Merge branch 'nov20' of github.com:bjodah/chempy into nov20

.ci/ci-01-install.sh

@@ -1,9 +1,9 @@
 #!/bin/bash
 set -euxo pipefail
+source /opt-3/cpython-v3.*-apt-deb/bin/activate
 export CPATH=$SUNDBASE/include:${CPATH:-}
 export LIBRARY_PATH=$SUNDBASE/lib
 export LD_LIBRARY_PATH=$SUNDBASE/lib
-source /opt-3/cpython-v3.*-apt-deb/bin/activate
 PYTHON=python
 INSTALL_PIP_FLAGS="--cache-dir $CACHE_ROOT/pip_cache ${INSTALL_PIP_FLAGS:-}"  # --user
 for pypkg in pyodeint pygslodeiv2 pycompilation pycodeexport pycvodes pykinsol sym pyodesys; do
@@ -40,17 +40,11 @@ for pypkg in pyodeint pygslodeiv2 pycompilation pycodeexport pycvodes pykinsol s
     #( cd /tmp; $PYTHON -m pytest -k "not pool_discontinuity_approx" --pyargs $pypkg )
 done
 
-$PYTHON -m pip install $INSTALL_PIP_FLAGS -e .[all]
 $PYTHON -c "import pycvodes; import pyodesys; import pygslodeiv2"
+$PYTHON -m pip install $INSTALL_PIP_FLAGS -e .[all]
+[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]
 #git fetch -tq
 $PYTHON setup.py sdist                    # test pip installable sdist (checks MANIFEST.in)
 git archive -o dist/chempy-head.zip HEAD  # test pip installable zip (symlinks break)
 mkdir -p deploy/public_html/branches/${CI_COMMIT_BRANCH}
 cp dist/chempy-* deploy/public_html/branches/${CI_COMMIT_BRANCH}/
-
-set +e
-[[ $($PYTHON setup.py --version) =~ ^[0-9]+.* ]]
-./scripts/run_tests.sh --cov chempy --cov-report html
-bash
-./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
-

.ci/ci-02-run-tests.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 set -euxo pipefail
 source /opt-3/cpython-v3.*-apt-deb/bin/activate
-
-[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]
-export \
-    PYODESYS_CVODE_FLAGS="-isystem $SUNDBASE/include -isystem /usr/include/suitesparse" \
-    PYODESYS_CVODE_LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib"
-
+export CPATH=$SUNDBASE/include:${CPATH:-}
+export LIBRARY_PATH=$SUNDBASE/lib
+export LD_LIBRARY_PATH=$SUNDBASE/lib
+PYTHON=python
+INSTALL_PIP_FLAGS="--cache-dir $CACHE_ROOT/pip_cache ${INSTALL_PIP_FLAGS:-}"  # --user
+$PYTHON -m pip install $INSTALL_PIP_FLAGS -e .[all]
 ./scripts/run_tests.sh --cov chempy --cov-report html
 ./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg

chempy/chemistry.py

@@ -482,10 +482,10 @@ def from_string(cls, string, substance_keys=None, globals_=None, **kwargs):
         >>> r4 = Reaction.from_string("A -> 2 B; 'k'", 'A B')
         >>> r4.rate(dict(A=3, B=5, k=7)) == {'A': -3*7, 'B': 2*3*7}
         True
-        >>> r5 = Reaction.from_string("A -> B; 1/molar/second", 'A B')
+        >>> r5 = Reaction.from_string("A -> B; 1/molar/second", 'A B') # doctest: +IGNORE_EXCEPTION_DETAIL
         Traceback (most recent call last):
             ...
-        ValueError: Unable to convert between units ...
+        ValueError: Incompatible units
 
 
         Notes

chempy/units.py

@@ -651,10 +651,10 @@ class Backend(object):
     >>> math.exp(3*km) == math.exp(3*m)
     True
     >>> be = Backend('math')
-    >>> be.exp(3*km)
+    >>> be.exp(3*km) # doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
         ...
-    ValueError: Unable to convert between units of "km" and "dimensionless"
+    ValueError: Incompatible units
     >>> import numpy as np
     >>> np.sum([1000*pq.metre/pq.kilometre, 1])
     1001.0