- The seg-fault in rdesigneur tests are due to BhallaLab#388.

.travis.yml

@@ -5,6 +5,8 @@ matrix:
   include:
   - os: linux
     dist: bionic
+    services:
+        - xvfb
   - os: osx
     osx_image: xcode11.3
 
@@ -21,6 +23,7 @@ addons:
   apt:
     update: true
 
+
 before_script:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.ci/travis_prepare_osx.sh; fi

CMakeLists.txt

@@ -409,15 +409,15 @@ foreach(_test_script ${PYDOC_TEST_SCRIPTS})
 endforeach()
 
 
-# CUSTOM TESTS. These tests may require some extra settings.
-# Run python tests. These are fast tests.
-set(PYMOOSE_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/py_custom)
-add_test(NAME test_long_sbml_multi
-    COMMAND ${PYTHON_EXECUTABLE} ${PYMOOSE_TEST_DIRECTORY}/test_long_sbml+exp+parser+multithreaded.py
-    WORKING_DIRECTORY ${PYMOOSE_TEST_DIRECTORY}
-    )
-set_tests_properties(test_long_sbml_multi PROPERTIES 
-    ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python;MOOSE_NUM_THREADS=4")
+## # CUSTOM TESTS. These tests may require some extra settings.
+## # Run python tests. These are fast tests.
+## set(PYMOOSE_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/py_custom)
+## add_test(NAME test_long_sbml_multi
+##     COMMAND ${PYTHON_EXECUTABLE} ${PYMOOSE_TEST_DIRECTORY}/test_long_sbml+exp+parser+multithreaded.py
+##     WORKING_DIRECTORY ${PYMOOSE_TEST_DIRECTORY}
+##     )
+## set_tests_properties(test_long_sbml_multi PROPERTIES 
+##     ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}/python;MOOSE_NUM_THREADS=4")
 
 # Alpha tests. These should not run by default.
 set(MOOSE_ALPHA_TEST_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests/alpha)
@@ -449,28 +449,6 @@ foreach(_test_script ${PY_ISSUES_SCRIPTS})
         )
 endforeach()
 
-# add pylint target.
-set(PYSCRIPTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/python )
-file(GLOB_RECURSE PY_SCRIPTS  "python/*.py")
-add_custom_target(pylint)
-foreach(_py_script ${PY_SCRIPTS})
-    get_filename_component( _py_name ${_py_script} NAME_WE)
-    file( READ ${_py_script} pytext)
-    string(MD5 _md5 "${pytext}")
-    set(TGT_NAME "${_py_name}-${_md5}" )
-    set(PYLINT_OPTIONS --disable=no-member --disable=no-name-in-module
-            --disable=invalid-unary-operand-type
-            --disable=import-error
-            --disable=no-method-argument
-        )
-    add_custom_target( ${TGT_NAME}
-        COMMAND ${PYTHON_EXECUTABLE} -m pylint -E ${PYLINT_OPTIONS} ${_py_script}
-        COMMENT "Running pylint on ${_py_script}"
-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-        )
-    add_dependencies(pylint ${TGT_NAME} )
-endforeach( )
-
 ############################ CPACK ######################################
 # This is not maintained anymore since packaging is done using OpenBuildService 
 include(${CMAKE_CURRENT_SOURCE_DIR}/cmake_moose_cpack.cmake)
@@ -499,3 +477,35 @@ add_custom_target(upload DEPENDS sdist
         ${PYMOOSE_SDIST_FILE}
     COMMENT "Uploading source distribution to PyPI"
     VERBATIM)
+
+####################### DEVELOPMENT ########################################
+
+# PYLINT target.
+set(PYSCRIPTS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/python)
+file(GLOB_RECURSE PY_SCRIPTS  "python/*.py")
+add_custom_target(pylint)
+foreach(_py_script ${PY_SCRIPTS})
+    get_filename_component( _py_name ${_py_script} NAME_WE)
+    file( READ ${_py_script} pytext)
+    string(MD5 _md5 "${pytext}")
+    set(TGT_NAME "${_py_name}-${_md5}" )
+    set(PYLINT_OPTIONS --disable=no-member --disable=no-name-in-module
+            --disable=invalid-unary-operand-type
+            --disable=import-error
+            --disable=no-method-argument
+        )
+    add_custom_target( ${TGT_NAME}
+        COMMAND ${PYTHON_EXECUTABLE} -m pylint -E ${PYLINT_OPTIONS} ${_py_script}
+        COMMENT "Running pylint on ${_py_script}"
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        )
+    add_dependencies(pylint ${TGT_NAME} )
+endforeach( )
+
+# Replicate Travis-CI building using docker
+add_custom_target(travis
+    COMMAND docker build -t bhallalab/travis:latest
+        -f ${CMAKE_CURRENT_SOURCE_DIR}/devel/docker/travis/Dockerfile .
+    COMMENT "Replicating Travis-CI building using Docker."
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    VERBATIM)

