Merge pull request #7 from theislab/feat/update_package

update dependences

.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.github/workflows/release.yml

@@ -0,0 +1,39 @@
+name: Release
+
+on:
+    push:
+        tags:
+            - "*.*.*"
+
+jobs:
+    release:
+        name: Release
+        runs-on: ubuntu-latest
+        steps:
+            # will use ref/SHA that triggered it
+            - name: Checkout code
+              uses: actions/checkout@v3
+
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.9"
+
+            - name: Install poetry
+              uses: abatilo/actions-poetry@v2.0.0
+              with:
+                  poetry-version: 1.4.2
+
+            - name: Build project for distribution
+              run: poetry build
+
+            - name: Check Version
+              id: check-version
+              run: |
+                  [[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] \
+                    || echo ::set-output name=prerelease::true
+
+            - name: Publish to PyPI
+              env:
+                  POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
+              run: poetry publish

.github/workflows/test.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: regvelo
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.9", "3.10", "3.11"]
+
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                  python-version: ${{ matrix.python-version }}
+            - name: Cache pip
+              uses: actions/cache@v2
+              with:
+                  path: ~/.cache/pip
+                  key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+                  restore-keys: |
+                      ${{ runner.os }}-pip-
+            - name: Install dependencies
+              run: |
+                  pip install pytest-cov
+                  pip install .[dev]
+            - name: Test with pytest
+              run: |
+                  pytest --cov-report=xml --cov=velovi
+            - name: After success
+              run: |
+                  bash <(curl -s https://codecov.io/bash)
+                  pip list

.gitignore

@@ -0,0 +1,137 @@
+# DS_Store
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# vscode
+.vscode/settings.json
+docs/api/reference/
+*.h5ad

.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/psf/black
+      rev: "23.1.0"
+      hooks:
+          - id: black
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.6
+      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: v0.0.254
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      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$'

docs/conf.py

@@ -21,7 +21,7 @@
 author = info["Weixu Wang"]
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
-repository_url = "https://github.com/theislab/RegVelo_repo"
+repository_url = "https://github.com/theislab/RegVelo"
 
 # The full version, including alpha/beta/rc tags
 release = info["Version"]