reorganizing dependencies, adding optinal deps, and adjusting workflows

.github/workflows/performance_benchmarks.yml

@@ -15,10 +15,10 @@ jobs:
       uses: actions/checkout@v3
       with:
         submodules: recursive
-    - name: Set up Python 3.12
+    - name: Set up Python 3.x
       uses: actions/setup-python@v2
       with:
-        python-version: 3.12
+        python-version: "3.x"
     - name: Install MPI
       uses: mpi4py/setup-mpi@v1
     - name: Install dependencies

.github/workflows/pylint.yml

@@ -9,10 +9,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.12
+    - name: Set up Python 3.x
       uses: actions/setup-python@v2
       with:
-        python-version: 3.12
+        python-version: "3.x"
     - name: Install MPI
       run: |
         sudo apt-get update

.github/workflows/pypi.yml

@@ -20,7 +20,7 @@ jobs:
         uses: mpi4py/setup-mpi@v1
       - name: Build using pip
         run: |
-          pip install .
+          pip install .[ONNX,TESTS]
       - name: Set safe forking var
         run: |
           echo "RDMAV_FORK_SAFE=1" >> $GITHUB_ENV
@@ -51,9 +51,6 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest pytest-cov pytest-mock
-        pip install coveralls
-        pip install build
         pip install -r requirements.txt
     - name: Build bingocpp
       run: |

.github/workflows/tests.yml

@@ -25,9 +25,6 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest pytest-cov pytest-mock
-        pip install coverage
-        pip install coveralls
         pip install -r requirements.txt
 
     - name: Set pythonpath

pyproject.toml

@@ -8,5 +8,28 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+dependencies = [
+    "mpi4py>=2.0.0,<4.0",
+    "numpy",
+    "scipy",
+    "dill",
+    "sympy",
+    "scikit-learn",
+    "smcpy",
+    "pybind11[global]",
+]
+
+[project.optional-dependencies]
+ONNX = ["onnx"]
+TESTS = [
+    "pytest",
+    "pytest-mock",
+    "pytest-timeout",
+    "pytest-cov",
+    "coverage",
+    "coveralls"
+]
+
 [tool.cibuildwheel]
 skip = "pp*"

requirements.txt

@@ -1,13 +1,18 @@
-# h5py==2.7.0
-# matplotlib==2.2.3
+# main
 mpi4py>=2.0.0,<4.0
 numpy>=1.14.3
-pytest>=3.6
-pytest-mock>=1.10.0
-pytest-timeout>=1.4.2
 scipy>=1.6.2
 dill>=0.2.9
 sympy>=1.0
 scikit-learn>=1.1
 smcpy>=0.1.4
 pybind11[global]
+# ONNX
+onnx
+# TESTS
+pytest>=3.6
+pytest-mock>=1.10.0
+pytest-timeout>=1.4.2
+pytest-cov
+coverage
+coveralls

setup.py

@@ -6,6 +6,7 @@
 
 from setuptools import Extension, setup
 from setuptools.command.build_ext import build_ext
+
 # from distutils.version import LooseVersion
 
 # Convert distutils Windows platform specifiers to CMake -A arguments
@@ -16,13 +17,15 @@
     "win-arm64": "ARM64",
 }
 
+
 def get_property(prop, project):
     result = re.search(
         r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
         open(project + "/__init__.py").read(),
     )
     return result.group(1)
 
+
 __version__ = get_property("__version__", "bingo")
 
 
@@ -78,7 +81,7 @@ def build_extension(self, ext: CMakeExtension) -> None:
                     ninja_executable_path = Path(ninja.BIN_DIR) / "ninja"
                     cmake_args += [
                         "-GNinja",
-                        '-DCMAKE_JOB_POOLS:STRING=compile=1;link=1'
+                        "-DCMAKE_JOB_POOLS:STRING=compile=1;link=1"
                         f"-DCMAKE_MAKE_PROGRAM:FILEPATH={ninja_executable_path}",
                     ]
                 except ImportError:
@@ -161,19 +164,7 @@ def build_extension(self, ext: CMakeExtension) -> None:
         "bingo.util",
         "bingo.variation",
     ],
-    install_requires=[
-        "mpi4py>=2.0.0,<4.0",
-        "numpy",
-        "pytest",
-        "pytest-mock",
-        "pytest-timeout",
-        "scipy",
-        "dill",
-        "sympy",
-        "scikit-learn",
-        "smcpy",
-        "pybind11[global]"
-    ],
+    install_requires=[],
     python_requires=">=3.9",
     classifiers=[
         "Programming Language :: Python :: 3.12",