Merge pull request #2 from scverse-bot/template-update-cobioda-scispy…

…-v0.4.0

Update template to v0.4.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "6a4338030e0c83a9034d607ed66abeff83e18840",
-  "checkout": null,
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "scispy",
@@ -13,9 +13,15 @@
       "project_repo": "https://github.com/bfxomics/scispy",
       "license": "MIT 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"
     }
   },

.github/workflows/release.yaml

@@ -1,30 +1,29 @@
 name: Release
 
 on:
-  push:
-    tags:
-      - "*.*.*"
+  release:
+    types: [published]
 
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:
   release:
-    name: Release
+    name: Upload release to PyPI
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scispy
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
-
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@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
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -5,6 +5,8 @@ on:
     branches: [main]
   pull_request:
     branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -21,13 +23,16 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            python: "3.9"
           - os: ubuntu-latest
             python: "3.10"
           - os: ubuntu-latest
-            python: "3.10"
+            python: "3.12"
+          - os: ubuntu-latest
+            python: "3.12"
             pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
 
     env:
       OS: ${{ matrix.os }}
@@ -54,6 +59,9 @@ jobs:
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
         run: |
-          pytest -v --cov --color=yes
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
       - name: Upload coverage
         uses: codecov/codecov-action@v3

.gitignore

@@ -18,6 +18,7 @@ __pycache__/
 /.pytest_cache/
 /.cache/
 /data/
+/node_modules/
 
 # docs
 /docs/generated/

.pre-commit-config.yaml

@@ -39,6 +39,9 @@ repos:
         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

.pre-commit-config.yaml.rej

@@ -0,0 +1,35 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -6,29 +6,18 @@ default_stages:
+   - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-  - repo: https://github.com/psf/black
+-    rev: "24.4.2"
+-    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
++  - repo: https://github.com/astral-sh/ruff-pre-commit
+     rev: v0.4.4
+     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: v4.6.0
+     hooks:

README.md.rej

@@ -0,0 +1,10 @@
+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 3.9 or newer installed on your system. If you don't have
++You need to have Python 3.10 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 scispy:

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

@@ -1,5 +1,5 @@
 # Configuration file for the Sphinx documentation builder.
-#
+
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -57,6 +57,7 @@
     "sphinx_autodoc_typehints",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
+    "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
@@ -108,12 +109,15 @@
 #
 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 @@
     # 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/conf.py.rej

@@ -0,0 +1,16 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -36,10 +36,10 @@ needs_sphinx = "4.0"
+
+ html_context = {
+     "display_github": True,  # Integrate GitHub
+-    "github_user": "bfxomics",  # Username
+-    "github_repo": project_name,  # Repo name
+-    "github_version": "main",  # Version
+-    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
++    "github_user": "bfxomics",
++    "github_repo": "https://github.com/bfxomics/scispy",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+
+ # -- General configuration ---------------------------------------------------