Merge pull request #250 from ianmkenney/clean_up_pyproject

Cleaning up pyproject.toml

devtools/conda-envs/env.yaml

@@ -0,0 +1,27 @@
+name: modelforge_env
+channels:
+  - conda-forge
+  - pytorch
+dependencies:
+  # Base depends
+  - python
+  - pip
+  - h5py
+  - tqdm
+  - toml
+  - qcportal>=0.50
+  - qcelemental
+  - pytorch>=2.1
+  - loguru
+  - lightning>=2.0.8
+  - tensorboard
+  - torchvision
+  - openff-units
+  - torchmetrics>=1.4
+  - pint=0.23
+  - rdkit
+  - retry
+  - sqlitedict
+  - pydantic>=2
+  - ray-all
+  - jax

pyproject.toml

@@ -1,9 +1,7 @@
 [build-system]
-requires = ["setuptools>=61.0", "versioningit~=2.0"]
+requires = ["setuptools>=61.0", "versioningit~=3.0"]
 build-backend = "setuptools.build_meta"
 
-# Self-descriptive entries which should always be present
-# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 [project]
 name = "modelforge"
 description = "Infrastructure to implement and train NNPs"
@@ -17,45 +15,27 @@ license = { text = "MIT" }
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: POSIX :: Linux",
+    "Environment :: GPU",
+    "Environment :: GPU :: NVIDIA CUDA",
 ]
-requires-python = ">=3.8"
-# Declare any run-time dependencies that should be installed with the package.
-#dependencies = [
-#    "importlib-resources;python_version<'3.10'",
-#]
+requires-python = ">=3.10"
 
-# Update the urls once the hosting is set up.
-#[project.urls]
-#"Source" = "https://github.com/<username>/modelforge/"
-#"Documentation" = "https://modelforge.readthedocs.io/"
-
-[project.optional-dependencies]
-test = [
-  "pytest>=6.1.2",
-  "pytest-runner"
-]
+[project.urls]
+Source = "https://github.com/choderalab/modelforge"
+Documentation = "https://modelforge.readthedocs.io/"
+Wiki = "https://github.com/choderalab/modelforge/wiki"
 
 [tool.setuptools]
-# This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details
-#
-# As of version 0.971, mypy does not support type checking of installed zipped
-# packages (because it does not actually import the Python packages).
-# We declare the package not-zip-safe so that our type hints are also available
-# when checking client code that uses our (installed) package.
-# Ref:
+# Disable zipping because mypy cannot read zip imports and this may affect downstream development.
 # https://mypy.readthedocs.io/en/stable/installed_packages.html?highlight=zip#using-installed-packages-with-mypy-pep-561
+# NOTE: We might consider removing this once we can test the code in a 
+# production environment since zipping the package may increase performance.
 zip-safe = false
-# Let setuptools discover the package in the current directory,
-# but be explicit about non-Python files.
-# See also:
-#   https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
-# Note that behavior is currently evolving with respect to how to interpret the
-# "data" and "tests" subdirectories. As of setuptools 63, both are automatically
-# included if namespaces is true (default), even if the package is named explicitly
-# (instead of using 'find'). With 'find', the 'tests' subpackage is discovered
-# recursively because of its __init__.py file, but the data subdirectory is excluded
-# with include-package-data = false and namespaces = false.
 include-package-data = true
+
 [tool.setuptools.packages.find]
 namespaces = false
 where = ["."]
@@ -66,6 +46,7 @@ modelforge = [
     "py.typed"
 ]
 
+# https://versioningit.readthedocs.io/en/stable/configuration.html#
 [tool.versioningit]
 default-version = "1+unknown"
 
@@ -75,9 +56,7 @@ dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 
 [tool.versioningit.vcs]
-# The method key:
-method = "git"  # <- The method name
-# Parameters to pass to the method:
+method = "git"
 match = ["*"]
 default-tag = "1.0.0"
 
@@ -90,7 +69,7 @@ file = "modelforge/_version.py"
 omit = [
     # Omit the tests
     "*/tests/*",
-    # Omit generated versioneer
+    # Omit generated versioningit
     "modelforge/_version.py"
 ]