Merge branch 'master' into develop

CHANGELOG.txt

-Changes in Release 2.x.x
+Changes in Release 2.2.0
 --------------------------------------------------------------------------------
 
  * Introduced CreateMeanlDDTHA function to evaluate the consistency of a
@@ -8,6 +8,7 @@ Changes in Release 2.x.x
    own code. You might have to adapt CMake flags when building OpenStructure to 
    variables specified here: 
    https://cmake.org/cmake/help/latest/module/FindPython.html
+ * Update container base image from ubuntu:18.04 to ubuntu:20.04
  * Several minor bug fixes and improvements.
 
 Changes in Release 2.1.0

CMakeLists.txt

@@ -14,7 +14,7 @@ cmake_policy(SET CMP0060 NEW)
 project(OpenStructure CXX C)
 set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
 set (OST_VERSION_MAJOR 2)
-set (OST_VERSION_MINOR 1)
+set (OST_VERSION_MINOR 2)
 set (OST_VERSION_PATCH 0)
 set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)

docker/Dockerfile

-FROM ubuntu:18.04
+FROM ubuntu:20.04
 
 # ARGUMENTS
 ###########
-ARG OPENSTRUCTURE_VERSION="2.1.0"
+ARG OPENSTRUCTURE_VERSION="2.2.0"
 ARG SRC_FOLDER="/usr/local/src"
 ARG CPUS_FOR_MAKE=2
 ARG MSMS_VERSION="2.6.1"
@@ -98,7 +98,7 @@ RUN cd ${SRC_FOLDER} && \
 #############
 WORKDIR /home
 ENV OST_ROOT="/usr/local"
-ENV PYTHONPATH="/usr/local/lib64/python3.6/site-packages"
+ENV PYTHONPATH="/usr/local/lib64/python3.8/site-packages"
 ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:/usr/local/openmm/lib/"
 ENV QT_X11_NO_MITSHM=1
 ENV OPENSTRUCTURE_VERSION=$OPENSTRUCTURE_VERSION

modules/bindings/pymod/dssp.py

@@ -110,6 +110,7 @@ def AssignDSSP(ent, pdb_path="", extract_burial_status=False, tmp_dir=None,
   # are handled in the parser LoadDSSP)
   temp_dssp_path=_ExecuteDSSP(pdb_path, dssp_bin)
   if not os.path.exists(temp_dssp_path):
+    _Cleanup(pdb_path, temp_dssp_path, entity_saved)
     raise RuntimeError('DSSP output file does not exist.')
   # assign DSSP to entity
   try:

modules/doc/install.rst

@@ -341,9 +341,9 @@ OpenStructure.
 
 `Homebrew <https://brew.sh/>`_ can be used to conveniently install all
 dependencies. The current Python version, as of writing these instructions, is
-3.8.5 but works so far. Boost comes as 1.73.0 which seems to be OK. Do not
+3.9.0 but works so far. Boost comes as 1.74.0 which seems to be OK. Do not
 forget to also install `boost-python3` (your system may have a lower version of
-Python than 3.8.5 but it seems like `boost-python3` was compiled for 3.8.5).
+Python than 3.9.0 but it seems like `boost-python3` was compiled for 3.9.0).
 Eigen and SQLite also seem to be unproblematic concerning higher version numbers.
 
 If you want to build the info module or the graphical user interface, make sure
@@ -373,11 +373,11 @@ C flags:
 
 .. code-block:: bash
 
-  cmake . -DPython_INCLUDE_DIR=/usr/local/opt/python@3.8/Frameworks/\
-  Python.framework/Versions/Current/include/python3.8/ \
-          -DPython_LIBRARY=/usr/local/opt/python@3.8/Frameworks/\
-  Python.framework/Versions/Current/lib/libpython3.8.dylib \
-          -DPython_ROOT_DIR=/usr/local/opt/python@3.8/ \
+  cmake . -DPython_INCLUDE_DIRS=/usr/local/opt/python@3.9/Frameworks/\
+  Python.framework/Versions/Current/include/python3.9/ \
+          -DPython_LIBRARIES=/usr/local/opt/python@3.9/Frameworks/\
+  Python.framework/Versions/Current/lib/libpython3.9.dylib \
+          -DPython_ROOT_DIR=/usr/local/opt/python@3.9/ \
           -DBOOST_ROOT=/usr/local \
           -DSYS_ROOT=/usr/local \
           -DOPTIMIZE=ON \

scripts/bump-version.py

@@ -42,6 +42,6 @@ lines = open(vfile).readlines()
 for i, line in enumerate(lines):
   if line.startswith("From: registry.scicore.unibas.ch/schwede/openstructure:"):
     lines[i] = 'From: registry.scicore.unibas.ch/schwede/openstructure:'+\
-      '%s' % version_string
+      '%s\n' % version_string
     break
 open(vfile, "w").writelines(lines)

singularity/Singularity

 BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:2.1.0-bionic
+From: registry.scicore.unibas.ch/schwede/openstructure:2.2.0-focal
 %post
 ##############################################################################
 # POST
@@ -54,7 +54,7 @@ cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
     "-m", "ipykernel",
         "-f", "{connection_file}",
     "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
-    "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.6/site-packages/ost/ost_startup.py']"
+    "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.8/site-packages/ost/ost_startup.py']"
   ],
   "env": {
   }
@@ -176,7 +176,7 @@ goes to CWD. Thus this sould work as expected out of the box.
 # NOTEBOOK ENV
 ##############################################################################
 export DNG_ROOT=$OST_ROOT
-export DNG_INITDIR=${DNG_ROOT}/lib64/python3.6/site-packages/ost
+export DNG_INITDIR=${DNG_ROOT}/lib64/python3.8/site-packages/ost
 
 
 %apprun IPython