Update GitHub Actions and dependency versions (#83)

nwb-extensions · Mar 31, 2024 · 7cb7618 · 7cb7618
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commit 7cb7618
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Showing 10 changed files with 56 additions and 79 deletions.
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -1,7 +1,6 @@
 name: Codespell
 on:
   push:
-  pull_request:
   workflow_dispatch:
 
 jobs:
@@ -10,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
-        uses: codespell-project/actions-codespell@v2
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -3,9 +3,6 @@ on:
   schedule:
     - cron: '0 5 * * *'  # once per day at midnight ET
   push:
-    branches:
-      - main
-  pull_request:
   workflow_dispatch:
 
 jobs:
@@ -15,6 +12,9 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -31,16 +31,11 @@ jobs:
         - { name: macos-python3.11   , os: macos-latest   , python-ver: "3.11" }
         - { name: macos-python3.12   , os: macos-latest   , python-ver: "3.12" }
     steps:
-    - name: Cancel non-latest runs
-      uses: styfle/[email protected]
-      with:
-        all_but_latest: true
-        access_token: ${{ github.token }}
-
-    - uses: actions/checkout@v4
+    - name: Checkout repo
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-ver }}
 

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
@@ -1,7 +1,6 @@
 name: Check Sphinx external links
 on:
   push:
-  pull_request:
   schedule:
     - cron: '0 5 * * 0'  # once every Sunday at midnight ET
   workflow_dispatch:
@@ -11,21 +10,15 @@ jobs:
     name: Check for broken Sphinx external links
     runs-on: ubuntu-latest
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/[email protected]
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ "{{" }} github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: "3.12"
 
       - name: Install Sphinx dependencies and package
         run: |

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/codespell.yml b/{{ cookiecutter.namespace }}/.github/workflows/codespell.yml
@@ -1,7 +1,6 @@
 name: Codespell
 on:
   push:
-  pull_request:
   workflow_dispatch:
 
 jobs:
@@ -10,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
-        uses: codespell-project/actions-codespell@v2
+        uses: codespell-project/actions-codespell@v2
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/ruff.yml b/{{ cookiecutter.namespace }}/.github/workflows/ruff.yml
@@ -1,7 +1,6 @@
 name: Ruff
 on:
   push:
-  pull_request:
   workflow_dispatch:
 
 jobs:
@@ -10,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Ruff
-        uses: chartboost/ruff-action@v1
+        uses: chartboost/ruff-action@v1
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
@@ -1,7 +1,6 @@
 name: Run all tests
 on:
   push:
-  pull_request:
   schedule:
     - cron: '0 5 * * 0'  # once every Sunday at midnight ET
   workflow_dispatch:
@@ -13,6 +12,9 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ "{{" }} github.workflow }}-${{ "{{" }} github.ref }}-${{ "{{" }} matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -39,19 +41,13 @@ jobs:
           - { name: macos-python3.12             , requirements: pinned     , python-ver: "3.12", os: macos-latest }
           - { name: macos-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: macos-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/[email protected]
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ "{{" }} github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ "{{" }} matrix.python-ver }}
 
@@ -111,6 +107,9 @@ jobs:
     defaults:
      run:
        shell: bash -l {0}  # needed for conda environment to work
+    concurrency:
+      group: ${{ "{{" }} github.workflow }}-${{ "{{" }} github.ref }}-${{ "{{" }} matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
@@ -123,18 +122,13 @@ jobs:
           - { name: conda-linux-python3.12           , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
           - { name: conda-linux-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ "{{" }} github.token }}
-
-      - uses: actions/checkout@v3
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           auto-activate-base: true

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml
@@ -1,7 +1,6 @@
 name: Run code coverage
 on:
   push:
-  pull_request:
   workflow_dispatch:
 
 jobs:
@@ -14,26 +13,23 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ "{{" }} github.workflow }}-${{ "{{" }} github.ref }}-${{ "{{" }} matrix.os }}
+      cancel-in-progress: true
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:  # used by codecov-action
       OS: ${{ "{{" }} matrix.os }}
-      PYTHON: '3.11'
+      PYTHON: '3.12'
     steps:
-      - name: Cancel any previous incomplete runs
-        uses: styfle/[email protected]
+      - name: Checkout repo
+        uses: actions/checkout@v4
         with:
-          all_but_latest: true
-          access_token: ${{ "{{" }} github.token }}
-
-      - uses: actions/checkout@v3
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # fetch tags
+          fetch-depth: 0  # tags are required to determine the version
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ "{{" }} env.PYTHON }}
 

diff --git a/{{ cookiecutter.namespace }}/pyproject.toml b/{{ cookiecutter.namespace }}/pyproject.toml
@@ -38,8 +38,8 @@ keywords = [
     'ndx-extension',
 ]
 dependencies = [
-    "pynwb>=2.5.0",
-    "hdmf>=3.10.0",
+    "pynwb>=2.6.0",
+    "hdmf>=3.13.0",
 ]
 
 # TODO: add URLs before release
@@ -108,10 +108,12 @@ exclude = [
   "__pycache__",
   "build/",
   "dist/",
+  "docs/source/conf.py",
 ]
 line-length = 120
 
 [tool.ruff.per-file-ignores]
+"src/pynwb/{{ cookiecutter.py_pkg_name }}/__init__.py" = ["E402", "F401"]
 "src/spec/create_extension_spec.py" = ["T201"]
 
 [tool.ruff.mccabe]

diff --git a/{{ cookiecutter.namespace }}/requirements-dev.txt b/{{ cookiecutter.namespace }}/requirements-dev.txt
@@ -1,15 +1,15 @@
 # pinned dependencies to reproduce an entire development environment to
 # run tests, check code style, and generate documentation
-black==23.9.1
+black==24.3.0
 codespell==2.2.6
-coverage==7.3.2
-hdmf==3.10.0
-hdmf-docutils==0.4.6
-pre-commit==3.4.0
-pynwb==2.5.0
-pytest==7.4.2
-pytest-cov==4.1.0
+coverage==7.4.4
+hdmf==3.13.0
+hdmf-docutils==0.4.7
+pre-commit==3.5.0
+pynwb==2.6.0
+pytest==8.1.1
+pytest-cov==5.0.0
+pytest-subtests==0.12.1
 python-dateutil==2.8.2
-pytest-subtests==0.6.0
-ruff==0.0.292
-tox==4.11.3
+ruff==0.3.4
+tox==4.14.2
diff --git a/{{ cookiecutter.namespace }}/requirements-min.txt b/{{ cookiecutter.namespace }}/requirements-min.txt
@@ -1,5 +1,5 @@
 # minimum versions of package dependencies for installation
 # these should match the minimum versions specified in pyproject.toml
 # NOTE: it may be possible to relax these minimum requirements
-pynwb==2.5.0
-hdmf==3.10.0
+pynwb==2.6.0
+hdmf==3.13.0