diff --git a/.github/workflows/openvariant_tester.yml b/.github/workflows/openvariant_tester.yml index 44a5976..5cfaf5f 100644 --- a/.github/workflows/openvariant_tester.yml +++ b/.github/workflows/openvariant_tester.yml @@ -24,27 +24,30 @@ jobs: build: runs-on: ubuntu-latest + env: + UV_LINK_MODE: copy + RUFF_FORMAT: github steps: - - uses: actions/checkout@v3 - - name: Set up the latest Python - uses: actions/setup-python@v3 + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 with: - python-version: "3.x" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest pytest-cov - pip install -e . - - name: Lint with flake8 + python-version-file: "pyproject.toml" + + - uses: astral-sh/setup-uv@v4 + + - name: Lint with Ruff run: | - # stop the build if there are Python syntax errors or undefined names - # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest + uv sync --extra linting --frozen + uv run ruff check openvariant + + - name: Test run: | - pytest --cov . + uv sync --extra tests --frozen + uv run pytest --cov . + - name: Upload coverage reports to Codecov with GitHub Action uses: codecov/codecov-action@v3 - + diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 62ee8fc..234afc7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -3,17 +3,18 @@ version: 2 build: os: "ubuntu-22.04" tools: - python: "3.12" + python: "3.10" apt_packages: - build-essential - libzmq3-dev - gcc - g++ - - python3-dev + commands: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv sync --extra docs --frozen + - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html sphinx: - configuration: docs/conf.py - -python: - install: - - requirements: requirements-docs.txt + configuration: docs/conf.py \ No newline at end of file diff --git a/openvariant/tasks/plugin.py b/openvariant/tasks/plugin.py index 163471e..c7bc5ba 100644 --- a/openvariant/tasks/plugin.py +++ b/openvariant/tasks/plugin.py @@ -31,49 +31,49 @@ def _add_action(name: str) -> None: init_file.write(f"import .{name} from {context_name}\n") init_file.close() with open(f"{path}/{name}/{name}.py", 'w') as plugin_file: - plugin_file.write(f"from openvariant.plugins.context import Context\n") - plugin_file.write(f"from openvariant.plugins.plugin import Plugin\n\n\n") + plugin_file.write("from openvariant.plugins.context import Context\n") + plugin_file.write("from openvariant.plugins.plugin import Plugin\n\n\n") plugin_file.write(f"class {context_name}(Context):\n") - plugin_file.write(f"\t\"\"\"\n") + plugin_file.write("\t\"\"\"\n") plugin_file.write(f"\t{context_name} class generated by OpenVariant\n\n") - plugin_file.write(f"\tAttributes\n") - plugin_file.write(f"\t-------\n") - plugin_file.write(f"\trow : dict\n") - plugin_file.write(f"\t\tMain method to execute data transformation in each row.\n") - plugin_file.write(f"\tfield_name : str\n") - plugin_file.write(f"\t\tName of the corresponding column that was described on the annotation schema.\n") - plugin_file.write(f"\tfile_path : str\n") - plugin_file.write(f"\t\tPath of the Input file that is being parsed.\n") - plugin_file.write(f"\t\"\"\"\n\n") - plugin_file.write(f"\tdef __init__(self, row: dict, field_name: str, file_path: str) -> None:\n") - plugin_file.write(f"\t\tsuper().__init__(row, field_name, file_path)\n") - plugin_file.write(f"\n\n") + plugin_file.write("\tAttributes\n") + plugin_file.write("\t-------\n") + plugin_file.write("\trow : dict\n") + plugin_file.write("\t\tMain method to execute data transformation in each row.\n") + plugin_file.write("\tfield_name : str\n") + plugin_file.write("\t\tName of the corresponding column that was described on the annotation schema.\n") + plugin_file.write("\tfile_path : str\n") + plugin_file.write("\t\tPath of the Input file that is being parsed.\n") + plugin_file.write("\t\"\"\"\n\n") + plugin_file.write("\tdef __init__(self, row: dict, field_name: str, file_path: str) -> None:\n") + plugin_file.write("\t\tsuper().__init__(row, field_name, file_path)\n") + plugin_file.write("\n\n") plugin_file.write(f"class {plugin_name}(Plugin):\n") - plugin_file.write(f"\t\"\"\"\n") + plugin_file.write("\t\"\"\"\n") plugin_file.write(f"\t{plugin_name} class generated by OpenVariant\n\n") - plugin_file.write(f"\tMethods\n") - plugin_file.write(f"\t-------\n") + plugin_file.write("\tMethods\n") + plugin_file.write("\t-------\n") plugin_file.write(f"\trun(context: {context_name})\n") - plugin_file.write(f"\t\tMain method to execute data transformation in each row.\n") - plugin_file.write(f"\t\"\"\"\n\n") + plugin_file.write("\t\tMain method to execute data transformation in each row.\n") + plugin_file.write("\t\"\"\"\n\n") plugin_file.write(f"\tdef run(self, context: {context_name}) -> dict:\n") - plugin_file.write(f"\t\t\"\"\"\n") - plugin_file.write(f"\t\tData transformation of a single row\n\n") - plugin_file.write(f"\t\tParameters\n") - plugin_file.write(f"\t\t-------\n") + plugin_file.write("\t\t\"\"\"\n") + plugin_file.write("\t\tData transformation of a single row\n\n") + plugin_file.write("\t\tParameters\n") + plugin_file.write("\t\t-------\n") plugin_file.write(f"\t\tcontext : {context_name}\n") - plugin_file.write(f"\t\t\tRepresentation of the row to be parsed.\n") - plugin_file.write(f"\t\t\n") - plugin_file.write(f"\t\tReturns\n") - plugin_file.write(f"\t\t-------\n") - plugin_file.write(f"\t\tfloat or int or str\n") - plugin_file.write(f"\t\t\tThe value of the field transformed.\n") - plugin_file.write(f"\t\t\"\"\"\n") - plugin_file.write(f"\n") - plugin_file.write(f"\t\t# This is an example code, modify if as you wish\n") - plugin_file.write(f"\t\tcontext.row[context.field_name] = \"Hello world! file:\" + context.file_path\n") - plugin_file.write(f"\n") - plugin_file.write(f"\t\treturn context.row[context.field_name]\n") + plugin_file.write("\t\t\tRepresentation of the row to be parsed.\n") + plugin_file.write("\t\t\n") + plugin_file.write("\t\tReturns\n") + plugin_file.write("\t\t-------\n") + plugin_file.write("\t\tfloat or int or str\n") + plugin_file.write("\t\t\tThe value of the field transformed.\n") + plugin_file.write("\t\t\"\"\"\n") + plugin_file.write("\n") + plugin_file.write("\t\t# This is an example code, modify if as you wish\n") + plugin_file.write("\t\tcontext.row[context.field_name] = \"Hello world! file:\" + context.file_path\n") + plugin_file.write("\n") + plugin_file.write("\t\treturn context.row[context.field_name]\n") class PluginActions(Enum): diff --git a/openvariant/variant/variant.py b/openvariant/variant/variant.py index 5bc7841..1e06d52 100644 --- a/openvariant/variant/variant.py +++ b/openvariant/variant/variant.py @@ -94,13 +94,18 @@ def _extract_header(file_path: str, original_header: list, annotation: Annotatio for field, ann in mapping_fields: ann_type = ann[0] - header_schema.update({field: AnnotationTypesProcess[ann_type].value(ann, original_header, file_path, - header_schema)}) + + class_name = ann_type + module_name = "openvariant.annotation.process" + ClassAnnotation = import_class_from_module(module_name, class_name) + instance = ClassAnnotation() + + header_schema.update({field: instance(ann, original_header, file_path, header_schema)}) return header_schema, annotation.columns @lru_cache(maxsize=256) -def _parse_field(value: float or int or str, func: Callable) -> str: +def _parse_field(value: float | int | str, func: Callable) -> str: """Getting the value of a specific annotation field. Cached with LRU policy""" result = func(value) return result if result is not None else str(float('nan')) diff --git a/openvariant/variant/where.py b/openvariant/variant/where.py index 1a43291..02e32c5 100644 --- a/openvariant/variant/where.py +++ b/openvariant/variant/where.py @@ -52,9 +52,9 @@ def _parse_where(where: str or None) -> List: WhereAttributesKeys.FIELD.value: wh[0], WhereAttributesKeys.VALUE.value: wh[2]} except KeyError: - raise ValueError(f"Unknown \"where\" syntax.") + raise ValueError("Unknown \"where\" syntax.") else: - raise ValueError(f"Unknown where syntax.") + raise ValueError("Unknown where syntax.") return [stmt] diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..f9d9524 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,142 @@ +[build-system] +requires = ["hatchling", "setuptools"] +build-backend = "hatchling.build" + +[project] +name = "open-variant" +version = "1.0.1" +description = "OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output." +authors = [ + { name = "BBGLab (Barcelona Biomedical Genomics Lab)", email = "bbglab@irbbarcelona.org" } +] +dependencies = [ + "pyyaml==6.0.1", + "tqdm==4.66.3", + "click==8.1.3", + "pyliftover==0.4.1", + "appdirs==1.4.4", +] +readme = "README.md" +requires-python = ">=3.10" +license = { file = "LICENSE" } +keywords = ["bioinformatics", "openvariant", "openvar", "bbglab"] + + +[project.urls] +Homepage = "https://github.com/bbglab/openvariant" +Documentation = "https://openvariant.readthedocs.io/" +Repository = "https://github.com/bbglab/openvariant" +Issues = "https://github.com/bbglab/openvariant/issues" + + +[project.scripts] +"openvar" = "openvariant.commands.openvar:openvar" + +[project.optional-dependencies] +docs = [ + "alabaster==0.7.12", + "asttokens==2.0.5", + "attrs==22.1.0", + "babel==2.10.3", + "backcall==0.2.0", + "beautifulsoup4==4.11.1", + "bleach==5.0.1", + "charset-normalizer==2.1.0", + "click==8.1.3", + "decorator==5.1.1", + "defusedxml==0.7.1", + "docutils==0.17.1", + "entrypoints==0.4", + "executing==0.9.1", + "fastjsonschema==2.16.1", + "idna==3.7", + "imagesize==1.4.1", + "jedi==0.18.1", + "jinja2==3.1.4", + "jsonschema==4.8.0", + "jupyter-client==7.3.4", + "jupyter-core==4.11.2", + "jupyterlab-pygments==0.2.2", + "markupsafe==2.1.1", + "matplotlib-inline==0.1.3", + "nbclient==0.6.6", + "nbformat==5.4.0", + "nbsphinx==0.8.9", + "nest-asyncio==1.5.5", + "open-variant==1.0.0", + "packaging==21.3", + "pandocfilters==1.5.0", + "parso==0.8.3", + "pexpect==4.8.0", + "pickleshare==0.7.5", + "prompt-toolkit==3.0.30", + "ptyprocess==0.7.0", + "pure-eval==0.2.2", + "pydata-sphinx-theme==0.8.1", + "pygments==2.15.0", + "pyparsing==3.0.9", + "pyrsistent==0.18.1", + "python-dateutil==2.8.2", + "pytz==2022.1", + "pyyaml==6.0.1", + "pyzmq==26.2.0", + "requests==2.32.2", + "ruamel-yaml==0.16.13", + "six==1.16.0", + "snowballstemmer==2.2.0", + "soupsieve==2.3.2.post1", + "sphinx-copybutton==0.5.0", + "sphinx==4.5.0", + "sphinx-gallery==0.10.1", + "sphinx-panels==0.6.0", + "sphinxcontrib-applehelp==1.0.2", + "sphinxcontrib-autoyaml==1.0.0", + "sphinxcontrib-devhelp==1.0.2", + "sphinxcontrib-htmlhelp==2.0.0", + "sphinxcontrib-jsmath==1.0.1", + "sphinxcontrib-qthelp==1.0.3", + "sphinxcontrib-serializinghtml==1.1.5", + "stack-data==0.3.0", + "tinycss2==1.1.1", + "tornado==6.4.2", + "tqdm==4.66.3", + "traitlets==5.3.0", + "urllib3==1.26.19", + "wcwidth==0.2.5", + "webencodings==0.5.1", + "ipython>=8.18.0", + "nbconvert==7.0.0rc0", + "mistune==2.0.3", + "sphinxcontrib-bibtex==2.6.3", + "setuptools>=58.2.0", +] +linting = [ + "flake8>=7.1.1", + "ruff>=0.8.3", +] +tests = [ + "coverage>=7.6.9", + "pytest-cov>=6.0.0", + "pytest>=8.3.4", +] + +[tool.hatch.metadata] +allow-direct-references = true + +[tool.hatch.build.targets.wheel] +packages = ["openvariant"] + +[tool.uv.sources] +open-variant = { workspace = true } + +[tool.ruff.lint] +select = ["F"] +ignore = ["F401"] + +[tool.ruff] +line-length = 127 + +[tool.ruff.format] +quote-style = "single" +indent-style = "space" +docstring-code-format = true diff --git a/requirements-docs.txt b/requirements-docs.txt deleted file mode 100644 index 93ed1be..0000000 --- a/requirements-docs.txt +++ /dev/null @@ -1,74 +0,0 @@ -alabaster==0.7.12 -asttokens==2.0.5 -attrs==22.1.0 -Babel==2.10.3 -backcall==0.2.0 -beautifulsoup4==4.11.1 -bleach==5.0.1 -charset-normalizer==2.1.0 -click==8.1.3 -decorator==5.1.1 -defusedxml==0.7.1 -docutils==0.17.1 -entrypoints==0.4 -executing==0.9.1 -fastjsonschema==2.16.1 -idna==3.7 -imagesize==1.4.1 -jedi==0.18.1 -Jinja2==3.1.4 -jsonschema==4.8.0 -jupyter-client==7.3.4 -jupyter-core==4.11.2 -jupyterlab-pygments==0.2.2 -MarkupSafe==2.1.1 -matplotlib-inline==0.1.3 -nbclient==0.6.6 -nbformat==5.4.0 -nbsphinx==0.8.9 -nest-asyncio==1.5.5 -open-variant==1.0.0 -packaging==21.3 -pandocfilters==1.5.0 -parso==0.8.3 -pexpect==4.8.0 -pickleshare==0.7.5 -prompt-toolkit==3.0.30 -ptyprocess==0.7.0 -pure-eval==0.2.2 -pydata-sphinx-theme==0.8.1 -Pygments==2.15.0 -pyparsing==3.0.9 -pyrsistent==0.18.1 -python-dateutil==2.8.2 -pytz==2022.1 -PyYAML==6.0.1 -pyzmq==26.2.0 -requests==2.32.2 -ruamel.yaml==0.16.13 -six==1.16.0 -snowballstemmer==2.2.0 -soupsieve==2.3.2.post1 -Sphinx==4.5.0 -sphinx-copybutton==0.5.0 -sphinx-gallery==0.10.1 -sphinx-panels==0.6.0 -sphinxcontrib-applehelp==1.0.2 -sphinxcontrib-autoyaml==1.0.0 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.0 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.5 -stack-data==0.3.0 -tinycss2==1.1.1 -tornado==6.4.2 -tqdm==4.66.3 -traitlets==5.3.0 -urllib3==1.26.19 -wcwidth==0.2.5 -webencodings==0.5.1 -ipython -nbconvert==7.0.0rc0 -mistune==2.0.3 -sphinxcontrib-bibtex==2.6.3 diff --git a/setup.py b/setup.py deleted file mode 100644 index 0517345..0000000 --- a/setup.py +++ /dev/null @@ -1,27 +0,0 @@ -from setuptools import setup, find_packages - -from pathlib import Path -this_directory = Path(__file__).parent -long_description = (this_directory / "README.md").read_text() - -setup( - name="open-variant", - version="1.0.0", - author="BBGLab - Barcelona Biomedical Genomics Lab", - author_email='bbglab@irbbarcelona.org', - description="OpenVariant provides different functionalities to read, parse and operate different multiple input " - "file formats, being able to customize the output.", - long_description=long_description, - long_description_content_type='text/markdown', - license='BSD 3-Clause License', - keywords='bioinformatics,openvariant,openvar,bbglab', - packages=find_packages(exclude=["tests.*", "tests"]), - include_package_data=True, - install_requires=['pyyaml', 'tqdm', 'click', 'pyliftover', 'appdirs'], - entry_points={ - 'console_scripts': [ - 'openvar = openvariant.commands.openvar:openvar', - ] - }, - url="https://github.com/bbglab/openvariant", -) diff --git 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