Update template to v0.3.1

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
-  "checkout": "main",
+  "commit": "586b1652162ff7994b0070a034023d64289ae416",
+  "checkout": "v0.3.1",
   "context": {
     "cookiecutter": {
       "project_name": "scib-metrics",
@@ -13,9 +13,15 @@
       "project_repo": "https://github.com/yoseflab/scib-metrics",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
       "_template": "https://github.com/scverse/cookiecutter-scverse"
     }
   },

.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/test.yaml

@@ -1,53 +1,67 @@
 name: Test
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
 
 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
-
-        strategy:
-            fail-fast: false
-            matrix:
-                python: ["3.8", "3.10"]
-                os: [ubuntu-latest]
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
 
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.9"
+          - os: ubuntu-latest
+            python: "3.11"
+          - os: ubuntu-latest
+            python: "3.11"
+            pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} 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"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+      - name: Install dependencies
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+      - name: Test
         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"
-
-            - 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: Upload coverage
-              uses: codecov/codecov-action@v3
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3

.pre-commit-config.yaml.rej

@@ -0,0 +1,89 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -1,50 +1,42 @@
+ 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/psf/black
+-      rev: "24.2.0"
+-      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: v4.0.0-alpha.8
+-      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/charliermarsh/ruff-pre-commit
+-      rev: v0.2.2
+-      hooks:
+-          - id: ruff
+-            args: [--fix, --exit-non-zero-on-fix]
+-    - repo: https://github.com/pre-commit/pre-commit-hooks
+-      rev: v4.5.0
+-      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
+-    - 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$'
++  - repo: https://github.com/pre-commit/mirrors-prettier
++    rev: v4.0.0-alpha.8
++    hooks:
++      - id: prettier
++  - repo: https://github.com/astral-sh/ruff-pre-commit
++    rev: v0.2.2
++    hooks:
++      - id: ruff
++        types_or: [python, pyi, jupyter]
++        args: [--fix, --exit-non-zero-on-fix]
++      - id: ruff-format
++        types_or: [python, pyi, jupyter]
++  - repo: https://github.com/pre-commit/pre-commit-hooks
++    rev: v4.5.0
++    hooks:
++      - id: detect-private-key
++      - id: check-ast
++      - id: end-of-file-fixer
++      - id: mixed-line-ending
++        args: [--fix=lf]
++      - id: trailing-whitespace
++      - id: check-case-conflict
++      # Check that there are no merge conflicts (could be generated by template sync)
++      - id: check-merge-conflict
++        args: [--assume-in-merge]
++  - repo: local
++    hooks:
++      - id: forbid-to-commit
++        name: Don't commit rej files
++        entry: |
++          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
++          Fix the merge conflicts manually and remove the .rej files.
++        language: fail
++        files: '.*\.rej$'

README.md.rej

@@ -0,0 +1,19 @@
+diff a/README.md b/README.md	(rejected hunks)
+@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the
+
+ ## Installation
+
+-You need to have Python 3.8 or newer installed on your system. If you don't have
++You need to have Python 3.9 or newer installed on your system. If you don't have
+ Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+ There are several alternative options to install scib-metrics:
+@@ -33,7 +33,7 @@ pip install scib-metrics
+ 1. Install the latest development version:
+
+ ```bash
+-pip install git+https://github.com/adamgayoso/scib-metrics.git@main
++pip install git+https://github.com/yoseflab/scib-metrics.git@main
+ ```
+
+ ## Release notes

docs/_static/css/custom.css

@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+    font-size: 0.8em;
+}

docs/conf.py

@@ -61,6 +61,7 @@
     "sphinx_autodoc_typehints",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
+    "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 

docs/conf.py.rej

@@ -0,0 +1,36 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -108,12 +109,15 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+ #
+ html_theme = "sphinx_book_theme"
+ html_static_path = ["_static"]
++html_css_files = ["css/custom.css"]
++
+ html_title = project_name
+
+ html_theme_options = {
+     "repository_url": repository_url,
+     "use_repository_button": True,
+     "path_to_docs": "docs/",
++    "navigation_with_keys": False,
+ }
+
+ pygments_style = "default"
+@@ -123,18 +127,3 @@ nitpick_ignore = [
+     # you can add an exception to this list.
+     #     ("py:class", "igraph.Graph"),
+ ]
+-
+-
+-def setup(app):
+-    """App setup hook."""
+-    app.add_config_value(
+-        "recommonmark_config",
+-        {
+-            "auto_toc_tree_section": "Contents",
+-            "enable_auto_toc_tree": True,
+-            "enable_math": True,
+-            "enable_inline_math": False,
+-            "enable_eval_rst": True,
+-        },
+-        True,
+-    )

docs/index.md.rej

@@ -0,0 +1,9 @@
+diff a/docs/index.md b/docs/index.md	(rejected hunks)
+@@ -8,7 +8,6 @@
+
+ api.md
+ changelog.md
+-template_usage.md
+ contributing.md
+ references.md
+

pyproject.toml

@@ -88,7 +88,7 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
     "E501",
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",
@@ -156,5 +156,5 @@ skip = [
     "docs/changelog.md",
     "docs/references.bib",
     "docs/references.md",
-    "docs/notebooks/example.ipynb"
+    "docs/notebooks/example.ipynb",
 ]