Merge pull request #154 from MolSSI-MDI/conda

Add conda test

.github/workflows/ci.yml

@@ -322,6 +322,7 @@ jobs:
           ls
 
       # Enable tmate debugging of manually-triggered workflows if the input option was provided
+      # To execute: Click the GitHub "Actions" tab, then "CI", then "Run Workflow", then set debugging to "true"
       - name: Setup tmate session
         uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
@@ -336,3 +337,82 @@ jobs:
         run: |
           codecov.exe -f coverage.xml -t "99465b5f-26b4-4487-8355-fbcac5249a05"
 
+
+
+  # Build for posix systems
+  conda:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ ubuntu-latest ]
+        mpilib: [null]
+
+    # The type of runner that the job will run on
+    runs-on: ${{ matrix.platform }}
+
+    env:
+      OMPI_MCA_btl_base_warn_component_unused: "0"
+      CODECOV_TOKEN: "99465b5f-26b4-4487-8355-fbcac5249a05"
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      # Install Miniconda
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-activate-base: true
+          activate-environment: ""
+
+      - name: Create source file with all required environment variables
+        shell: bash -el {0}
+        run: |
+          # Create a source file that will contain environment variables used in additional steps
+          # Environment variabls are not normally preserved between steps, so the source file is necessary
+          touch env.source
+
+          # Set MDI_TESTS, which defines which tests will be performed for this job
+          [ "${{ matrix.mpilib }}" == "" ] && echo 'export MDI_TESTS="not mpi"' >> env.source
+
+          cat env.source
+
+      - name: Install dependencies
+        shell: bash -el {0}
+        run: |
+          source env.source
+          sudo apt-get clean
+          sudo apt-get update
+          sudo apt-get install gfortran
+          conda install -y -c conda-forge numpy
+          conda install -y -c conda-forge pytest
+          conda install -y -c conda-forge pymdi
+
+      - name: Install local build
+        shell: bash -el {0}
+        run: |
+          source env.source
+          mkdir build
+          cd build
+          cmake -Dtest_codes=ON -DCMAKE_INSTALL_PREFIX=./install ..
+          make VERBOSE=1
+          #make install
+          rm MDI_Library/__init__.py
+          rm MDI_Library/mdi.py
+          ls
+          ls MDI_Library
+
+      # Enable tmate debugging of manually-triggered workflows if the input option was provided
+      # To execute: Click the GitHub "Actions" tab, then "CI", then "Run Workflow", then set debugging to "true"
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+
+      - name: Run test scripts
+        shell: bash -el {0}
+        run: |
+          source env.source
+          conda list
+          cd tests
+          pytest -vv -k "${MDI_TESTS}"

tests/MDI_Test_Codes/driver_ipicomp_py/driver_ipicomp_py.py

@@ -3,6 +3,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/driver_plug_py/driver_plug_py.py

@@ -3,6 +3,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/driver_py/driver_py.py

@@ -3,6 +3,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/engine_py/engine_py.py

@@ -3,6 +3,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/lib_py/lib_py.py

@@ -3,6 +3,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_double.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_fake_method.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_fake_opt.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_fake_role.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_no_hostname.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_no_method.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_no_name.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_no_port_d.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_no_port_e.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_no_role.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_hostname.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_language.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_method.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_name.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_out.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_port.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_init_noarg_role.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/MDI_Test_Codes/misc_py/ut_tmethod.py

@@ -4,6 +4,7 @@
 
 try: # Check for local build
     import MDI_Library as mdi
+    testvar = mdi.MDI_COMMAND_LENGTH
 except: # Check for installed package
     import mdi
 

tests/test_element.py

@@ -18,6 +18,10 @@ def import_mdi():
     try: # Check for local build
         sys.path.append('../build')
         import MDI_Library as mdi
+        try:
+            testvar = mdi.MDI_COMMAND_LENGTH
+        except AttributeError:
+            import mdi
     except ImportError: # Check for installed package
         import mdi
     return mdi
@@ -41,4 +45,4 @@ def test_atomic_number_unrecognized():
     mdi = import_mdi()
 
     with pytest.raises(Exception):
-        mdi.MDI_String_to_atomic_number("YY")
+        mdi.MDI_String_to_atomic_number("YY")

tests/test_uninit.py

@@ -21,6 +21,10 @@ def import_mdi():
     try: # Check for local build
         sys.path.append('../build')
         import MDI_Library as mdi
+        try:
+            testvar = mdi.MDI_COMMAND_LENGTH
+        except AttributeError:
+            import mdi
     except ImportError: # Check for installed package
         import mdi
     return mdi

tests/test_unit.py

@@ -21,6 +21,10 @@ def import_mdi():
     try: # Check for local build
         sys.path.append('../build')
         import MDI_Library as mdi
+        try:
+            testvar = mdi.MDI_COMMAND_LENGTH
+        except AttributeError:
+            import mdi
     except ImportError: # Check for installed package
         import mdi
     return mdi

tests/valgrind.supp

@@ -327,3 +327,41 @@
    fun:start_thread
    fun:clone
 }
+
+
+{
+   Leak from test import
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:malloc
+   fun:_PyMem_RawMalloc
+   fun:PyObject_Malloc
+   fun:PyFloat_FromDouble
+   fun:fill_time
+   fun:_pystat_fromstructstat
+   fun:posix_do_stat
+   fun:os_stat_impl
+   fun:os_stat
+   fun:cfunction_vectorcall_FASTCALL_KEYWORDS
+   fun:_PyObject_VectorcallTstate
+   fun:PyObject_Vectorcall
+}
+
+
+{
+   Leak from test import 2
+   Memcheck:Leak
+   match-leak-kinds: definite
+   fun:malloc
+   fun:_PyMem_RawMalloc
+   fun:PyObject_Malloc
+   fun:PyFloat_FromDouble
+   fun:float_abs
+   fun:PyNumber_Absolute
+   fun:builtin_abs
+   fun:cfunction_vectorcall_O
+   fun:_PyObject_VectorcallTstate
+   fun:PyObject_Vectorcall
+   fun:call_function
+   fun:_PyEval_EvalFrameDefault
+}