From 147d3634b4817d312e102aaaa1cf5cd6ad248f8e Mon Sep 17 00:00:00 2001
From: Remco de Boer <29308176+redeboer@users.noreply.github.com>
Date: Sun, 9 Jul 2023 15:59:23 +0200
Subject: [PATCH 1/2] MAINT!: merge setup.cfg into pyproject.toml

---
 .constraints/py3.8.txt             |   1 +
 .cspell.json                       |   1 -
 .cspell/this-project.txt           |   1 +
 .editorconfig                      |  29 ++++----
 .github/workflows/ci-docs.yml      |  14 ++--
 .github/workflows/requirements.yml |   2 +-
 environment.yml                    |   2 +-
 pyproject.toml                     | 115 ++++++++++++++++++++++++++++-
 setup.cfg                          | 101 -------------------------
 setup.py                           |   6 --
 10 files changed, 138 insertions(+), 134 deletions(-)
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt
index 95b6a754..720cc409 100644
--- a/.constraints/py3.8.txt
+++ b/.constraints/py3.8.txt
@@ -203,4 +203,5 @@ wrapt==1.15.0
 zipp==3.16.0
 
 # The following packages are considered to be unsafe in a requirements file:
+# polarimetry
 # setuptools
diff --git a/.cspell.json b/.cspell.json
index 7e4ea04f..868b983b 100644
--- a/.cspell.json
+++ b/.cspell.json
@@ -66,7 +66,6 @@
     "miscellchecks/**.C",
     "pyproject.toml",
     "pytest.ini",
-    "setup.cfg",
     "tox.ini"
   ],
   "language": "en-US",
diff --git a/.cspell/this-project.txt b/.cspell/this-project.txt
index 19b35221..f57bb220 100644
--- a/.cspell/this-project.txt
+++ b/.cspell/this-project.txt
@@ -25,6 +25,7 @@ pdfnb
 phsp
 pushd
 PyPI
+pyproject
 pyright
 pytest
 PYTHONHASHSEED
diff --git a/.editorconfig b/.editorconfig
index 00343fce..d3d78df8 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -1,16 +1,13 @@
-root = true
-
-[*]
-end_of_line = lf
-indent_style = space
-insert_final_newline = true
-trim_trailing_whitespace = true
-
-[Makefile]
-indent_style = tab
-
-[*.{py,toml}]
-indent_size = 4
-
-[setup.cfg]
-indent_size = 4
+root = true
+
+[*]
+end_of_line = lf
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[Makefile]
+indent_style = tab
+
+[*.{py,toml}]
+indent_size = 4
diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml
index 3ebdee9c..425ea524 100644
--- a/.github/workflows/ci-docs.yml
+++ b/.github/workflows/ci-docs.yml
@@ -106,27 +106,27 @@ jobs:
         uses: actions/cache@v3
         with:
           key: |
-            sympy-${{hashFiles('.constraints/py3.*.txt', 'setup.cfg')}}-${{hashFiles('src/**')}}-${{hashFiles('docs/**.ipynb')}}
+            sympy-${{hashFiles('.constraints/py3.*.txt')}}-${{hashFiles('src/**')}}-${{hashFiles('docs/**.ipynb')}}
           restore-keys: |
-            sympy-${{hashFiles('.constraints/py3.*.txt', 'setup.cfg')}}-${{hashFiles('src/**')}}
-            sympy-${{hashFiles('.constraints/py3.*.txt', 'setup.cfg')}}
+            sympy-${{hashFiles('.constraints/py3.*.txt')}}-${{hashFiles('src/**')}}
+            sympy-${{hashFiles('.constraints/py3.*.txt')}}
           path: ~/.sympy-cache*/
       - name: Fetch Jupyter cache
         uses: actions/cache@v3
         with:
           key: |
-            jupyter-cache-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'setup.cfg', 'src/**')}}-${{hashFiles('docs/**')}}
+            jupyter-cache-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'src/**')}}-${{hashFiles('docs/**')}}
           restore-keys: |
-            jupyter-cache-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'setup.cfg', 'src/**')}}
+            jupyter-cache-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'src/**')}}
           path: |
             ./docs/_build/.jupyter_cache
       - name: Fetch output files
         uses: actions/cache@v3
         with:
           key: |
-            output-files-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'setup.cfg', 'src/**')}}-${{hashFiles('docs/**')}}
+            output-files-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'src/**')}}-${{hashFiles('docs/**')}}
           restore-keys: |
-            output-files-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'setup.cfg', 'src/**')}}
+            output-files-${{hashFiles('.constraints/py3.*.txt', 'data/**', 'src/**')}}
             output-files
           path: |
             ./docs/_images
diff --git a/.github/workflows/requirements.yml b/.github/workflows/requirements.yml
index b8f8c9e0..dac6b208 100644
--- a/.github/workflows/requirements.yml
+++ b/.github/workflows/requirements.yml
@@ -12,7 +12,7 @@ on:
     paths:
       - .constraints/py3.*.txt
       - .pre-commit-config.yaml
-      - setup.cfg
+      - pyproject.toml
   schedule:
     - cron: "0 3 7 */3 *"
   workflow_dispatch:
diff --git a/environment.yml b/environment.yml
index a17671fc..2908c369 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,7 +3,7 @@ channels:
   - defaults
 dependencies:
   - python==3.8.*
-  - pip
+  - pip>=21.3 # pyproject.toml
   - pip:
       - |
         -c .constraints/py3.8.txt
diff --git a/pyproject.toml b/pyproject.toml
index 66bfa969..db7b741c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,10 +1,123 @@
 [build-system]
+build-backend = "setuptools.build_meta"
 requires = [
-    "setuptools>=36.2.1", # environment markers
+    "setuptools>=61.2",
     "setuptools_scm",
     "wheel",
 ]
 
