Fix conflicts

Author: sarakonradi

.github/ISSUE_TEMPLATE/documentation_improvement.md

@@ -2,7 +2,7 @@
 name: Documentation improvement
 about: Request a documentation improvement
 title: ''
-labels: 'C: Documentation'
+labels: ''
 assignees: ''
 
 ---

.gitignore

@@ -25,13 +25,10 @@ install/
 /libtool
 /nest/nest
 /nest/static_modules.h
-/pynest/do_tests.py
 /pynest/setup.py
 /reports/
 /sli/sli
 /testsuite/do_tests.sh
-/topology/setup.py
-/topology/doc/Topology_UserManual.out
 /doc/doxygen/
 /doc/_build/
 /doc/xml/
@@ -60,8 +57,10 @@ CPackSourceConfig.cmake
 doc/set_rcsinfo.cmake
 doc/fulldoc.conf
 doc/normaldoc.conf
-doc/userdocs/
+doc/models/
 doc/pynestkernel_mock.py
+doc/from_cpp/
+doc/microcircuit/
 lib/sli/rcsinfo.sli
 extras/nest_vars.sh
 

.travis.yml

@@ -18,56 +18,56 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
-
 # This is the Travis CI top-level script to setup and run the NEST
 # build and test environment.
 
+
 language: python
 
-# Using the Sudo-enabled Ubuntu Bionic (18.04 LTS).
 sudo: required
 dist: bionic
 
 env:
   global:
     - MAKEFLAGS="-j 2"
 stages:
-   - Staticcheck
-   - MPI-Threading-GSL-Python
-   - Python-Full-build-Clang7-OsX
-   - ARM64
-
-# list of build stages to run. Stages with the same name get run in parallel.
+   - Static-Code-Analysis
+   - Linux-GCC
+   - Linux-Clang
+   - macOS
 
