new formatting and template

theislab · Apr 24, 2024 · 675dcc3 · 675dcc3
1 parent 389807e
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diff --git a/.github/workflows/sync.yaml b/.github/workflows/sync.yaml
@@ -1,44 +1,44 @@
 name: Sync Template
 
 on:
-    workflow_dispatch:
+  workflow_dispatch:
 
 jobs:
-    sync:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-            - name: Install dependencies
-              # for now, pin cookiecutter version, due to https://github.com/cruft/cruft/issues/166
-              run: python -m pip install --upgrade cruft "cookiecutter<2" pre-commit toml
-            - name: Find Latest Tag
-              uses: oprypin/[email protected]
-              id: get-latest-tag
-              with:
-                  repository: scverse/cookiecutter-scverse
-                  releases-only: false
-                  sort-tags: true
-                  regex: '^v\d+\.\d+\.\d+$' # vX.X.X
-            - name: Sync
-              run: |
-                  cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
-            - name: Create Pull Request
-              uses: peter-evans/create-pull-request@v4
-              with:
-                  commit-message: Automated template update from cookiecutter-scverse
-                  branch: template-update
-                  title: Automated template update from cookiecutter-scverse
-                  body: |
-                      A new version of the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse/releases)
-                      got released. This PR adds all new changes to your repository and helps to to stay in sync with
-                      the latest best-practice template maintained by the scverse team.
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        # for now, pin cookiecutter version, due to https://github.com/cruft/cruft/issues/166
+        run: python -m pip install --upgrade cruft "cookiecutter<2" pre-commit toml
+      - name: Find Latest Tag
+        uses: oprypin/[email protected]
+        id: get-latest-tag
+        with:
+          repository: scverse/cookiecutter-scverse
+          releases-only: false
+          sort-tags: true
+          regex: '^v\d+\.\d+\.\d+$' # vX.X.X
+      - name: Sync
+        run: |
+          cruft update --checkout ${{ steps.get-latest-tag.outputs.tag }} --skip-apply-ask --project-dir .
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v4
+        with:
+          commit-message: Automated template update from cookiecutter-scverse
+          branch: template-update
+          title: Automated template update from cookiecutter-scverse
+          body: |
+            A new version of the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse/releases)
+            got released. This PR adds all new changes to your repository and helps to to stay in sync with
+            the latest best-practice template maintained by the scverse team.
 
-                      **If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
-                      manually merge these changes.**
+            **If a merge conflict arised, a `.rej` file with the rejected patch is generated. You'll need to
+            manually merge these changes.**
 
-                      For more information about the template sync, please refer to the
-                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
+            For more information about the template sync, please refer to the
+            [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,85 +1,38 @@
 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: 22.3.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v2.5.1
-      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/asottile/blacken-docs
-      rev: v1.12.1
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.10.1
-      hooks:
-          - id: isort
-    - repo: https://github.com/asottile/yesqa
-      rev: v1.3.0
-      hooks:
-          - id: yesqa
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.1.0
-      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: https://github.com/myint/autoflake
-      rev: v1.4
-      hooks:
-          - id: autoflake
-            args:
-                - --in-place
-                - --remove-all-unused-imports
-                - --remove-unused-variable
-                - --ignore-init-module-imports
-    - repo: https://github.com/PyCQA/flake8
-      rev: 4.0.1
-      hooks:
-          - id: flake8
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v2.31.1
-      hooks:
-          - id: pyupgrade
-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
-    - 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$'
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.2
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'
diff --git a/.pre-commit-config.yaml.rej b/.pre-commit-config.yaml.rej
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,16 +1,16 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-    os: ubuntu-20.04
-    tools:
-        python: "3.10"
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
 sphinx:
-    configuration: docs/conf.py
-    # disable this for more lenient docs builds
-    fail_on_warning: false
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
 python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-              - doc
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
diff --git a/.readthedocs.yaml.rej b/.readthedocs.yaml.rej
diff --git a/README.md b/README.md
@@ -45,7 +45,6 @@ See the [changelog][changelog].
 For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
 If you found a bug, please use the [issue tracker][issue-tracker].
 
-
 ## Credits
 
 Some of the data for `DatasetHartmann` is distributed in this package.

diff --git a/README.md.rej b/README.md.rej
diff --git a/docs/api.md b/docs/api.md
@@ -14,4 +14,4 @@
 .. automodule:: geome.datamodule
     :members:
 
-```
+```