+[project]
+authors = [
+    { name = "Mikhail Mikhasenko" },
+    { name = "Remco de Boer" },
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering",
+    "Typing :: Typed",
+]
+dependencies = [
+    "IPython",
+    "PyYAML",
+    "ampform >=0.14.1",
+    "attrs >=20.1.0",
+    "cloudpickle",
+    "matplotlib",
+    "numpy",
+    "sympy >=1.10",
+    "tensorwaves[jax] >=0.4.5",
+    'typing-extensions; python_version <"3.8.0"',
+]
+description = "Symbolic expressions that describe an aligned polarimeter vector field"
+dynamic = ["version"]
+license = { text = "GPLv3 or later" }
+name = "polarimetry"
+requires-python = ">=3.7"
+
+[project.optional-dependencies]
+dev = [
+    "polarimetry[doc]",
+    "polarimetry[jupyter]",
+    "polarimetry[sty]",
+    "polarimetry[test]",
+    "sphinx-autobuild",
+    "tox >=1.9",
+]
+doc = [
+    "cairosvg",
+    "ipympl",
+    "ipywidgets",
+    "kaleido",
+    "matplotlib-inline !=0.1.5",
+    "myst-nb >=0.14",
+    "pandas",
+    "plotly",
+    "psutil",
+    "scipy",
+    "sphinx-book-theme",
+    "sphinx-codeautolink[ipython]",
+    "sphinx-copybutton",
+    "sphinx-design",
+    "sphinx-reredirects",
+    "sphinx-togglebutton",
+    "sphinxcontrib-bibtex >=2.2",
+    "sphinxcontrib-svg2pdfconverter",
+    "svgutils",
+    "tqdm",
+    'importlib-metadata; python_version <"3.8.0"',
+]
+jupyter = [
+    "jupyterlab >=3.0",
+    "jupyterlab-code-formatter",
+    "jupyterlab-myst",
+    "polarimetry[doc]",
+    'ypy-websocket <0.8.3; python_version <"3.8.0"',
+]
+sty = [
+    "black",
+    "pre-commit >=1.4.0",
+    "pytest",
+    "ruff",
+]
+test = [
+    "nbmake",
+    "pytest >=6.0",
+    "pytest-xdist",
+    'nbmake <1.3; python_version<"3.8.0"',
+]
+
+[project.readme]
+content-type = "text/markdown"
+file = "README.md"
+
+[tool.setuptools]
+include-package-data = false
+package-dir = { "" = "src" }
+
+[tool.setuptools.packages.find]
+namespaces = false
+where = ["src"]
+
+[tool.setuptools.package-data]
+"polarimetry.lhcb" = [
+    "model-definitions.yaml",
+    "particle-definitions.yaml",
+]
+
+
 [tool.setuptools_scm]
 write_to = "src/polarimetry/version.py"
 
