Merge pull request #41 from kabilar/main

Update GitHub Actions

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: false
 contact_links:
   - name: DataJoint Contribution Guideline
-    url: https://docs.datajoint.org/python/community/02-Contribute.html
+    url: https://datajoint.com/docs/community/contribute/
     about: Please make sure to review the DataJoint Contribution Guidelines

.github/workflows/release.yaml

@@ -0,0 +1,18 @@
+name: Release
+on:
+  workflow_dispatch:
+jobs:
+  make_github_release:
+    uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
+  pypi_release:
+    needs: make_github_release
+    uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
+    secrets:
+      TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
+      TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
+    with:
+      UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
+  mkdocs_release:
+    uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
+    permissions: 
+      contents: write

.github/workflows/test.yaml

@@ -0,0 +1,32 @@
+name: Test
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        py_ver: ["3.9", "3.10"]
+        mysql_ver: ["8.0", "5.7"]
+        include:
+          - py_ver: "3.8"
+            mysql_ver: "5.7"
+          - py_ver: "3.7"
+            mysql_ver: "5.7"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 "black[jupyter]"
+      - name: Run style tests
+        run: |
+          python_version=${{matrix.py_ver}}
+          black element_animal --check --verbose --target-version py${python_version//.}
+

CHANGELOG.md

@@ -3,7 +3,12 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.1.7] - 2023 05-11
+## [0.1.8] - 2023-06-20
+
++ Update - GitHub Actions workflows
++ Fix - Remove Google Analytics key
+
+## [0.1.7] - 2023-05-11
 
 + Fix - `.ipynb` dark mode output for all notebooks.
 + Update - CHANGELOG markdown from "-" to "+" for consistency with other
@@ -53,6 +58,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `subject` schema
 + Add - `genotyping` schema
 
+[0.1.8]: https://github.com/datajoint/element-animal/releases/tag/0.1.8
 [0.1.7]: https://github.com/datajoint/element-animal/releases/tag/0.1.7
 [0.1.6]: https://github.com/datajoint/element-animal/releases/tag/0.1.6
 [0.1.5]: https://github.com/datajoint/element-animal/releases/tag/0.1.5

README.md

@@ -1,3 +1,5 @@
+[![PyPI version](https://badge.fury.io/py/element-animal.svg)](http://badge.fury.io/py/element-animal)
+
 # Element Animal
 
 DataJoint Element for storing animal meta data, genotype, and surgery information.

docs/.docker/pip_requirements.txt

@@ -7,4 +7,6 @@ mdx-truly-sane-lists
 mkdocs-gen-files
 mkdocs-literate-nav
 mkdocs-exclude-search
-mkdocs-markdownextradata-plugin
+mkdocs-markdownextradata-plugin
+mkdocs-jupyter
+mkdocs-section-index

docs/docker-compose.yaml

@@ -1,6 +1,4 @@
 # MODE="LIVE|QA|PUSH" PACKAGE=element_animal UPSTREAM_REPO=https://github.com/datajoint/element-animal.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
-#
-# navigate to http://localhost/
 version: "2.4"
 services:
   docs:
@@ -14,7 +12,6 @@ services:
       - PACKAGE
       - UPSTREAM_REPO
       - MODE
-      - GOOGLE_ANALYTICS_KEY 
       - PATCH_VERSION
     volumes:
       - ../docs:/main/docs

docs/mkdocs.yaml

@@ -42,17 +42,14 @@ nav:
 #     UPSTREAM_REPO=https://github.com/datajoint/element-{ELEMENT}.git \
 #     HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
 #     ```
-# 02. Site analytics depend on a local environment variable GOOGLE_ANALYTICS_KEY
-#     You can find this in LastPass or declare with any string to suppress errors
-# 03. The API section will pull docstrings.
+# 02. The API section will pull docstrings.
 #     A. Follow google styleguide e.g.,
 #        https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
 #        With typing suggestions: https://docs.python.org/3/library/typing.html
 #     B. To pull a specific workflow fork, change ./docs/src/api/make_pages.py#L19
-# 04. To see your fork of the workflow-{element} in this render, change the
+# 03. To see your fork of the workflow-{element} in this render, change the
 #     URL in ./docs/src/api/make_pages.py#L19 to your fork.
-# 05. For redirecting options For redirect options, see 'redirects' below.
-# 06. To deploy this site on your fork,
+# 04. To deploy this site on your fork,
 #     A. declare a branch called gh-pages
 #     B. go to the your fork > settings > pages
 #     C. direct pages to render from the gh-pages branch at root
@@ -87,9 +84,6 @@ theme:
 plugins:
   - markdownextradata: {}
   - search
-  # - redirects: # OPTIONAL REDIRECTS
-  #     redirect_maps:
-  #       "index.md": "getting_started.md"
   - mkdocstrings:
       default_handler: python
       handlers:
@@ -126,13 +120,12 @@ markdown_extensions:
       linenums: true
   - pymdownx.inlinehilite
   - pymdownx.snippets
-
+  - pymdownx.magiclink # Displays bare URLs as links
+  - pymdownx.tasklist: # Renders check boxes in tasks lists
+      custom_checkbox: true
 extra:
   PATCH_VERSION: !ENV PATCH_VERSION
   generator: false # Disable watermark
-  analytics:
-    provider: google
-    property: !ENV GOOGLE_ANALYTICS_KEY
   version:
     provider: mike
   social:

element_animal/subject.py

@@ -11,7 +11,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: bool = True
+    linking_module: bool = True,
 ):
     """Activate this schema.