Csse layout setuptools (#469)

* fixup PR numbers in changelog * pyproject.toml * qcel address * unduplicate cov directive * adjust address * fully right address * avoid new geometric * more geometric
MolSSI · Feb 4, 2025 · 7decb78 · 7decb78
1 parent 5577d35
commit 7decb78
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -180,7 +180,7 @@ jobs:
       #if: false
       run: |
         conda remove qcelemental --force
-        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_layout_536f_rb2025_take2' --no-deps
+        python -m pip install 'git+https://github.com/MolSSI/QCElemental.git@next2025' --no-deps
 
       # note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412
       #       alt. is micromamba but not yet ready for setup-miniconda https://github.com/conda-incubator/setup-miniconda/issues/75
@@ -269,7 +269,7 @@ jobs:
       #if: false
       run: |
         conda remove qcelemental --force
-        python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_layout_536f_rb2025_take2' --no-deps
+        python -m pip install 'git+https://github.com/MolSSI/QCElemental.git@next2025' --no-deps
 
     - name: Environment Information
       run: |

diff --git a/.codecov.yml → codecov.yml b/.codecov.yml → codecov.yml
diff --git a/devtools/conda-envs/disp-win.yaml b/devtools/conda-envs/disp-win.yaml
@@ -5,7 +5,7 @@ channels:
 dependencies:
   - dftd3-python =1.2.0
   - gcp-correction
-  - geometric
+  - geometric=1.0
   - optking
   - pymdi
 

diff --git a/devtools/conda-envs/mrchem.yaml b/devtools/conda-envs/mrchem.yaml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - mrchem >=1.1=*openmpi*
-  - geometric
+  - geometric=1.0
   - optking
 
     # Core

diff --git a/devtools/conda-envs/openmm.yaml b/devtools/conda-envs/openmm.yaml
@@ -7,7 +7,7 @@ dependencies:
   - openff-toolkit
   - openff-forcefields
   - openmmforcefields
-  - geometric
+  - geometric=1.0
   - torsiondrive
 
     # Core

diff --git a/devtools/conda-envs/opt-disp-cf.yaml b/devtools/conda-envs/opt-disp-cf.yaml
@@ -11,7 +11,7 @@ dependencies:
   - dftd3-python
   - dftd4-python
   - gcp-correction
-  - geometric
+  - geometric=1.0
   - optking
   - pymdi
   - qcmanybody

diff --git a/devtools/conda-envs/opt-disp.yaml b/devtools/conda-envs/opt-disp.yaml
@@ -16,7 +16,7 @@ dependencies:
   - dftd4-python=3.3.0
   - mp2d >=1.1
   - gcp
-  - geometric
+  - geometric=1.0
   - optking
   - pymdi
 

diff --git a/devtools/conda-envs/psi.yaml b/devtools/conda-envs/psi.yaml
@@ -6,7 +6,7 @@ dependencies:
   - psi4=1.5
   - libint2=*=hc9558a2_9
   - dftd3
-  - geometric
+  - geometric=1.0
   - intel-openmp!=2019.5
   - pymdi
 

diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -70,12 +70,13 @@ Misc.
 
 MUST (Unmerged)
 +++++++++++++++
-- (:pr:`462`) 
-- (:pr:`462`) adapt harnesses for TD.initial_molecules -> TD.initial_molecule and TD.optimization_history -> TD.scan_results
-- (:pr:`462`) rdkit, store ``AtomicResult.properties.return_gradient`` and ``calcinfo_natom``. mrchem, store ``AtomicResult.properties.return_gradient``.
-- (:pr:`462`) lightly Adapt harnesses for Mol v3
-- (:pr:`462`) Use packaging instead of setuptools to provide version parsing
-- (:pr:`462`) torsiondrive now accepts protocols. use ``protocols={"scan_results": "all"}`` if going to be converted to v1.
+- (:pr:`469`) setup.py replaced by pyproject.toml with setuptools backend and replaced versioneer with setuptools-scm
+- (:pr:`469`) remove __git_revision__ and get_information("git_revision") removed with versioneer
+- (:pr:`468`) adapt harnesses for TD.initial_molecules -> TD.initial_molecule and TD.optimization_history -> TD.scan_results
+- (:pr:`468`) rdkit, store ``AtomicResult.properties.return_gradient`` and ``calcinfo_natom``. mrchem, store ``AtomicResult.properties.return_gradient``.
+- (:pr:`468`) lightly Adapt harnesses for Mol v3
+- (:pr:`468`) Use packaging instead of setuptools to provide version parsing
+- (:pr:`468`) torsiondrive now accepts protocols. use ``protocols={"scan_results": "all"}`` if going to be converted to v1.
 - (:pr:`461`) torsiondrive rewritten in v2.
 - (:pr:`461`) berny harness rewritten in v2. optking and geometric natively speak v1, so adapted as well as can be.
 - (:pr:`461`) allow nwchemdriver w/o driver=energy. provenance now nwchemdriver not nwchemrelax

