poetry to setuptools; min py38 (#361)

* Update pyproject.toml * Update CI.yaml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update CI.yaml * Update CI.yaml * Update pyproject.toml * Update Lint.yml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update CI.yaml * Update README.md * Update test.sh * Update format.sh * Update build_docs.sh * Update changelog.rst * Update PULL_REQUEST_TEMPLATE.md * Update CONTRIBUTING.md * Update .github/workflows/CI.yaml
MolSSI · Nov 26, 2024 · c38fa3c · c38fa3c
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -7,6 +7,6 @@
 <!-- Provide a brief single sentence for the changelog. -->
 
 ## Status
-<!-- Please `poetry install; bash scripts/format.sh` in the base folder. -->
+<!-- Please `bash scripts/format.sh` in the base folder or use pre-commit. -->
 - [ ] Code base linted
 - [ ] Ready to go
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
         pydantic-version: ["2"]
         runs-on: [ubuntu-latest, windows-latest]
     name: "🐍 ${{ matrix.python-version }} • ${{ matrix.pydantic-version }} • ${{ matrix.runs-on }}"
@@ -30,16 +30,14 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Checkout Code
         uses: actions/checkout@v3
-      - name: Install poetry
-        run: pip install poetry
-      - name: Install repo with poetry (full deps)
-        if: matrix.python-version != '3.9'
-        run: poetry install --no-interaction --no-ansi --all-extras
-      - name: Install repo with poetry (min deps)
-        if: matrix.python-version == '3.9'
-        run: poetry install --no-interaction --no-ansi --extras test
+      - name: Install QCElemental (full deps)
+        if: matrix.python-version != '3.8' && matrix.python-version != '3.10'
+        run: pip install '.[test,viz,align,standard]'
+      - name: Install QCElemental (min deps)
+        if: matrix.python-version == '3.8' || matrix.python-version == '3.10'
+        run: pip install '.[test]'
       - name: Run tests
-        run: poetry run pytest -rws -v --cov=qcelemental --color=yes --cov-report=xml  #-k "not pubchem_multiout_g"
+        run: pytest -rws -v --cov=qcelemental --color=yes --cov-report=xml  #-k "not pubchem_multiout_g"
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3 # NEEDS UPDATE TO v3 https://github.com/codecov/codecov-action
       - name: QCSchema Examples Deploy
@@ -64,12 +62,10 @@ jobs:
           python-version: "3.10"
       - name: Setup Graphviz
         uses: ts-graphviz/setup-graphviz@v2
-      - name: Install poetry
-        run: pip install poetry
       - name: Install repo
-        run: poetry install --no-interaction --no-ansi
+        run: pip install '.[docs]'
       - name: Build Documentation
-        run: bash scripts/build_docs.sh
+        run: sphinx-build docs/ build/docs
       - name: GitHub Pages Deploy
         uses: JamesIves/[email protected]
         if: github.event_name == 'push' && github.repository == 'MolSSI/QCElemental' && ( startsWith( github.ref, 'refs/tags/' ) || github.ref == 'refs/heads/master' )

diff --git a/.github/workflows/Lint.yml b/.github/workflows/Lint.yml
@@ -10,11 +10,11 @@ jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
       - name: Install black
         run: pip install "black>=22.1.0,<23.0a0"
       - name: Check code formatting with black
@@ -23,26 +23,24 @@ jobs:
   isort:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
-      - name: Install poetry
-        run: pip install poetry
+          python-version: "3.8"
       - name: Install repo
-        run: poetry install --no-interaction --no-ansi
+        run: pip install '.[lint]'
       - name: Check import formatting with isort
-        run: poetry run isort --check-only --diff .
+        run: isort --check-only --diff .
 # TODO: Support flake8 when the repo is ready :)
 # flake8:
 #   runs-on: ubuntu-latest
 #   steps:
-#     - uses: actions/checkout@v3
+#     - uses: actions/checkout@v4
 #     - name: Set up Python
 #       uses: actions/setup-python@v4
 #       with:
-#         python-version: "3.7"
+#         python-version: "3.8"
 #     - name: Install flake8
 #       run: pip install flake8
 #     - name: Flake8
@@ -52,7 +50,7 @@ jobs:
 # mypy:
 #   runs-on: ubuntu-latest
 #   steps:
-#     - uses: actions/checkout@v3
+#     - uses: actions/checkout@v4
 #     - name: Set up Python
 #       uses: actions/setup-python@v4
 #       with:

