GitLab

Updated instructions on running the test installation script

Conda testing

run_tests to TestingError so users only ever have one exception to catch.

SyntaxWarning otherwise). So move those imports back to the module level and
save any error messages for when the tests are actually run (if ever).

python -m simtk.testInstallation

runs the tests, whereas

python -c "import simtk.testInstallation"

does not.

import of the new testInstallation module and a command to run the tests.

This way, we only have one place where we need to maintain this code, yet the
current workflow of "run testInstallation.py" still works.

Also copy the test PDB file to the data/ directory, since we rather need it...

Workaround for CUDA bug

DrudeForce did not implement getBondedParticles()

Added error codes from CUDA 5.0

Fixep

Install benchmark.py script

most important and we don't want false positives.

At some point, at least, TP4 was the residue label for water (I think tleap
currently translates most of the water residue labels to WAT, but there are at
least some -- like $AMBERHOME/test/tip4p/prmtop -- that use older labels).

Remove what appears to be a debug message.

Minor optimization to sorting

[WIP]Fix byte handling to work for both Py2 and Py3

Further documentation updates for 6.2

Make sure files are appropriately closed by PDBFile()

can't validate the that this object does anything more than simply write without
exceptions (i.e., we can't tell if the DCD file is actually _valid_)

CustomIntegrator throws an exception if variable names are ambiguous

Python 3 compatitbility

Fixed a bug in neighbor list construction