Updated the dependencies in test/environment.yml as the minimum
python version has been bumped to 3.9 and rdkit is not being
installed through pypi. mdanalysis is also being installed through
conda install -c conda-forga mdanalysis rather than
pip install mdanalysis because the pip version seem lacking
dependencies and is causing crashing when pytest is run. This is
fixed by simply using the conda version of the package, presumably
because it installs the required binaries that are missing in the
pip version.
Also updated readme.rst to reflect that mdanalysis needs to be
installed from conda and that stk and rdkit do not need to be
installed explicitly, as they are requirements in setup.py.
Finally, removed the prefix and name keys from
tests/environment.yml as these can modify global environments on the
users computer. Instead the environmnent file should be used in an
active environment in the following way
conda env update --file tests/environment.yml
which will simply add the dependencies in tests/environment.yml to
the current active environment, instead of creating a new global
enivonrment, as was being done previously.
Also update the comparison of some floating point tests
to only check for an accuracy of 1E-6 as there appears to
be some non-determinism across machines and in GitHub's
CI.
Related Issues: #148
Updated the dependencies in
test/environment.ymlas the minimum python version has been bumped to 3.9 andrdkitis not being installed throughpypi.mdanalysisis also being installed throughconda install -c conda-forga mdanalysisrather thanpip install mdanalysisbecause thepipversion seem lacking dependencies and is causing crashing whenpytestis run. This is fixed by simply using thecondaversion of the package, presumably because it installs the required binaries that are missing in thepipversion.Also updated
readme.rstto reflect thatmdanalysisneeds to be installed fromcondaand thatstkandrdkitdo not need to be installed explicitly, as they are requirements insetup.py.Finally, removed the
prefixandnamekeys fromtests/environment.ymlas these can modify global environments on the users computer. Instead the environmnent file should be used in an active environment in the following waywhich will simply add the dependencies in
tests/environment.ymlto the current active environment, instead of creating a new global enivonrment, as was being done previously.Also update the comparison of some floating point tests to only check for an accuracy of
1E-6as there appears to be some non-determinism across machines and in GitHub's CI.Co-authored-by: Austin Mroz austin.mroz@gmail.com