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -16,21 +16,25 @@ We welcome contributions from external contributors, and this document describes
   git clone https://github.com/{YOUR-GITHUB-USERNAME}/QCElemental.git
   cd QCElemental
   ```
+<!--
 - Install [poetry](https://python-poetry.org/) if you do not have it on your system. Poetry will manage package dependencies and virtual environments for you.
   ```sh
   curl -sSL https://install.python-poetry.org | python3 -
   ```
+-->
 - Install QCElemental.
 
   ```sh
-  poetry install
+  pip install .
   ```
 
+<!--
 - Activate your new virtual environment. Many editors--like VS Code--will do this for you automatically when you open a directory that has been installed with `poetry`.
 
   ```sh
   poetry shell
   ```
+-->
 
 - Check your installation by running the tests.
 
@@ -84,12 +88,12 @@ We welcome contributions from external contributors, and this document describes
 - Build packages for distribution. Build artifacts will be in `dist/`:
 
   ```sh
-  poetry build
+  python -m build
   ```
 
 - Distribute built packages to PyPi:
   ```sh
-  poetry publish --username {pypi_username} --password {pypi_password}
+  python -m twine upload dist/*
   ```
 
 ## Additional Resources

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 [![codecov](https://img.shields.io/codecov/c/github/MolSSI/QCElemental.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/MolSSI/QCElemental)
 [![Documentation Status](https://img.shields.io/github/actions/workflow/status/MolSSI/QCElemental/CI.yaml?label=docs&logo=readthedocs&logoColor=white)](https://molssi.github.io/QCElemental/)
 [![Chat on Slack](https://img.shields.io/badge/chat-on_slack-green.svg?longCache=true&style=flat&logo=slack)](https://join.slack.com/t/qcarchive/shared_invite/enQtNDIzNTQ2OTExODk0LTE3MWI0YzBjNzVhNzczNDM0ZTA5MmQ1ODcxYTc0YTA1ZDQ2MTk1NDhlMjhjMmQ0YWYwOGMzYzJkZTM2NDlmOGM)
-![python](https://img.shields.io/badge/python-3.7+-blue.svg)
+![python](https://img.shields.io/badge/python-3.8+-blue.svg)
 
 **Documentation:** [GitHub Pages](https://molssi.github.io/QCElemental/)
 
@@ -16,7 +16,7 @@ This project also contains a generator, validator, and translator for [Molecule
 
 ## ✨ Getting Started
 
-- Installation. QCElemental supports Python 3.7+. We reserve the right to move to Python 3.9+ at no notice for new releases.
+- Installation. QCElemental supports Python 3.8+. We reserve the right to move to Python 3.9+ at no notice for new releases.
 
   ```sh
   python -m pip install qcelemental

diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -33,6 +33,7 @@ New Features
 ++++++++++++
 * Downstream code should ``from qcelemental.models.v1 import Molecule, AtomicResult`` etc. to assure medium-term availability of existing models.
 * New pydantic v2 models available as ``from qcelemental.models.v2 import Molecule, AtomicResult`` etc.
+- (:pr:`361`) Switch from poetry to setuptools build backend. 
 
