Migrate from setup.cfg to pyproject.toml (#774)

* fix authors, readme, versioning, python-requires
* add empty setup.cfg to allow for dev installs
* removed setup.py stub
* added todo in manifest
* move flake8 cfg from setup.cfg to .flake8 as it does not support pyproject.toml
* require pytest >=6 for pyproject.toml support
  Only this tool refuses pep518, so we let its config reside in an explicit file.
* add src dir for coverage.run
* fix pytest config section
* [conda-recipe] use pyproject.toml to expand dependencies and entry points (thx @kenodegard).
* request toml feature for build environment.
* use "build" package to create wheel and sdist
* [conda-recipe] build a compattible conda env from pyproject.toml via jinja
* [conda-recipe] version gets set by env variable
* set Development Status classifier to "beta"

Co-authored-by: CagtayFabry <CagtayFabry@users.noreply.github.com>

.flake8

@@ -0,0 +1,22 @@
+# flake8 maintainer does not like pyproject.toml:
+# https://github.com/PyCQA/flake8/issues/234#issuecomment-812800722
+
+[flake8]
+# References:
+# https://flake8.readthedocs.io/en/latest/user/configuration.html
+# https://flake8.readthedocs.io/en/latest/user/error-codes.html
+
+# Note: there cannot be spaces after comma's here
+ignore =
+    W503,W504  # line break after binary operator
+    E203       # E203 whitespace before ':' (not PEP8 compliant anyway)
+    C408        # allow dict() over literal {}
+
+max-line-length = 88
+select = C,E,F,W,B,B950 # black formatting options
+per-file-ignores =
+    aws_setup.py:E501
+exclude =
+    __init__.py
+    doc/conf.py
+no-accept-encodings = True

.github/workflows/build_pkg.yml

@@ -52,6 +52,9 @@ jobs:
       - name: conda list
         run: conda list
 
+      - name: set pkg version
+        run: echo "SETUPTOOLS_SCM_PRETEND_VERSION=$(python -m setuptools_scm)" >> $GITHUB_ENV
+
       - name: Build from local conda recipe
         run: conda mambabuild -c conda-forge .
 
@@ -83,11 +86,11 @@ jobs:
       - name: pip installs
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools setuptools_scm wheel twine
+          pip install setuptools setuptools_scm wheel twine build
 
-      - name: build package
+      - name: build package + create src archive (stored in dist folder)
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
 
       - uses: actions/upload-artifact@v3
         with:

.github/workflows/pytest.yml

@@ -38,6 +38,7 @@ jobs:
 
       - uses: CagtayFabry/pydeps2env@main
         with:
+          file: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: 'test vis'
           setup_requires: 'include'
@@ -133,6 +134,7 @@ jobs:
 
       - uses: CagtayFabry/pydeps2env@main
         with:
+          file: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: 'test'
           setup_requires: 'include'

.github/workflows/static_analysis.yml

@@ -36,6 +36,7 @@ jobs:
 
       - uses: CagtayFabry/pydeps2env@main
         with:
+          file: 'pyproject.toml'
           channels: 'conda-forge defaults'
           extras: ''
           setup_requires: 'include'

CHANGELOG.rst

@@ -15,10 +15,13 @@ added
 changes
 =======
 
+-  ``weldx`` now requires pip to install (previously it could be installed by directly invoking setup.py) [:pull:`774`].
+   From a users perspective nothing changes here, as the package was always recommended to be installed via pip.
 -  Updated the outdated tutorial about the `LocalCoordinateSystem` [:pull:`775`]
 - ``weld_seam`` is now a required field in the ``multi_pass_weld`` schema [:pull:`790`]
 - Add section about time-dependent spatial data to the `CoordinateSystemManager` tutorial [:pull:`792`]
 
+
 fixes
 =====
 

MANIFEST.in

@@ -1,3 +1,5 @@
+global-exclude .*
+
 recursive-include weldx/schemas *.yaml
 recursive-include weldx/manifests *.yaml
 include CITATION.cff
@@ -7,5 +9,6 @@ prune .github
 prune devtools
 prune doc
 prune tutorials
+prune build
 
