[ENH] package with pyproject.tom and lint (#46)

* package with pyproject.toml, add isort / codespell, apply linting via pre-commit

* update pre-commit

* run tests

* rm breakpoints

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update test_rs2redcap_redcap2rs.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: Yibei Chen <yibeichan@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+doctests = True
+exclude =
+    **/__init__.py
+    **/tests/*
+    *build/
+    docs/sphinxext/
+    docs/tools/
+    reproschema/_version.py
+max-line-length=79
+extend-ignore = B001, B006, B016, E501, E722, F821

.gitattributes

@@ -5,9 +5,9 @@ name: Python package
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:

.github/workflows/pythonpackage.yml

@@ -21,11 +21,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine pyyaml
+        pip install setuptools twine pyyaml build
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py bdist_wheel
+        python -m build
         twine upload dist/*

.github/workflows/pythonpublish.yml

@@ -1,3 +1,6 @@
+# autogenerated by hacthling
+reproschema/_version.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.gitignore

@@ -8,7 +8,43 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
+
+# Sorts Python imports alphabetically and by section with `isort`.
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: [--profile, black, --settings-path, pyproject.toml]
+
 -   repo: https://github.com/psf/black
     rev: 24.4.2
     hooks:
     -   id: black
+
+# Checks for spelling errors
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    -   id: codespell
+        args: [--toml, pyproject.toml]
+        additional_dependencies: [tomli]
+
+# Format TOML files
+-   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.13.0
+    hooks:
+    -   id: pretty-format-toml
+        args: [--autofix, --indent, '4']
+
+# Check that Python code complies with PEP8 guidelines
+# flake8 uses pydocstyle to check docstrings: https://flake8.pycqa.org/en/latest/
+# flake8-docstrings: https://pypi.org/project/flake8-docstrings/
+# flake8-use-fstring forces to use fstrings: https://pypi.org/project/flake8-use-fstring/
+# flake8-functions checks functions quality: https://pypi.org/project/flake8-functions/
+# flake8-bugbear detects some common bugs: https://github.com/PyCQA/flake8-bugbear
+-   repo: https://github.com/pyCQA/flake8
+    rev: 7.1.0
+    hooks:
+    -   id: flake8
+        args: [--config, .flake8, --verbose, reproschema]
+        additional_dependencies: [flake8-bugbear]

.pre-commit-config.yaml

@@ -0,0 +1,3 @@
+datas
+Varios
+deamon

codespell_ignore_words.txt

@@ -0,0 +1,84 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling", "hatch-vcs"]
+
+[project]
+authors = [{name = "Repronim developers", email = "info@repronim.org"}]
+dependencies = [
+    "click",
+    "etelemetry",
+    "pyshacl",
+    "PyLD",
+    "requests",
+    "requests_cache",
+    "pyyaml",
+    "beautifulsoup4",
+    "lxml",
+    "pydantic >= 2.0"
+]
+description = "Reproschema Python library"
+# Version from setuptools_scm
+dynamic = ["version"]
+license = {text = "Apache License, 2.0"}
+maintainers = [{name = "Repronim developers", email = "info@repronim.org"}]
+name = "reproschema-py"
+readme = "README.md"
+requires-python = ">=3.8"
+
+[project.optional-dependencies]
+all = ["reproschema-py[doc]", "reproschema-py[test]"]
+dev = ["reproschema-py[doc]", "reproschema-py[test]", "black", "pre-commit"]
+doc = [
+    "packaging",
+    "sphinx >= 2.1.2",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-apidoc ~= 0.3.0",
+    "sphinxcontrib-napoleon",
+    "sphinxcontrib-versioning"
+]
+docs = ["reproschema-py[doc]"]
+# For running unit and docstring tests
+test = [
+    "pytest >= 4.4.0",
+    "pytest-cov",
+    "pytest-env",
+    "pytest-xdist",
+    "pytest-rerunfailures",
+    "codecov"
+]
+tests = ["reproschema-py[test]"]
+
+[project.scripts]
+reproschema = "reproschema.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/ReproNim/reproschema-py"
+
+[tool.black]
+line-length = 79
+
+[tool.codespell]
+ignore-words = "codespell_ignore_words.txt"
+skip = "./.git"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "reproschema/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["reproschema"]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.isort]
+combine_as_imports = true
+line_length = 79
+profile = "black"
+skip_gitignore = true
+
+[tool.pytest.ini_options]
+addopts = "-ra --strict-config --strict-markers --doctest-modules --showlocals -v"
+doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
+junit_family = "xunit2"
+minversion = "6.0"
+xfail_strict = true

pyproject.toml

@@ -1,10 +1,7 @@
 import logging
 import os
 
-from ._version import get_versions
-
-__version__ = get_versions()["version"]
-del get_versions
+from reproschema._version import __version__
 
 #
 # Basic logger configuration
@@ -40,12 +37,11 @@ def set_logger_level(lgr, level):
 try:
     import etelemetry
 
-    etelemetry.check_available_version("repronim/reproschema-py", __version__, lgr=lgr)
+    etelemetry.check_available_version(
+        "repronim/reproschema-py", __version__, lgr=lgr
+    )
 except Exception as exc:
     lgr.warning(
-        "Failed to check for a more recent version available with etelemetry: %s", exc
+        "Failed to check for a more recent version available with etelemetry: %s",
+        exc,
     )
-
-from . import _version
-
-__version__ = _version.get_versions()["version"]