diff --git a/.bumpversion.cfg b/.bumpversion.cfg new file mode 100644 index 0000000..f539f35 --- /dev/null +++ b/.bumpversion.cfg @@ -0,0 +1,7 @@ +[bumpversion] +current_version = 0.0.1 +commit = True +tag = True +files = pyproject.toml lipyd/_metadata.py +parse = (?P\d+)\.(?P\d+)\.(?P\d+) +serialize = {major}.{minor}.{patch} diff --git a/.codecov.yaml b/.codecov.yaml new file mode 100644 index 0000000..829e56c --- /dev/null +++ b/.codecov.yaml @@ -0,0 +1,17 @@ +# Based on pydata/xarray +codecov: + require_ci_to_pass: no + +coverage: + status: + project: + default: + # Require 1% coverage, i.e., always succeed + target: 1 + patch: false + changes: false + +comment: + layout: diff, flags, files + behavior: once + require_base: no diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..f2cb21b --- /dev/null +++ b/.coveragerc @@ -0,0 +1,22 @@ +[paths] +source = + project_name + */site-packages/Lipyd + +[run] +branch = true +parallel = true +source = Lipyd +omit = */__init__.py + +[report] +exclude_lines = + \#.*pragma:\s*no.?cover + + if __name__ == .__main__. + + ^\s*raise AssertionError\b + ^\s*raise NotImplementedError\b + ^\s*return NotImplemented\b +show_missing = true +precision = 2 diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..2fe0ce0 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,12 @@ +root = true + +[*] +indent_style = space +indent_size = 4 +end_of_line = lf +charset = utf-8 +trim_trailing_whitespace = true +insert_final_newline = true + +[Makefile] +indent_style = tab diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml new file mode 100644 index 0000000..67bdf24 --- /dev/null +++ b/.github/workflows/build.yaml @@ -0,0 +1,23 @@ +name: Package build + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + package: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.10 + uses: actions/setup-python@v2 + with: + python-version: '3.10' + - 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 diff --git a/.github/workflows/sphinx_autodoc.yaml b/.github/workflows/sphinx_autodoc.yaml new file mode 100644 index 0000000..770a6c6 --- /dev/null +++ b/.github/workflows/sphinx_autodoc.yaml @@ -0,0 +1,55 @@ +name: Sphinx build docs on push +on: +- push + +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Check out main + uses: actions/checkout@main + - name: Setup Python + uses: actions/setup-python@v2 + with: + python-version: 3.10.5 + - name: Load cached Poetry installation + uses: actions/cache@v2 + with: + path: ~/.local + key: poetry-0 + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + - name: Poetry disable modern-installation + run: poetry config installer.modern-installation false + - name: Load cached venv + id: cached-poetry-dependencies + uses: actions/cache@v2 + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} + - name: Install dependencies + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: poetry install --no-interaction --no-root + - name: Install library + run: poetry install --no-interaction + - name: Build documentation + run: poetry run make html --directory docs/ + - name: Commit files + run: | + git config --local user.email "action@github.com" + git config --local user.name "GitHub Action" + touch docs/_build/html/.nojekyll + git add -f docs/_build/ + git commit -m "Update autodoc" -a + # using https://github.com/marketplace/actions/push-git-subdirectory-as-branch + - name: Deploy + uses: s0/git-publish-subdir-action@develop + env: + REPO: self + BRANCH: gh-pages + FOLDER: docs/_build/html + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml new file mode 100644 index 0000000..9203d90 --- /dev/null +++ b/.github/workflows/test.yaml @@ -0,0 +1,57 @@ +name: Test + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + + test: + runs-on: ${{ matrix.os }} + defaults: + run: + shell: bash -e {0} + + strategy: + fail-fast: false + matrix: + python: [3.8, 3.9, 3.10] + os: [ubuntu-latest, macos-latest] + + env: + OS: ${{ matrix.os }} + PYTHON: ${{ matrix.python }} + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python }} + cache: pip + cache-dependency-path: '**/pyproject.toml' + + - name: Install test dependencies + run: | + python -m pip install --upgrade pip wheel + pip install codecov + - name: Install dependencies + run: | + pip install ".