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 1c49668f..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,101 +0,0 @@
-[metadata]
-name = polarimetry
-description = Symbolic expressions that describe an aligned polarimeter vector field
-author = Mikhail Mikhasenko, Remco de Boer, Miriam Fritsch
-long_description = file: README.md
-long_description_content_type = text/markdown
-classifiers =
-    Development Status :: 4 - Beta
-    Intended Audience :: Developers
-    Intended Audience :: Education
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-    Natural Language :: English
-    Operating System :: OS Independent
-    Programming Language :: Python
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-    Topic :: Scientific/Engineering
-    Topic :: Scientific/Engineering :: Physics
-    Typing :: Typed
-license = GPLv3 or later
-
-[options]
-python_requires = >=3.7
-setup_requires =
-    setuptools_scm
-install_requires =
-    ampform >=0.14.1  # Kibble and Kallen functions
-    attrs >=20.1.0  # on_setattr and https://www.attrs.org/en/stable/api.html#next-gen
-    cloudpickle
-    IPython
-    matplotlib
-    numpy
-    sympy >=1.10  # module sympy.printing.numpy and array expressions with shape kwarg
-    tensorwaves[jax] >=0.4.5  # lambdify sympy.Indexed
-    typing-extensions; python_version <"3.8.0"
-    PyYAML
-packages = find:
-package_dir =
-    =src
-
-[options.extras_require]
-doc =
-    cairosvg
-    importlib-metadata; python_version <"3.8.0"
-    ipympl
-    ipywidgets
-    kaleido  # plotly static figure export
-    matplotlib-inline !=0.1.5  # problem with plt.ioff()
-    myst-nb >=0.14  # nb_render_markdown_format for Markdown tables
-    pandas
-    plotly
-    psutil
-    scipy
-    sphinx-book-theme
-    sphinx-codeautolink[ipython]
-    sphinx-codeautolink !=0.14.0  # https://github.com/ComPWA/polarimetry/actions/runs/4044891117/jobs/6955624561
-    sphinx-copybutton
-    sphinx-design
-    sphinx-reredirects
-    sphinx-togglebutton
-    sphinxcontrib-bibtex >=2.2  # bibtex_reference_style
-    sphinxcontrib-svg2pdfconverter
-    svgutils
-    tqdm
-jupyter =
-    %(doc)s
-    jupyterlab >=3.0
-    jupyterlab-code-formatter
-    jupyterlab-myst
-    ypy-websocket <0.8.3; python_version <"3.8.0"
-test =
-    nbmake
-    nbmake <1.3; python_version<"3.8.0"
-    pytest >=6.0  # pyproject.toml
-    pytest-xdist
-format =
-    black
-sty =
-    %(format)s
-    ruff
-    pytest  # for type hints
-    pre-commit >=1.4.0
-dev =
-    %(doc)s
-    %(jupyter)s
-    %(sty)s
-    %(test)s
-    sphinx-autobuild
-    tox >=1.9  # for skip_install, use_develop
-
-[options.packages.find]
-where = src
-
-[options.package_data]
-polarimetry.lhcb =
-    model-definitions.yaml
-    particle-definitions.yaml
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 93296978..00000000
--- a/setup.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from setuptools import setup
-
-setup(
-    use_scm_version=True,
-    setup_requires=["setuptools_scm"],
-)

