Adopt pyproject.toml

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="[email protected],[email protected]" \
     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" ]

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 = "[email protected]"},
+]
+# TODO maintainers = [{name = "Brett Cannon", email = "[email protected]"}]
+
+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",
+]