devel/docker/travis/Dockerfile

@@ -1,20 +1,18 @@
-FROM ubuntu:xenial
+FROM ubuntu:bionic
 MAINTAINER Dilawar Singh <dilawars@ncbs.res.in>
 
 # Install dependencies.
-RUN apt update && apt install -y git cmake gcc g++ make vim-athena \
-        libboost-all-dev libgsl-dev \
+RUN apt update && apt install -y cmake gcc g++ make \
+        libboost-all-dev libgsl-dev libblas-dev \
+        python3-pip python-pip \
+        python3-numpy python-numpy python3-matplotlib python-matplotlib \
+        python-tk python3-tk \
+        python-setuptools python3-setuptools \
+        python-dev python3-dev \
         && rm -rf /var/lib/apt/lists/*
 
-RUN apt update && apt install -y python3-pip python-pip \
-        python3-numpy python-numpy \
-        python3-matplotlib python-matplotlib \
-        && rm -rf /var/lib/apt/lists/*
-
-RUN git config --global user.name "Dilawar Singh" \
-  && git config --global user.email "dilawars@ncbs.res.in"
-RUN git clone https://github.com/dilawar/vim ~/.vim -b minimal --depth 1
 WORKDIR /root
+RUN ls -ltrah
 COPY . moose-core/
-RUN ls -lta
+RUN ls -ltarh
 CMD cd moose-core && ./.ci/travis_build_linux.sh

kinetics/PoolBase.cpp

@@ -225,8 +225,7 @@ const Cinfo* PoolBase::initCinfo()
 static const Cinfo* poolCinfo = PoolBase::initCinfo();
 
 //////////////////////////////////////////////////////////////
-PoolBase::PoolBase()
-    : concInit_( 0.0 )
+PoolBase::PoolBase() : concInit_( 0.0 )
 {;}
 
 PoolBase::~PoolBase()

kinetics/PoolBase.h

@@ -153,6 +153,7 @@ class PoolBase
 
     //////////////////////////////////////////////////////////////////
     static const Cinfo* initCinfo();
+
 private:
     double concInit_; /// Initial concentration.
     // We don't store the conc here as this is computed on the fly

ksolve/Stoich.cpp

@@ -193,16 +193,17 @@ const Cinfo* Stoich::initCinfo()
     // MsgDest Definitions
     //////////////////////////////////////////////////////////////
     static DestFinfo unzombify( "unzombify",
-                                "Restore all zombies to their native state",
-                                new OpFunc0< Stoich >( &Stoich::unZombifyModel )
-                              );
+            "Restore all zombies to their native state",
+            new OpFunc0< Stoich >( &Stoich::unZombifyModel )
+            );
+
     static DestFinfo scaleBufsAndRates( "scaleBufsAndRates",
-                                        "Args: voxel#, volRatio\n"
-                                        "Handles requests for runtime volume changes in the specified "
-                                        "voxel#, Used in adaptors changing spine vols.",
-                                        new OpFunc2< Stoich, unsigned int, double >(
-                                            &Stoich::scaleBufsAndRates )
-                                      );
+            "Args: voxel#, volRatio\n"
+            "Handles requests for runtime volume changes in the specified "
+            "voxel#, Used in adaptors changing spine vols.",
+            new OpFunc2< Stoich, unsigned int, double >(
+                &Stoich::scaleBufsAndRates )
+            );
 
     //////////////////////////////////////////////////////////////
     // SrcFinfo Definitions
@@ -274,6 +275,7 @@ Stoich::Stoich()
 Stoich::~Stoich()
 {
     unZombifyModel();
+
     // Note that we cannot do the unZombify here, because it is too
     // prone to problems with the ordering of the delete operations
     // relative to the zombies.

ksolve/Stoich.h

@@ -483,6 +483,7 @@ class Stoich
     //////////////////////////////////////////////////////////////////
     static const unsigned int PoolIsNotOnSolver;
     static const Cinfo* initCinfo();
+
 private:
     /**
      * True if the stoich matrix is set up to handle only one-way