Merge pull request #232 from blakecaldwell/hnn_core_v2

[MRG] hnn-core integration

.travis.yml

@@ -4,68 +4,28 @@ matrix:
   include:
       # OSX
       - os: osx
-        name: "MacOS sierra"
-        osx_image: xcode9.2
-        env:
-          - PYTHON_VERSION=3.7
-          - NEURON_VERSION=7.7
-
-      - os: osx
-        name: "MacOS el capitan"
-        osx_image: xcode8
-        env:
-          - PYTHON_VERSION=3.7
-          - NEURON_VERSION=7.7
-
-      - os: osx
-        name: "MacOS mojave"
-        osx_image: xcode11.3
-        env:
-          - PYTHON_VERSION=3.7
-          - NEURON_VERSION=7.7
+        name: "MacOS Catalina"
+        osx_image: xcode12
 
-      - os: osx
-        name: "MacOS high sierra"
-        osx_image: xcode10.1
+      # WSL
+      - os: windows
+        name: "WSL"
         env:
-          - PYTHON_VERSION=3.7
-          - NEURON_VERSION=7.7
+          - WSL_INSTALL=1
+          - USE_CONDA=0
 
       # Windows
       - os: windows
         name: "Windows"
         env:
-          - PYTHON_VERSION=3.7
-          - NEURON_VERSION=7.7
+          - WSL_INSTALL=0
 
       # Linux
-      - os: linux
-        dist: xenial
-        name: "Ubuntu xenial"
-        env:
-          - NEURON_VERSION=7.7
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - xvfb
-
       - os: linux
         dist: bionic
-        name: "Ubuntu bionic"
+        name: "Ubuntu Bionic"
         env:
-          - NEURON_VERSION=7.7
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - xvfb
-
-      - os: linux
-        dist: disco
-        name: "Ubuntu disco"
-        env:
-          - NEURON_VERSION=7.7
+          - USE_CONDA=1
         apt:
           sources:
             - ubuntu-toolchain-r-test
@@ -75,112 +35,74 @@ matrix:
       - os: linux
         dist: focal
         name: "Ubuntu focal"
-        env:
-          - NEURON_VERSION=7.7
         apt:
           sources:
             - ubuntu-toolchain-r-test
           packages:
             - xvfb
 
 before_install:
-  - set -e  # error on any command failure
-  - | # function exports
-    export TRAVIS_TESTING=1
-
-    if [[ "${TRAVIS_OS_NAME}" == "windows" ]]; then
-      # for start_vcxsrv_print and stop_vcxsrv
-      source "scripts/docker_functions.sh"
-      set_globals
-    fi
-
-    # source utility functions
-    export LOGFILE="hnn_travis.log"
-    source scripts/utils.sh
-    export -f cleanup
-
   - |
-    if [ "${TRAVIS_OS_NAME}" == "osx" ]; then  # install osx prerequisites
-      echo "Installing macOS prerequisites"
-
-      scripts/setup-travis-mac.sh
-      export PATH=${HOME}/Miniconda3/bin:$PATH
-      export PATH=$PATH:/Applications/NEURON-${NEURON_VERSION}/nrn/x86_64/bin
-      export PYTHONPATH=/Applications/NEURON-${NEURON_VERSION}/nrn/lib/python:$PYTHONPATH
-      export PYTHON=python3
-
-      source activate hnn && echo "activated conda HNN environment"
-    fi
-  - | # windows
-    if [ "${TRAVIS_OS_NAME}" == "windows" ]; then
-      echo "Installing windows prerequisites"
-
-      scripts/setup-travis-windows.sh
+    # Step 0: set common environment variables
 
-      # add miniconda python to the path
-      export PATH=$PATH:$HOME/Miniconda3/Scripts
-      export PATH=$HOME/Miniconda3/envs/hnn/:$PATH
-      export PATH=$HOME/Miniconda3/envs/hnn/Scripts:$PATH
-      export PATH=$HOME/Miniconda3/envs/hnn/Library/bin:$PATH
-
-      # for using X server
-      export PATH="$PATH:/c/Program\ Files/VcXsrv"
-
-      # for MESA dll's
-      export PATH=$PATH:/c/tools/msys64/mingw64/bin
+    set -e
+    export TRAVIS_TESTING=1
+    export DISPLAY=:0
+    export LOGFILE="hnn_travis.log"
+    export PATH="$PATH:$HOME/.local/bin"
 
