ye11owSub · ye11owSub · May 12, 2024
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -13,37 +13,12 @@ jobs:
     - name: Install system dependencies
       run: >
         sudo apt-get update;
-        sudo apt-get --no-install-recommends install
-        catch2
-        cmake
-        libfreetype6-dev
-        libglew-dev
-        libglm-dev
-        libmsgpack-dev
-        libnetcdf-dev
-        libpng-dev
-        libxml2-dev
-        python-is-python3
-        python3-biopython
-        python3-dev
-        python3-setuptools
-        python3-numpy
-        python3-pil
-        python3-pytest
-
-    - name: Install collada2gltf
-      run: |
-        wget -nv https://anaconda.org/schrodinger/collada2gltf/2.1.4/download/linux-64/collada2gltf-2.1.4-h6bb024c_0.tar.bz2
-        sudo tar xf collada2gltf-*.tar.bz2 -C / bin/collada2gltf
-
-    - name: Get additional sources
-      run: |
-        git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
-        cp -R mmtf-cpp/include/mmtf* include/
+        sudo apt-get --no-install-recommends install python3-dev python3-pytest
 
     - name: Build
       run: |
-        python setup.py --testing install --prefix=install-prefix
+        python -m pip install --upgrade pip;
+        pip install '.[test]' -Csetup-args=-Dtesting=true --prefix=install-prefix
       env:
         DEBUG: 1
 
@@ -72,7 +47,7 @@ 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 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest
+        conda install -y -c conda-forge -c python glew pytest
 
     - name: Conda info
       shell: cmd
@@ -92,7 +67,7 @@ jobs:
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        python setup.py --testing install --prefix=%GITHUB_WORKSPACE%\\install-prefix
+        pip install . -Csetup-args=-Dtesting=true --prefix=%GITHUB_WORKSPACE%\\install-prefix
 
     - name: Test
       shell: cmd
@@ -104,34 +79,13 @@ jobs:
 
     runs-on: macos-latest
 
-    env:
-      CONDA_ROOT: "/tmp/miniconda"
-
     steps:
     - uses: actions/checkout@v4.0.0
-    - name: Set up Miniconda and Build
-      run: |-
-        curl -L -o $CONDA_ROOT.sh https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-MacOSX-x86_64.sh
-        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 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest
-        conda info
-
-    - name: Get additional sources
-      run: |
-        git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
-        cp -R mmtf-cpp/include/mmtf* ${CONDA_ROOT}/include/
-        git clone --depth 1 --single-branch --branch cpp_master https://github.com/msgpack/msgpack-c.git
-        cp -R msgpack-c/include/msgpack* ${CONDA_ROOT}/include/
-
     - name: Build PyMOL
       run: |-
         export MACOSX_DEPLOYMENT_TARGET=12.0
-        export PATH="$CONDA_ROOT/bin:$PATH"
-        python setup.py install --prefix=${GITHUB_WORKSPACE}/install-prefix
+        pip install '.[test]' -Csetup-args=-Dtesting=true --prefix=${GITHUB_WORKSPACE}/install-prefix
 
     - name: Test
       run: |-
-        export PATH="$CONDA_ROOT/bin:$PATH"
         ${GITHUB_WORKSPACE}/install-prefix/bin/pymol -ckqy testing/testing.py --run all
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,5 @@
 *.d
 generated
 build
+subprojects/*
+!subprojects/*.wrap
diff --git a/CMakeLists.txt b/CMakeLists.txt
diff --git a/INSTALL b/INSTALL
@@ -1,14 +1,13 @@
 
 ----------------------------------------------------------------------
-INSTALLATION VIA COMPILATION 
+INSTALLATION VIA COMPILATION
 ----------------------------------------------------------------------
 
 See also: http://pymolwiki.org/index.php/Linux_Install
 
 REQUIREMENTS
 
     - C++17 compiler (e.g. gcc 8+)
-    - CMake (3.13+)
     - Python 3.9+
     - Pmw (Python Megawidgets) (optional, for legacy GUI/plugins)
       https://github.com/schrodinger/pmw-patched
@@ -50,7 +49,7 @@ SETUP OPTIONS
 
