Merge branch 'main' into mmg/rename-to-github-owner

UCL-ARC · Oct 22, 2024 · a2026e1 · a2026e1
2 parents ebf2649 + df14157
commit a2026e1
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -84,7 +84,7 @@
       "login": "sfmig",
       "name": "sfmig",
       "avatar_url": "https://avatars.githubusercontent.com/u/33267254?v=4",
-      "profile": "https://sfmig.github.io/",
+      "profile": "https://github.com/sfmig",
       "contributions": [
         "bug",
         "code",
@@ -240,6 +240,15 @@
         "code",
         "question"
       ]
+    },
+    {
+      "login": "llapira",
+      "name": "llapira",
+      "avatar_url": "https://avatars.githubusercontent.com/u/48060852?v=4",
+      "profile": "https://github.com/LLapira",
+      "contributions": [
+        "bug"
+      ]
     }
   ]
 }
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,7 +1,6 @@
 ---
 name: Bug Report
 description: Create a Report to Help us Improve
-title: "A one-line description of your problem"
 labels:
   - bug
 body:

diff --git a/.github/ISSUE_TEMPLATE/documentation.yml b/.github/ISSUE_TEMPLATE/documentation.yml
@@ -1,7 +1,6 @@
 ---
 name: Documentation
 description: How Can We Improve the Documentation
-title: "What needs improving in the documentation?"
 labels:
   - documentation
 body:

diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,7 +1,6 @@
 ---
 name: Feature Request
 description: Suggest a Way to Improve This Project
-title: "Feature suggestion: What should be added?"
 labels:
   - enhancement
 body:
@@ -18,8 +17,6 @@ body:
     attributes:
       label: Describe the Solution You'd Like
       description: A clear and concise description of what you want to happen.
-    validations:
-      required: true
   - id: alternatives
     type: textarea
     attributes:

diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml
@@ -1,7 +1,6 @@
 ---
 name: Question
 description: General Questions About Using the Cookiecutter Template
-title: "The title of your question."
 labels:
   - question
 body:

diff --git a/.github/ISSUE_TEMPLATE/task.yml b/.github/ISSUE_TEMPLATE/task.yml
@@ -1,7 +1,6 @@
 ---
 name: Task
 description: A Task to be Completed
-title: "Task: What needs to be done?"
 labels:
   - task
 body:

diff --git a/.github/ISSUE_TEMPLATE/website.yml b/.github/ISSUE_TEMPLATE/website.yml
@@ -1,7 +1,6 @@
 ---
 name: Website
 description: How Can We Improve the Website
-title: "Website Improvement:"
 labels:
   - website
 body:

diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml
@@ -15,19 +15,22 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Link Checker
         id: lychee
         uses: lycheeverse/lychee-action@2b973e86fc7b1f6b36a93795fe2c9c6ae1118621 # v1.10.0
         with:
           # Exclude the image.sc forum (which works) but returns 403 from
           # github runners and exclude relative links to other pages. Ignore
-          # the whole of the project slug README since the links are
+          # gnu.org and fsf.org because they're often down but are still the right
+          # websites to link to!
+          #
+          # Ignore the whole of the project slug README since the links are
           # necessarily not real links - i.e. demos and to be filled by
           # cookiecutter values.
           args:
-            "--verbose --exclude https://forum.image.sc/ --exclude docs/pages
+            "--verbose --exclude https://forum.image.sc/ --exclude http://www.gnu.org --exclude http://fsf.org --exclude docs/pages
             --exclude-path '{{cookiecutter.project_slug}}/README.md'  -- ."
           fail: true
           jobSummary: true

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Cache pre-commit
         uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
@@ -21,7 +21,7 @@ jobs:
           key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
           python-version: "3.x"
 
@@ -35,7 +35,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Cache pre-commit
         uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
@@ -44,7 +44,7 @@ jobs:
           key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
 
       - name: Set up python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
           python-version: "3.x"
 

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -33,11 +33,11 @@ jobs:
       BUNDLE_GEMFILE: ${{ github.workspace }}/docs/Gemfile
     steps:
       - name: Checkout
-        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: "3.1" # Not needed with a .ruby-version file
+          ruby-version: "3.3" # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
           cache-version: 0 # Increment this number if you need to re-download cached gems
       - name: Setup Pages

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -18,13 +18,13 @@ jobs:
           - ubuntu-latest
           - windows-latest
         python-version:
-          - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
 
     steps:
       - name: Checkout source
-        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Cache tox
         uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
@@ -33,16 +33,16 @@ jobs:
           key: test-${{ hashFiles('pyproject.toml') }}
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: pyproject.toml
 
       - name: Install dependencies
-        run: python -m pip install tox tox-gh-actions
+        run: python -m pip install tox tox-gh
 
       - name: Run tests
-        run: tox
+        run: tox run
         env:
-          OS: ${{ matrix.os }}
+          TOX_GH_MAJOR_MINOR: ${{ matrix.python-version }}
diff --git a/.markdownlint.yaml b/.markdownlint.yaml
@@ -0,0 +1,2 @@
+---
+MD013: false
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,14 +1,20 @@
 exclude: ^{{cookiecutter.project_slug}}/
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.6.8
     hooks:
       - id: ruff
         args:
           - --config=pyproject.toml
       - id: ruff-format
         args:
           - --config=pyproject.toml
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.42.0
+    hooks:
+      - id: markdownlint-fix
+        args:
+          - --dot
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5
     hooks:
@@ -18,7 +24,7 @@ repos:
     hooks:
       - id: toml-sort-fix
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.11.2
     hooks:
       - id: mypy
         args:
@@ -43,7 +49,7 @@ repos:
           - --fix=lf
       - id: trailing-whitespace
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.4
+    rev: 0.29.3
     hooks:
       # Schemas taken from https://www.schemastore.org/json/
       - id: check-jsonschema

diff --git a/.renovaterc.json5 b/.renovaterc.json5
@@ -2,7 +2,7 @@
   $schema: "https://docs.renovatebot.com/renovate-schema.json",
   extends: [
     "github>UCL-ARC/.github//renovate/default-config.json",
+    ":assignAndReview(team:collaborations-python-tooling)",
     ":maintainLockFilesMonthly",
   ],
-  reviewers: ["paddyroddy", "samcunliffe"],
 }
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,3 +1,5 @@
+# Contributing Guide
+
 This template and our [recommendation pages][website] were made by [research
 software engineers] at [UCL's Centre for Advanced Research Computing][UCL ARC].
 We made it with research software projects in mind, but whoever you are, we hope