+    if [[ "${WSL_INSTALL}" -eq 1 ]]; then
       # for sharing with WSL environment
-      export WSLENV=TRAVIS_TESTING/u
-
-      # set other variables for neuron and HNN
-      export PATH=$PATH:/c/nrn/bin
-      export DISPLAY="localhost:0"
-      export NEURONHOME=/c/nrn
-      export PYTHON=python
+      export OMPI_MCA_btl_vader_single_copy_mechanism=none
+      export WSLENV=TRAVIS_TESTING/u:DISPLAY/u:OMPI_MCA_btl_vader_single_copy_mechanism/u:WSL_INSTALL/u
     fi
-  - | # Linux
-    if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
-      echo "Installing Linux prerequisites"
-
-      export DISPLAY=:0
-      export PATH=/usr/bin:/usr/local/bin:$PATH
-
-      echo "Starting fake Xserver"
-      Xvfb $DISPLAY -listen tcp -screen 0 1024x768x24 > /dev/null &
-
-      echo "Starting Ubuntu install script"
-      installer/ubuntu/hnn-ubuntu.sh
+  - |
+    # Step 1: install prerequisites
 
-      NLOPT_LIB=$(ls -d $HOME/.local/lib/python*/site-packages)
-      echo $NLOPT_LIB
-      export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NLOPT_LIB
-      export PYTHON=python3
+    if [[ "${WSL_INSTALL}" -eq 1 ]]; then
+      powershell.exe -ExecutionPolicy Bypass -File ./scripts/setup-travis-wsl.ps1
+      # scripts/setup-travis-wsl.sh
+    else
+      echo "Installing ${TRAVIS_OS_NAME} prerequisites"
+      scripts/setup-travis-${TRAVIS_OS_NAME}.sh
 
-      # test X server
-      xset -display $DISPLAY -q > /dev/null;
+      source "$HOME/Miniconda3/etc/profile.d/conda.sh"
+      conda activate hnn
     fi
 
 install:
-  - | # for mac build HNN .mod files
-    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      make -j2
+  - |
+    # Step 2: install hnn Python module and modules for testing
+
+    if [[ "${WSL_INSTALL}" -ne 1 ]]; then
+      pip install flake8 pytest pytest-cov coverage coveralls mne pytest-qt
+      python setup.py install
+    else
+      wsl -- pip install flake8 pytest pytest-cov coverage coveralls mne \
+                 pytest-qt
+      wsl -- python3 setup.py install --user
     fi
-  - | # testing packages
-    pip install flake8 pytest pytest-cov coverage coveralls mne
 
 script:
-  - | # Check that the GUI starts on host OS
-    echo "Testing GUI on host OS..."
-    $PYTHON hnn.py
-  - | # Run py.test that includes running a simulation and verifying results
-    echo "Running Python tests on host OS..."
-    py.test --cov=. tests/
-  - | # Test WSL-based version on windows (needs VcXsrv)
-    if [[ "${TRAVIS_OS_NAME}" == "windows" ]]; then
-      find_command_suggested_path "vcxsrv" "/c/Program Files/VcXsrv" && \
-        start_vcxsrv_print || script_fail
-      wsl -- bash -e //home/hnn_user/hnn/scripts/run-travis-wsl.sh
-      stop_vcxsrv || script_fail
+  - |
+    # Step 3: run CI tests with py.test
+
+    if [[ "${WSL_INSTALL}" -eq 1 ]]; then
+      wsl -- //home/hnn_user/hnn/scripts/run-pytest.sh
+    else
+      if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
+        # NEURON will fail to import if DISPLAY is set
+        unset DISPLAY
+      elif [[ "${TRAVIS_OS_NAME}" == "windows" ]]; then
+        # Python will search path to find neuron dll's
+        export PATH=$PATH:/c/nrn/bin
+
+        # run tests first as a user with a space (TODO)
+        # runas //user:"test user" //wait "bash" "scripts/run-pytest.sh" < "$HOME/test_user_creds"
+        # echo "Finished test with 'test user'"
+      fi
+
+      scripts/run-pytest.sh
     fi
 
 after_success: