Merge branch 'cmake' into cmake_win

.github/workflows/build.yml

@@ -72,7 +72,7 @@ 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 pytest
+        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
@@ -84,27 +84,28 @@ jobs:
       shell: cmd
       run: |
         git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
-        cp -R mmtf-cpp/include/mmtf* include/
+        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=install-prefix
+        python setup.py --testing install --prefix=%GITHUB_WORKSPACE%\\install-prefix
 
     - name: Test
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        install-prefix\\Scripts\\pymol.bat -ckqy testing\\testing.py --run all
+        %GITHUB_WORKSPACE%\\install-prefix\\Scripts\\pymol.bat -ckqy testing\\testing.py --run all
 
   build-MacOS:
 
     runs-on: macos-latest
 
     env:
       CONDA_ROOT: "/tmp/miniconda"
-      MAMBAFORGE_EXEC: ${{github.workspace}}\..\tmp\mambaforge.exe
 
     steps:
     - uses: actions/[email protected]
@@ -114,21 +115,23 @@ 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 catch2=2.13.3 glm libnetcdf collada2gltf pytest
+        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* include/
+        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=install-prefix
+        python setup.py install --prefix=${GITHUB_WORKSPACE}/install-prefix
 
     - name: Test
       run: |-
         export PATH="$CONDA_ROOT/bin:$PATH"
-        ./install-prefix/bin/pymol -ckqy testing/testing.py --run all
+        ${GITHUB_WORKSPACE}/install-prefix/bin/pymol -ckqy testing/testing.py --run all

layer2/ObjectMolecule.cpp

@@ -2388,7 +2388,7 @@ static ObjectMolecule *ObjectMoleculeReadTOPStr(PyMOLGlobals * G, ObjectMolecule
      */
 
     if(ok && isNew)
-      ok &= ObjectMoleculeConnect(I, cset, false);
+      ok = ObjectMoleculeConnect(I, cset, false);
     if(cset->Symmetry && (!I->Symmetry)) {
       I->Symmetry.reset(new CSymmetry(*cset->Symmetry));
       CHECKOK(ok, I->Symmetry);

setup.py

@@ -119,17 +119,18 @@ def is_conda_env():
 
 def guess_msgpackc():
     for prefix in prefix_path:
-        f = os.path.join(prefix, 'include', 'msgpack', 'version_master.h')
+        for suffix in ['h', 'hpp']:
+            f = os.path.join(prefix, 'include', 'msgpack', f'version_master.{suffix}')
 
-        try:
-            m = re.search(r'MSGPACK_VERSION_MAJOR\s+(\d+)', open(f).read())
-        except EnvironmentError:
-            continue
+            try:
+                m = re.search(r'MSGPACK_VERSION_MAJOR\s+(\d+)', open(f).read())
+            except EnvironmentError:
+                continue
 
-        if m is not None:
-            major = int(m.group(1))
-            if major > 1:
-                return 'c++11'
+            if m is not None:
+                major = int(m.group(1))
+                if major > 1:
+                    return 'c++11'
 
     return 'no'
 
@@ -451,7 +452,10 @@ def make_launch_script(self):
     def_macros += [("_PYMOL_NO_MSGPACKC", None)]
 else:
     if options.use_msgpackc == 'c++11':
-        def_macros += [("MMTF_MSGPACK_USE_CPP11", None)]
+        def_macros += [
+            ("MMTF_MSGPACK_USE_CPP11", None),
+            ("MSGPACK_NO_BOOST", None),
+        ]
     else:
         libs += ['msgpackc']
 

testing/tests/api/externing.py

@@ -1,4 +1,5 @@
 import os
+import sys
 from pymol import cmd, testing, stored
 
 def touch(filename):
@@ -9,8 +10,17 @@ class TestExterning(testing.PyMOLTestCase):
     def testCdLsPwd(self):
         with testing.mkdtemp() as path:
             cmd.cd(path)
-            self.assertEqual(os.getcwd(),
-                    os.path.realpath(path))
+            if sys.platform == 'win32':
+                import ctypes
+                def get_long_path_name(path):
+                    buf = ctypes.create_unicode_buffer(260)
+                    ctypes.windll.kernel32.GetLongPathNameW(path, buf, len(buf))
+                    return buf.value
+                self.assertEqual(get_long_path_name(os.getcwd()),
+                                 get_long_path_name(os.path.realpath(path)))
+            else:
+                self.assertEqual(os.getcwd(),
+                        os.path.realpath(path))
 
             touch('foo1.txt')
             touch('foo2.txt')