From 6329cfade41abc4c3b9f47908ad87e9d3221897b Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Fri, 4 Aug 2023 17:01:45 +0200 Subject: [PATCH] Switch from setup.py to pyproject.toml and poetry --- .github/workflows/main.yml | 7 +- .gitignore | 2 +- README.rst | 1 + poetry.lock | 4096 ++++++++++++++++++ pyproject.toml | 61 + requirements.txt | 10 - requirements_dev.txt | 3 - sequana_pipetools/snaketools/file_factory.py | 4 +- setup.py | 68 - tests/snaketools/test_filefactory.py | 4 +- tests/snaketools/test_sequana_config.py | 15 +- tests/test_manager.py | 2 +- 12 files changed, 4176 insertions(+), 97 deletions(-) create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 requirements.txt delete mode 100644 requirements_dev.txt delete mode 100644 setup.py diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6aeeb90..334edd7 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -33,16 +33,15 @@ jobs: - name: Install dependencies run: | pip install coveralls pytest-cov - pip install -r requirements_dev.txt - name: install package itself run: | - pip install . - pip install sequana_fastqc + pip install poetry + poetry install - name: testing run: | - pytest --cov-report term --cov=sequana_pipetools + poetry run pytest --cov-report term --cov=sequana_pipetools - name: coveralls run: | echo $COVERALLS_REPO_TOKEN diff --git a/.gitignore b/.gitignore index 7c6f977..2425034 100644 --- a/.gitignore +++ b/.gitignore @@ -24,7 +24,7 @@ doc/_build *.egg-info/ .installed.cfg *.egg - +poetry.lock # PyInstaller # Usually these files are written by a python script from a template diff --git a/README.rst b/README.rst index 1225c75..b05a493 100644 --- a/README.rst +++ b/README.rst @@ -253,6 +253,7 @@ Changelog ========= ====================================================================== Version Description ========= ====================================================================== +0.13.0 * switch to 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"zope.testing"] +testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] + +[metadata] +lock-version = "2.0" +python-versions = ">=3.8" +content-hash = "cc4d21e087d8f278c4c3541763846b43a5dac9f7becd58ea1c5a3c64bda00ff6" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..97ea1b5 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,61 @@ +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + + +#maintainer ?#maintainer email +[tool.poetry] +name = "sequana_pipetools" +version = "0.13.0" +description = "A set of tools to help building or using Sequana pipelines" +authors = ["Sequana Team"] +license = "BSD-3" +repository = "https://github.com/sequana/sequana_pipetools" +readme = "README.rst" +keywords = ["snakemake", "sequana", "pipelines"] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Education", + "Intended Audience :: End Users/Desktop", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.10", + "Topic :: Software Development :: Libraries :: Python Modules", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Information Analysis", +] +packages = [ + { include = "sequana_pipetools" } +] + +[tool.poetry.dependencies] +python = ">=3.8" +deprecated = ">=1.2.13" +easydev = ">=0.12.1" +parse = ">=1.19.0" +"ruamel.yaml" = ">=0.17.32" +packaging = ">=23.1" +pykwalify = ">=1.8" +importlib_resources = ">=5.4.0" +pyyaml = ">=1.3" +aiohttp = ">=3.8.4" +tqdm = ">=4.65" +charset-normalizer = "^2" + + +[tool.poetry.scripts] +sequana_completion = "sequana_pipetools.scripts.completion:main" +sequana_slurm_status = "sequana_pipetools.scripts.slurm:main" + + +[tool.poetry.group.dev.dependencies] +black = "^23.7.0" +pytest = "^7.4.0" +mock = "^5.1.0" +pytest-mock = "^3.11.1" +sequana-fastqc = "^1.7.1" +pytest-cov = "^4.1.0" + diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index b2ffd40..0000000 --- a/requirements.txt +++ /dev/null @@ -1,10 +0,0 @@ -deprecated -easydev -parse -ruamel.yaml -packaging -pykwalify -importlib_resources -pyyaml -aiohttp -tqdm diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index 0ef276e..0000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,3 +0,0 @@ -pytest -mock -git+https://github.com/sequana/fastqc.git@main#egg=sequana-fastqc diff --git a/sequana_pipetools/snaketools/file_factory.py b/sequana_pipetools/snaketools/file_factory.py index 3dc8de3..9d59368 100644 --- a/sequana_pipetools/snaketools/file_factory.py +++ b/sequana_pipetools/snaketools/file_factory.py @@ -198,8 +198,10 @@ def _pathname(self): pathname = set(self.pathnames) if len(pathname) == 1: return list(pathname)[0] + os.sep + elif len(pathname) == 0: + raise ValueError(f"found no pathname; no input files found in {self.patten} ?") else: - raise ValueError("found more than one pathname") + raise ValueError(f"found more than one pathname {pathname}.") pathname = property(_pathname, doc="the common relative path") diff --git a/setup.py b/setup.py deleted file mode 100644 index 7f110ad..0000000 --- a/setup.py +++ /dev/null @@ -1,68 +0,0 @@ -from setuptools import setup, find_packages - - -_MAJOR = 0 -_MINOR = 12 -_MICRO = 5 - -version = f"{_MAJOR}.{_MINOR}.{_MICRO}" -release = f"{_MAJOR}.{_MINOR}" - -metainfo = { - "authors": {"main": ("thomas cokelaer", "thomas.cokelaer@pasteur.fr")}, - "version": version, - "license": "new BSD", - "url": "https://github.com/sequana/sequana_pipetools", - "description": "A set of tools to help building or using Sequana pipelines", - "platforms": ["Linux", "Unix", "MacOsX", "Windows"], - "keywords": ["snakemake, sequana, pipelines"], - "classifiers": [ - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Education", - "Intended Audience :: End Users/Desktop", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Topic :: Software Development :: Libraries :: Python Modules", - "Topic :: Scientific/Engineering :: Bio-Informatics", - "Topic :: Scientific/Engineering :: Information Analysis", - "Topic :: Scientific/Engineering :: Mathematics", - "Topic :: Scientific/Engineering :: Physics", - ], -} - - -setup( - name="sequana_pipetools", - version=version, - maintainer=metainfo["authors"]["main"][0], - maintainer_email=metainfo["authors"]["main"][1], - author=metainfo["authors"]["main"][0], - author_email=metainfo["authors"]["main"][1], - long_description=open("README.rst").read(), - keywords=metainfo["keywords"], - description=metainfo["description"], - license=metainfo["license"], - platforms=metainfo["platforms"], - url=metainfo["url"], - classifiers=metainfo["classifiers"], - # package installation - packages=find_packages(exclude=["tests*"]), - install_requires=open("requirements.txt").read(), - tests_require=["pytest", "coverage", "pytest-cov", "sequana_fastqc"], - # This is recursive include of data files - exclude_package_data={"": ["__pycache__"]}, - package_data={ - "": ["*.yaml", "*.rules", "*.json", "requirements.txt", "*png"], - }, - zip_safe=False, - entry_points={ - "console_scripts": [ - "sequana_completion=sequana_pipetools.scripts.completion:main", - "sequana_slurm_status=sequana_pipetools.scripts.slurm:main", - ] - }, -) diff --git a/tests/snaketools/test_filefactory.py b/tests/snaketools/test_filefactory.py index 5ff9d3a..204b942 100644 --- a/tests/snaketools/test_filefactory.py +++ b/tests/snaketools/test_filefactory.py @@ -22,12 +22,12 @@ def inner_test(ff): ff.extensions # list - list_files = glob.glob("*.py") + list_files = glob.glob("*.*") ff = snaketools.FileFactory(list_files) inner_test(ff) # glob - ff = snaketools.FileFactory("*py") + ff = snaketools.FileFactory("*.*") inner_test(ff) ff = snaketools.FastQFactory(test_dir + "/data/Hm2*fastq.gz", verbose=True) diff --git a/tests/snaketools/test_sequana_config.py b/tests/snaketools/test_sequana_config.py index 0b84c45..a91939c 100644 --- a/tests/snaketools/test_sequana_config.py +++ b/tests/snaketools/test_sequana_config.py @@ -83,13 +83,14 @@ def test_sequana_config(tmpdir): # test all installed pipelines saving/reading config file output = tmpdir.join("test.yml") for pipeline in snaketools.pipeline_names: - config_filename = Module(pipeline)._get_config() - cfg1 = SequanaConfig(config_filename) - - cfg1.save(output) - cfg2 = SequanaConfig(str(output)) - assert cfg2._yaml_code == cfg1._yaml_code - assert cfg1.config == cfg2.config + if "_fastqc" in pipeline: + config_filename = Module(pipeline)._get_config() + cfg1 = SequanaConfig(config_filename) + + cfg1.save(output) + cfg2 = SequanaConfig(str(output)) + assert cfg2._yaml_code == cfg1._yaml_code + assert cfg1.config == cfg2.config # test config with a _directory or _file based on the fastqc pipeline cfg = SequanaConfig(s.config) diff --git a/tests/test_manager.py b/tests/test_manager.py index cda1a19..70a0cec 100644 --- a/tests/test_manager.py +++ b/tests/test_manager.py @@ -155,7 +155,7 @@ def test_copy_requirements(tmpdir): requirements = [ # "phiX174.fa", str(tmp_require), - "https://raw.githubusercontent.com/sequana/sequana/master/README.rst", + "https://raw.githubusercontent.com/sequana/sequana/main/README.rst", "__init__.py", "setup.py", ]