Merge branch 'schrodinger:master' into patch-1

.clang-format

@@ -0,0 +1,62 @@
+---
+Language:        Cpp
+AccessModifierOffset: -2
+ConstructorInitializerIndentWidth: 4
+AlignEscapedNewlinesLeft: false
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+AlwaysBreakAfterDefinitionReturnType: false
+AlwaysBreakTemplateDeclarations: false
+AlwaysBreakBeforeMultilineStrings: false
+BreakBeforeBraces: Linux
+BreakBeforeBinaryOperators: None
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: true
+BinPackParameters: true
+BinPackArguments: true
+ColumnLimit:     80
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+DerivePointerAlignment: false
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: false
+IndentWrappedFunctionNames: false
+IndentFunctionDeclarationAfterType: false
+MaxEmptyLinesToKeep: 1
+KeepEmptyLinesAtTheStartOfBlocks: true
+NamespaceIndentation: None
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakString: 1000
+PenaltyBreakFirstLessLess: 120
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+SpacesBeforeTrailingComments: 1
+Cpp11BracedListStyle: true
+Standard:        Cpp11
+IndentWidth:     2
+TabWidth:        8
+UseTab:          Never
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpacesInAngles:  false
+SpaceInEmptyParentheses: false
+SpacesInCStyleCastParentheses: false
+SpaceAfterCStyleCast: true
+SpacesInContainerLiterals: true
+SpaceBeforeAssignmentOperators: true
+ContinuationIndentWidth: 4
+CommentPragmas:  '^ IWYU pragma:'
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+SpaceBeforeParens: ControlStatements
+DisableFormat:   false
+AlignAfterOpenBracket: DontAlign
+...
+

.github/workflows/build.yml

@@ -1,20 +1,21 @@
 name: CI
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
-  build:
+  build-Linux:
 
     runs-on: ubuntu-22.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4.0.0
 
     - name: Install system dependencies
       run: >
         sudo apt-get update;
         sudo apt-get --no-install-recommends install
         catch2
+        cmake
         libfreetype6-dev
         libglew-dev
         libglm-dev
@@ -25,7 +26,7 @@ jobs:
         python-is-python3
         python3-biopython
         python3-dev
-        python3-distutils
+        python3-setuptools
         python3-numpy
         python3-pil
         python3-pytest
@@ -49,3 +50,88 @@ jobs:
     - name: Test
       run: |
         ./install-prefix/bin/pymol -ckqy testing/testing.py --run all
+
+  build-Windows:
+
+    runs-on: windows-latest
+
+    env:
+      CONDA_ROOT: ${{github.workspace}}\..\tmp\mambaforge
+      MAMBAFORGE_EXEC: ${{github.workspace}}\..\tmp\mambaforge.exe
+
+    steps:
+    - uses: actions/[email protected]
+    - name: Download miniconda
+      shell: cmd
+      run: |-
+        if not exist %CONDA_ROOT% mkdir %CONDA_ROOT%
+        curl -L -o %MAMBAFORGE_EXEC% https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Mambaforge-24.3.0-0-Windows-x86_64.exe
+        start /wait %MAMBAFORGE_EXEC% /S /D=%CONDA_ROOT%
+
+    - name: Set up Miniconda
+      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
+
+    - name: Conda info
+      shell: cmd
+      run: |-
+        CALL %CONDA_ROOT%\\Scripts\\activate.bat
+        conda info
+
+    - name: Get additional sources
+      shell: cmd
+      run: |
+        git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
+        cp -R mmtf-cpp/include/mmtf* %CONDA_ROOT%/Library/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%/Library/include/
+
+    - name: Build PyMOL
+      shell: cmd
+      run: |
+        CALL %CONDA_ROOT%\\Scripts\\activate.bat
+        python setup.py --testing install --prefix=%GITHUB_WORKSPACE%\\install-prefix
+
+    - name: Test
+      shell: cmd
+      run: |
+        CALL %CONDA_ROOT%\\Scripts\\activate.bat
+        %GITHUB_WORKSPACE%\\install-prefix\\Scripts\\pymol.bat -ckqy testing\\testing.py --run all
+
+  build-MacOS:
+
+    runs-on: macos-latest
+
+    env:
+      CONDA_ROOT: "/tmp/miniconda"
+
+    steps:
+    - uses: actions/[email protected]
+    - 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
+
+    - name: Test
+      run: |-
+        export PATH="$CONDA_ROOT/bin:$PATH"
+        ${GITHUB_WORKSPACE}/install-prefix/bin/pymol -ckqy testing/testing.py --run all

CMakeLists.txt

@@ -0,0 +1,31 @@
+cmake_minimum_required(VERSION 3.13)
+
+project(${TARGET_NAME})
+
+set(CMAKE_VERBOSE_MAKEFILE on)
+
+add_library(${TARGET_NAME} SHARED ${ALL_SRC})
+
+target_compile_options(${TARGET_NAME} PRIVATE ${ALL_COMP_ARGS})
+
+set_target_properties(${TARGET_NAME} PROPERTIES SUFFIX ${SHARED_SUFFIX})
+
+target_compile_features(${TARGET_NAME} PRIVATE cxx_std_17)
+
+set_target_properties(${TARGET_NAME} PROPERTIES PREFIX "")
+
+target_include_directories(${TARGET_NAME} PUBLIC ${ALL_INC_DIR})
+
+target_link_directories(${TARGET_NAME} PUBLIC ${ALL_LIB_DIR})
+
+
+if(APPLE)
+    set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -undefined dynamic_lookup")
+endif()
+
+target_link_libraries(${TARGET_NAME}
+    ${ALL_LIB}
+    ${ALL_EXT_LINK}
+)
+
+target_compile_definitions(${TARGET_NAME} PUBLIC ${ALL_DEF})

ChangeLog

@@ -2,6 +2,38 @@
 CHANGE LOG
 =========================================================================
 
+2024-04-09 Jarrett Johnson, Thomas Stewart, Thomas Holder, Anton Butsev
+
+	* 3.0.0
+
+	* Panels
+	  - Nucleic Acid Builder supported
+	  - Scenes Panel (Basic version)
+	  - Improved APBS electrostatics plugin integrated
+
+	* Distance/Bonding detection
+	  - Halogen-bond detection and display
+
+	* Python API
+	  - `fnab` command (sequence to nucleic acid chain)
+	  - Improved CGO builder API
+	  - get_sasa_relative() `subsele` argument added
+	  - new clip modes/API
+	  - iterate() adds `explicit_valence` and `explicit_degree`
+	  - `cell_centered` setting added
+	  - by grid-cell background gradient `bg_gradient=2`
+	  - look_at() added
+	  - experimental `curve_new` / `move_on_curve`
+
+	* Developer
+	  - C++17 required
+	  - pymol-testing integrated
+	  - pytest introduced
+	  - Github Actions CI
+
+	* And many other fixes and small additions provided by developers
+	  and the community...
+
 2021-05-10 Jarrett Johnson, Thomas Holder, Thomas Stewart
 
 	* 2.5.0

INSTALL

@@ -8,7 +8,8 @@ See also: http://pymolwiki.org/index.php/Linux_Install
 REQUIREMENTS
 
     - C++17 compiler (e.g. gcc 8+)
-    - Python 3.6+
+    - CMake (3.13+)
+    - Python 3.9+
     - Pmw (Python Megawidgets) (optional, for legacy GUI/plugins)
       https://github.com/schrodinger/pmw-patched
     - OpenGL

contrib/champ/champ_module.c

@@ -1053,7 +1053,7 @@ static PyMethodDef champ_methods[] = {
   {NULL,		                    NULL}     /* sentinel */        
 };
 
-PyObject * PyInit__champ(void)
+PyMODINIT_FUNC PyInit__champ(void)
 {
   static struct PyModuleDef moduledef = {
     PyModuleDef_HEAD_INIT,

contrib/champ/os_memory.c

@@ -176,7 +176,15 @@ void *OSMemoryMalloc(unsigned int size,const char *file,int line,int type)
   rec=(DebugRec*)malloc(sizeof(DebugRec)+size);
   if(!rec)
     return(NULL);
-  strcpy(rec->file,file);
+
+  int len = strlen(file);
+  int max_size = sizeof(rec->file) - 1;
+  if (len > max_size) {
+    strcpy(rec->file, file + len - max_size);
+  } else {
+    strcpy(rec->file, file);
+  }
+  rec->file[max_size - 1] = '\0';
   rec->line=line;
   rec->size=size;
   rec->type=type;
@@ -196,7 +204,15 @@ void *OSMemoryCalloc(unsigned int count,unsigned int size,const char *file,int l
   rec=(DebugRec*)calloc(1,sizeof(DebugRec)+size);
   if(!rec)
     return(NULL);
-  strcpy(rec->file,file);
+
+  int len = strlen(file);
+  int max_size = sizeof(rec->file) - 1;
+  if (len > max_size) {
+    strcpy(rec->file, file + len - max_size);
+  } else {
+    strcpy(rec->file, file);
+  }
+  rec->file[max_size - 1] = '\0';
   rec->line=line;
   rec->size=size;
   rec->type=type;

create_shadertext.py

@@ -7,7 +7,6 @@
 from collections import defaultdict
 from os.path import dirname
 from subprocess import Popen, PIPE
-from distutils import dir_util
 
 def create_all(generated_dir, pymoldir="."):
     '''
@@ -30,7 +29,7 @@ def __init__(self, filename):
             self.out = cStringIO.StringIO()
             self.filename = filename
         else:
-            dir_util.mkpath(os.path.dirname(filename))
+            os.makedirs(os.path.dirname(filename), exist_ok=True)
             self.out = open(filename, "w")
             self.filename = None
     def close(self):

data/shaders/bezier.fs

@@ -1,8 +1,5 @@
-#version 450
-
-out vec4 outColor;
 
 void main()
 {
-    outColor = vec4(1.0, 1.0, 0.0f, 1.0);
+    gl_FragColor = vec4(1.0, 1.0, 0.0f, 1.0);
 }

data/shaders/bezier.vs

@@ -1,6 +1,4 @@
-#version 450
-
-layout (location = 0) in vec3 position;
+attribute vec3 position;
 
 void main()
 {