Merge pull request #735 from stan-dev/setup/move-to-pyproject

Move to pyproject.toml setup, deduplicate dependencies

Author: WardBrian

.github/workflows/main.yml

@@ -56,12 +56,16 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies (python)
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip wheel build
+
+      - name: Build package
         run: |
-          python -m pip install --upgrade pip wheel build
-          pip install -r requirements.txt
-          pip install -r requirements-test.txt
-          pip install codecov
+          python -m build
+          python -m pip install .[test]
+
+      - name: Show libraries
+        run: python -m pip freeze
 
       - name: Run flake8, pylint, mypy
         if: matrix.python-version == '3.11'
@@ -70,22 +74,6 @@ jobs:
           pylint -v cmdstanpy test
           mypy cmdstanpy
 
-      - name: Build wheel
-        run: python -m build
-
-      - name: Install wheel (Linux, macOS)
-        if: matrix.os != 'windows-latest'
-        run: pip install dist/*.whl
-
-      - name: Install wheel (Windows)
-        if: matrix.os == 'windows-latest'
-        run: |
-          $whl = Get-ChildItem -Path dist -Filter *.whl | Select-Object -First 1
-          pip install "$whl"
-
-      - name: Show libraries
-        run: python -m pip freeze
-
       - name: CmdStan installation cacheing
         id: cache-cmdstan
         if: ${{ !startswith(needs.get-cmdstan-version.outputs.version, 'git:') }}
@@ -118,13 +106,8 @@ jobs:
           cd run_tests
           pytest -v ../test --cov=../cmdstanpy
 
-      - name: Run model with requirements-optional.txt
-        run: |
-          cd run_tests
-          python -m pip install -r ../requirements-optional.txt
-          python ../test/example_script.py
-
       - name: Submit codecov
         run: |
+          pip install codecov
           cd run_tests
           codecov

.github/workflows/release.yml

@@ -32,9 +32,8 @@ jobs:
 
       - name: Install dependencies (python)
         run: |
-          python -m pip install --upgrade pip wheel twine codecov "sphinx>5,<6" nbsphinx ipython ipykernel "pydata-sphinx-theme<0.9" requests sphinx-copybutton xarray matplotlib
-          pip install -r requirements.txt
-          pip install -e .
+          python -m pip install --upgrade pip wheel build twine requests
+          pip install -e .[doc,test]
 
       - name: Install CmdStan
         run: |
@@ -80,7 +79,7 @@ jobs:
           git push -f origin master
 
       - name: Build wheel
-        run: python setup.py sdist bdist_wheel
+        run: python -m build
 
       - name: Install bdist_wheel
         run: pip install dist/*.whl

.pre-commit-config.yaml

@@ -23,7 +23,6 @@ repos:
     rev: v1.5.0
     hooks:
       - id: mypy
-        # Copied from setup.cfg
         exclude: ^test/
         additional_dependencies: [ numpy >= 1.22]
   # local uses the user-installed pylint, this allows dependency checking

MANIFEST.in

@@ -1,6 +1,4 @@
 # This file is used to include extra files in source distributions.
-# (Source distributions are generated by running `python setup.py sdist`.)
 
-include requirements*.txt
 include LICENSE.md
 include cmdstanpy/py.typed

docsrc/env.yml

@@ -5,18 +5,12 @@ channels:
 dependencies:
   - python=3.9
   - ipykernel
-  - ipython
-  - ipywidgets
-  - numpy>=1.15
+  - numpy
   - pandas
   - xarray
-  - sphinx>5,<6
-  - nbsphinx
-  - pydata-sphinx-theme>0.7,<0.9
-  - sphinx-copybutton
   - matplotlib-base
   - pip
   - cmdstan
   - tqdm
   - pip:
-      - -e ../
+      - -e ../.[docs]

pyproject.toml

@@ -1,3 +1,68 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cmdstanpy"
+description = "Python interface to CmdStan"
+readme = "README.md"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "Stan Dev Team" }]
+requires-python = ">=3.8"
+dependencies = ["pandas", "numpy>=1.21", "tqdm", "stanio>=0.4.0,<2.0.0"]
+dynamic = ["version"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/stan-dev/cmdstanpy"
+"Bug Tracker" = "https://github.com/stan-dev/cmdstanpy/issues"
+
+[project.scripts]
+install_cmdstan = "cmdstanpy.install_cmdstan:__main__"
+install_cxx_toolchain = "cmdstanpy.install_cxx_toolchain:__main__"
+
+[tool.setuptools.dynamic]
+version = { attr = "cmdstanpy._version.__version__" }
+
+[tool.setuptools]
+packages = ["cmdstanpy", "cmdstanpy.stanfit", "cmdstanpy.utils"]
+
+[tool.setuptools.package-data]
+"cmdstanpy" = ["py.typed"]
+
+[project.optional-dependencies]
+all = ["xarray"]
+test = [
+    "flake8",
+    "pylint",
+    "pytest",
+    "pytest-cov",
+    "pytest-order",
+    "mypy",
+    "xarray",
+]
+docs = [
+    "sphinx>5,<6",
+    "pydata-sphinx-theme<0.9",
+    "nbsphinx",
+    "ipython",
+    "ipykernel",
+    "ipywidgets",
+    "sphinx-copybutton",
+    "xarray",
+    "matplotlib",
+]
+
+
 [tool.black]
 line-length = 80
 skip-string-normalization = true
@@ -23,8 +88,8 @@ strict_equality = true
 disallow_untyped_calls = true
 
 [[tool.mypy.overrides]]
-module = [
-    'tqdm.auto',
-    'pandas',
-    ]
+module = ['tqdm.auto', 'pandas']
 ignore_missing_imports = true
+
+[tool.coverage.run]
+source = ["cmdstanpy"]