Update template to v0.6.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
-  "checkout": "v0.5.0",
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "dso-core",
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,10 +1,13 @@
 name: Feature request
-description: Suggest an idea for DSO
+description: Propose a new feature for dso-core
+labels: enhancement
 body:
   - type: textarea
     id: description
     attributes:
       label: Description of feature
-      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+      description: Please describe your suggestion for a new feature. It might help to
+        describe a problem or use case, plus any alternatives that you have
+        considered.
     validations:
       required: true

.github/workflows/build.yaml

@@ -0,0 +1,33 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

.github/workflows/release.yaml

@@ -0,0 +1,34 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dso
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -0,0 +1,103 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+  # more details.
+  get-environments:
+    runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+  test:
+    needs: get-environments
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.env.python }}
+          cache-dependency-glob: pyproject.toml
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+      - name: generate coverage report
+        run: |
+          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@release/v1
+          with:
+            jobs: ${{ toJSON(needs) }}

.gitignore

@@ -17,6 +17,7 @@ uv.lock
 # Tests and coverage
 /data/
 /node_modules/
+/.coverage*
 
 # docs
 /docs/generated/

.pre-commit-config.yaml

@@ -7,54 +7,49 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.3
+    rev: 0.37.2
     hooks:
       - id: check-jsonschema
         files: "src/dso/templates/schema.json"
-        args: ["--check-metaschema"]
+        args: [ "--check-metaschema" ]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.3
+    rev: 0.37.2
     hooks:
       - id: check-jsonschema
         files: "src/dso/templates/index.json"
-        args: ["--schemafile", "src/dso/templates/schema.json"]
+        args: [ "--schemafile", "src/dso/templates/schema.json" ]
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.2.2
+    rev: v2.4.15
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.6.0
+    rev: v2.21.2
     hooks:
       - id: pyproject-fmt
         exclude: ^src/dso/templates/.*$
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.21.2
+    hooks:
+      - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.15.12
     hooks:
-      - id: ruff
-        types_or: [python, pyi, jupyter]
-        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-check
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix, --exit-non-zero-on-fix ]
       - id: ruff-format
-        types_or: [python, pyi, jupyter]
+        types_or: [ python, pyi, jupyter ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
       - id: end-of-file-fixer
       - id: mixed-line-ending
-        args: [--fix=lf]
+        args: [ --fix=lf ]
       - id: trailing-whitespace
       - id: check-case-conflict
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
-        args: [--assume-in-merge]
-  - repo: local
-    hooks:
-      - id: forbid-to-commit
-        name: Don't commit rej files
-        entry: |
-          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-          Fix the merge conflicts manually and remove the .rej files.
-        language: fail
-        files: '.*\.rej$'
+        args: [ --assume-in-merge ]

.readthedocs.yaml

@@ -0,0 +1,15 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    build:
+      html:
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT

biome.jsonc

@@ -1,5 +1,6 @@
 {
     "$schema": "https://biomejs.dev/schemas/2.2.2/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {

docs/conf.py

@@ -92,6 +92,7 @@
 nb_execution_mode = "off"
 nb_merge_streams = True
 typehints_defaults = "braces"
+click_extra_enable_exec_directives = True
 
 source_suffix = {
     ".rst": "restructuredtext",