[dev,test]" + - name: Install pip dependencies + run: | + python -m pip install --upgrade pip + - name: Test + env: + MPLBACKEND: agg + PLATFORM: ${{ matrix.os }} + DISPLAY: :42 + run: | + pytest -v --cov --color=yes + - name: Upload coverage + env: + CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }} + run: | + codecov --no-color --required --flags unittests diff --git a/.gitignore b/.gitignore index ce583b6..474b0fe 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,23 @@ -build/ -dist/ +*~ +__pycache__/ +/build/ +/docs/_build/ +/docs/generated/ +.DS_Store +/.vscode/ +/*.egg-info/ +*.egg +*.prof +*.coverage +*.pickle +/out/ +*.log +/dist/ +*.pye *.pyc -*.egg-info/ +*.kate-swp +/.tox/ +/.idea/ +/.pytest_cache/ +/.cache/ +/data/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..58fc995 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,110 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +fail_fast: false +default_language_version: + python: python3 +default_stages: +- commit +- push +minimum_pre_commit_version: 2.7.1 +repos: +- repo: https://github.com/deeenes/unexport + rev: 0.4.0-patch0-3 + hooks: + - id: unexport + args: [--refactor, --single_quotes] + exclude: __init__.py$ +- repo: https://github.com/google/yapf + rev: v0.40.2 + hooks: + - id: yapf + additional_dependencies: [toml] + stages: [manual] +- repo: https://github.com/psf/black + rev: 24.4.2 + hooks: + - id: black + additional_dependencies: [toml] + stages: [manual] +- repo: https://github.com/Instagram/Fixit + rev: 9d59f968e84bd2773f34b0069eeeaad3ce783254 + hooks: + - id: fixit-run-rules + stages: [manual] +- repo: https://github.com/timothycrosley/isort + rev: 5.13.2 + hooks: + - id: isort + additional_dependencies: [toml] +- repo: https://github.com/snok/pep585-upgrade + rev: v1.0 + hooks: + - id: upgrade-type-hints + args: [--futures=true] +- repo: https://github.com/asottile/add-trailing-comma + rev: v3.1.0 + hooks: + - id: add-trailing-comma +- repo: https://github.com/myint/unify + rev: v0.5 + hooks: + - id: unify +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: detect-private-key + - id: check-ast + - id: check-docstring-first + - id: end-of-file-fixer + - id: check-added-large-files + - id: mixed-line-ending + args: [--fix=lf] + exclude: ^docs/make.bat$ + - id: trailing-whitespace + exclude: ^.bumpversion.cfg$ + - id: check-merge-conflict + - id: check-case-conflict + - id: check-symlinks + - id: check-yaml + args: [--unsafe] + - id: check-ast + - id: fix-encoding-pragma + args: [--remove] # for Python3 codebase, it's not necessary + - id: requirements-txt-fixer +- repo: https://github.com/john-hen/Flake8-pyproject + rev: 1.2.3 + hooks: + - id: Flake8-pyproject + additional_dependencies: + - flake8-docstrings + - flake8-comprehensions + - flake8-bugbear + - git+https://github.com/saezlab/flake8-kwargs-spaces.git +- repo: https://github.com/rstcheck/rstcheck + rev: v6.2.0 + hooks: + - id: rstcheck + exclude: docs +- repo: https://github.com/asottile/blacken-docs + rev: 1.16.0 + hooks: + - id: blacken-docs +- repo: https://github.com/asottile/pyupgrade + rev: v3.16.0 + hooks: + - id: pyupgrade + args: [--py3-plus, --py38-plus, --keep-runtime-typing] +- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks + rev: v2.13.0 + hooks: + - id: pretty-format-yaml + args: [--autofix, --indent, '4'] +- repo: https://github.com/pre-commit/pygrep-hooks + rev: v1.10.0 + hooks: + - id: python-no-eval + - id: python-use-type-annotations + - id: python-check-blanket-noqa + - id: rst-backticks + - id: rst-directive-colons + - id: rst-inline-touching-normal diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..56363c4 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,22 @@ +version: 2 + +sphinx: + builder: html + configuration: docs/source/conf.py + fail_on_warning: true + +formats: +- htmlzip +- pdf + +build: + os: ubuntu-22.04 + tools: + python: 3.10 + +python: + install: + - method: pip + path: . + extra_requirements: + - docs diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..ef7e7ef --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ +GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {one line to give the program's name and a brief idea of what it does.} + Copyright (C) {year} {name of author} + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..a67fa61 --- /dev/null +++ b/README.md @@ -0,0 +1,11 @@ +# Lipyd + +[![Tests][badge-tests]][link-tests] +[![Documentation][badge-docs]][link-docs] + +[badge-tests]: https://img.shields.io/github/actions/workflow/status/saezlab/lipyd/test.yaml?branch=main +[link-tests]: https://github.com/saezlab/lipyd/actions/workflows/test.yml +[badge-docs]: https://img.shields.io/readthedocs/lipyd +[link-docs]: https://lipyd.readthedocs.io + +Python module for lipidomics LC MS/MS data processing diff --git a/docs/Makefile b/docs/Makefile index eb2ee7d..c7c0696 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,11 +1,11 @@ # Minimal makefile for Sphinx documentation # -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SPHINXPROJ = emese -SOURCEDIR = . +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = src BUILDDIR = _build # Put it first so that "make" without argument is like "make help". @@ -17,4 +17,4 @@ help: # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \ No newline at end of file + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..5b28825 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=src +set BUILDDIR=_build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/src/conf.py b/docs/src/conf.py new file mode 100644 index 0000000..a519a51 --- /dev/null +++ b/docs/src/conf.py @@ -0,0 +1,125 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +from datetime import datetime +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import sys +import pathlib + +here = pathlib.Path(__file__).parent +sys.path.insert(0, str(here.parent)) + +import lipyd # noqa: E402 + +# -- Project information ----------------------------------------------------- + +project = 'lipyd' +version = lipyd.__version__ +author = ', '.join(lipyd.__author__) +years = '-'.join(sorted({'2022', f'{datetime.now():%Y}'})) +copyright = f'{years}, Saez Lab' +repository_url = 'https://github.com/saezlab/lipyd' + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named "sphinx.ext.*") or your custom +# ones. +extensions = [ + 'myst_parser', + 'sphinx.ext.autodoc', + 'sphinx.ext.intersphinx', + 'sphinx.ext.autosummary', + 'sphinx.ext.napoleon', + 'sphinx.ext.todo', # not for output but to remove warnings + 'sphinx.ext.githubpages', + 'sphinx.ext.viewcode', + 'sphinx.ext.ifconfig', + 'sphinxcontrib.bibtex', + 'sphinx_autodoc_typehints', + 'sphinx.ext.mathjax', + 'sphinx_copybutton', + 'sphinx_last_updated_by_git', + 'sphinxcontrib.fulltoc', + 'sphinx_remove_toctrees', + 'nbsphinx', + 'IPython.sphinxext.ipython_console_highlighting', +] + +autosummary_generate = True +autodoc_member_order = 'groupwise' +default_role = 'literal' +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_include_init_with_doc = False +napoleon_use_rtype = True # having a separate entry generally helps readability +napoleon_use_param = True + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = 'en' + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = ['.rst', '.md'] + +# The master toctree document. +master_doc = 'contents' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'] + + +# -- Autodoc configuration --------------------------------------------------- + +autodoc_mock_imports = [] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'manni' + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. + +html_theme = 'pydata_sphinx_theme' +html_theme_options = { + 'navigation_depth': 2, + 'collapse_navigation': True, +} +html_context = { + 'display_github': True, # Integrate GitHub + 'github_user': 'saezlab', # Username + 'github_repo': project, # Repo name + 'github_version': 'main', # Version + 'conf_py_path': '/docs/', # Path in the checkout to the docs root +} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +nitpick_ignore = [ + # If building the documentation fails because + # of a missing link that is outside your control, + # you can add an exception to this list. + # ("py:class", "igraph.Graph"), +] diff --git a/docs/src/developer_docs.md b/docs/src/developer_docs.md new file mode 100644 index 0000000..3017a37 --- /dev/null +++ b/docs/src/developer_docs.md @@ -0,0 +1,58 @@ +## Pre-commit documentation + +[Pre-commit](https://pre-commit.com/) checks are fast programs that +check code for errors, inconsistencies and code styles, before the code +is committed. This is a brief documentation of pre-commits checks +pre-sets in the scverse-template. + +The following pre-commit checks for code style and format. + +- [black](https://black.readthedocs.io/en/stable/): standard code + formatter in Python. +- [autopep8](https://github.com/hhatto/autopep8): code formatter to + conform to [PEP8](https://peps.python.org/pep-0008/) style guide. +- [isort](https://pycqa.github.io/isort/): sort module imports into + sections and types. +- [prettier](https://prettier.io/docs/en/index.html): standard code + formatter for non-Python files (e.g. YAML). +- [blacken-docs](https://github.com/asottile/blacken-docs): black on + python code in docs. + +The following pre-commit checks for errors, inconsistencies and typing. + +- [flake8](https://flake8.pycqa.org/en/latest/): standard check for errors in Python files. + - [flake8-tidy-imports](https://github.com/adamchainz/flake8-tidy-imports): + tidy module imports. + - [flake8-docstrings](https://github.com/PyCQA/flake8-docstrings): + pydocstyle extension of flake8. + - [flake8-rst-docstrings](https://github.com/peterjc/e8-rst-docstrings): + extension of `flake8-docstrings` for `rst` docs. + - [flake8-comprehensions](https://github.com/adamchainz/e8-comprehensions): + write better list/set/dict comprehensions. + - [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear): + find possible bugs and design issues in program. + - [flake8-blind-except](https://github.com/elijahandrews/flake8-blind-except): + checks for blind, catch-all `except` statements. +- [yesqa](https://github.com/asottile/yesqa): + remove unneccesary `# noqa` comments, follows additional dependencies listed above. + Not included in this template. +- [autoflake](https://github.com/PyCQA/autoflake): + remove unused imports and variables. Not included in this template. +- [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks. + - **detect-private-key**: checks for the existence of private keys. + - **check-ast**: check whether files parse as valid python. + - **end-of-file-fixer**:check files end in a newline and only a newline. + - **mixed-line-ending**: checks mixed line ending. + - **trailing-whitespace**: trims trailing whitespace. + - **check-case-conflict**: check files that would conflict with case-insensitive file systems. +- [pyupgrade](https://github.com/asottile/pyupgrade): + upgrade syntax for newer versions of the language. + +### Notes on pre-commit checks + +- **flake8**: to ignore errors, you can add a comment `# noqa` to the offending line. + You can also specify the error id to ignore with e.g. `# noqa: E731`. + Check [flake8 guide](https://flake8.pycqa.org/en/3.1.1/user/ignoring-errors.html) for