 jobs:
+  # list of build stages to run. Stages with the same name get run in parallel.
   include:
-    - stage: Staticcheck
-      python: 3.6.10
-      env: xTHREADING=0 xMPI=0 xSIONLIB=0 xGSL=0 xLIBNEUROSIM=0 xLTDL=0 xREADLINE=0 xLIBBOOST=0 xPYTHON=0 xMUSIC=0 xSTATIC_ANALYSIS=1 xRUN_BUILD_AND_TESTSUITE=0 CACHE_NAME=JOB   # only static code analysis
-    - stage: MPI-Threading-GSL-Python
-      python: 3.6.10
-      env: xTHREADING=1 xMPI=1 xSIONLIB=0 xGSL=1 xLIBNEUROSIM=0 xLTDL=1 xREADLINE=1 xLIBBOOST=1 xPYTHON=1 xMUSIC=0 xSTATIC_ANALYSIS=0 xRUN_BUILD_AND_TESTSUITE=1 CACHE_NAME=JOB
-    - stage: MPI-Threading-GSL-Python
-      python: 3.6.10
-      env: xTHREADING=0 xMPI=1 xSIONLIB=0 xGSL=0 xLIBNEUROSIM=0 xLTDL=1 xREADLINE=1 xLIBBOOST=1 xPYTHON=0 xMUSIC=0 xSTATIC_ANALYSIS=0 xRUN_BUILD_AND_TESTSUITE=1 CACHE_NAME=JOB   # only MPI
-    - stage: MPI-Threading-GSL-Python
-      python: 3.6.10
-      env: xTHREADING=1 xMPI=0 xSIONLIB=0 xGSL=0 xLIBNEUROSIM=0 xLTDL=1 xREADLINE=1 xLIBBOOST=1 xPYTHON=0 xMUSIC=0 xSTATIC_ANALYSIS=0 xRUN_BUILD_AND_TESTSUITE=1 CACHE_NAME=JOB   # only threading
-    - stage: MPI-Threading-GSL-Python
-      python: 3.6.10
-      env: xTHREADING=0 xMPI=0 xSIONLIB=0 xGSL=0 xLIBNEUROSIM=0 xLTDL=0 xREADLINE=0 xLIBBOOST=0 xPYTHON=1 xMUSIC=0 xSTATIC_ANALYSIS=0 xRUN_BUILD_AND_TESTSUITE=1 CACHE_NAME=JOB   # Only Python
-    - stage: Python-Full-build-Clang7-OsX
-      python: 3.6.10
-      env: xTHREADING=1 xMPI=1 xSIONLIB=1 xGSL=1 xLIBNEUROSIM=1 xLTDL=1 xREADLINE=1 xLIBBOOST=1 xPYTHON=1 xMUSIC=1 xSTATIC_ANALYSIS=0 xRUN_BUILD_AND_TESTSUITE=1 CACHE_NAME=JOB   # full
-    - stage: Python-Full-build-Clang7-OsX
+    - stage: Static-Code-Analysis
+      python: 3.8.2
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=STATIC_CODE_ANALYSIS
+    - stage: Linux-GCC
+      python: 3.8.2
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=MINIMAL
+    - stage: Linux-GCC
+      python: 3.8.2
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=MPI_ONLY
+    - stage: Linux-GCC
+      python: 3.8.2
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=OPENMP_ONLY
+    - stage: Linux-GCC
+      python: 3.8.2
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=FULL
+    - stage: Linux-Clang
       language: cpp
-      env: MATRIX_EVAL="CC=clang-7 && CXX=clang++-7" xRUN_BUILD_AND_TESTSUITE=1
-    - stage: Python-Full-build-Clang7-OsX
+      python: 3.6.10
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=MINIMAL xNEST_BUILD_COMPILER=CLANG xNEST_PYTHON_VERSION=3.6.10
+    - stage: macOS
       os: osx
-      osx_image: xcode10.3 # Python 3.7.5 running on macOS 10.14.4
+      osx_image: xcode12   # Python 3.8.3 running on macOS 10.15.5
       language: shell      # language 'python' results in errors on macOS
-      env: xTHREADING=1 xMPI=0 xGSL=1 xLIBNEUROSIM=0 xLTDL=1 xREADLINE=1 xPYTHON=1 xMUSIC=0 xSTATIC_ANALYSIS=0 xRUN_BUILD_AND_TESTSUITE=1 CACHE_NAME=JOB   # Without MUSIC, MPI and Libneurosim
-#https://docs.travis-ci.com/user/installing-dependencies#Installing-Packages-with-the-APT-Addon
+      env: CACHE_NAME=JOB xNEST_BUILD_TYPE=FULL_NO_EXTERNAL_FEATURES
+      cache:
+        directories:
+          - $HOME/.cache
+          - $HOME/.pyenv/versions
+          - /usr/local/Homebrew
 addons:
    apt:
     sources:
@@ -91,7 +91,6 @@ addons:
      - pkg-config
      - openmpi-bin
      - libopenmpi-dev
-     - python3-nose
      - libpcre3
      - libpcre3-dev
      - llvm-9-dev
@@ -103,7 +102,6 @@ addons:
      - libboost-python-dev
      - libboost-program-options-dev
      - libboost-test-dev
-     - python3-mpi4py
 cache:
    directory:
      - $HOME/.cache
@@ -130,23 +128,20 @@ before_install:
        /usr/bin/c++ --version
      fi
    - |
-     if [ "$xRUN_BUILD_AND_TESTSUITE" = "1" ]; then
+     if [ "$xNEST_BUILD_TYPE" != "STATIC_CODE_ANALYSIS" ]; then
          echo "+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +"
          echo "+         P R E P A R E   N E S T   B U I L D   E N V I R O N M E N T         +"
          echo "+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +"
-         echo ${MATRIX_EVAL}
-         eval "${MATRIX_EVAL}"
          cp extras/install_csa-libneurosim.sh $HOME
          cp extras/install_music.sh $HOME
          cp extras/install_sionlib.sh $HOME
          cp extras/install_libboost.sh $HOME
          cd $HOME/build
          echo $PATH
-         # Upgrade pip and setuptools
-         if [ MATRIX_EVAL="CC=clang-7 && CXX=clang++-7" ]; then
-           pyenv install --list
-           pyenv global 3.6.7
+         if [ "$xNEST_BUILD_COMPILER" = "CLANG" ]; then
+             pyenv global $xNEST_PYTHON_VERSION
          fi
+
          if [ "$TRAVIS_OS_NAME" = "osx" ]; then
            brew --version
            brew update
@@ -158,32 +153,40 @@ before_install:
            brew unlink gcc
            brew install gcc@8
            brew link gcc@8
-           brew list
-           brew leaves
-           brew cask list
+           find /usr/local/Cellar/ -name Python\.h
+           find /usr/local/Cellar/ -name \*python\*dylib
          fi
-         if [ "$TRAVIS_OS_NAME" = "linux" ]; then
+
+         if [ "$TRAVIS_OS_NAME" != "osx" ]; then
+           # Upgrade pip and setuptools
            pip install --upgrade pip setuptools
+           pip install nose
+         else
+           # updating pip breaks on osx, must install man-page free nose
+           wget https://arken.nmbu.no/~plesser/nose-1.3.7noman-py3-none-any.whl
+           pip install nose-1.3.7noman-py3-none-any.whl
          fi
-
          # Installing additional packages using pip as they only have
          # outdated versions in the Travis package whitelist.
          # terminaltables is required by parse_travis_log.py to create
          # the build summary.
-         pip install cython scipy matplotlib terminaltables
+         pip install cython scipy matplotlib terminaltables junitparser mpi4py
          pip install numpy==1.16.5
+         pip list
      fi
 