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,108 @@
+[build-system]
+requires = ["setuptools>=61.0", "setuptools-scm>=8.0"]
+build-backend = "setuptools.build_meta"
+
+[project.urls]
+homepage = "https://github.com/MolSSI/QCEngine"
+changelog = "https://github.com/MolSSI/QCEngine/blob/master/docs/source/changelog.rst"
+documentation = "https://molssi.github.io/QCEngine/"
+issues = "https://github.com/MolSSI/QCEngine/issues"
+
+[project]
+name = "qcengine"
+#version = "0.31.0"
+dynamic = ["version"]
+requires-python = ">=3.8"
+description = "A compute wrapper for Quantum Chemistry, ingesting and producing QCSchema for a variety of QC programs."
+authors = [
+  { name="The QCArchive Development Team", email="[email protected]" },
+]
+license = { file="LICENSE" }
+readme = "README.md"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3",
+    "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",
+]
+
+dependencies = [
+    "pyyaml",
+    "py-cpuinfo",
+    "psutil",
+    "qcelemental>=0.50a1,<0.70.0",
+    "pydantic >=2.1",
+    "pydantic-settings",
+    # "typing_extensions; python_version<'3.9'",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov",
+    "codecov",
+    "packaging",
+]
+lint = [
+    "pre-commit",
+    "black >=22.1.0,<23.0a0",  # if running outside of pre-commit
+    "isort >=5.13.2",  # if running outside of pre-commit
+    # "mypy",
+    # "autoflake",
+    # "flake8",
+]
+docs = [  # probably >=py39
+    "numpydoc",
+    # "docutils",
+    "sphinx >=7.0.0",
+    "sphinxcontrib-napoleon",
+    "sphinx-rtd-theme",
+    "autodoc-pydantic>=2.0",
+    # "sphinx-automodapi",
+    # "sphinx-autodoc-typehints",
+    # "pydantic ==2.5.0",  # for now
+    # "pydantic-settings ==2.2.0",  # for now
+]
+
+[project.scripts]
+qcengine = "qcengine.cli:main"
+
 [tool.black]
 line-length = 120
-target-version = ['py37', 'py38']
+target-version = ['py38']
+
+[tool.isort]
+profile = "black"
+line_length = 120
+
+[tool.setuptools]
+packages = ["qcengine"]
+
+[aliases]
+test="pytest"
+
+[tool.setuptools.package-data]
+
+[tool.setuptools_scm]
+
+[tool.versioningit.vcs]
+default-tag = "0.0.99" # useful for CI/shallow clones
+
+[tool.pytest.ini_options]
+#filterwarnings = [
+#    "ignore::DeprecationWarning",
+#    "ignore::PendingDeprecationWarning",
+#]
+markers = [
+    "long",
+    """slow: marks tests as slow (deselect with '-m "not slow"')""",
+    "smoke",
+]
diff --git a/qcengine/__init__.py b/qcengine/__init__.py
@@ -1,7 +1,13 @@
 """
 Base file for the dqm_compute module.
 """
+from importlib.metadata import version
 
+__version__ = version("qcengine")
+__git_revision__ = "(no longer provided)"
+del version
+
+# isort: off
 from . import config, exceptions
 from .compute import compute, compute_procedure
 from .config import get_config
@@ -11,7 +17,4 @@
 from .programs import get_program, list_all_programs, list_available_programs, register_program, unregister_program
 from .stock_mols import get_molecule
 
-# Handle versioneer
-__version__ = get_information("version")
-__git_revision__ = get_information("git_revision")
-del get_information
+# isort: on