add pre-commit

Signed-off-by: zethson <[email protected]>
theislab · May 21, 2022 · bb4d523 · bb4d523
1 parent 8f557cd
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diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,51 +1,51 @@
 name-template: "1.0.0 🌈"
 tag-template: 1.0.0
 categories:
-    - title: "🚀 Features"
-      labels:
-          - feature
-          - enhancement
-    - title: "🐛 Bug Fixes"
-      labels:
-          - fix
-          - bugfix
-          - bug
-    - title: "🧰 Maintenance"
-      label: chore
-    - title: ":package: Dependencies"
-      labels:
-          - dependencies
-          - build
-          - dependabot
-          - DEPENDABOT
+  - title: "🚀 Features"
+    labels:
+      - feature
+      - enhancement
+  - title: "🐛 Bug Fixes"
+    labels:
+      - fix
+      - bugfix
+      - bug
+  - title: "🧰 Maintenance"
+    label: chore
+  - title: ":package: Dependencies"
+    labels:
+      - dependencies
+      - build
+      - dependabot
+      - DEPENDABOT
 version-resolver:
-    major:
-        labels:
-            - major
-    minor:
-        labels:
-            - minor
-    patch:
-        labels:
-            - patch
-    default: patch
+  major:
+    labels:
+      - major
+  minor:
+    labels:
+      - minor
+  patch:
+    labels:
+      - patch
+  default: patch
 autolabeler:
-    - label: chore
-      files:
-          - "*.md"
-      branch:
-          - '/docs{0,1}\/.+/'
-    - label: bug
-      branch:
-          - /fix\/.+/
-      title:
-          - /fix/i
-    - label: enhancement
-      branch:
-          - /feature\/.+/
-      body:
-          - "/JIRA-[0-9]{1,4}/"
+  - label: chore
+    files:
+      - "*.md"
+    branch:
+      - '/docs{0,1}\/.+/'
+  - label: bug
+    branch:
+      - /fix\/.+/
+    title:
+      - /fix/i
+  - label: enhancement
+    branch:
+      - /feature\/.+/
+    body:
+      - "/JIRA-[0-9]{1,4}/"
 template: |
-    ## Changes
+  ## Changes
 
-    $CHANGES
+  $CHANGES
diff --git a/.github/workflows/build_book.yml b/.github/workflows/build_book.yml
@@ -6,26 +6,26 @@ jobs:
   build-book:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
 
-    - name: Setup environment
-      run: pip install --upgrade jupyter-book jupytext beautifulsoup4
+      - name: Setup environment
+        run: pip install --upgrade jupyter-book jupytext beautifulsoup4
 
-    - name: Cache jupyter-cache folder
-      uses: actions/cache@v2
-      env:
-       cache-name: jupyter-cache
-      with:
-        path: jupyter-book/_build/.jupyter_cache
-        key: v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
-        restore-keys: |
-          v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
-          v1-${{ github.ref }}
-          v1-refs/heads/master
-    - name: Build the JupyterBook
-      run: make
+      - name: Cache jupyter-cache folder
+        uses: actions/cache@v2
+        env:
+          cache-name: jupyter-cache
+        with:
+          path: jupyter-book/_build/.jupyter_cache
+          key: v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
+          restore-keys: |
+            v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
+            v1-${{ github.ref }}
+            v1-refs/heads/master
+      - name: Build the JupyterBook
+        run: make
diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml
@@ -1,19 +1,19 @@
 name: Labeler
 
 on:
-    push:
-        branches:
-            - main
-            - master
+  push:
+    branches:
+      - main
+      - master
 
 jobs:
-    labeler:
-        runs-on: ubuntu-latest
-        steps:
-            - name: Check out the repository
-              uses: actions/[email protected]
+  labeler:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repository
+        uses: actions/[email protected]
 
-            - name: Run Labeler
-              uses: crazy-max/[email protected]
-              with:
-                  skip-delete: true
+      - name: Run Labeler
+        uses: crazy-max/[email protected]
+        with:
+          skip-delete: true
diff --git a/.github/workflows/publish_book.yml b/.github/workflows/publish_book.yml
@@ -1,40 +1,40 @@
 name: Publish book
 
 on:
-    release:
-        types: [published]
+  release:
+    types: [published]
 
 jobs:
   build-book:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
 
-    - name: Setup environment
-      run: pip install --upgrade jupyter-book jupytext beautifulsoup4
+      - name: Setup environment
+        run: pip install --upgrade jupyter-book jupytext beautifulsoup4
 
