Merge branch 'develop' of https://github.com/veg/hyphy into develop

.coveralls.condarc

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - defaults
+always_yes: True
+auto_update_conda: True

.coveralls.env.yml

@@ -0,0 +1,4 @@
+name: hyphy-test-env
+dependencies:
+  - pip
+  - openmpi

.github/workflows/coverage.yml

@@ -0,0 +1,42 @@
+name: Test Coverage
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+jobs:
+  coverage:
+    name: Coveralls Report
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run:
+          python -m pip install --upgrade pip;
+          python -m pip install --upgrade wheel;
+          python -m pip install --upgrade cpp-coveralls;
+      - name: Get HyPhy code
+        uses: actions/checkout@v2
+      - name: Install and activate miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: 'hyphy-test-env'
+          environment-file: '.coveralls.env.yml'
+          condarc-file: '.coveralls.condarc'
+      - name: Build HyPhy
+        run:
+          cmake .;
+          make -j HYPHYDEBUG;
+          ln -s HYPHYDEBUG hyphy;
+          ln -s HYPHYDEBUG HYPHYMP;
+      - name: Run unit tests
+        run:
+          PATH=.:$PATH ./run_unit_tests.sh || true;
+      - name: Generate coverage information
+        run:
+          coveralls --gcov-options '\-lp';
+        env:
+          COVERALLS_REPO_TOKEN: ${{ secrets.coveralls_token }}

.travis.yml

@@ -149,4 +149,4 @@ jobs:
       install:
         - if [ "$CXX" = "g++" ]; then export CXX="g++-8" CC="gcc-8"; fi
         - cmake . 
-        - make
+        - make

src/core/matrix.cpp

@@ -2263,7 +2263,7 @@ bool    _Matrix::IncreaseStorage    (void) {
         } else {
             theData = (hyFloat*) MemReallocate(theData, lDim*sizeof(void*));
             for (long i = lDim-allocationBlock; i < lDim; i++) {
-                theData [i] = ZEROPOINTER;
+                theData [i] = ZEROOBJECT;
             }
         }
     } else {