 Enhancements
 ++++++++++++

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,126 +1,103 @@
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["setuptools>=61.0", "setuptools-scm>=8.0"]
+build-backend = "setuptools.build_meta"
 
+[project.urls]
+homepage = "https://github.com/MolSSI/QCElemental"
+changelog = "https://github.com/MolSSI/QCElemental/docs/changelog.rst"
+documentation = "http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/"
+issues = "https://github.com/MolSSI/QCElemental/issues"
 
-[tool.poetry]
+[project]
 name = "qcelemental"
-version = "0.28.0"
+#version = "0.28.0"
+dynamic = ["version"]
+requires-python = ">=3.8"
 description = "Core data structures for Quantum Chemistry."
-authors = ["The QCArchive Development Team <[email protected]>"]
-license = "BSD-3-Clause"
+authors = [
+  { name="The QCArchive Development Team", email="[email protected]" },
+]
+license = { file="LICENSE" }
 readme = "README.md"
-homepage = "https://github.com/MolSSI/QCElemental"
-documentation = "http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3 :: Only",
     "Programming Language :: Python :: 3",
-    "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",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Framework :: Pydantic",
     "Framework :: Pydantic :: 2",
 ]
-
-[tool.poetry.dependencies]
-numpy = [
-    { version = ">=1.12.0", python = "3.8" },
-    { version = ">=1.26.1,<2.0", python = ">=3.9,<3.10" },
-    { version = ">=1.26.1", python = ">=3.9,<3.13" },
-]
-packaging = [
-    { version = ">=24.0", python = ">=3.7,<3.8" },
-    { version = ">=24.1", python = ">=3.8" },
-]
-# qcel is compatible with most any numpy, v1 or v2, but numpy v2 only works with pint >=0.24, which is only available for py >=3.10
-python = "^3.7.1"
-pint = [
-    { version = ">=0.10", python = ">=3.7,<3.9" },
-    { version = ">=0.23", python = ">=3.9,<3.10" },
-    { version = ">=0.24", python = ">=3.10,<3.13" },
+dependencies = [
+    "numpy >=1.12.0; python_version=='3.8'",
+    "numpy >=1.26.1; python_version>='3.9'",
+    "pint >=0.10; python_version=='3.8'",
+    "pint >=0.24; python_version>='3.9'",
+    "pydantic >=2.0",
 ]
-pydantic = ">=2.0"
-nglview = { version = "^3.0.3", optional = true }
-ipykernel = { version = "<6.0.0", optional = true }
-importlib-metadata = { version = ">=4.8", python = "<3.8" }
-networkx = { version = "<3.0", optional = true }
-scipy = [
-    { version = ">=1.6.0", python = "<3.9", optional = true },
-    { version = ">=1.9.0", python = ">=3.9,<3.13", optional = true },
-]
-pytest = { version = "^7.2.2", optional = true }
-
-[tool.poetry.extras]
-viz = ["nglview", "ipykernel"]
-align = ["networkx", "scipy"]
-test = ["pytest"]
 