From 652b75e9c7b80d2d7cb1ffd57ad11ad14972e42f Mon Sep 17 00:00:00 2001
From: GitHub <noreply@github.com>
Date: Tue, 11 Jul 2023 08:15:53 +0000
Subject: [PATCH 2/2] MAINT: update pip constraints and pre-commit

---
 .constraints/py3.10.txt |  7 ++++---
 .constraints/py3.11.txt |  7 ++++---
 .constraints/py3.7.txt  | 11 ++++++-----
 .constraints/py3.8.txt  |  6 +++---
 .constraints/py3.9.txt  |  7 ++++---
 .pre-commit-config.yaml |  2 +-
 6 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/.constraints/py3.10.txt b/.constraints/py3.10.txt
index 8ccb5e70..1663f396 100644
--- a/.constraints/py3.10.txt
+++ b/.constraints/py3.10.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.10.txt --resolver=backtracking --strip-extras
+#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.10.txt --resolver=backtracking --strip-extras --unsafe-package=pip --unsafe-package=polarimetry --unsafe-package=setuptools
 #
 accessible-pygments==0.0.4
 alabaster==0.7.13
@@ -17,7 +17,7 @@ attrs==23.1.0
 babel==2.12.1
 backcall==0.2.0
 beautifulsoup4==4.12.2
-black==23.3.0
+black==23.7.0
 bleach==6.0.0
 cachetools==5.3.1
 cairocffi==1.6.0
@@ -122,7 +122,7 @@ platformdirs==3.8.1
 plotly==5.15.0
 pluggy==1.2.0
 pre-commit==3.3.3
-prometheus-client==0.17.0
+prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 psutil==5.9.5
 ptyprocess==0.7.0
@@ -201,4 +201,5 @@ wrapt==1.15.0
 zipp==3.16.0
 
 # The following packages are considered to be unsafe in a requirements file:
+# polarimetry
 # setuptools
diff --git a/.constraints/py3.11.txt b/.constraints/py3.11.txt
index c6dcf8ab..502a726b 100644
--- a/.constraints/py3.11.txt
+++ b/.constraints/py3.11.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
-#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.11.txt --resolver=backtracking --strip-extras
+#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.11.txt --resolver=backtracking --strip-extras --unsafe-package=pip --unsafe-package=polarimetry --unsafe-package=setuptools
 #
 accessible-pygments==0.0.4
 alabaster==0.7.13
@@ -17,7 +17,7 @@ attrs==23.1.0
 babel==2.12.1
 backcall==0.2.0
 beautifulsoup4==4.12.2
-black==23.3.0
+black==23.7.0
 bleach==6.0.0
 cachetools==5.3.1
 cairocffi==1.6.0
@@ -121,7 +121,7 @@ platformdirs==3.8.1
 plotly==5.15.0
 pluggy==1.2.0
 pre-commit==3.3.3
-prometheus-client==0.17.0
+prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 psutil==5.9.5
 ptyprocess==0.7.0
@@ -199,4 +199,5 @@ wrapt==1.15.0
 zipp==3.16.0
 
