convert to proper python project, create CLI tool stub

Author: apirogov

.pre-commit-config.yaml

@@ -5,43 +5,22 @@ exclude: "^{{ cookiecutter.*"  # <-- added
 repos:
   # GH Actions
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: '0.22.0'
+    rev: '0.27.2'
     hooks:
     - id: check-github-workflows
 
-  # General Python linters and formatters
-  - repo: https://github.com/pycqa/isort
-    rev: '5.12.0'
+  # Code Quality
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
     hooks:
-      - id: isort
-        args: ['--profile', 'black']
-  - repo: https://github.com/ambv/black
-    rev: '23.1.0'
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.1.1
-    hooks:
-    -   id: autoflake
-
-  # Quality
-  - repo: https://github.com/pycqa/flake8
-    rev: '6.0.0'
-    hooks:
-      - id: flake8
-        additional_dependencies:
-          - Flake8-pyproject==1.2.3
-          - flake8-bugbear==23.3.23
-          - dlint==0.14.1
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: '6.3.0'
-    hooks:
-      - id: pydocstyle
-        additional_dependencies: ["tomli==2.0.1"]
-        files: "^src/"
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.1.1'
+    rev: 'v1.7.1'
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]
@@ -60,18 +39,18 @@ repos:
     hooks:
       - id: validate-cff
   - repo: https://github.com/fsfe/reuse-tool
-    rev: 'v1.1.2'
+    rev: 'v2.1.0'
     hooks:
       - id: reuse
 
   - repo: https://github.com/Materials-Data-Science-and-Informatics/somesy
-    rev: 'v0.1.0'
+    rev: 'v0.2.0'
     hooks:
       - id: somesy
 
   # Various general + format-specific helpers
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-symlinks
     - id: trailing-whitespace

.reuse/dep5

@@ -11,6 +11,6 @@ Files: .gitignore pyproject.toml poetry.lock .pre-commit-config.yaml .somesy.tom
 Copyright: 2023 Forschungszentrum Jülich GmbH - Institute for Materials Data Science and Informatics (IAS9) - Stefan Sandfeld <s.sandfeld@fz-juelich.de>
 License: CC0-1.0
 
-Files: tests/* hooks/*
+Files: src/* tests/* hooks/*
 Copyright: 2023 Forschungszentrum Jülich GmbH - Institute for Materials Data Science and Informatics (IAS9) - Stefan Sandfeld <s.sandfeld@fz-juelich.de>
 License: MIT

codemeta.json

@@ -57,14 +57,34 @@
             "runtimePlatform": "Python 3",
             "version": "^2.1.1"
         },
+        {
+            "@type": "SoftwareApplication",
+            "identifier": "pydantic",
+            "name": "pydantic",
+            "runtimePlatform": "Python 3",
+            "version": "^2.5.2"
+        },
         {
             "@type": "SoftwareApplication",
             "identifier": "python",
             "name": "python",
             "runtimePlatform": "Python 3",
             "version": "^3.8"
+        },
+        {
+            "@type": "SoftwareApplication",
+            "identifier": "typer",
+            "name": "typer",
+            "runtimePlatform": "Python 3",
+            "version": "^0.9.0"
         }
     ],
+    "targetProduct": {
+        "@type": "CommandLineApplication",
+        "executableName": "fair-python-cookiecutter",
+        "name": "fair-python-cookiecutter",
+        "runtimePlatform": "Python 3"
+    },
     "url": "https://materials-data-science-and-informatics.github.io/fair-python-cookiecutter",
     "version": "0.1.0"
 }

poetry.lock

@@ -7,21 +7,37 @@ authors = ["Anton Pirogov <a.pirogov@fz-juelich.de>"]
 maintainers = ["Anton Pirogov <a.pirogov@fz-juelich.de>"]
 license = "MIT"
 
