Moving to Ruff and pyproject.toml

.github/workflows/test.yml

@@ -19,7 +19,7 @@ jobs:
         os:
           - ubuntu-latest
           - macos-latest
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     runs-on: ${{ matrix.os }}
     name: Run pytest
     steps:
@@ -44,7 +44,6 @@ jobs:
           which python
           python -m pip install --upgrade pip
           python -m pip install -r requirements.txt
-          conda config --remove channels defaults
           conda config --add channels conda-forge 
           conda config --add channels nodefaults
           $CONDA/bin/conda init bash
@@ -60,7 +59,6 @@ jobs:
           which python
           python -m pip install --upgrade pip
           python -m pip install -r requirements.txt
-          conda config --remove channels defaults
           conda config --add channels conda-forge 
           conda config --add channels nodefaults
           $CONDA/bin/conda init bash

.pre-commit-config.yaml

@@ -44,13 +44,6 @@ repos:
         language: system
         types: [python]
         require_serial: true
-      # - id: flake8
-      #   name: flake8
-      #   entry: flake8
-      #   language: system
-      #   types: [python]
-      #   args: ["--config='{{ cookiecutter.repo_name }}/setup.cfg'"]
-      #   require_serial: true
   - repo: https://github.com/prettier/pre-commit
     rev: v2.1.2
     hooks:

docs/docs/structure.md

@@ -311,23 +311,19 @@ You can write reports in markdown and put them in `outputs/reports` and referenc
 │   ├── pipeline/                    |  Pipeline components
 │   └── utils/                       |  Utilities
 ├── docs/                            |  DOCUMENTATION
+├── pyproject.toml                   |  PROJECT METADATA AND CONFIGURATION
 ├── environment.yaml                 |  CONDA ENVIRONMENT SPECIFICATION (optional component)
-├── requirements.txt                 |  PYTHON DEPENDENCIES NEEDED TO RUN THE CODE
-├── requirements_dev.txt             |  PYTHON DEV DEPENDENCIES (e.g. building docs/running tests)
 ├── inputs/                          |  INPUTS (should be immutable)
-├── jupytext.toml                    |  JUPYTEXT CONFIGURATION
 ├── LICENSE                          |
-├── outputs/                          |  OUTPUTS PRODUCED FROM THE PROJECT
+├── outputs/                         |  OUTPUTS PRODUCED FROM THE PROJECT
 ├── Makefile                         |  TASKS TO COORDINATE PROJECT (`make` shows available commands)
 ├── README.md                        |
-├── setup.py                         |  ALLOWS US TO PIP INSTALL src/
-├── setup.cfg                        |  ADDITIONAL PROJECT CONFIGURATION, e.g. flake8
 ├── .pre-commit-config.yaml          |  DEFINES CHECKS THAT MUST PASS BEFORE git commit SUCCEEDS
 ├── .gitignore                       |  TELLS git WHAT FILES WE DON'T WANT TO COMMIT
 ├── .github/                         |  GITHUB CONFIGURATION
 ├── .env                             |  SECRETS (never commit to git!)
 ├── .envrc                           |  SHARED PROJECT CONFIGURATION VARIABLES
-├── .cookiecutter                    |  COOKIECUTTER SETUP & CONFIGURATION (user can safely ignore)
+└── .cookiecutter                    |  COOKIECUTTER SETUP & CONFIGURATION (user can safely ignore)
 ```
 
 ## The Makefile

requirements.txt

@@ -2,4 +2,5 @@ mkdocs
 mkdocs-material
 mkdocs-material-extensions
 cookiecutter
+tomli
 pytest

tests/test_creation.py

@@ -1,14 +1,14 @@
 import os
 import re
 import sys
+import tomli
 from contextlib import contextmanager
 from pathlib import Path
 from subprocess import CalledProcessError, check_output
 from typing import List
 
 import pytest
 
-
 @contextmanager
 def ch_dir(path):
     """Context Manager to change directory to `path`."""
@@ -42,13 +42,6 @@ def test_project_name(self):
         name = "NestaTestCookie".lower()
         assert project.name == name
 
-    def test_author(self):
-        """Test author set in `setup.py`."""
-        setup_ = self.path / "setup.py"
-        args = ["python", setup_, "--author"]
-        p = "".join(shell(args))
-        assert p == "Nesta"
-
     def test_readme(self):
         """Test README.md exists with no curlies."""
         readme_path = self.path / "README.md"
@@ -57,28 +50,29 @@ def test_readme(self):
         with open(readme_path) as fin:
             assert "# NestaTestCookie".lower() == next(fin).strip()
 
-    def test_version(self):
-        """Test version set in `setup.py`."""
-        setup_ = self.path / "setup.py"
-        args = ["python", setup_, "--version"]
-        p = "".join(shell(args))
-        assert p == "0.1.0"
-
     def test_license(self):
         """Test LICENSE exists with no curlies."""
         license_path = self.path / "LICENSE"
         assert license_path.exists()
         assert no_curlies(license_path)
 
-    def test_license_type(self):
-        """Test License set appropriately in `setup.py`."""
-        setup_ = self.path / "setup.py"
-        args = ["python", setup_, "--license"]
-        p = "".join(shell(args))
+    def test_metadata(self):
+        """Test project metadata in pyproject.toml."""
+        pyproject_path = self.path / "pyproject.toml"
+        assert pyproject_path.exists()
+        assert no_curlies(pyproject_path)
+
+        with open(pyproject_path, "rb") as f:
+            pyproject = tomli.load(f)
+
+        project = pyproject.get("project", {})
+        assert project.get("name") == "nestatestcookie"
+        assert project.get("version") == "0.1.0"
+        assert any(author.get("name") == "Nesta" for author in project.get("authors", []))
         if pytest.param.get("openess") == "private":
-            assert p == "proprietary"
+            assert project.get("license", {}).get("text") == "proprietary"
         else:
-            assert p == "MIT"
+            assert project.get("license", {}).get("text") == "MIT"
 
     def test_makefile(self):
         """Test Makefile exists with no curlies."""
@@ -93,7 +87,7 @@ def test_curlies(self):
             ".env",
             ".envrc",
             "README.md",
-            "setup.cfg",
+            "pyproject.toml",
             "docs/conf.py",
             "docs/index.rst",
             f"{repo_name}/config/logging.yaml",

{{ cookiecutter.repo_name }}/.pre-commit-config.yaml

@@ -1,12 +1,6 @@
 repos:
   - repo: local
     hooks:
-      - id: black
-        name: black
-        entry: black
-        language: system
-        types: [python]
-        require_serial: true
       - id: check-added-large-files
         name: Check for added large files
         entry: check-added-large-files
@@ -37,24 +31,17 @@ repos:
         entry: check-yaml
         language: system
         types: [yaml]
-      # - id: reorder-python-imports
-      #   name: Reorder python imports
-      #   entry: reorder-python-imports
-      #   language: system
-      #   types: [python]
-      # - id: flake8
-      #   name: flake8
-      #   entry: flake8
-      #   language: system
-      #   types: [python]
-      #   args: ["--config=.flake8"]
-      #   require_serial: true
       - id: no-commit-to-branch
         name: Prevent commits to dev / master
         entry: no-commit-to-branch
         language: python
         args: ["-b", dev, "-b", master, "-b", main]
         pass_filenames: false
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      - id: ruff
+      - id: ruff-format
   - repo: https://github.com/prettier/pre-commit
     rev: v2.1.2
     hooks:

{{ cookiecutter.repo_name }}/Makefile

@@ -63,10 +63,18 @@ pip-install:
 	@pip install -e ".[dev]"
 
 .PHONY: conda-remove
-## Remove the conda-environment cleanly, using -f so works even if no environment to be removed
+## Remove the conda-environment cleanly
 conda-remove:
-	conda env remove -n ${REPO_NAME}
-	rm -f .cookiecutter/state/conda-create*
+	@echo "Checking if conda environment ${REPO_NAME} exists"
+	@if conda info --envs | grep -q ${REPO_NAME}; then \
+		if conda info --envs | grep '*' | grep -q ${REPO_NAME}; then \
+			echo "Error: Conda environment ${REPO_NAME} is currently active. Please run `conda deactivate` before proceeding."; \
+			exit 1; \
+		fi; \
+		conda env remove -n ${REPO_NAME}; \
+		echo "Removing conda-create state files"; \
+		rm -f .cookiecutter/state/conda-create*; \
+	fi
 	@direnv reload
 
 .PHONY: clean
@@ -97,9 +105,9 @@ endef
 .cookiecutter/state/setup-git:
 	@echo -n "Installing and configuring git pre-commit hooks"
 	@(eval "$$(conda shell.bash activate "${REPO_NAME}")"\
-	 &&pre-commit install --install-hooks)\
+	 && pre-commit install --install-hooks)\
 	 > [email protected] 2>&1\
-	 || $(call err,Git pre-commit setup failed)
+	 || (cat [email protected] && $(call err,Git pre-commit setup failed))
 	@touch $@
 	@echo " DONE"
 

{{ cookiecutter.repo_name }}/docs/conf.py

@@ -2,7 +2,6 @@
 
 from datetime import datetime
 
-
 project = "{{ cookiecutter.project_name }}"
 author = "{{ cookiecutter.author_name }}"
 copyright = f"{datetime.now().year}, {author}"

{{ cookiecutter.repo_name }}/pyproject.toml

@@ -0,0 +1,61 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["{{ cookiecutter.repo_name }}"]
+
+[project]
+name = "{{ cookiecutter.project_name }}"
+version = "0.1.0"
+description = "{{ cookiecutter.description }}"
+authors = [{name = "{{ cookiecutter.author_name }}"}]
+license = {text = "{% if cookiecutter.openness == 'public' %}MIT{% else %}proprietary{% endif %}"}
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = []
+
+[project.urls]
+repository = "https://github.com/nestauk/{{ cookiecutter.repo_name }}"
+issues = "https://github.com/nestauk/{{ cookiecutter.repo_name }}/issues"
+
+[project.optional-dependencies]
+dev = [
+    "ipykernel",
+    "jupytext",
+    "ruff",
+    "Sphinx",
+    "sphinxcontrib-napoleon",
+    "sphinx-rtd-theme",
+    "pytest",
+    "pre-commit",
+    "pre-commit-hooks"
+]
+
+[tool.jupytext]
+# Always pair ipynb notebooks to py:percent files
+default_jupytext_formats = "ipynb,py:percent"
+# Comment out magics (allows code formatting)
+comment_magics = true
+# Strip cell-level metadata (avoid polluting git diffs)
+default_cell_metadata_filter = "-all"
+
+[tool.ruff.lint]
+select = ["ANN", "B", "C", "D", "E", "F", "I", "N", "W"]
+# S101 - warns about assert being removed when compiled
+# D100 - warns about missing module-level docstrings
+ignore = ["S101", "D100"]
+mccabe = { max-complexity = 10 }
+
+[tool.ruff.lint.isort]
+known-first-party = ["{{ cookiecutter.repo_name }}"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+"**/__init__.py" = ["F401", "E402", "D104"]
+
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = "dynamic"