Merge branch 'master' into fix-datajoint#1218

Author: yambottle

.devcontainer/devcontainer.json

@@ -28,7 +28,7 @@
 	// "runServices": [],
 	// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
 	"shutdownAction": "stopCompose",
-	"onCreateCommand": "python3 -m pip install -q -e .[test]",
+	"onCreateCommand": "python3 -m pip install -q -e .[dev]",
 	"features": {
 		"ghcr.io/devcontainers/features/git:1": {},
 		"ghcr.io/devcontainers/features/docker-in-docker:2": {},

.github/workflows/close_inactive_issues.yaml .github/workflows/close_inactive_issues_prs.yaml

@@ -1,7 +1,8 @@
-name: Close inactive issues
+name: Close inactive issues and PRs
 on:
   schedule:
     - cron: "30 1 * * *"
+  workflow_dispatch:
 
 jobs:
   close-issues:
@@ -12,11 +13,21 @@ jobs:
     steps:
       - uses: actions/stale@v9
         with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          operations-per-run: 500 # API rate limit
+          ## issues
+          # stale
           days-before-issue-stale: 45 # for initial period, suggest 15
           stale-issue-label: "stale"
           stale-issue-message: "This issue is stale because it has been open for 45 days with no activity."
+          # close
           days-before-issue-close: 365 # for initial period, suggest 30
           close-issue-message: "This issue was closed because it has been inactive for 365 days since being marked as stale, please reopen if it's still applicable."
+          ## PRs
+          # stale
           days-before-pr-stale: 45 # for initial period, suggest 15
+          stale-pr-label: "stale"
+          stale-pr-message: "This PR is stale because it has been open for 45 days with no activity."
+          # close
           days-before-pr-close: 365 # for initial period, suggest 30
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          close-pr-message: "This PR was closed because it has been inactive for 365 days since being marked as stale, please reopen if it's still applicable."

.github/workflows/development.yaml

@@ -1,12 +1,10 @@
 name: Manual docs release
 on:
   workflow_dispatch:
+  workflow_call:
 jobs:
   publish-docs:
     runs-on: ubuntu-latest
-    env:
-      DOCKER_CLIENT_TIMEOUT: "120"
-      COMPOSE_HTTP_TIMEOUT: "120"
     steps:
       - uses: actions/checkout@v4
       - name: Deploy docs

.github/workflows/docs.yaml

@@ -0,0 +1,29 @@
+name: Test
+on:
+  push:
+    branches:
+      - "**" # every branch
+      - "!gh-pages" # exclude gh-pages branch
+      - "!stage*" # exclude branches beginning with stage
+  pull_request:
+    branches:
+      - "**" # every branch
+      - "!gh-pages" # exclude gh-pages branch
+      - "!stage*" # exclude branches beginning with stage
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    # enforce the same check as pre-commit
+    # but only run important checks
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: codespell --all-files
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: black --all-files
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: flake8 --all-files