 INSTALLATION
 
-    python setup.py install --prefix=~/someplace
+    pip install . --prefix=~/someplace
 
 RUNNING PyMOL
 

diff --git a/contrib/champ/meson.build b/contrib/champ/meson.build
@@ -0,0 +1,26 @@
+files_names = [
+      'champ.c',
+      'champ_module.c',
+      'chiral.c',
+      'err2.c',
+      'feedback2.c',
+      'list.c',
+      'os_memory.c',
+      'sort.c',
+      'strblock.c',
+      'vla.c',
+]
+champ_src_files = []
+
+foreach file_name : files_names
+  champ_src_files += files(file_name)
+endforeach
+
+py.extension_module(
+  '_champ',
+  champ_src_files,
+  include_directories : include_directories('.'),
+  install: true,
+  subdir: 'chempy/champ'
+)
+
diff --git a/contrib/uiuc/plugins/meson.build b/contrib/uiuc/plugins/meson.build
diff --git a/create_shadertext.py b/create_shadertext.py
@@ -130,5 +130,4 @@ def create_buildinfo(outputdir, pymoldir='.'):
         ''' % (time.time(), sha), file=out)
 
 if __name__ == "__main__":
-    create_shadertext(*sys.argv[1:6])
-    create_buildinfo(dirname(sys.argv[4]), dirname(dirname(sys.argv[1])))
+    create_all("build")
diff --git a/layer0/meson.build b/layer0/meson.build
@@ -0,0 +1,42 @@
+src_files += files(
+  'Bezier.cpp',
+  'Block.cpp',
+  'CarveHelper.cpp',
+  'ccealignmodule.cpp',
+  'ContourSurf.cpp',
+  'Crystal.cpp',
+  'Err.cpp',
+  'Feedback.cpp',
+  'Field.cpp',
+  'File.cpp',
+  'GenericBuffer.cpp',
+  'GFXManager.cpp',
+  'GraphicsUtil.cpp',
+  'Isosurf.cpp',
+  'Map.cpp',
+  'marching_cubes.cpp',
+  'Match.cpp',
+  'Matrix.cpp',
+  'MemoryDebug.cpp',
+  'MemoryUsage.cpp',
+  'MyPNG.cpp',
+  'os_gl.cpp',
+  'Parse.cpp',
+  'Pixmap.cpp',
+  'PostProcess.cpp',
+  'ShaderMgr.cpp',
+  'ShaderPreprocessor.cpp',
+  'ShaderPrg.cpp',
+  'Sphere.cpp',
+  'Tetsurf.cpp',
+  'Texture.cpp',
+  'Tracker.cpp',
+  'Triangle.cpp',
+  'TTT.cpp',
+  'Util.cpp',
+  'Util2.cpp',
+  'Vector.cpp',
+  'Word.cpp',
+)
+
+include_dirs += include_directories('.')
diff --git a/layer1/meson.build b/layer1/meson.build
@@ -0,0 +1,50 @@
+src_files += files(
+    'Basis.cpp',
+    'ButMode.cpp',
+    'Camera.cpp',
+    'CGO.cpp',
+    'CGOGL.cpp',
+    'CGORenderer.cpp',
+    'Character.cpp',
+    'COLLADA.cpp',
+    'Color.cpp',
+    'Control.cpp',
+    'Extrude.cpp',
+    'Font.cpp',
+    'FontGLUT.cpp',
+    'FontGLUT8x13.cpp',
+    'FontGLUT9x15.cpp',
+    'FontGLUTHel10.cpp',
+    'FontGLUTHel12.cpp',
+    'FontGLUTHel18.cpp',
+    'FontType.cpp',
+    'Movie.cpp',
+    'Ortho.cpp',
+    'P.cpp',
+    'PConv.cpp',
+    'Picking.cpp',
+    'Pop.cpp',
+    'PyMOLObject.cpp',
+    'Ray.cpp',
+    'Rep.cpp',
+    'Scene.cpp',
+    'SceneMouse.cpp',
+    'ScenePicking.cpp',
