Add writer_kwargs to MDAReporter and speed up testing (#9)

* Add code for serializing simulation.

(cherry picked from commit 5e1584c)

* Add serialized XML files for integrator, system, and state.

(cherry picked from commit 17b11e1)

* Move villin.pdb to sit alongside other serialized simulation files.

(cherry picked from commit 44f4304)

* Add a writer_kwargs argument to MDAReporter.

(cherry picked from commit b3032d6)

* Update Changelog.

(cherry picked from commit 9c7e1a8)

* Update tests to use a serialized simulation, this makes it so we don't have to reinstantiate the simulation with each test and SIGNIFICANTLY speeds up the test suite.

* Update changelog

* Better document test data creation.

* Correct outputs for describeNextReport and add testing.

CHANGELOG.md

@@ -16,13 +16,15 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
 
-## [Unreleased]
+## v0.1.1
 
 ### Authors
-<!-- GitHub usernames of contributors to this release -->
+- @sef43, @richardjgowers, @orionarcher
 
 ### Added
-<!-- New added features -->
+- Serialized simulation used in testing to speed up
+- Added writer_kwargs to `MDAReporter` instantiation
+- Added `MDAReporter` core logic and documentation
 
 ### Fixed
 <!-- Bug fixes -->

mdareporter/data/files.py

@@ -16,4 +16,8 @@
 from pkg_resources import resource_filename
 
 MDANALYSIS_LOGO = resource_filename(__name__, "mda.txt")
-VILLIN_PDB = resource_filename(__name__, "villin.pdb")
+VILLIN_PDB = resource_filename(__name__, "villin_simulation/villin.pdb")
+INTEGRATOR_XML = resource_filename(__name__, "villin_simulation/integrator.xml")
+SYSTEM_XML = resource_filename(__name__, "villin_simulation/system.xml")
+STATE_XML = resource_filename(__name__, "villin_simulation/state.xml")
+

mdareporter/data/villin_simulation/README.md

@@ -0,0 +1,3 @@
+This directory contains a serialized simulation for use in testing.
+
+The `integrator.xml`, `state.xml`, and `system.xml` here were generated by serialize_simulation.py.

mdareporter/data/villin_simulation/integrator.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" ?>
+<Integrator constraintTolerance="1e-05" friction="1" randomSeed="0" stepSize=".004" temperature="300" type="LangevinMiddleIntegrator" version="1"/>

mdareporter/data/villin_simulation/serialize_simulation.py

@@ -0,0 +1,39 @@
+from openmm.app import ForceField, Simulation, PME, HBonds
+from openmm import LangevinMiddleIntegrator
+from openmm.unit import nanometer, picosecond, kelvin
+
+from openmm.app import PDBFile, Topology
+from openmm.openmm import XmlSerializer
+from mdareporter.data.files import VILLIN_PDB
+
+
+pdb = PDBFile(VILLIN_PDB)
+
+forcefield = ForceField("amber14-all.xml", "amber14/tip3pfb.xml")
+system = forcefield.createSystem(
+    pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1 * nanometer, constraints=HBonds
+)
+integrator = LangevinMiddleIntegrator(300 * kelvin, 1 / picosecond, 0.004 * picosecond)
+simulation = Simulation(pdb.topology, system, integrator)
+simulation.context.setPositions(pdb.positions)
+simulation.minimizeEnergy()
+
+
+pdb.writeFile(
+    simulation.topology,
+    simulation.context.getState(getPositions=True).getPositions(),
+    open("output.pdb", "w"),
+)
+system_xml = XmlSerializer.serialize(system)
+integrator_xml = XmlSerializer.serialize(integrator)
+state_xml = XmlSerializer.serialize(
+    simulation.context.getState(getPositions=True, getVelocities=True)
+)
+
+# write to files
+with open("system.xml", "w") as f:
+    f.write(system_xml)
+with open("integrator.xml", "w") as f:
+    f.write(integrator_xml)
+with open("state.xml", "w") as f:
+    f.write(state_xml)