template update scverse scverse tutorials v0.2.21 (#108)

Co-authored-by: scverse-bot <None>
Co-authored-by: grst <grst@users.noreply.github.com>
Co-authored-by: Philipp A <flying-sheep@web.de>

.codecov.yaml

@@ -1,17 +1,17 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
+  require_ci_to_pass: no
 
 coverage:
-    status:
-        project:
-            default:
-                # Require 1% coverage, i.e., always succeed
-                target: 1
-        patch: false
-        changes: false
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
 
 comment:
-    layout: diff, flags, files
-    behavior: once
-    require_base: no
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

.cruft.json

@@ -1,23 +1,23 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
-    "checkout": "main",
-    "context": {
-        "cookiecutter": {
-            "project_name": "scverse-tutorials",
-            "package_name": "scverse_tutorials",
-            "project_description": "A very interesting piece of code",
-            "author_full_name": "scverse team",
-            "author_email": "core-team@scverse.org",
-            "github_user": "scverse",
-            "project_repo": "https://github.com/scverse/scverse-tutorials",
-            "license": "BSD 3-Clause License",
-            "_copy_without_render": [
-                ".github/workflows/**.yaml",
-                "docs/_templates/autosummary/**.rst"
-            ],
-            "_template": "https://github.com/scverse/cookiecutter-scverse"
-        }
-    },
-    "directory": null
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "23a9eaaf101dc9b6d31976f32f7345e1b209b071",
+  "checkout": "v0.2.21",
+  "context": {
+    "cookiecutter": {
+      "project_name": "scverse-tutorials",
+      "package_name": "scverse_tutorials",
+      "project_description": "A very interesting piece of code",
+      "author_full_name": "scverse team",
+      "author_email": "core-team@scverse.org",
+      "github_user": "scverse",
+      "project_repo": "https://github.com/scverse/scverse-tutorials",
+      "license": "BSD 3-Clause License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
 }

.editorconfig

@@ -8,5 +8,11 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

.github/workflows/execute-nbs.yaml

@@ -1,80 +1,80 @@
 name: Execute notebooks
 on:
-    pull_request:
-        branches: [main]
-        paths:
-            - "docs/**"
-            - "environment.yml"
+  pull_request:
+    branches: [main]
+    paths:
+      - "docs/**"
+      - "environment.yml"
 
 jobs:
-    runnbs:
-        runs-on: ubuntu-latest
-        concurrency:
-            group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-            cancel-in-progress: true
-        defaults:
-            run:
-                shell: bash -el {0}
-        steps:
-            - uses: actions/checkout@v2
-              with:
-                  repository: ${{ github.event.pull_request.head.repo.full_name }}
-                  ref: ${{ github.head_ref }}
-            - name: Cache conda
-              uses: actions/cache@v2
-              env:
-                  # Increase this value to reset cache if env file has not changed
-                  CACHE_NUMBER: 0
-              with:
-                  path: ~/conda_pkgs_dir
-                  key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-            - name: Cache notebooks
-              uses: actions/cache@v2
-              env:
-                  # Increase this value to reset cache if env file has not changed
-                  CACHE_NUMBER: 0
-              with:
-                  path: .jupyter_cache
-                  key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-            - uses: conda-incubator/setup-miniconda@v2
-              with:
-                  activate-environment: tutorials
-                  channel-priority: strict
-                  environment-file: environment.yml
-                  miniforge-variant: Mambaforge
-                  miniforge-version: latest
-                  use-mamba: true
-                  use-only-tar-bz2: true # This needs to be set for caching to work properly!
+  runnbs:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.head_ref }}
+      - name: Cache conda
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if env file has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+      - name: Cache notebooks
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if env file has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: .jupyter_cache
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: tutorials
+          channel-priority: strict
+          environment-file: environment.yml
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
+          use-only-tar-bz2: true # This needs to be set for caching to work properly!
 
-            - name: execute notebooks
-              run: |
-                  mkdir -p .jupyter_cache
-                  # set kernel to "python3" (just in case someone used a custom conda env kernel locally)
-                  for f in docs/notebooks/*.ipynb ; do
-                      jupytext --to notebook --set-kernel python3 $f
-                  done
+      - name: execute notebooks
+        run: |
+          mkdir -p .jupyter_cache
+          # set kernel to "python3" (just in case someone used a custom conda env kernel locally)
+          for f in docs/notebooks/*.ipynb ; do
+              jupytext --to notebook --set-kernel python3 $f
+          done
 