 install:
    - |
-     if [ "$xRUN_BUILD_AND_TESTSUITE" = "1" ]; then
+     if [ "$xNEST_BUILD_TYPE" != "STATIC_CODE_ANALYSIS" ]; then
          which cython
          cython --version
          which python
          python --version
          which pip
          pip list
-         if [ "$TRAVIS_OS_NAME" = "linux" ]; then which nosetests; nosetests --version; nosetests --plugins; fi
+         which nosetests
+         nosetests --version
+         nosetests --plugins
          which cmake
          cmake --version
          echo ${CC}
@@ -199,13 +202,13 @@ script:
    - set -o pipefail
    - ./extras/travis_build.sh 2>&1 | tee travis_build.sh.log
    - |
-     if [ "$xRUN_BUILD_AND_TESTSUITE" = "1" ]; then
+     if [ "$xNEST_BUILD_TYPE" != "STATIC_CODE_ANALYSIS" ]; then
         python extras/parse_travis_log.py travis_build.sh.log ;
      fi
 
 before_deploy:
    - |
-     if [ "$xRUN_BUILD_AND_TESTSUITE" = "1" ]; then
+     if [ "$xNEST_BUILD_TYPE" != "STATIC_CODE_ANALYSIS" ]; then
          cd $TRAVIS_BUILD_DIR/build
          tar -zcvf reports.tar.gz ./reports
          tar -zcvf docs.tar.gz $TRAVIS_BUILD_DIR/result/share/doc/nest/*.*
@@ -215,19 +218,19 @@ before_deploy:
      fi
 
 # S3 Deployment (Uploading the Travis CI build artefacts to Amazon S3).
-deploy:
-  provider: s3
-  access_key_id:
-    secure: $ARTIFACTS_KEY
-  secret_access_key:
-    secure: $ARTIFACTS_SECRET
-  bucket: "nest-travis-artefacts"
-  region: eu-central-1
-  skip_cleanup: true
-  on:
-    repo: nest/nest-simulator
-    branch: master
-    condition: xRUN_BUILD_AND_TESTSUITE = 1
-  local-dir: "$TRAVIS_BUILD_DIR/build/artefacts_upload"
-  upload-dir: "$TRAVIS_REPO_SLUG/$TRAVIS_BUILD_NUMBER/$TRAVIS_JOB_NUMBER"
-  acl: bucket_owner_full_control
+#deploy:
+#  provider: s3
+#  access_key_id:
+#    secure: $ARTIFACTS_KEY
+#  secret_access_key:
+#    secure: $ARTIFACTS_SECRET
+#  bucket: "nest-travis-artefacts"
+#  region: eu-central-1
+#  skip_cleanup: true
+#  on:
+#    repo: nest/nest-simulator
+#    branch: master
+#    condition: $xNEST_BUILD_TYPE != STATIC_CODE_ANALYSIS
+#  local-dir: "$TRAVIS_BUILD_DIR/build/artefacts_upload"
+#  upload-dir: "$TRAVIS_REPO_SLUG/$TRAVIS_BUILD_NUMBER/$TRAVIS_JOB_NUMBER"
+#  acl: bucket_owner_full_control

