Important cookietemple template update 2.1.1 released!

.cookietemple.yml

@@ -1,9 +1,9 @@
-cookietemple_version: '1.3.2 # <<COOKIETEMPLE_NO_BUMP>>'
+cookietemple_version: '1.4.1 # <<COOKIETEMPLE_NO_BUMP>>'
 domain: cli
 language: python
 project_slug: sc-toolbox
 project_slug_no_hyphen: sc_toolbox
-template_version: '2.0.0 # <<COOKIETEMPLE_NO_BUMP>>'
+template_version: '2.1.1 # <<COOKIETEMPLE_NO_BUMP>>'
 template_handle: cli-python
 github_username: schillerlab
 creator_github_username: zethson
@@ -16,5 +16,5 @@ email: [email protected]
 project_name: sc-toolbox
 project_short_description: A collection of project templates and useful code snippets
   for single-cell data analysis with Scanpy.
-version: 0.1.0
+version: 0.12.0
 license: MIT

.github/dependabot.yml

@@ -3,8 +3,8 @@ updates:
     - package-ecosystem: github-actions
       directory: "/"
       schedule:
-          interval: daily
-      open-pull-requests-limit: 5
+          interval: weekly
+      open-pull-requests-limit: 3
       target-branch: development
       labels:
           - DEPENDABOT
@@ -14,8 +14,8 @@ updates:
     - package-ecosystem: pip
       directory: "/.github/workflows"
       schedule:
-          interval: daily
-      open-pull-requests-limit: 5
+          interval: weekly
+      open-pull-requests-limit: 3
       target-branch: development
       labels:
           - DEPENDABOT
@@ -25,8 +25,8 @@ updates:
     - package-ecosystem: pip
       directory: "/docs"
       schedule:
-          interval: daily
-      open-pull-requests-limit: 5
+          interval: weekly
+      open-pull-requests-limit: 3
       target-branch: development
       labels:
           - DEPENDABOT
@@ -36,8 +36,8 @@ updates:
     - package-ecosystem: pip
       directory: "/"
       schedule:
-          interval: daily
-      open-pull-requests-limit: 5
+          interval: weekly
+      open-pull-requests-limit: 3
       target-branch: development
       labels:
           - DEPENDABOT

.github/labels.yml

@@ -64,3 +64,6 @@
 - name: wontfix
   description: This will not be worked on
   color: ffffff
+- name: skip-changelog
+  description: Changes that should be omitted from the release notes
+  color: ededed

.github/pull_request_template.md

@@ -8,7 +8,6 @@
 -   [ ] Referenced issue is linked
 -   [ ] If you've fixed a bug or added code that should be tested, add tests!
 -   [ ] Documentation in `docs` is updated
--   [ ] `CHANGELOG.rst` is updated
 
 **Description of changes**
 

.github/release-drafter.yml

@@ -1,5 +1,8 @@
-name-template: "0.1.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.1.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.12.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.12.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+exclude-labels:
+    - "skip-changelog"
+
 categories:
     - title: "🚀 Features"
       labels:

.github/workflows/build_package.yml

@@ -9,14 +9,14 @@ jobs:
         strategy:
             matrix:
                 os: [macos-latest, ubuntu-latest, windows-latest]
-                python: [3.7, 3.8, 3.9]
+                python: [3.8, 3.9]
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v3
               with:
                   python-version: ${{ matrix.python }}
 
@@ -26,8 +26,7 @@ jobs:
                   poetry --version
 
             - name: Build package
-              run: |
-                  poetry build --ansi
+              run: poetry build --ansi
 
             - name: Install required twine packaging dependencies
               run: pip install setuptools wheel twine

.github/workflows/publish_package.yml

@@ -2,7 +2,7 @@ name: Publish sc-toolbox to PyPI
 
 on:
     release:
-        types: [created]
+        types: [published]
 
 jobs:
     release:
@@ -15,7 +15,7 @@ jobs:
                   fetch-depth: 2
 
             - name: Set up Python
-              uses: actions/setup-python@v2.1.4
+              uses: actions/setup-python@v3
               with:
                   python-version: "3.9"
 

.github/workflows/run_cookietemple_lint.yml

@@ -3,22 +3,20 @@ name: cookietemple lint
 on: [push]
 
 jobs:
-    build:
+    run:
         runs-on: ubuntu-latest
 
         steps:
             - uses: actions/checkout@v2
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v1
+              uses: actions/setup-python@v3
               with:
                   python-version: 3.9
 
             - name: Install cookietemple
-              run: |
-                  pip install cookietemple==1.3.2
+              run: pip install cookietemple==1.4.1
 
             - name: Run cookietemple lint
-              run: |
-                  cookietemple lint . --skip-external
+              run: cookietemple lint .

.github/workflows/run_tests.yml

@@ -66,24 +66,22 @@ jobs:
               uses: actions/[email protected]
 
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v2.1.4
+              uses: actions/setup-python@v2.2.2
               with:
                   python-version: ${{ matrix.python-version }}
 
             - name: Install Poetry
               run: |
-                  pip install poetry
+                  pipx install poetry
                   poetry --version
 
-            - name: Install Nox
+            - name: Install nox nox-poetry rich
               run: |
-                  pip install nox nox-poetry
+                  pipx install nox
+                  pipx inject nox nox-poetry
+                  pipx inject nox rich
                   nox --version
 
-            - name: Install Rich
-              run: |
-                  pip install rich
-
             - name: Compute pre-commit cache key
               if: matrix.session == 'pre-commit'
               id: pre-commit-cache
@@ -100,7 +98,7 @@ jobs:
                   print("::set-output name=result::{}".format(result))
 
             - name: Restore pre-commit cache
-              uses: actions/[email protected].4
+              uses: actions/[email protected].7
               if: matrix.session == 'pre-commit'
               with:
                   path: ~/.cache/pre-commit
@@ -109,19 +107,18 @@ jobs:
                       ${{ steps.pre-commit-cache.outputs.result }}-
 
             - name: Run Nox
-              run: |
-                  nox --force-color --python=${{ matrix.python-version }}
+              run: nox --force-color --python=${{ matrix.python-version }}
 
             - name: Upload coverage data
               if: always() && matrix.session == 'tests'
-              uses: "actions/upload-artifact@v2.2.3"
+              uses: actions/upload-artifact@v3
               with:
                   name: coverage-data
                   path: ".coverage.*"
 
             - name: Upload documentation
               if: matrix.session == 'docs-build'
-              uses: actions/upload-artifact@v2.2.3
+              uses: actions/upload-artifact@v3
               with:
                   name: docs
                   path: docs/_build
@@ -131,39 +128,35 @@ jobs:
         needs: tests
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v3
 
             - name: Set up Python 3.8
-              uses: actions/setup-python@v2.1.4
+              uses: actions/setup-python@v3
               with:
                   python-version: 3.8
 
             - name: Install Poetry
               run: |
-                  pip install poetry
+                  pipx install poetry
                   poetry --version
 
-            - name: Install Nox
+            - name: Install nox nox-poetry rich
               run: |
-                  pip install nox nox-poetry
+                  pipx install nox
+                  pipx inject nox nox-poetry
+                  pipx inject nox rich
                   nox --version
 
-            - name: Install Rich
-              run: |
-                  pip install rich
-
             - name: Download coverage data
-              uses: actions/download-artifact@v2.0.9
+              uses: actions/download-artifact@v3
               with:
                   name: coverage-data
 
             - name: Combine coverage data and display human readable report
-              run: |
-                  nox --force-color --session=coverage
+              run: nox --force-color --session=coverage
 
             - name: Create coverage report
-              run: |
-                  nox --force-color --session=coverage -- xml
+              run: nox --force-color --session=coverage -- xml -i
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v1.3.2
+              uses: codecov/codecov-action@v2.1.0

.github/workflows/sync_project.yml

@@ -10,14 +10,14 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Setup Python
-              uses: actions/setup-python@v1
+              uses: actions/setup-python@v3
               with:
                   python-version: 3.8
 
             - name: Install cookietemple
               run: pip install cookietemple
 
-            - uses: actions/checkout@v2.1
+            - uses: actions/checkout@v2
               with:
                   fetch-depth: 0
                   token: "${{ secrets.CT_SYNC_TOKEN }}"

.pre-commit-config.yaml

@@ -27,25 +27,38 @@ repos:
             language: system
             types: [text]
             stages: [commit, push, manual]
+            exclude: docs/
           - id: flake8
             name: flake8
             entry: flake8
             language: system
             types: [python]
             require_serial: true
-          - id: reorder-python-imports
-            name: Reorder python imports
-            entry: reorder-python-imports
+          - id: pyupgrade
+            name: pyupgrade
+            description: Automatically upgrade syntax for newer versions.
+            entry: pyupgrade
             language: system
             types: [python]
-            args: [--application-directories=src]
+            args: [--py38-plus]
           - id: trailing-whitespace
             name: Trim Trailing Whitespace
             entry: trailing-whitespace-fixer
             language: system
             types: [text]
             stages: [commit, push, manual]
-    - repo: https://github.com/prettier/pre-commit
-      rev: v2.1.2
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v2.5.1
       hooks:
           - id: prettier
+    - repo: https://github.com/pycqa/isort
+      rev: 5.8.0
+      hooks:
+          - id: isort
+            name: isort (python)
+          - id: isort
+            name: isort (cython)
+            types: [cython]
+          - id: isort
+            name: isort (pyi)
+            types: [pyi]

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021, Lukas Heumos
+Copyright (c) 2022, Lukas Heumos
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -54,22 +54,14 @@ Usage
 Please see the `Command-line Reference <Usage_>`_ for details.
 
 
-Contributing
-------------
-
-Contributions are very welcome. To learn more, see the `Contributor Guide`_.
-
-
 Credits
 -------
 
 This package was created with cookietemple_ using Cookiecutter_ based on Hypermodern_Python_Cookiecutter_.
 
 .. _cookietemple: https://cookietemple.com
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _MIT: http://opensource.org/licenses/MIT
 .. _PyPI: https://pypi.org/
 .. _Hypermodern_Python_Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python
 .. _pip: https://pip.pypa.io/
-.. _Contributor Guide: CONTRIBUTING.rst
 .. _Usage: https://sc-toolbox.readthedocs.io/en/latest/usage.html

cookietemple.cfg

@@ -1,10 +1,11 @@
 [bumpversion]
-current_version = 0.1.0
+current_version = 0.12.0
 
 [bumpversion_files_whitelisted]
-init_file = src/sc_toolbox/__init__.py
+init_file = sc_toolbox/__init__.py
 dot_cookietemple = .cookietemple.yml
 conf_py = docs/conf.py
+main_file = sc_toolbox/__main__.py
 
 [bumpversion_files_blacklisted]
 poetry = pyproject.toml