-# Note that all the versions below are a farce for poetry's benefit.
-#   One needs a fairly recent sphinx, pydantic, and autodoc-pydantic for a
-#   successful docs build, and that likely requires py 3.9."
-
-[tool.poetry.group.dev.dependencies]
-black = ">=22.1.0,<23.0a0"
-mypy = "^1.1.1"
-isort = "5.11.5"
-flake8 = [
-    { version = "<6.0.0", python = "<3.8.1" },
-    { version = "6.0.0", python = ">=3.8.1,<4.0.0" }
-]
-pre-commit = [
-    { version = "<3.2.0", python = "<3.9" },
-    { version = "^3.8.0", python = ">=3.9,<4.0.0" }
-]
-pytest-cov = "^4.0.0"
-autoflake = "^2.0.2"
-jsonschema = { version = "^4.23.0", python = ">=3.8,<4.0.0" }
-msgpack = { version = "^1.0.8", python = ">=3.8,<4.0.0" }
-numpydoc = [
-    { version = "^1.5.0", python = "<3.9" },
-    { version = "^1.8.0", python = ">=3.9,<4.0.0" }
+[project.optional-dependencies]
+standard = [
+    "msgpack",
+    "jsonschema",
 ]
-docutils = [
-    { version = "<0.19", python = "<3.9" },
-    { version = "0.20.1", python = ">=3.9,<4.0.0" }
+viz = [
+    "nglview",  # !py38  # insufficient on pypi as also need `dot`. python-graphviz sufficient in conda.
+    "setuptools; python_version>='3.12'",  # nglview needs pkg_resources
+    "ipykernel <6.0",
 ]
-sphinx = [
-    { version = "<6.0.0", python = "<3.9" },
-    { version = "^7.0.0", python = ">=3.9,<4.0.0" }
+align = [
+    "networkx <3.0", 
+    "scipy",
 ]
-sphinxcontrib-napoleon = "^0.7"
-sphinx-rtd-theme = [
-    { version = "^1.2.0", python = "<3.9" },
-    { version = "^2.0.0", python = ">=3.9,<4.0.0" }
+test = [
+    "pytest",
+    "pytest-cov",
+    "codecov",
 ]
-autodoc-pydantic = [
-    { version = "^2.0.0", python = "<3.8" },
-    { version = "^2.1.0", python = ">=3.8,<4.0" }
+lint = [
+    "pre-commit",
+    "black >=22.1.0,<23.0a0",  # if running outside of pre-commit
+    "isort ==5.11.5",  # if running outside of pre-commit
+    # "mypy",
+    # "autoflake",
+    # "flake8",
 ]
-sphinx-automodapi = [
-    { version = "^0.15.0", python = "<3.8" },
-    { version = "^0.17.0", python = ">=3.8,<4.0.0" }
+docs = [  # probably >=py39
+    "numpydoc",
+    "docutils",
+    "sphinx >=7.0.0",
+    "sphinxcontrib-napoleon",
+    "sphinx-rtd-theme",
+    "autodoc-pydantic",
+    "sphinx-automodapi",
+    "sphinx-autodoc-typehints",
+    "pydantic ==2.5.0",  # for now
+    "pydantic-settings ==2.2.0",  # for now
 ]
-sphinx-autodoc-typehints = [
-    { version = "^1.22", python = "<3.10" },
-    { version = "^2.3", python = ">=3.10,<4.0.0" }
-]
-graphviz = "^0.20.0"  # insufficient on pypi as also need `dot`. python-graphviz sufficient in conda.
+
+#[tool.poetry.dependencies]
+#packaging = ">=24.1"
+#pytest = { version = "^7.2.2", optional = true }
+
+#[tool.poetry.group.dev.dependencies]
+#msgpack = "^1.0.8"
+#    { version = "^1.22", python = "<3.10" },
+#    { version = "^2.3", python = ">=3.10,<4.0.0" }
+#]
 
 [tool.black]
 line-length = 120
-target-version = ['py37']
+target-version = ['py38']
 
 [tool.isort]
-force_grid_wrap = 0
-include_trailing_comma = true
+profile = "black"
 line_length = 120
-multi_line_output = 3
-use_parentheses = true
 
 [tool.coverage.run]
 branch = true
@@ -135,3 +112,13 @@ init_forbid_extra = true
 init_typed = true
 warn_required_dynamic_aliases = true
 warn_untyped_fields = true
+
+[tool.setuptools]
+packages = ["qcelemental"]
+
+[tool.setuptools.package-data]
+
+[tool.setuptools_scm]
+
+[tool.versioningit.vcs]
+default-tag = "0.0.99" # useful for CI/shallow clones
diff --git a/scripts/build_docs.sh b/scripts/build_docs.sh
@@ -1,3 +1,3 @@
 set -xe
 # Run tests
-poetry run sphinx-build docs/ build/docs
+sphinx-build docs/ build/docs