-                  # First remove all notebooks from the project, then add all again.
-                  # This does not remove them from the cache. This step is required since a notebook could be in the cache, but not in the PR.
-                  jcache notebook clear --force
-                  jcache notebook add docs/notebooks/*.ipynb
-                  jcache project execute --timeout 1800
+          # First remove all notebooks from the project, then add all again.
+          # This does not remove them from the cache. This step is required since a notebook could be in the cache, but not in the PR.
+          jcache notebook clear --force
+          jcache notebook add docs/notebooks/*.ipynb
+          jcache project execute --timeout 1800
 
-            - name: output logs
-              run: |
-                  jcache notebook list
-                  for f in docs/notebooks/*.ipynb ; do
-                    jcache notebook info --tb $f
-                  done
+      - name: output logs
+        run: |
+          jcache notebook list
+          for f in docs/notebooks/*.ipynb ; do
+            jcache notebook info --tb $f
+          done
 
-            # write changed outputs back to the ipynb files
-            # will fail if there was an execution error
-            - name: merge notebooks
-              run: |
-                  for f in docs/notebooks/*.ipynb ; do
-                    jcache notebook merge $f $f
-                  done
+      # write changed outputs back to the ipynb files
+      # will fail if there was an execution error
+      - name: merge notebooks
+        run: |
+          for f in docs/notebooks/*.ipynb ; do
+            jcache notebook merge $f $f
+          done
 
-            - uses: stefanzweifel/git-auto-commit-action@v4
-              with:
-                  commit_message: Render notebooks
+      - uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: Render notebooks

.github/workflows/make-tutorials-json.yml

@@ -1,60 +1,60 @@
 name: Make JSON of tutorial registry
 on:
-    pull_request:
-        branches: [main]
-    push:
-        branches: [main]
-    schedule:
-        - cron: "0 2 * * *"
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  schedule:
+    - cron: "0 2 * * *"
 
 concurrency:
-    group: "pages"
-    cancel-in-progress: true
+  group: "pages"
+  cancel-in-progress: true
 
 jobs:
-    mkjson:
-        runs-on: ubuntu-latest
+  mkjson:
+    runs-on: ubuntu-latest
 
-        steps:
-            - name: Checkout repository
-              uses: actions/checkout@v3
-            - uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-                  cache: "pip" # caching pip dependencies
-            - name: Install dependencies for validation script
-              run: pip install jsonschema pillow requests pyyaml
-            - name: Execute validation script and create output directory
-              run: |
-                  ./tutorial-registry/validate.py --outdir=build
-            - name: Upload GitHub Pages artifact
-              uses: actions/upload-pages-artifact@v1
-              with:
-                  path: "build"
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip" # caching pip dependencies
+      - name: Install dependencies for validation script
+        run: pip install jsonschema pillow requests pyyaml
+      - name: Execute validation script and create output directory
+        run: |
+          ./tutorial-registry/validate.py --outdir=build
+      - name: Upload GitHub Pages artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: "build"
 
-    deploy:
-        runs-on: ubuntu-latest
-        needs: mkjson
+  deploy:
+    runs-on: ubuntu-latest
+    needs: mkjson
 
-        # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
-        permissions:
-            pages: write # to deploy to Pages
-            id-token: write
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write # to deploy to Pages
+      id-token: write
 
-        environment:
-            name: github-pages
-            url: ${{ steps.deployment.outputs.page_url }}
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
 
-        if: github.ref == 'refs/heads/main' && github.event_name != 'schedule'
-        steps:
-            - name: Deploy to GitHub Pages
-              id: deployment
-              uses: actions/deploy-pages@v1
-            - name: Trigger website build
-              run: |
-                  curl -XPOST \
-                  -u "scverse-bot:${{ secrets.BOT_GH_TOKEN }}" \
-                  -H "Accept: application/vnd.github.everest-preview+json" \
-                  -H "Content-Type: application/json" \
-                  https://api.github.com/repos/scverse/scverse.github.io/actions/workflows/gh-pages.yml/dispatches \
-                  --data '{"ref": "main"}'
+    if: github.ref == 'refs/heads/main' && github.event_name != 'schedule'
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1
+      - name: Trigger website build
+        run: |
+          curl -XPOST \
+          -u "scverse-bot:${{ secrets.BOT_GH_TOKEN }}" \
+          -H "Accept: application/vnd.github.everest-preview+json" \
+          -H "Content-Type: application/json" \
+          https://api.github.com/repos/scverse/scverse.github.io/actions/workflows/gh-pages.yml/dispatches \
+          --data '{"ref": "main"}'

.github/workflows/release.yaml

@@ -0,0 +1,30 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "*.*.*"
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install hatch
+        run: pip install hatch
+
+      - name: Build project for distribution
+        run: hatch build
+
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}