RMG-Py v2.1.8 release

Author: mliu49

Makefile

@@ -6,13 +6,10 @@
 
 DASPK=$(shell python -c 'import pydas.daspk; print pydas.daspk.__file__')
 DASSL=$(shell python -c 'import pydas.dassl; print pydas.dassl.__file__')
-RDKIT_VERSION=$(shell python -c 'import rdkit; print rdkit.__version__')
 
-.PHONY : all minimal main solver cantherm clean decython documentation QM mopac_travis
+.PHONY : all minimal main solver check cantherm clean decython documentation mopac_travis
 
-all: main solver QM
-
-noQM: main solver
+all: main solver check
 
 minimal:
 	python setup.py build_ext minimal --build-lib . --build-temp build --pyrex-c-in-temp
@@ -39,86 +36,75 @@ endif
 cantherm:
 	python setup.py build_ext cantherm --build-lib . --build-temp build --pyrex-c-in-temp
 
-QM:
-	@ echo "Checking if you have symmetry..."
-	@ echo "symmetry -h"
-	@ echo "Checking you have rdkit..."
-	@ python -c 'import rdkit; print rdkit.__file__'
-	@ echo "Checking rdkit version..."
-ifneq ($(RDKIT_VERSION),)
-	@ echo "Found rdkit version $(RDKIT_VERSION)"
-else
-	$(error RDKit version out of date, please install RDKit version 2015.03.1 or later with InChI support);
-endif
-	@ echo "Checking rdkit has InChI support..."
-	@ python -c 'from rdkit import Chem; assert Chem.inchi.INCHI_AVAILABLE, "RDKit installed without InChI Support. Please install with InChI."'
+check:
+	@ python utilities.py check-dependencies
 
 documentation:
 	$(MAKE) -C documentation html
 	@ echo "Start at: documentation/build/html/index.html"
 
 clean:
-	python setup.py clean --build-temp build
-	rm -rf build/
-	find . -name '*.so' -exec rm -f '{}' \;
-	find . -name '*.pyc' -exec rm -f '{}' \;
-	
+	@ echo "Removing build directory..."
+	@ python setup.py clean --build-temp build
+	@ echo "Removing compiled files..."
+	@ python utilities.py clean
+	@ echo "Cleanup completed."
+
 clean-solver:
-	rm -r build/pyrex/rmgpy/solver/
-	rm -r build/build/pyrex/rmgpy/solver/
-	find rmgpy/solver/ -name '*.so' -exec rm -f '{}' \;
-	find rmgpy/solver/ -name '*.pyc' -exec rm -f '{}' \;
+	@ echo "Removing solver build directories..."
+ifeq ($(OS),Windows_NT)
+	@ -rd /s /q build\pyrex\rmgpy\solver
+	@ -rd /s /q build\build\pyrex\rmgpy\solver
+else
+	@ -rm -r build/pyrex/rmgpy/solver/
+	@ -rm -r build/build/pyrex/rmgpy/solver/
+endif
+	@ echo "Removing compiled files..."
+	@ python utilities.py clean-solver
+	@ echo "Cleanup completed."
 
 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:
-ifeq ($(OS),Windows_NT)
-	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
-	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 endif
+	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 
 test-unittests:
-ifeq ($(OS),Windows_NT)
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 endif
+	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 
 test test-unittests-non-auth:
-ifeq ($(OS),Windows_NT)
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
-	nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 endif
+	nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 
 test-functional:
-ifeq ($(OS),Windows_NT)
-	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
-else
+ifneq ($(OS),Windows_NT)
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
-	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
 endif
+	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
 
 test-database:
 	nosetests -v -d testing/databaseTest.py	
-eg0: noQM
+eg0: all
 	mkdir -p testing/eg0
 	rm -rf testing/eg0/*
 	cp examples/rmg/superminimal/input.py testing/eg0/input.py
 	@ echo "Running eg0: superminimal (H2 oxidation) example"
 	python rmg.py testing/eg0/input.py
-eg1: noQM
+eg1: all
 	mkdir -p testing/eg1
 	rm -rf testing/eg1/*
 	cp examples/rmg/minimal/input.py testing/eg1/input.py
@@ -168,7 +154,7 @@ eg7: all
 	@ echo "Running eg7: gri_mech_rxn_lib example"
 	python rmg.py testing/eg7/input.py
 
-scoop: noQM
+scoop: all
 	mkdir -p testing/scoop
 	rm -rf testing/scoop/*
 	cp examples/rmg/minimal/input.py testing/scoop/input.py

documentation/source/_static/RMG-logo.pdf

@@ -0,0 +1,81 @@
+@import url("classic.css");
+
+/* ----- sidebar styles ----- */
+
+div.sidebarlogo {
+    text-align: center;
+    padding: 20px;
+}
+
+div.sphinxsidebarwrapper {
+    padding: 0;
+}
+
+#sidebar .icon {
+    float: left;
+    width: 40px;
+    padding: 5px;
+}
+
+#sidebar div.menuitem {
+    padding: 5px;
+}
+
+#sidebar div.menutext {
+    text-align: left;
+    margin-left: 50px;
+    padding: 1px 5px;
+}
+
+#sidebar div.menutitle {
+    color: #F04040;
+    font-size: 125%;
+    vertical-align: bottom;
+}
+
+#sidebar div.menudesc {
+    color: #FFFFFF;
+    font-size: 90%;
+    vertical-align: top;
+}
+
+#rmgsidebar a {
+    text-decoration: none;
+}
+
+#rmgsidebar div.menuitem {
+    min-height: 50px;
+}
+
+#rmgsidebar div.menuitem:hover {
+    background-color: #606060;
+}
+
+/* ----- table styles ----- */
+
+th {
+    background-color: transparent;
+}
+
+table.rmg {
+    border-top: 2px solid #000000;
+    border-bottom: 2px solid #000000;
+    border-collapse: collapse;
+    margin: 10px 10px 20px 30px;
+}
+
+table.rmg thead {
+    border-bottom: 1px solid #000000;
+}
+
+table.rmg th,
+table.rmg td {
+    padding: 5px;
+}
+
+/* ----- code block styles ----- */
+
+pre {
+    border-top: 1px solid #F04040;
+    border-bottom: 1px solid #F04040;
+}