Release 0.9.5

[mikemhenry]

Quick release to get our citations in order, see #948

[mikemhenry]

@jchodera if you could take a look at this when you get a chance that would be great! Also would it be okay for me to merge the release on conda-forge as well? Thanks!

[jchodera]

Shoot, sorry for not catching this earlier:

1. Can we update CITATION.cff to include middle initials in "given names", e.g. "John" -> "John D." to reflect current publication practice?
2. Any idea why builds are failing?

[jchodera]

It looks like at least some of these failures are due to the change in how diameter is computed for solvating systems: openmm/openmm#3480

_____________________________ test_position_output _____________________________
[gw1] linux -- Python 3.8.12 /usr/share/miniconda/envs/test/bin/python

    def test_position_output():
        """
        Test that the hybrid returns the correct positions for the new and old systems after construction
        """
        from perses.annihilation.relative import HybridTopologyFactory
        import numpy as np
    
        # Generate topology proposal
>       topology_proposal, old_positions, new_positions = utils.generate_solvated_hybrid_test_topology()

perses/tests/test_relative.py:489: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
perses/tests/utils.py:533: in generate_solvated_hybrid_test_topology
    new_positions, _ = geometry_engine.propose(top_proposal, solvated_positions, beta)
perses/rjmc/geometry.py:237: in propose
    logp_proposal, new_positions, rjmc_info, atoms_with_positions_reduced_potential, final_context_reduced_potential, neglected_angle_terms, omitted_terms = self._logp_propose(top_proposal, current_positions, beta, direction='forward', validate_energy_bookkeeping = validate_energy_bookkeeping)
perses/rjmc/geometry.py:641: in _logp_propose
    final_context = openmm.Context(final_system, final_system_integrator, platform)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <openmm.openmm.Context;  >
args = (<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x7f58aa7020f0> >, <openmm.openmm.VerletIn...at 0x7f58a8c4bc00> >, <openmm.openmm.Platform; proxy of <Swig Object of type 'OpenMM::Platform *' at 0x7f58a8a90870> >)

    def __init__(self, *args):
        r"""
        __init__(self, system, integrator) -> Context
        __init__(self, system, integrator, platform) -> Context
        __init__(self, system, integrator, platform, properties) -> Context
        __init__(self, other) -> Context
        Construct a new Context in which to run a simulation, explicitly specifying what Platform should be used to perform calculations and the values of platform-specific properties.
    
        Parameters
        ----------
        system : System
            the System which will be simulated
        integrator : Integrator
            the Integrator which will be used to simulate the System
        platform : Platform
            the Platform to use for calculations
        properties : map< std::string, std::string >
            a set of values for platform-specific properties. Keys are the property names.
        """
>       _openmm.Context_swiginit(self, _openmm.new_Context(*args))
E       openmm.OpenMMException: NonbondedForce: The cutoff distance cannot be greater than half the periodic box size.

/usr/share/miniconda/envs/test/lib/python3.8/site-packages/openmm/openmm.py:7[257](https://github.com/choderalab/perses/runs/5400530956?check_suite_focus=true#step:9:257): OpenMMException

[codecov]

Codecov Report

Merging #950 (b830141) into main (25200de) will decrease coverage by 0.93%.
The diff coverage is n/a.

❗ Current head b830141 differs from pull request most recent head 754436c. Consider uploading reports for the commit 754436c to get more accurate results

[jchodera]

Let's address the failing nightlies by increasing the buffer size for the tests that are failing. We should also open an issue to change defaults and recommendations/examples as well as box shape in advance of the next OpenMM release. Once we add middle initials to the citations to match what folks generally publish under, this is then ready to go!

[zhang-ivy]

#952 adds the middle initials to the citation file!

[mikemhenry]

@jchodera Just to be clear we want to

- [ ] fix failing tests by increasing the buffer size

• add middle initials (Fix citation file #952)

Then do the release?
Note: Going to fix failing tests from padding a different way

[jchodera]

@jchodera Just to be clear we want to

Correct!