pertpy 0.5.0__tar.gz → 0.7.0__tar.gz

pertpy-0.7.0/.editorconfig

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+# 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

pertpy-0.7.0/.gitattributes

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+* text=auto eol=lf

pertpy-0.7.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+    - type: markdown
+      attributes:
+          value: |
+              **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+              detailing how to provide the necessary information for us to reproduce your bug. In brief:
+                * Please provide exact steps how to reproduce the bug in a clean Python environment.
+                * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+                * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+                  available datasets or to share a subset of your data.
+
+    - type: textarea
+      id: report
+      attributes:
+          label: Report
+          description: A clear and concise description of what the bug is.
+      validations:
+          required: true
+
+    - type: textarea
+      id: versions
+      attributes:
+          label: Version information
+          description: |
+              Please paste below the output of
+
+              ```python
+              import session_info
+              session_info.show(html=False, dependencies=True)
+              ```
+          placeholder: |
+              -----
+              anndata             0.8.0rc2.dev27+ge524389
+              session_info        1.0.0
+              -----
+              asttokens           NA
+              awkward             1.8.0
+              backcall            0.2.0
+              cython_runtime      NA
+              dateutil            2.8.2
+              debugpy             1.6.0
+              decorator           5.1.1
+              entrypoints         0.4
+              executing           0.8.3
+              h5py                3.7.0
+              ipykernel           6.15.0
+              jedi                0.18.1
+              mpl_toolkits        NA
+              natsort             8.1.0
+              numpy               1.22.4
+              packaging           21.3
+              pandas              1.4.2
+              parso               0.8.3
+              pexpect             4.8.0
+              pickleshare         0.7.5
+              pkg_resources       NA
+              prompt_toolkit      3.0.29
+              psutil              5.9.1
+              ptyprocess          0.7.0
+              pure_eval           0.2.2
+              pydev_ipython       NA
+              pydevconsole        NA
+              pydevd              2.8.0
+              pydevd_file_utils   NA
+              pydevd_plugins      NA
+              pydevd_tracing      NA
+              pygments            2.12.0
+              pytz                2022.1
+              scipy               1.8.1
+              setuptools          62.5.0
+              setuptools_scm      NA
+              six                 1.16.0
+              stack_data          0.3.0
+              tornado             6.1
+              traitlets           5.3.0
+              wcwidth             0.2.5
+              zmq                 23.1.0
+              -----
+              IPython             8.4.0
+              jupyter_client      7.3.4
+              jupyter_core        4.10.0
+              -----
+              Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+              Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+              -----
+              Session information updated at 2022-07-07 17:55

pertpy-0.7.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+    - name: Scverse Community Forum
+      url: https://discourse.scverse.org/
+      about: If you have questions about “How to do X”, please ask them here.

pertpy-0.7.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new feature for pertpy
+labels: enhancement
+body:
+    - type: textarea
+      id: description
+      attributes:
+          label: Description of feature
+          description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+      validations:
+          required: true

pertpy-0.7.0/.github/labels.yml

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+---
+# Labels names are important as they are used by Release Drafter to decide
+# regarding where to record them in changelog or if to skip them.
+#
+# The repository labels will be automatically configured using this file and
+# the GitHub Action https://github.com/marketplace/actions/github-labeler.
+- name: breaking
+  description: Breaking Changes
+  color: bfd4f2
+- name: bug
+  description: Something isn't working
+  color: d73a4a
+- name: build
+  description: Build System and Dependencies
+  color: bfdadc
+- name: ci
+  description: Continuous Integration
+  color: 4a97d6
+- name: dependencies
+  description: Pull requests that update a dependency file
+  color: 0366d6
+- name: documentation
+  description: Improvements or additions to documentation
+  color: 0075ca
+- name: duplicate
+  description: This issue or pull request already exists
+  color: cfd3d7
+- name: enhancement
+  description: New feature or request
+  color: a2eeef
+- name: github_actions
+  description: Pull requests that update Github_actions code
+  color: "000000"
+- name: good first issue
+  description: Good for newcomers
+  color: 7057ff
+- name: help wanted
+  description: Extra attention is needed
+  color: 008672
+- name: invalid
+  description: This doesn't seem right
+  color: e4e669
+- name: performance
+  description: Performance
+  color: "016175"
+- name: python
+  description: Pull requests that update Python code
+  color: 2b67c6
+- name: question
+  description: Further information is requested
+  color: d876e3
+- name: refactoring
+  description: Refactoring
+  color: ef67c4
+- name: removal
+  description: Removals and Deprecations
+  color: 9ae7ea
+- name: style
+  description: Style
+  color: c120e5
+- name: testing
+  description: Testing
+  color: b1fc6f
+- 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

pertpy-0.7.0/.github/pull_request_template.md

@@ -0,0 +1,21 @@
+<!-- Many thanks for contributing to this project! -->
+
+**PR Checklist**
+
+<!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
+
+-   [ ] Referenced issue is linked
+-   [ ] If you've fixed a bug or added code that should be tested, add tests!
+-   [ ] Documentation in `docs` is updated
+
+**Description of changes**
+
+<!-- Please state what you've changed and how it might affect the user. -->
+
+**Technical details**
+
+<!-- Please state any technical details such as limitations, reasons for additional dependencies, benchmarks etc. here. -->
+
+**Additional context**
+
+<!-- Add any other context or screenshots here. -->

pertpy-0.7.0/.github/release-drafter.yml

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+name-template: "0.7.0 🌈"
+tag-template: 0.7.0
+exclude-labels:
+    - "skip-changelog"
+
+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
+version-resolver:
+    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}/"
+template: |
+    ## Changes
+
+    $CHANGES

pertpy-0.7.0/.github/workflows/build.yml

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+name: Check Build
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    package:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Set up Python 3.11
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.11"
+                  cache: "pip"
+                  cache-dependency-path: "**/pyproject.toml"
+
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+
+            - name: Build package
+              run: python -m build
+
+            - name: Check package
+              run: twine check --strict dist/*.whl

pertpy-0.7.0/.github/workflows/labeler.yml

@@ -0,0 +1,19 @@
+name: Labeler
+
+on:
+    push:
+        branches:
+            - main
+            - master
+
+jobs:
+    labeler:
+        runs-on: ubuntu-latest
+        steps:
+            - name: Check out the repository
+              uses: actions/checkout@v4
+
+            - name: Run Labeler
+              uses: crazy-max/ghaction-github-labeler@v4.1.0
+              with:
+                  skip-delete: true

pertpy-0.7.0/.github/workflows/release.yml

@@ -0,0 +1,30 @@
+name: Release
+
+on:
+    push:
+        tags:
+            - "*.*.*"
+
+jobs:
+    release:
+        name: Release
+        runs-on: ubuntu-latest
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v4
+
+            - name: Set up Python 3.11
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.11"
+
+            - 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
+              with:
+                  password: ${{ secrets.PYPI_TOKEN }}

pertpy-0.7.0/.github/workflows/release_drafter.yml

@@ -0,0 +1,19 @@
+name: Release Drafter
+on:
+    push:
+        branches:
+            - main
+    pull_request:
+        branches:
+            - main
+        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 }}"

pertpy-0.7.0/.github/workflows/test.yml

@@ -0,0 +1,64 @@
+name: Test
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - os: ubuntu-latest
+                      python: "3.10"
+                    - os: ubuntu-latest
+                      python: "3.11"
+                    - os: ubuntu-latest
+                      python: "3.11"
+                      pip-flags: "--pre"
+
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+            - uses: actions/checkout@v4
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v5
+              with:
+                  python-version: ${{ matrix.python }}
+                  cache: "pip"
+                  cache-dependency-path: "**/pyproject.toml"
+
+            - name: Install test dependencies
+              run: python -m pip install --upgrade uv wheel
+            - name: Install dependencies
+              run: uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda]"
+
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: coverage run -m pytest -v --color=yes
+
+            - name: Show coverage report
+              run: coverage report -m
+
+            - name: Upload coverage
+              uses: codecov/codecov-action@v3
+              with:
+                  fail_ci_if_error: true
+                  verbose: true

pertpy-0.7.0/.gitignore

@@ -0,0 +1,157 @@
+# 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
+.pertpy_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/
+docs/usage/*
+!docs/usage/usage.md
+
+# 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
+.pytype/
+
+# Pyre type checker
+.pyre/
+
+# Jetbrains IDE
+.idea/
+
+# Coala
+*.orig
+
+# Datasets
+*.h5ad
+*.h5md
+*.h5mu
+
+# Test cache
+cache
+
+# Apple stuff
+.DS_Store
+
+lightning_logs/*
+*/lightning_logs/*
+
+node_modules

pertpy-0.7.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "docs/notebooks"]
+	path = docs/tutorials/notebooks
+	url = https://github.com/theislab/pertpy-tutorials/

pertpy-0.7.0/.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+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: v4.0.0-alpha.8
+      hooks:
+          - id: prettier
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.3.5
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+          - id: ruff-format
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.6.0
+      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/pre-commit/mirrors-mypy
+      rev: v1.9.0
+      hooks:
+          - id: mypy
+            args: [--no-strict-optional, --ignore-missing-imports]
+            additional_dependencies:
+                ["types-pkg-resources", "types-requests", "types-attrs"]
+    - 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$'

pertpy-0.7.0/.readthedocs.yml

@@ -0,0 +1,22 @@
+version: 2
+build:
+    os: ubuntu-22.04
+    tools:
+        python: "3.11"
+    jobs:
+        pre_build:
+            - python -c "import pertpy"
+            - pip freeze
+sphinx:
+    configuration: docs/conf.py
+    fail_on_warning: false
+python:
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - doc
+              - coda
+
+submodules:
+    include: all