 # The following packages are considered to be unsafe in a requirements file:
+# polarimetry
 # setuptools
diff --git a/.constraints/py3.7.txt b/.constraints/py3.7.txt
index 41ee4964..1d0b211b 100644
--- a/.constraints/py3.7.txt
+++ b/.constraints/py3.7.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.7
 # by the following command:
 #
-#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.7.txt --resolver=backtracking --strip-extras
+#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.7.txt --resolver=backtracking --strip-extras --unsafe-package=pip --unsafe-package=polarimetry --unsafe-package=setuptools
 #
 accessible-pygments==0.0.4
 aiofiles==22.1.0
@@ -52,7 +52,7 @@ identify==2.5.24
 idna==3.4
 imagesize==1.4.1
 iminuit==2.18.0
-importlib-metadata==6.7.0 ; python_version < "3.8.0"
+importlib-metadata==6.7.0
 importlib-resources==5.12.0
 iniconfig==2.0.0
 ipykernel==6.16.2
@@ -102,7 +102,7 @@ nbclassic==1.0.0
 nbclient==0.5.13
 nbconvert==7.6.0
 nbformat==5.8.0
-nbmake==1.2.1 ; python_version < "3.8.0"
+nbmake==1.2.1
 nest-asyncio==1.5.6
 nodeenv==1.8.0
 notebook==6.5.4
@@ -123,7 +123,7 @@ platformdirs==3.8.1
 plotly==5.15.0
 pluggy==1.2.0
 pre-commit==2.21.0
-prometheus-client==0.17.0
+prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 psutil==5.9.5
 ptyprocess==0.7.0
@@ -198,8 +198,9 @@ wheel==0.40.0
 widgetsnbextension==4.0.8
 wrapt==1.15.0
 y-py==0.5.9
-ypy-websocket==0.8.2 ; python_version < "3.8.0"
+ypy-websocket==0.8.2
 zipp==3.15.0
 
 # The following packages are considered to be unsafe in a requirements file:
+# polarimetry
 # setuptools
diff --git a/.constraints/py3.8.txt b/.constraints/py3.8.txt
index 720cc409..55c1394f 100644
--- a/.constraints/py3.8.txt
+++ b/.constraints/py3.8.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.8
 # by the following command:
 #
-#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.8.txt --resolver=backtracking --strip-extras
+#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.8.txt --resolver=backtracking --strip-extras --unsafe-package=pip --unsafe-package=polarimetry --unsafe-package=setuptools
 #
 accessible-pygments==0.0.4
 alabaster==0.7.13
@@ -17,7 +17,7 @@ attrs==23.1.0
 babel==2.12.1
 backcall==0.2.0
 beautifulsoup4==4.12.2
-black==23.3.0
+black==23.7.0
 bleach==6.0.0
 cachetools==5.3.1
 cairocffi==1.6.0
@@ -124,7 +124,7 @@ platformdirs==3.8.1
 plotly==5.15.0
 pluggy==1.2.0
 pre-commit==3.3.3
-prometheus-client==0.17.0
+prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 psutil==5.9.5
 ptyprocess==0.7.0
diff --git a/.constraints/py3.9.txt b/.constraints/py3.9.txt
index c8bef6ef..c095822e 100644
--- a/.constraints/py3.9.txt
+++ b/.constraints/py3.9.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.9
 # by the following command:
 #
-#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.9.txt --resolver=backtracking --strip-extras
+#    pip-compile --extra=dev --no-annotate --output-file=.constraints/py3.9.txt --resolver=backtracking --strip-extras --unsafe-package=pip --unsafe-package=polarimetry --unsafe-package=setuptools
 #
 accessible-pygments==0.0.4
 alabaster==0.7.13
@@ -17,7 +17,7 @@ attrs==23.1.0
 babel==2.12.1
 backcall==0.2.0
 beautifulsoup4==4.12.2
-black==23.3.0
+black==23.7.0
 bleach==6.0.0
 cachetools==5.3.1
 cairocffi==1.6.0
@@ -123,7 +123,7 @@ platformdirs==3.8.1
 plotly==5.15.0
 pluggy==1.2.0
 pre-commit==3.3.3
-prometheus-client==0.17.0
+prometheus-client==0.17.1
 prompt-toolkit==3.0.39
 psutil==5.9.5
 ptyprocess==0.7.0
@@ -202,4 +202,5 @@ wrapt==1.15.0
 zipp==3.16.0
 
 # The following packages are considered to be unsafe in a requirements file:
+# polarimetry
 # setuptools
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0255cc2b..4d269aa6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -32,7 +32,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black