Update template to v0.2.22 (icbi-lab#32)

* Update template to v0.2.22 * Fix merge conflicts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix missing comma * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: scverse-bot <None> Co-authored-by: Gregor Sturm <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
vjmarteau · Aug 24, 2023 · ada5984 · ada5984
1 parent 24317b6
commit ada5984
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Showing 16 changed files with 221 additions and 229 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
diff --git a/.cruft.json b/.cruft.json
@@ -1,23 +1,23 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
-    "checkout": "main",
-    "context": {
-        "cookiecutter": {
-            "project_name": "atlas_protocol",
-            "package_name": "atlas_protocol_scripts",
-            "project_description": "A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022). ",
-            "author_full_name": "Gregor Sturm",
-            "author_email": "[email protected]",
-            "github_user": "icbi-lab",
-            "project_repo": "https://github.com/icbi-lab/atlas_protocol",
-            "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": "605f95714130c960bce12eab98a4e023e8932249",
+  "checkout": "v0.2.22",
+  "context": {
+    "cookiecutter": {
+      "project_name": "atlas_protocol",
+      "package_name": "atlas_protocol_scripts",
+      "project_description": "A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022). ",
+      "author_full_name": "Gregor Sturm",
+      "author_email": "[email protected]",
+      "github_user": "icbi-lab",
+      "project_repo": "https://github.com/icbi-lab/atlas_protocol",
+      "license": "BSD 3-Clause License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
 }
diff --git a/.editorconfig b/.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
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -1,29 +1,29 @@
 name: Check Build
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
 
 concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: true
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-    package:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v3
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
-            - name: Install build dependencies
-              run: python -m pip install --upgrade pip wheel twine build
-            - name: Build package
-              run: python -m build
-            - name: Check package
-              run: twine check --strict dist/*.whl
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl
diff --git a/.github/workflows/release.yaml b/.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 }}
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -1,51 +1,51 @@
 name: Test
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
 
 concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: true
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-    test:
-        runs-on: ${{ matrix.os }}
-        defaults:
-            run:
-                shell: bash -e {0} # -e to fail on error
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
 
-        strategy:
-            fail-fast: false
-            matrix:
-                python: ["3.8", "3.10"]
-                os: [ubuntu-latest]
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.9", "3.10"]
+        os: [ubuntu-latest]
 
-        env:
-            OS: ${{ matrix.os }}
-            PYTHON: ${{ matrix.python }}
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
 
-        steps:
-            - uses: actions/checkout@v3
-            - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v4
-              with:
-                  python-version: ${{ matrix.python }}
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
 
-            - name: Install test dependencies
-              run: |
-                  python -m pip install --upgrade pip wheel
-            - name: Install dependencies
-              run: |
-                  pip install ".[dev,test]"
-            - name: Test
-              env:
-                  MPLBACKEND: agg
-                  PLATFORM: ${{ matrix.os }}
-                  DISPLAY: :42
-              run: |
-                  pytest -v --cov --color=yes
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+      - name: Install dependencies
+        run: |
+          pip install ".[dev,test]"
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          pytest -v --cov --color=yes
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,70 +1,70 @@
 fail_fast: false
 default_language_version:
-    python: python3
+  python: python3
 default_stages:
-    - commit
-    - push
+  - commit
+  - push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/mwouts/jupytext
-      rev: v1.15.0
-      hooks:
-          - id: jupytext
-            args:
-                [
-                    --sync,
-                    --pipe-fmt,
-                    py:percent,
-                    --pipe,
-                    black,
-                    --pipe,
-                    "ruff --fix {}",
-                ]
-            additional_dependencies:
-                - black==22.3.0 # Matches hook
-                - ruff==0.0.261
-            files: "^(docs/notebooks|_preprocessing)/.*$"
-    - repo: https://github.com/psf/black
-      rev: "23.7.0"
-      hooks:
-          - id: black
-    - repo: https://github.com/asottile/blacken-docs
-      rev: 1.16.0
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.2
-      hooks:
-          - id: prettier
-            # Newer versions of node don't work on systems that have an older version of GLIBC
-            # (in particular Ubuntu 18.04 and Centos 7)
-            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
-            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
-            # https://github.com/jupyterlab/jupyterlab/issues/12675
-            language_version: "17.9.1"
-    - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.285
-      hooks:
-          - id: ruff
-            args: [--fix, --exit-non-zero-on-fix]
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      hooks:
-          - id: detect-private-key
-          - id: check-ast
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: trailing-whitespace
-          - id: check-case-conflict
-          - 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$'
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.15.0
+    hooks:
+      - id: jupytext
+        args:
+          [
+            --sync,
+            --pipe-fmt,
+            py:percent,
+            --pipe,
+            black,
+            --pipe,
+            "ruff --fix {}",
+          ]
+        additional_dependencies:
+          - black==22.3.0 # Matches hook
+          - ruff==0.0.261
+        files: "^(docs/notebooks|_preprocessing)/.*$"
+  - repo: https://github.com/psf/black
+    rev: "23.7.0"
+    hooks:
+      - id: black
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.2
+    hooks:
+      - id: prettier
+        # Newer versions of node don't work on systems that have an older version of GLIBC
+        # (in particular Ubuntu 18.04 and Centos 7)
+        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+        # https://github.com/jupyterlab/jupyterlab/issues/12675
+        language_version: "17.9.1"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.285
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - 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$'