CMakeLists.txt

@@ -75,9 +75,6 @@ set( with-version-suffix "" CACHE STRING "Set a user defined version suffix. [de
 set( enable-bluegene OFF CACHE STRING "Configure for BlueGene." )
 option( k-computer "Enable K computer." OFF )
 
-set( disable-timing OFF CACHE BOOL "Disable measurements via Stopwatches. [default OFF]" )
-set( disable-counts ON CACHE BOOL "Disable measurements of call counts. [default ON]" )
-
 set( target-bits-split "standard" CACHE STRING "Split of the 64-bit target neuron identifier type. 'standard' is recommended for most users. If running on more than 262144 MPI processes or more than 512 threads, change to 'hpc'. [default standard]" )
 
 ################################################################################
@@ -191,26 +188,26 @@ message("-- NEST version: ${NEST_VERSION_STRING}")
 ##################         Enable Testing Targets             ##################
 ################################################################################
 enable_testing()
-set( TEST_LOGFILE ${PROJECT_BINARY_DIR}/reports/installcheck.log )
-file( MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/reports/ )
+set( TEST_OPTS "" )
 
 if ( HAVE_PYTHON )
-  add_custom_target( installcheck
-    COMMAND ${CMAKE_COMMAND} -E env
-      PYTHON="${PYTHON}"
-      ${CMAKE_INSTALL_FULL_DATADIR}/extras/do_tests.sh --test-pynest
-    WORKING_DIRECTORY "${PROJECT_BINARY_DIR}"
-    COMMENT "Execute NEST's testsuite...."
-  )
-else ()
-  add_custom_target( installcheck
-    COMMAND ${CMAKE_COMMAND} -E env
-      ${CMAKE_INSTALL_FULL_DATADIR}/extras/do_tests.sh
-    WORKING_DIRECTORY "${PROJECT_BINARY_DIR}"
-    COMMENT "Execute NEST's testsuite...."
-  )
+  set( TEST_OPTS "${TEST_OPTS};--with-python=${PYTHON}" )
+endif ()
+
+if ( HAVE_MUSIC )
+  set( TEST_OPTS "${TEST_OPTS};--with-music=${MUSIC_EXECUTABLE}" )
 endif ()
 
+add_custom_target( installcheck
+  COMMAND ${CMAKE_COMMAND} -E env
+    ${CMAKE_INSTALL_FULL_DATADIR}/extras/do_tests.sh
+	--prefix=${CMAKE_INSTALL_PREFIX}
+	--report-dir="${PROJECT_BINARY_DIR}/reports"
+	${TEST_OPTS}
+  WORKING_DIRECTORY "${PROJECT_BINARY_DIR}"
+  COMMENT "Executing NEST's testsuite..."
+)
+
 # N.B. to ensure "make install" is always run before "make installcheck", we
 # would ideally like to add:
 #   add_dependencies( installcheck install )
@@ -235,9 +232,7 @@ add_subdirectory( models )
 add_subdirectory( sli )
 add_subdirectory( nest )
 add_subdirectory( nestkernel )
-add_subdirectory( precise )
 add_subdirectory( testsuite )
-add_subdirectory( topology )
 if ( HAVE_PYTHON )
   add_subdirectory( pynest )
 endif ()
@@ -286,7 +281,6 @@ set( ALL_LIBS
   "-lrandom"
   "-lsli"
   "-lnestkernel"
-  "-ltopology"
   "${OpenMP_CXX_FLAGS}"
   "${LTDL_LIBRARIES}"
   "${READLINE_LIBRARIES}"
@@ -339,16 +333,6 @@ configure_file(
     "${PROJECT_BINARY_DIR}/pynest/setup.py" @ONLY
 )
 
-configure_file(
-    "${PROJECT_SOURCE_DIR}/pynest/do_tests.py.in"
-    "${PROJECT_BINARY_DIR}/pynest/do_tests.py" @ONLY
-)
-
-configure_file(
-    "${PROJECT_SOURCE_DIR}/testsuite/do_tests.sh.in"
-    "${PROJECT_BINARY_DIR}/testsuite/do_tests.sh" @ONLY
-)
-
 configure_file(
     "${PROJECT_SOURCE_DIR}/extras/nest-config.in"
     "${PROJECT_BINARY_DIR}/extras/nest-config" @ONLY