+    'SceneRay.cpp',
+    'SceneRender.cpp',
+    'SceneView.cpp',
+    'ScrollBar.cpp',
+    'Seq.cpp',
+    'Setting.cpp',
+    'Shaker.cpp',
+    'Symmetry.cpp',
+    'SymOp.cpp',
+    'SymOpPConv.cpp',
+    'SymOpTools.cpp',
+    'Text.cpp',
+    'TypeFace.cpp',
+    'View.cpp',
+    'Wizard.cpp',
+)
+
+include_dirs += include_directories('.')
diff --git a/layer2/meson.build b/layer2/meson.build
@@ -0,0 +1,56 @@
+src_files += files(
+    'AssemblyHelpers.cpp',
+    'AtomInfo.cpp',
+    'AtomInfoHistory.cpp',
+    'BondTypeHistory.cpp',
+    'CifFile.cpp',
+    'CifMoleculeReader.cpp',
+    'CoordSet.cpp',
+    'DistSet.cpp',
+    'GadgetSet.cpp',
+    'HydrogenAdder.cpp',
+    'MmodTyping.cpp',
+    'MmtfMoleculeReader.cpp',
+    'Mol2Typing.cpp',
+    'MolV3000.cpp',
+    'ObjectAlignment.cpp',
+    'ObjectCallback.cpp',
+    'ObjectCGO.cpp',
+    'ObjectCurve.cpp',
+    'ObjectDist.cpp',
+    'ObjectGadget.cpp',
+    'ObjectGadgetRamp.cpp',
+    'ObjectGroup.cpp',
+    'ObjectMap.cpp',
+    'ObjectMesh.cpp',
+    'ObjectMolecule.cpp',
+    'ObjectMolecule2.cpp',
+    'ObjectMolecule3.cpp',
+    'ObjectSlice.cpp',
+    'ObjectSurface.cpp',
+    'ObjectVolume.cpp',
+    'RepAngle.cpp',
+    'RepCartoon.cpp',
+    'RepCylBond.cpp',
+    'RepDihedral.cpp',
+    'RepDistDash.cpp',
+    'RepDistLabel.cpp',
+    'RepDot.cpp',
+    'RepEllipsoid.cpp',
+    'RepLabel.cpp',
+    'RepMesh.cpp',
+    'RepNonbonded.cpp',
+    'RepNonbondedSphere.cpp',
+    'RepRibbon.cpp',
+    'RepSphere.cpp',
+    'RepSphereGenerate.cpp',
+    'RepSphereImmediate.cpp',
+    'RepSurface.cpp',
+    'RepWireBond.cpp',
+    'Sculpt.cpp',
+    'SculptCache.cpp',
+    'SideChainHelper.cpp',
+    'VFont.cpp',
+)
+
+include_dirs += include_directories('.')
diff --git a/layer3/meson.build b/layer3/meson.build
@@ -0,0 +1,20 @@
+src_files += files(
+    'AtomIterators.cpp',
+    'CifDataValueFormatter.cpp',
+    'Editor.cpp',
+    'Executive.cpp',
+    'ExecutivePython.cpp',
+    'Interactions.cpp',
+    'MaeExportHelpers.cpp',
+    'MoleculeExporter.cpp',
+    'MovieScene.cpp',
+    'PlugIOManager.cpp',
+    'RingFinder.cpp',
+    'Seeker.cpp',
+    'Selector.cpp',
+    'SelectorTmp.cpp',
+    'SpecRec.cpp',
+    'SpecRecSpecial.cpp',
+)
+
+include_dirs += include_directories('.')
diff --git a/layer4/meson.build b/layer4/meson.build
@@ -0,0 +1,7 @@
+src_files += files(
+    'Cmd.cpp',
+    'Menu.cpp',
+    'PopUp.cpp',
+)
+
+include_dirs += include_directories('.')
diff --git a/layer5/meson.build b/layer5/meson.build
@@ -0,0 +1,7 @@
+src_files += files(
+    'main.cpp',
+    'PyMOL.cpp',
+    'TestPyMOL.cpp'
+)
+
+include_dirs += include_directories('.')