pytest

.github/workflows/CI.yml

@@ -65,11 +65,16 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - name: Checkout RMG-Py
+      - name: Checkout RMG-Py - Resuable Workflow
+        if: github.repository == 'ReactionMechanismGenerator/RMG-database'
         uses: actions/checkout@v3
         with:
           repository: ReactionMechanismGenerator/RMG-Py
 
+      - name: Clone RMG-Py - RMG-Py
+        if: github.repository != 'ReactionMechanismGenerator/RMG-database'
+        uses: actions/checkout@v3
+
       # configures the mamba environment manager and builds the environment
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
@@ -185,12 +190,9 @@ jobs:
           julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' || true 
 
       # 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/*
@@ -76,9 +74,6 @@ bin/symmetry
 ipython/*
 !ipython/*.ipynb
 
-# Q2DTor
-external/Q2DTor
-
 # egg files (pip install -e)
 RMG_Py.egg-info/*
 
@@ -96,3 +91,24 @@ scripts/treegen_backup.log
 test/regression/*
 !test/regression/*/input.py
 !test/regression/*/regression_input.py
+
+# testing files
+test/arkane/data/two_parameter_arrhenius_fit/arkane.log
+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

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
 
 all: pycheck main solver check
 
@@ -40,34 +40,23 @@ clean-solver:
 install:
 	@ python utilities.py check-pydas
 	python setup.py install
-
-q2dtor:
-	@ echo -e "\nInstalling Q2DTor...\n"
-	@ echo -e "Q2DTor is a software for calculating the partition functions and themodynamic properties\
-	of molecular systems with two or more torsional modes developed by David Ferro Costas (david.ferro@usc.es)\
-	 and Antonio Fernandez Ramos (qf.ramos@usc.es) at the Universidade de Santiago de Compostela. Arkane can\
-	  integrate Q2DTor to compute the quantum mechanical partition function of 2D rotors.  \n\nFor use of 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
 
 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 +74,22 @@ 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
@@ -140,3 +126,15 @@ eg4: all
 	cp examples/thermoEstimator/input.py testing/eg4/input.py
 	@ echo "Running thermo data estimator example. This tests QM."
 	python scripts/thermoEstimator.py testing/eg4/input.py
+
+q2dtor:
+	@ echo -e "\nInstalling Q2DTor...\n"
+	@ echo -e "Q2DTor is a software for calculating the partition functions and themodynamic properties\
+	of molecular systems with two or more torsional modes developed by David Ferro Costas (david.ferro@usc.es)\
+	 and Antonio Fernandez Ramos (qf.ramos@usc.es) at the Universidade de Santiago de Compostela. Arkane can\
+	  integrate Q2DTor to compute the quantum mechanical partition function of 2D rotors.  \n\nFor use of 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
+	@ mkdir -p external
+	@ git clone https://github.com/cathedralpkg/Q2DTor external/Q2DTor