-    - name: Cache jupyter-cache folder
-      uses: actions/cache@v2
-      env:
-       cache-name: jupyter-cache
-      with:
-        path: jupyter-book/_build/.jupyter_cache
-        key: v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
-        restore-keys: |
-          v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
-          v1-${{ github.ref }}
-          v1-refs/heads/master
+      - name: Cache jupyter-cache folder
+        uses: actions/cache@v2
+        env:
+          cache-name: jupyter-cache
+        with:
+          path: jupyter-book/_build/.jupyter_cache
+          key: v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
+          restore-keys: |
+            v1-${{ github.ref }}-${{ hashFiles('notebook_scripts/**/*.py') }}
+            v1-${{ github.ref }}
+            v1-refs/heads/master
 
-    - name: Build the JupyterBook
-      run: make
+      - name: Build the JupyterBook
+        run: make
 
-    - name: Deploy to Github Pages
-      uses: peaceiris/actions-gh-pages@v3
-      with:
+      - name: Deploy to Github Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./jupyter-book/_build/html/
diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml
@@ -1,19 +1,19 @@
 name: Release Drafter
 on:
-    push:
-        branches:
-            - development
-    pull_request:
-        branches:
-            - development
-        types:
-            - opened
-            - reopened
-            - synchronize
+  push:
+    branches:
+      - development
+  pull_request:
+    branches:
+      - development
+    types:
+      - opened
+      - reopened
+      - synchronize
 jobs:
-    update_release_draft:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: release-drafter/release-drafter@v5
-              env:
-                  GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+  update_release_draft:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: release-drafter/release-drafter@v5
+        env:
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,16 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v2.6.2
+      hooks:
+          - id: prettier
+    - repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+          - id: black-jupyter
diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ In case of questions or problems, please get in touch by posting an issue in thi
 
 ## Adapting the notebooks to other datasets:
 
-All notebooks for the various steps can be found in the [jupyter book folder](extended-single-cell-best-practices/tree/master/jupyter-book). 
+All notebooks for the various steps can be found in the [jupyter book folder](extended-single-cell-best-practices/tree/master/jupyter-book).
 These can easily be reused for your own projects.
 
 ## Acknowledgements

diff --git a/jupyter-book/_config.yml b/jupyter-book/_config.yml
@@ -14,8 +14,8 @@ exclude_patterns:
   - "README.md"
 
 execute:
-  execute_notebooks           : 'off'
-  timeout                     : 600000
+  execute_notebooks: "off"
+  timeout: 600000
 
 parse:
   myst_enable_extensions:
@@ -26,10 +26,10 @@ parse:
     - html_image
 
 html:
-  home_page_in_navbar         : false
-  use_edit_page_button        : true
-  use_repository_button       : true
-  use_issues_button           : true
+  home_page_in_navbar: false
+  use_edit_page_button: true
+  use_repository_button: true
+  use_issues_button: true
   favicon: _static/favicon.ico
   comments:
     hypothesis: true
@@ -40,11 +40,11 @@ html:
     </div>
 
 latex:
-  latex_engine                : "xelatex"
+  latex_engine: "xelatex"
   latex_documents:
     targetname: book.tex
 
-notebook_interface            : "notebook"
+notebook_interface: "notebook"
 
 sphinx:
   config:
@@ -60,12 +60,12 @@ sphinx:
     language: en
 
 bibtex_bibfiles:
-    - references.bib
+  - references.bib
 
 repository:
-  url                         : https://github.com/theislab/extended-single-cell-tutorial
-  branch                      : master
+  url: https://github.com/theislab/extended-single-cell-tutorial
+  branch: master
 
 binder:
-  binderhub_url               : "https://mybinder.org"
-  text                        : "Launch binder"
+  binderhub_url: "https://mybinder.org"
+  text: "Launch binder"