adding building with pyproject.toml

.github/workflows/build.yml

@@ -30,6 +30,7 @@ jobs:
         python3-numpy
         python3-pil
         python3-pytest
+        python3-pip
 
     - name: Install collada2gltf
       run: |
@@ -43,13 +44,14 @@ jobs:
 
     - name: Build
       run: |
-        python setup.py --testing install --prefix=install-prefix
+        pip install --upgrade pip
+        pip install -v --config-settings testing=True .
       env:
         DEBUG: 1
 
     - name: Test
       run: |
-        ./install-prefix/bin/pymol -ckqy testing/testing.py --run all
+        pymol -ckqy testing/testing.py --run all
 
   build-Windows:
 
@@ -72,7 +74,7 @@ jobs:
       shell: cmd
       run: |-
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyqt glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest
+        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyqt glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest pip python-build
 
     - name: Conda info
       shell: cmd
@@ -92,13 +94,13 @@ jobs:
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        python setup.py --testing install --prefix=%GITHUB_WORKSPACE%\\install-prefix
+        pip install -v --config-settings testing=True .
 
     - name: Test
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        %GITHUB_WORKSPACE%\\install-prefix\\Scripts\\pymol.bat -ckqy testing\\testing.py --run all
+        pymol -ckqy testing\\testing.py --run all
 
   build-MacOS:
 
@@ -115,7 +117,7 @@ jobs:
         bash $CONDA_ROOT.sh -b -p $CONDA_ROOT
         export PATH="$CONDA_ROOT/bin:$PATH"
         conda config --set quiet yes
-        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyqt glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest
+        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyqt glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest pip python-build
         conda info
 
     - name: Get additional sources
@@ -129,9 +131,9 @@ jobs:
       run: |-
         export MACOSX_DEPLOYMENT_TARGET=12.0
         export PATH="$CONDA_ROOT/bin:$PATH"
-        python setup.py install --prefix=${GITHUB_WORKSPACE}/install-prefix
+        pip install -v --config-settings testing=True .
 
     - name: Test
       run: |-
         export PATH="$CONDA_ROOT/bin:$PATH"
-        ${GITHUB_WORKSPACE}/install-prefix/bin/pymol -ckqy testing/testing.py --run all
+        pymol -ckqy testing/testing.py --run all

_custom_build/backend.py

@@ -0,0 +1,36 @@
+# Adopted from pillow and pycapnp
+
+import sys
+
+from setuptools.build_meta import build_wheel
+
+backend_class = build_wheel.__self__.__class__
+
+
+class _CustomBuildMetaBackend(backend_class):
+    def run_setup(self, setup_script="setup.py"):
+        if self.config_settings:
+            flags = [
+                f"--{k}={v}"
+                for k, v in self.config_settings.items()
+            ]
+            sys.argv = sys.argv[:1] + ["build_ext"] + flags + sys.argv[1:]
+        return super().run_setup(setup_script)
+
+    def build_wheel(
+        self, wheel_directory, config_settings=None, metadata_directory=None
+    ):
+        self.config_settings = config_settings
+        return super().build_wheel(wheel_directory, config_settings, metadata_directory)
+
+    def build_editable(
+        self, wheel_directory, config_settings=None, metadata_directory=None
+    ):
+        self.config_settings = config_settings
+        return super().build_editable(
+            wheel_directory, config_settings, metadata_directory
+        )
+
+_backend = _CustomBuildMetaBackend()
+build_wheel = _backend.build_wheel
+build_editable = _backend.build_editable

pyproject.toml

@@ -0,0 +1,49 @@
+[project]
+name = "pymol"
+readme = "README.md"
+requires-python = ">=3.9"
+dynamic=["version"]
+license = {file = "LICENSE"}
+description = """
+PyMOL is a Python-enhanced molecular graphics tool.
+It excels at 3D visualization of proteins, small molecules, density,
+surfaces, and trajectories. It also includes molecular editing,
+ray tracing, and movies. Open Source PyMOL is free to everyone!
+"""
+authors = [
+  {name = "Schrodinger", email = "[email protected]"},
+]
+dependencies = [
+  "numpy>=1.26.4,<2",
+]
+
+[build-system]
+build-backend = "backend"
+backend-path = ["_custom_build"]
+requires = [
+  "numpy>=1.26.4,<2",
+  "setuptools>=69.2.0",
+]
+
+[project.optional-dependencies]
+test = [
+  "pillow==10.3.0",
+  "pytest==8.2.2",
+]
+
+[project.urls]
+Homepage = "https://pymol.org"
+Documentation = "https://pymol.org/dokuwiki"
+Repository = "https://github.com/schrodinger/pymol-open-source"
+"Bug Tracker" = "https://github.com/schrodinger/pymol-open-source/issues"
+Changelog = "https://github.com/schrodinger/pymol-open-source/blob/master/ChangeLog"
+
+[project.scripts]
+pymol = "pymol:launch"
+
+[tool.setuptools.packages.find]
+where = ["modules"]
+
+[tool.setuptools.package-data]
+pmg_qt = ["forms/*.ui"]
+