-global-exclude .*
+# TODO: sdist contains files in parent, which are not part of the source dist (e.g. unversioned files etc. in repo)

devtools/conda.recipe/meta.yaml

@@ -1,29 +1,34 @@
-{% set data = load_setup_py_data() %}
+{% set pyproject = load_file_data("../../pyproject.toml", from_recipe_dir=True)  %}
+{% set proj = pyproject.get('project') %}
 
 package:
   name: weldx
-  version: {{ data.get("version") }}
+  version: {{ environ.get('SETUPTOOLS_SCM_PRETEND_VERSION', 999) }}
 
 source:
     path: ../..
 
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION
+  script: "{{ PYTHON }} -m pip install . -vv"
   entry_points:
-  {% for e in data['entry_points']['console_scripts'] %}
-    - {{ e }}
+  {% for module, entrypoints in proj.get('entry-points').items() %}
+  {% for name, path in entrypoints.items() %}
+    - {{ name }} = {{ module }}.{{ path }}
+  {% endfor %}
   {% endfor %}
 requirements:
   host:
     - pip
     - setuptools_scm
     - python
   run:
-    - python >=3.8,<3.10
-    # dependencies are defined in setup.py
-    {% for dep in data['install_requires'] %}
+    - python {{ proj.get("requires-python") }}
+    # dependencies are defined in pyproject.toml
+    {% for dep in proj.get('dependencies') %}
     - {{ dep.lower() }}
     {% endfor %}
 
@@ -33,7 +38,7 @@ test:
     - pytest
     - pytest-xdist
     - black
-    # requires wx-widgets here, so we can properly load the visualization sub-package.
+    # require wx-widgets here, so we can properly load the visualization sub-package.
     - weldx_widgets
   files:
     - conftest.py