reference. +- You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file. + Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` or pre-commit + specific config files, such as `.prettierrc.yml` for **prettier** and `.flake8` for **flake8**. diff --git a/docs/src/index.rst b/docs/src/index.rst new file mode 100644 index 0000000..53cb4b9 --- /dev/null +++ b/docs/src/index.rst @@ -0,0 +1,30 @@ +############ +Introduction +############ + +Created from a project template. Please write the docs of your project here, +and remove the parts below (or edit ``README.rst`` in the project root). + +.. include:: ../../README.rst + +######### +Reference +######### + +project_name +============ + +.. automodule:: project_name + :members: + +########################### +Indices, Tables, and Search +########################### + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + + +.. toctree:: + :maxdepth: 4 diff --git a/lipyd/__init__.py b/lipyd/__init__.py new file mode 100644 index 0000000..59d6524 --- /dev/null +++ b/lipyd/__init__.py @@ -0,0 +1,25 @@ +#!/usr/bin/env python + +# +# This file is part of the `lipyd` Python module +# +# Copyright 2024 +# Heidelberg University Hospital +# +# File author(s): Saez Lab (omnipathdb@gmail.com) +# +# Distributed under the GPLv3 license +# See the file `LICENSE` or read a copy at +# https://www.gnu.org/licenses/gpl-3.0.txt +# + +""" +Python module for lipidomics LC MS/MS data processing. +""" + +__all__ = [ + '__version__', + '__author__', +] + +from ._metadata import __author__, __version__ diff --git a/lipyd/_metadata.py b/lipyd/_metadata.py new file mode 100644 index 0000000..6ba2e78 --- /dev/null +++ b/lipyd/_metadata.py @@ -0,0 +1,82 @@ +#!/usr/bin/env python + +# +# This file is part of the `lipyd` Python module +# +# Copyright 2024 +# Heidelberg University Hospital +# +# File author(s): Saez Lab (omnipathdb@gmail.com) +# +# Distributed under the GPLv3 license +# See the file `LICENSE` or read a copy at +# https://www.gnu.org/licenses/gpl-3.0.txt +# + +""" +Package metadata (version, authors, etc). +""" + +__all__ = ['get_metadata'] + +import os +import pathlib +import importlib.metadata + +import toml + +_VERSION = '0.0.1' + + +def get_metadata(): + """ + Basic package metadata. + + Retrieves package metadata from the current project directory or from + the installed package. + """ + + here = pathlib.Path(__file__).parent + pyproj_toml = 'pyproject.toml' + meta = {} + + for project_dir in (here, here.parent): + + toml_path = str(project_dir.joinpath(pyproj_toml).absolute()) + + if os.path.exists(toml_path): + + pyproject = toml.load(toml_path) + + meta = { + 'name': pyproject['tool']['poetry']['name'], + 'version': pyproject['tool']['poetry']['version'], + 'author': pyproject['tool']['poetry']['authors'], + 'license': pyproject['tool']['poetry']['license'], + 'full_metadata': pyproject, + } + + break + + if not meta: + + try: + + meta = { + k.lower(): v for k, v in + importlib.metadata.metadata(here.name).items() + } + + except importlib.metadata.PackageNotFoundError: + + pass + + meta['version'] = meta.get('version', None) or _VERSION + + return meta + + +metadata = get_metadata() +__version__ = metadata.get('version', None) +__author__ = metadata.get('author', None) +__license__ = metadata.get('license', None) diff --git a/pyproject.toml b/pyproject.toml index 1de0a2c..f33f1d7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,12 +1,20 @@ -[package] +[build-system] +requires = ["poetry_core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + +[tool.poetry] name = "lipyd" -summary = """A module for lipidomics LC MS/MS data analysis.""" -url = "https://saezlab.github.io/lipyd" -author = "Dénes Türei" -author-email = "turei.denes@gmail.com" -license = "GPLv3" +version = "0.0.1" +description = "Python module for lipidomics LC MS/MS data processing" +license = "GNU General Public License Version 3" +authors = [ + "Saez Lab " +] +packages = [ + { include = "lipyd" } +] classifiers = [ - "Development Status :: 3 - Alpha", + "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", @@ -16,21 +24,134 @@ classifiers = [ "Natural Language :: English", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", + "Topic :: Scientific/Engineering :: Bio-Informatics" +] +homepage = "https://saezlab.github.io/lipyd" +repository = "https://github.com/saezlab/lipyd" +documentation = "https://lipyd.readthedocs.io/" +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.9" +toml = "*" + +[tool.poetry.dev-dependencies] +pytest = ">=6.0" +tox = ">=3.20.1" +pre-commit = ">=2.17.0" +bump2version = "*" +coverage = ">=6.0" +distlib = "*" +sphinx = ">=5.0.0" +sphinx-last-updated-by-git = ">=0.3" +sphinx-autodoc-typehints = ">=1.18.0" +sphinxcontrib-fulltoc = ">=1.2.0" +sphinxcontrib-bibtex = "*" +sphinx-copybutton = "*" +myst-parser = "*" +myst-nb = "*" +jupyterlab = "*" +pydata-sphinx-theme = "*" +sphinx-remove-toctrees = "*" +jupyter-contrib-nbextensions = { git = "https://github.com/deeenes/jupyter_contrib_nbextensions.git", branch = "master" } +nbsphinx = { git = "https://github.com/deeenes/nbsphinx.git", branch = "timings" } + +[tool.poetry.urls] +"Bug Tracker" = "https://github.com/saezlab/lipyd/issues" + +[tool.black] +line-length = 80 +target-version = ['py31*'] +include = '\.pyi?$' +exclude = ''' +( + /( + \.eggs + | \.git + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | _build + | buck-out + | build + | dist + )/ +) +''' + +[tool.isort] +from_first = true +line_length = 80 +multi_line_output = 3 +include_trailing_comma = true +use_parentheses = true +known_num="numpy,pandas" +sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER" +no_lines_before="LOCALFOLDER" +balanced_wrapping = true +force_grid_wrap = 0 +length_sort = "1" +indent = " " +skip = [] + +[tool.flake8] +extend-select = ["CE101"] +ignore = [ + "D200", "D202", "D401", "D105", + "W503", "W504", + "E731", "E131", "E251", "E303" +] +per-file-ignores = [ + "docs/src/conf.py:D100", + "tests/*:D100,D101,D102", + "*/__init__.py:F401" +] +max-line-length = 80 +count = true +exclude = [ + ".git", + "__pycache__", + "build", + "docs/_build", + "dist" ] -[package.dependencies] -runtime = [] +[tool.yapf] +based_on_style = "facebook" +split_penalty_before_if_expr = 0 +split_penalty_import_names = 0 +split_penalty_comprehension = 0 +split_penalty_for_added_line_split = 0 +split_penalty_after_opening_bracket = 0 +split_before_first_argument = true +split_before_named_assigns = true +split_complex_comprehension = true -[package.build] -dependencies = [ - "setuptools", - "wheel", - "numpy" +[tool.rstcheck] +report_level = "INFO" +ignore_directives = [ + "automodule", + "toctree", ] +ignore_roles = ["ref"] +ignore_messages = '(Unknown target name:.*|No (directive|role) entry for "(auto)?(class|method|property|function|func|mod|attr)" in module "docutils\.parsers\.rst\.languages\.en"\.)' -[build-system] -requires = [ - "setuptools", - "wheel", - "numpy" +[tool.coverage.run] +source = ["lipyd"] +omit = [ + "**/test_*.py", +] + +[tool.pytest.ini_options] +testpaths = [ + "tests", +] +xfail_strict = true +addopts = [ + # "-Werror", # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below + "--import-mode=importlib", # allow using test files with same name +] +filterwarnings = [ + # "ignore:.*U.*mode is deprecated:DeprecationWarning", ] diff --git a/tests/test_twentythree.py b/tests/test_twentythree.py new file mode 100644 index 0000000..f1e089d --- /dev/null +++ b/tests/test_twentythree.py @@ -0,0 +1,10 @@ +import lipyd + +__all__ = ['Test23'] + + +class Test23: + + def test_twentythree(self): + + assert lipyd.twentythree() == 23 diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..dc1262d --- /dev/null +++ b/tox.ini @@ -0,0 +1,9 @@ +[tox] +skipsdist = true +envlist = py310 + +[testenv] +whitelist_externals = poetry +commands = + poetry install -v + poetry run pytest