune requirements
 recursive-include requirements *.txt
 recursive-include src *.py *.pyx
+include CITATION.cff
 exclude .flake8
 exclude .gitignore
 exclude .pre-commit-config.yaml