Conversion from nose to pytest

.github/workflows/CI.yml

@@ -149,20 +149,19 @@ jobs:
           make
 
       # RMS installation and linking to Julia
-      # Allow these installs to 'fail' (as they do in RMG-Tests) with the command || True trick
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" || true
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' || true 
+          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
+
+      - name: Install Q2DTor
+        run: echo "" | make q2dtor
 
       # non-regression testing
-      - name: Unit tests
-        run: make test-unittests
-      - name: Functional tests
-        run: make test-functional
-      - name: Database tests
-        run: make test-database
+      - name: Run Unit, Functional, and Database Tests
+        # aggregate into one command so we only have to eat the collection time once
+        run: make test-all
 
       # Regression Testing - Test Execution
       - name: Regression Tests - Execution

.github/workflows/docs.yml

@@ -16,10 +16,6 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
-      - name: Patch the environment file
-        run: |
-          echo -e "\n  - libstdcxx-ng < 13\n" >> environment.yml
-          cat environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:

.gitignore

@@ -27,10 +27,8 @@ documentation/build/*
 # (These will be unique to each developer's setup)
 make.inc
 
-# Example output files
-examples/*
-!examples/*/input.py
-!examples/**/*.ipynb
+# output files
+rmgpy/output/*
 
 # NetBeans project files
 nbproject/*
@@ -88,11 +86,34 @@ RMG_Py.egg-info/*
 # RMG configuration file
 rmgpy/rmgrc
 
+# treegen log files
 scripts/treegen.log
-
 scripts/treegen_backup.log
 
 # regression testing files - ignore everything but input and regression input
 test/regression/*
 !test/regression/*/input.py
 !test/regression/*/regression_input.py
+
+# testing files
+test/arkane/data/two_parameter_arrhenius_fit/arkane.log
+test/arkane/data/two_parameter_arrhenius_fit/output.py
+test/arkane/data/two_parameter_arrhenius_fit/chem.inp
+test/rmgpy/test_data/temp_dir_for_testing/cantera/chem001.yaml
+rmgpy/test_data/copied_kinetic_lib/
+testing/qm/*
+test_log.txt
+
+# example directory - save the inputs but not the outputs
+# cantera input files
+examples/**/chem.inp
+# log files from the runs
+examples/**/arkane.log
+# results from the runs
+examples/**/species_dictionary.txt
+examples/**/output*py
+examples/**/network*py
+examples/**/dictionary.txt
+examples/**/reactions.py
+examples/**/RMG_libraries
+examples/**/species

Dockerfile

@@ -62,7 +62,7 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 # 1. Build RMG
 # 2. Install and link Julia dependencies for RMS
 RUN make && \
-    julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \
+    julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator' && \
     python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" 
 
 # RMG-Py should now be installed and ready - trigger precompilation and test run

Makefile

@@ -4,7 +4,7 @@
 #
 ################################################################################
 
-.PHONY : all minimal main solver check pycheck arkane clean install decython documentation mopac_travis test
+.PHONY : all minimal main solver check pycheck arkane clean install decython documentation test q2dtor
 
 all: pycheck main solver check
 
@@ -50,24 +50,25 @@ q2dtor:
  and HinderedRotor2D within Arkane please cite:  \n\nD. Ferro-Costas, M. N. D. S.Cordeiro, D. G. Truhlar, A.\
 		  Fernández-Ramos, Comput. Phys. Commun. 232, 190-205, 2018.\n"
 	@ read -p "Press ENTER to continue" dummy
-	@ git clone https://github.com/mjohnson541/Q2DTor.git external/Q2DTor --branch arkanepy3
-
+	@ mkdir -p external
+	@ git clone https://github.com/cathedralpkg/Q2DTor external/Q2DTor
+
 decython:
 	# de-cythonize all but the 'minimal'. Helpful for debugging in "pure python" mode.
 	find . -name *.so ! \( -name _statmech.so -o -name quantity.so -o -regex '.*rmgpy/solver/.*' \) -exec rm -f '{}' \;
 	find . -name *.pyc -exec rm -f '{}' \;
 
 test-all:
-	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
+	python-jl -m pytest
 
 test test-unittests:
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy arkane
+	python-jl -m pytest -m "not functional and not database"
 
 test-functional:
-	nosetests --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy arkane
+	python-jl -m pytest -m "functional"
 
 test-database:
-	nosetests --nocapture --nologcapture --verbose --detailed-errors testing/databaseTest.py
+	python-jl -m pytest -m "database"
 
 eg0: all
 	mkdir -p testing/eg0
@@ -85,25 +86,22 @@ eg1: all
 	coverage run rmg.py -p testing/eg1/input.py
 	coverage report
 	coverage html
+
 eg2: all
 	mkdir -p testing/eg2
 	rm -rf testing/eg2/*
 	cp examples/rmg/1,3-hexadiene/input.py testing/eg2/input.py
 	coverage erase
-	@ echo "Running eg2: 1,3-hexadiene example with coverage tracking AND profiling"
-	coverage run rmg.py -p testing/eg2/input.py
-	coverage report
-	coverage html
+	@ echo "Running eg2: 1,3-hexadiene example with profiling"
+	python rmg.py -p testing/eg2/input.py
 
 eg3: all
 	mkdir -p testing/eg3
 	rm -rf testing/eg3/*
 	cp examples/rmg/liquid_phase/input.py testing/eg3/input.py
 	coverage erase
-	@ echo "Running eg3: liquid_phase example with coverage tracking AND profiling"
-	coverage run rmg.py -p testing/eg3/input.py
-	coverage report
-	coverage html
+	@ echo "Running eg3: liquid_phase example with profiling"
+	python rmg.py -p testing/eg3/input.py
 
 eg5: all
 	mkdir -p testing/eg5

arkane/common.py

@@ -367,7 +367,7 @@ def check_conformer_energy(energies, path):
     is not 0.5 kcal/mol (or more) higher than any other energies in the scan. If so, print and 
     log a warning message.  
     """
-    energies = np.array(energies, np.float64)
+    energies = np.array(energies, float)
     e_diff = (energies[0] - np.min(energies)) * constants.E_h * constants.Na / 1000
     if e_diff >= 2:  # we choose 2 kJ/mol to be the critical energy
         logging.warning(f'The species corresponding to {os.path.basename(path)} is different in energy from the '
@@ -628,7 +628,7 @@ def get_center_of_mass(coords, numbers=None, symbols=None):
         raise IndexError('Either symbols or numbers must be given.')
     if numbers is not None:
         symbols = [symbol_by_number[number] for number in numbers]
-    center, total_mass = np.zeros(3, np.float64), 0
+    center, total_mass = np.zeros(3, float), 0
     for coord, symbol in zip(coords, symbols):
         mass = get_element_mass(symbol)[0]
         center += mass * coord
@@ -661,7 +661,7 @@ def get_moment_of_inertia_tensor(coords, numbers=None, symbols=None):
     if len(coords) != len(symbols):
         raise InputError(f'The number of atoms ({len(symbols)}) is not equal to the number of '
                          f'atomic coordinates ({len(list(coords))})')
-    tensor = np.zeros((3, 3), np.float64)
+    tensor = np.zeros((3, 3), float)
     center_of_mass = get_center_of_mass(coords=coords, numbers=numbers, symbols=symbols)
     for symbol, coord in zip(symbols, coords):
         mass = get_element_mass(symbol)[0]