pyproject.toml

@@ -1,7 +1,192 @@
+[project]
+name = "weldx"
+dynamic = [  # see: https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#dynamic-metadata
+    "version",  # version gets derived from git by setuptools_scm.
+]
+authors = [
+    {name="Cagtay Fabry", email="cagtay.fabry@bam.de"},
+    {name="Volker Hirthammer", email="volker.hirthammer@bam.de"},
+    {name="Martin K. Scherer", email="martin.scherer@bam.de"},
+]
+description = "Python API for the WelDX file format and standard"
+readme = {file = "README.rst", content-type="text/x-rst"}
+license = {file = "LICENSE", name="BSD License"}
+keywords = [
+    "welding",
+    "weldx",
+    "bam", # TODO: add more keywords here! think of them as in a journal article.
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Natural Language :: English",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Physics", # TODO: add more topics here!
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+]
+
+# Dependencies
+requires-python = ">=3.8,<3.11"
+dependencies = [
+    "numpy >=1.20",
+    "asdf >=2.8.2",
+    "pandas >=1.0",
+    "xarray >=0.19",
+    "scipy >=1.4,!=1.6.0,!=1.6.1",
+    "sympy >=1.6",
+    "pint >=0.18",
+    "pint-xarray >=0.2.1",
+    "bottleneck >=1.3.3",
+    "boltons",
+    "bidict",
+    "networkx >=2,!=2.7.0,!=2.8.1",
+    "fs",
+    "meshio",
+    "psutil",
+    "IPython",
+]
+
+[project.urls]
+documentation = "https://weldx.readthedocs.io"
+repository = "https://github.com/BAMweldx/weldx"
+bug_tracker = "https://github.com/BAMweldx/weldx/issues"
+changelog = "https://github.com/BAMweldx/weldx/blob/master/CHANGELOG.rst"
+
+[project.optional-dependencies]
+test = [
+    "pytest >=6",
+    "pytest-cov",
+    "pytest-xdist",
+    "nbval",
+  ]
+vis = [
+    "weldx_widgets >= 0.2",
+]
+
+# ASDF extension entry points.
+
+[project.entry-points."asdf.extensions"]
+weldx = "weldx.asdf.extension:get_extensions"
+weldx_validators = "weldx.asdf._extension:WeldxValidatorExtension"
+
+[project.entry-points."asdf.resource_mappings"]
+weldx_schemas = "weldx.asdf.extension:get_resource_mappings"
+
+# console scripts
+[project.scripts]
+welding_schema = "weldx.asdf.cli.welding_schema:main"
+
+# Build system config, pip creates a temporary env with "requires" pkgs.
 [build-system]
 requires = [
   "wheel",
   "setuptools >= 40.9.0",
-  "setuptools_scm",
+  "setuptools_scm[toml]>=6.2",
 ]
 build-backend = "setuptools.build_meta"
+
+
+# Tool configs
+[tool.setuptools.packages.find]
+where = ["."]
+
+[tool.setuptools_scm]
+write_to = "weldx/_version.py"
+write_to_template = '__version__ = "{version}"'
+
+[tool.pydocstyle]
+# convention numpy is currently equivalent to ignoring 'D107', 'D203', 'D212', 'D213', 'D402', 'D413'
+convention = "numpy"
+match = "(?!__)(?!_version)(?!conftest).*\\.py"
+match_dir = "^(?!(tests|tags|asdf)).*"
+
+[tool.pytest.ini_options]
+addopts = "--tb=short --color=yes -rsw --cov=weldx --cov-report=term-missing:skip-covered --doctest-modules"
+#addopts = --tb=short --color=yes -rs -p no:cov
+testpaths = "weldx"
+# custom test markers, see https://docs.pytest.org/en/latest/example/markers.html#mark-examples
+markers = "slow: marks tests as slow to run (skipped by default, enable with --runslow option)"
+asdf_schema_root = "weldx/schemas/weldx.bam.de/weldx"  # TODO: couldn't we just use the entry points to resolve this?
+#asdf_schema_tests_enabled = true
+#asdf_schema_skip_tests =
+#    weldx.bam.de/weldx/datamodels/single_pass_weld-1.0.0.schema.yaml
+norecursedirs = "doc"
+filterwarnings = [
+    "ignore::DeprecationWarning:traittypes.*:",
+    "ignore:Passing method to :FutureWarning:xarray.*:",
+    "error::pint.UnitStrippedWarning",
+]
+
+[tool.isort]
+profile = "black"
+default_section = "THIRDPARTY"
+known_first_party = "weldx"
+sections = "FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER" # TODO: or list?
+
+[tool.coverage.run]
+source = ["weldx"]
+
+[tool.coverage.report]
+omit = [
+    "weldx/_version.py",
+    "weldx/tests/*",
+]
+exclude_lines = [
+# Have to re-enable the standard pragma
+    "pragma: no cover",
+
+# ignore class __repr__-like functions:
+    "def __repr__",
+    "def __str__",
+    "def _ipython_display_",
+]
+
+[tool.mypy]
+python_version = "3.9"
+files = "weldx"
+ignore_missing_imports = true # TODO: this is bad!
+strict_optional = false
+pretty = true
+allow_redefinition = true
+show_error_context = true
+show_error_codes = true
+show_column_numbers = true
+sqlite_cache = true
+
+# MyPy per-module options:
+[[tool.mypy.overrides]]
+module = "weldx.asdf.*"
+ignore_errors = true
+
+[[tool.mypy.overrides]]
+module = "weldx.tags.*"
+ignore_errors = true
+
+[[tool.mypy.overrides]]
+module = "weldx.tests.*"
+ignore_errors = true
+
+[[tool.mypy.overrides]]
+module = "weldx.welding.groove.*"
+ignore_errors = true
+
+# TODO: remove after refactoring the geometry module
+[[tool.mypy.overrides]]
+module = "weldx.geometry.*"
+ignore_errors = true
+
+# this is a workaround for an xarray related mypy bug
+# see https://github.com/python/mypy/pull/9495
+# and https://github.com/space-physics/msise00/commit/8b59a9383dd6fcc54b7dac74eb95a350308d7b62
+# TODO: is this still mandatory?
+[[tool.mypy.overrides]]
+module = "xarray"
+follow_imports = "skip"
+ignore_errors = true