diff --git a/Dockerfile b/Dockerfile index c88abcb1ce..945d6d5e8e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,16 +1,19 @@ FROM python:3.12-slim@sha256:740d94a19218c8dd584b92f804b1158f85b0d241e5215ea26ed2dcade2b9d138 +COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" # Do not pick up python packages from $HOME ENV PYTHONNUSERSITE=1 -# Update pip to latest version -RUN python -m pip install --upgrade pip - +RUN uv venv /opt/venv +# Use the virtual environment automatically +ENV VIRTUAL_ENV=/opt/venv +# Place entry points in the environment at the front of the path +ENV PATH="/opt/venv/bin:$PATH" # Install dependencies -COPY requirements.txt requirements.txt -RUN python -m pip install -r requirements.txt +COPY pyproject.toml . +RUN uv pip install -r pyproject.toml # Install Nextflow dependencies RUN apt-get update \ @@ -41,7 +44,7 @@ COPY . /usr/src/nf_core WORKDIR /usr/src/nf_core # Install nf-core -RUN python -m pip install . +RUN uv pip install -e . # Set up entrypoint and cmd for easy docker usage ENTRYPOINT [ "nf-core" ] diff --git a/pyproject.toml b/pyproject.toml index 8168bd7c11..e8d86175b8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,92 @@ +[project] +name = "nf-core" +version = "2.14.2dev" +requires-python = ">=3.8.1, <4" +description = "Helper tools for use with nf-core Nextflow pipelines." +readme = "README.md" +keywords=[ + "nf-core", + "nextflow", + "bioinformatics", + "workflow", + "pipeline", + "biology", + "sequencing", + "NGS", + "next generation sequencing", +] +authors = [ + {name = "Phil Ewels", email = "phil.ewels@scilifelab.se"}, +] +# TODO maintainers = [{name = "Brett Cannon", email = "brett@example.com"}] + +dependencies = [ + "click", + "filetype", + "GitPython", + "PyGithub", + "jinja2", + "jsonschema>=3.0", + "markdown>=3.3", + "packaging", + "pillow", + "pdiff", + "pre-commit", + "prompt_toolkit>=3.0.3", + "pydantic>=2.2.1", + "pyyaml", + "questionary>=1.8.0", + "refgenie", + "requests", + "requests_cache", + "rich-click==1.8.*", + "rich>=13.3.1", + "tabulate", + "textual==0.71.0", + "trogon", + "pdiff", + "setuptools; python_version >= '3.12'", +] +# TODO include_package_data=True, +# TODO zip_safe=False, + +[project.urls] +Repository = "https://github.com/nf-core/tools" +# TODO https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls + + +# [project.entry_points] +# "console_scripts" = ["nf-core=nf_core.__main__:run_nf_core"] +# "refgenie.hooks.post_update" = ["nf-core-refgenie=nf_core.pipelines.refgenie:update_config"] + +[tool.uv] +dev-dependencies = [ + "mypy", + "myst_parser", + "pytest-cov", + "pytest-datafiles", + "responses", + "ruff", + "Sphinx", + "sphinx-rtd-theme", + "textual-dev==1.5.1", + "types-PyYAML", + "types-requests", + "types-jsonschema", + "types-Markdown", + "types-PyYAML", + "types-requests", + "types-setuptools", + "pytest-textual-snapshot==0.4.0", + "pytest-workflow>=2.0.0", + "pytest>=8.0.0", + "ruff", +] + +[tool.uv.workspace] +# members = ["packages/*", "examples/*"] +exclude = ["docs"] + [build-system] build-backend = "setuptools.build_meta" requires = ["setuptools>=40.6.0", "wheel"] @@ -33,3 +122,10 @@ known-first-party = ["nf_core"] [tool.ruff.lint.pep8-naming] extend-ignore-names = ["mocked_*", "*allOf", "*URI*"] + +# TODO Add mypy +# TODO Add pytest.ini + +classifiers = [ + "License :: OSI Approved :: MIT License", +] diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index 2c7bb0c8cf..0000000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,20 +0,0 @@ -mypy -myst_parser -pytest-cov -pytest-datafiles -responses -ruff -Sphinx -sphinx-rtd-theme -textual-dev==1.5.1 -types-PyYAML -types-requests -types-jsonschema -types-Markdown -types-PyYAML -types-requests -types-setuptools -pytest-textual-snapshot==0.4.0 -pytest-workflow>=2.0.0 -pytest>=8.0.0 -ruff diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 524b739e89..0000000000 --- a/requirements.txt +++ /dev/null @@ -1,24 +0,0 @@ -click -filetype -GitPython -PyGithub -jinja2 -jsonschema>=3.0 -markdown>=3.3 -packaging -pillow -pdiff -pre-commit -prompt_toolkit>=3.0.3 -pydantic>=2.2.1 -pyyaml -questionary>=1.8.0 -refgenie -requests -requests_cache -rich-click==1.8.* -rich>=13.3.1 -tabulate -textual==0.71.0 -trogon -pdiff diff --git a/setup.py b/setup.py deleted file mode 100644 index 8f32daa904..0000000000 --- a/setup.py +++ /dev/null @@ -1,43 +0,0 @@ -#!/usr/bin/env python - -from setuptools import find_packages, setup - -version = "2.14.2dev" - -with open("README.md") as f: - readme = f.read() - -with open("requirements.txt") as f: - required = f.read().splitlines() - -setup( - name="nf-core", - version=version, - description="Helper tools for use with nf-core Nextflow pipelines.", - long_description=readme, - long_description_content_type="text/markdown", - keywords=[ - "nf-core", - "nextflow", - "bioinformatics", - "workflow", - "pipeline", - "biology", - "sequencing", - "NGS", - "next generation sequencing", - ], - author="Phil Ewels", - author_email="phil.ewels@scilifelab.se", - url="https://github.com/nf-core/tools", - license="MIT", - entry_points={ - "console_scripts": ["nf-core=nf_core.__main__:run_nf_core"], - "refgenie.hooks.post_update": ["nf-core-refgenie=nf_core.pipelines.refgenie:update_config"], - }, - python_requires=">=3.8, <4", - install_requires=required, - packages=find_packages(exclude=("docs")), - include_package_data=True, - zip_safe=False, -) diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0 deleted file mode 160000 index ee82f320cb..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 deleted file mode 160000 index f7fe48cf9d..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 deleted file mode 160000 index dce3324acb..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit dce3324acbbe32f905afae8553e042f39404b37e diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0 deleted file mode 160000 index e2638dca91..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec diff --git 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