-keywords = ["fair", "metadata", "python", "cookiecutter", "template"]
+readme = "README.md"
 repository = "https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter"
 homepage = "https://materials-data-science-and-informatics.github.io/fair-python-cookiecutter"
 documentation = "https://materials-data-science-and-informatics.github.io/fair-python-cookiecutter"
+
+keywords = ["fair", "metadata", "python", "cookiecutter", "template"]
 # ---- managed by somesy, see .somesy.toml ----
 
 classifiers = [
     "Intended Audience :: Science/Research",
     "Intended Audience :: Developers",
 ]
-readme = "README.md"
+
+# the Python packages that will be included in a built distribution:
+packages = [{include = "fair_python_cookiecutter", from = "src"}]
+
+# always include basic info for humans and core metadata in the distribution,
+# include files related to test and documentation only in sdist:
+include = [
+  "*.md", "LICENSE", "LICENSES", ".reuse/dep5", "CITATION.cff", "codemeta.json",
+  "mkdocs.yml", "docs", "tests",
+  { path = "mkdocs.yml", format = "sdist" },
+  { path = "docs", format = "sdist" },
+  { path = "tests", format = "sdist" },
+]
 
 [tool.poetry.dependencies]
 python = "^3.8"
 cookiecutter = "^2.1.1"
+typer = "^0.9.0"
+pydantic = "^2.5.2"
 
 [tool.poetry.group.dev.dependencies]
 poethepoet = "^0.18.1"
@@ -48,6 +64,9 @@ anybadge = "^1.14.0"
 interrogate = "^1.5.0"
 black = "^23.3.0"
 
+[tool.poetry.scripts]
+fair-python-cookiecutter = "fair_python_cookiecutter.main:app"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
@@ -63,14 +82,46 @@ docs = "mkdocs build"  # run this to generate local documentation
 # -------------------
 
 [tool.pytest.ini_options]
+pythonpath = ["src"]
 addopts = "--ignore='{{ cookiecutter.__project_slug }}'"
+# addopts = "--cov-report=term-missing:skip-covered"
+filterwarnings = [
+"ignore::DeprecationWarning:pkg_resources.*",
+"ignore::DeprecationWarning:pyshacl.*",
+# Example:
+# "ignore::DeprecationWarning:importlib_metadata.*",
+]
 
-[tool.flake8]
-ignore = ["W503"]
-max-line-length = 88
+[tool.coverage.run]
+source = ["fair_python_cookiecutter"]
 
-[tool.pydocstyle]
-convention = "google"
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "if self.debug:",
+    "if settings.DEBUG",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if 0:",
+    "if TYPE_CHECKING:",
+    "if __name__ == .__main__.:",
+    "class .*\\bProtocol\\):",
+    "@(abc\\.)?abstractmethod",
+]
+
+[tool.ruff.lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = []
+# TODO: check that ruff substitutes
+# - flake8-bugbear
+# - dlint
+# - pydocstyle (google style)
+# - black
+# - autoflake
+# - isort
 
 [tool.bandit]
 exclude_dirs = ["tests"]
+

pyproject.toml

@@ -0,0 +1,5 @@
+"""somesy package."""
+import importlib_metadata
+
+# Set version, it will use version from pyproject.toml if defined
+__version__: str = importlib_metadata.version(__package__ or __name__)

src/fair_python_cookiecutter/__init__.py

@@ -0,0 +1,18 @@
+"""Main entry point for the somesy CLI."""
+import logging
+
+import typer
+from cookiecutter.config import get_user_config
+
+logger = logging.getLogger("fair_python_cookiecutter")
+
+app = typer.Typer()
+
+
+@app.command()
+def main():
+    """Main entry point for creating a project from the template."""
+    typer.echo("hello world!")
+
+    conf = get_user_config()
+    print(conf.get("fair-python-cookiecutter"))

src/fair_python_cookiecutter/main.py

@@ -72,8 +72,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ "ubuntu-latest" ]
-        python-version: [ "3.8", "3.9", "3.10" ]
+        os: [ "ubuntu-latest", "macos-latest", "windows-latest" ]
+        python-version: [ "3.8", "3.9", "3.10", "3.11" ]
     runs-on: ${{ matrix.os }}
 
     steps: