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Add unit tests from pyrosetta.tests to PyRosetta testing server: Pull…
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… request #3808

Add unit tests from pyrosetta.tests to PyRosetta testing server

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An additional 14 commit messages were squashed into this commit:
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Removing pyrosetta.tests.protocols.indexed_structure_store.test_search unit test due to missing imports
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PEP8 updates to T900_distributed.py
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Add pip-installable 'scipy' to temporary testing virtual environment; PEP8
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Resort to declaring explicit list of unit tests available in pyrosetta.tests for testing on the PyRosetta testing server
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Update T900_distributed.py to print list of automatically discovered unit tests to PyRosetta testing server tracer
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Implementing automatic unit test discovery in pyrosetta.tests, skipping test_gil.py unit test
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Testing updated test_gil.py unit test on PyRosetta testing server.
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Assertion bug fix and updating docstrings.
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Update test_dask.py unit test to run in temporary directory, and update unittest framework in other unit tests.
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Add pip-installable 'dask' and 'distributed' to temporary testing virtual environment
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Temporarily remove pyrosetta.tests.distributed.test_gil unit tests from PyRosetta testing server
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Add pip-installable 'blosc' to temporary testing virtual environment
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Removing dependency on unittest.TestLoader().discover() and declaring pyrosetta.tests.distributed unit tests explicitly
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Updating T900 tests covering pyrosetta.tests.distributed test suites with unittest framework
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Old repository SHA1: 1e0f021a01a3fe9a27617789f896bdd30ec32798
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@klimaj
klimaj authored Feb 20, 2019
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175 changes: 175 additions & 0 deletions source/src/python/PyRosetta/src/pyrosetta/tests/bindings/core/test_pose.py
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# :noTabs=true:
#
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org.
# (c) Questions about this can be addressed to University of Washington CoMotion, email: [email protected].

import pyrosetta
import pyrosetta.rosetta.core.pose as pose
import unittest


pyrosetta.init(extra_options="-constant_seed", set_logging_handler="logging")

class TestPoseResidueAccessor(unittest.TestCase):

def test_residues(self):

pose1 = pyrosetta.pose_from_sequence('ACDEFGHI')

# Test __len__
self.assertEqual(0, len(pose.Pose().residues))
self.assertEqual(8, len(pose1.residues))
self.assertEqual(8, len(pose1)) # Deprecated

# Test __iter__
self.assertEqual(0, len(list(pose.Pose().residues)))
self.assertEqual(8, len(list(pose1.residues)))
self.assertEqual(8, len(list(pose1))) # Deprecated

# Test __getitem__
# assert(pose1.residues[0] == ValueError)
# assert(pose1.residues[0:] == ValueError)
self.assertEqual(
pose1.residues[1].annotated_name(), 'A[ALA:NtermProteinFull]')

self.assertEqual(pose1.residues[6].annotated_name(), 'G')
self.assertEqual(pose1.residues[8].annotated_name(), 'I[ILE:CtermProteinFull]')
self.assertEqual(pose1.residues[-1].annotated_name(), 'I[ILE:CtermProteinFull]')
self.assertEqual(pose1.residues[-3].annotated_name(), 'G')
self.assertEqual(pose1.residues[-8].annotated_name(), 'A[ALA:NtermProteinFull]')
self.assertEqual(
''.join([res.annotated_name() for res in pose.Pose().residues[:]]), '')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[:]]),
'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[1:9]]),
'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[:-3]]), 'A[ALA:NtermProteinFull]CDEF')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[3:]]), 'DEFGHI[ILE:CtermProteinFull]')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[-6:8]]), 'DEFGH')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[-6:8:2]]), 'DFH')
self.assertEqual(
''.join([res.annotated_name() for res in pose1.residues[-6:8:3]]), 'DG')
self.assertEqual(
''.join([res.annotated_name() for res in pose1[1:9]]), 'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]') # Deprecated
self.assertEqual(
''.join([res.annotated_name() for res in pose1[-6:8]]), 'DEFGH') # Deprecated

# #Test __iadd__
# gly_residue = pose1.residues[6]
# pose1.residues += gly_residue
# self.assertEqual(
# ''.join([res.annotated_name() for res in pose1.residues]), 'A[ALA:NtermProteinFull]CDEFGHIG[GLY:CtermProteinFull]')

# pose2 = Pose()
# pose2.residues += pose1.residues[1]
# for _ in range(3):
# pose2.residues += gly_residue
# pose2.residues += pose1.residues[-1]
# pose2.residues += gly_residue
# self.assertEqual(
# ''.join([res.annotated_name() for res in pose2.residues]), 'A[ALA:NtermProteinFull]GGGGG[GLY:CtermProteinFull]')

# #Test __imul__
# pose3 = Pose()
# pose3.residues *= pose1.residues[5]
# self.assertEqual(''.join([res.annotated_name() for res in pose3.residues]), 'F')
# pose3.residues *= pose1.residues[5]
# self.assertEqual(''.join([res.annotated_name() for res in pose3.residues]), 'FF')
# pose3.residues *= pose1.residues[5]
# self.assertEqual(''.join([res.annotated_name() for res in pose3.residues]), 'FFF')


class TestPoseScoresAccessor(unittest.TestCase):

def test_scores(self):

test_pose = pyrosetta.pose_from_sequence("TESTTESTTEST")

self.assertDictEqual(dict(test_pose.scores), {})

# Test proper overwrite of extra scores of varying types.
test_pose.scores["foo"] = "bar"
self.assertDictEqual(dict(test_pose.scores), {"foo" : "bar"})
test_pose.scores["foo"] = 1
self.assertDictEqual(dict(test_pose.scores), {"foo" : 1.0})

test_pose.scores["bar"] = 2
self.assertDictEqual(dict(test_pose.scores), {"foo" : 1.0, "bar" : 2.0})

# Test score deletion
del test_pose.scores["foo"]
self.assertDictEqual(dict(test_pose.scores), {"bar" : 2.0})

# Test exception when setting reserved names
with self.assertRaises(ValueError):
test_pose.scores["fa_atr"] = "invalid"

# Test score update after scoring
self.assertNotIn("fa_atr", test_pose.scores)
pyrosetta.get_score_function()(test_pose)
self.assertIn("fa_atr", test_pose.scores)

# Test clear w/ energies
with self.assertRaises(ValueError):
del test_pose.scores["fa_atr"]

test_pose.energies().clear()
self.assertNotIn("fa_atr", test_pose.scores)
self.assertDictEqual(dict(test_pose.scores), {"bar" : 2.0})

test_pose.scores.clear()
self.assertDictEqual(dict(test_pose.scores), dict())


class TestPoseResidueLabelAccessor(unittest.TestCase):

def test_labels(self):

test_pose = pyrosetta.pose_from_sequence("TESTTESTTEST")

self.assertSequenceEqual(
list(test_pose.reslabels), [set()] * len(test_pose.residues))

test_pose.reslabels[1].add("foo")
test_pose.reslabels[-1].add("bar")
test_pose.reslabels[-1].add("blah")
self.assertSequenceEqual(
list(test_pose.reslabels),
[{"foo"}] + [set()] * (len(test_pose.residues) - 2) + [{"bar", "blah"}])

self.assertSequenceEqual(
test_pose.reslabels.mask["foo"],
[True] + [False] * (len(test_pose.residues) - 1))
self.assertSequenceEqual(
test_pose.reslabels.mask["bar"],
[False] * (len(test_pose.residues) - 1) + [True])
self.assertSequenceEqual(
test_pose.reslabels.mask["blah"],
[False] * (len(test_pose.residues) - 1) + [True])

self.assertSetEqual(set(test_pose.reslabels.mask), {"foo", "bar", "blah"})

test_pose.reslabels[-1].clear()
self.assertSequenceEqual(
list(test_pose.reslabels),
[{"foo"}] + [set()] * (len(test_pose.residues) - 1))

test_pose.reslabels[-1].add("bar")
test_pose.reslabels[-1].add("blah")
test_pose.reslabels[-1].discard("blah")
self.assertSequenceEqual(
list(test_pose.reslabels),
[{"foo"}] + [set()] * (len(test_pose.residues) - 2) + [{"bar"}])


if __name__ == "__main__":
unittest.main()
48 changes: 25 additions & 23 deletions source/src/python/PyRosetta/src/pyrosetta/tests/distributed/test_concurrency.py
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Original file line number Diff line number Diff line change
@@ -1,27 +1,33 @@
import unittest
import threading
import time
# :noTabs=true:
#
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org.
# (c) Questions about this can be addressed to University of Washington CoMotion, email: [email protected].

import numpy
import time
import threading
import unittest

import pyrosetta.distributed.io as io
import pyrosetta.distributed.tasks.rosetta_scripts as rosetta_scripts
import pyrosetta.distributed.tasks.score as score


class TestConcurrentScripts(unittest.TestCase):

def test_concurrent_on_task(self):

protocol = rosetta_scripts.SingleoutputRosettaScriptsTask("""
<ROSETTASCRIPTS>
<MOVERS>
<FastRelax name="score" repeats="1" />
</MOVERS>
<PROTOCOLS>
<Add mover_name="score"/>
</PROTOCOLS>
<MOVERS>
<FastRelax name="score" repeats="1"/>
</MOVERS>
<PROTOCOLS>
<Add mover_name="score"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
""")

Expand All @@ -37,21 +43,17 @@ def run_task(seq):
test_pose = io.pose_from_sequence(seq)
protocol = rosetta_scripts.SingleoutputRosettaScriptsTask("""
<ROSETTASCRIPTS>
<MOVERS>
<FastRelax name="score" repeats="1" />
</MOVERS>
<PROTOCOLS>
<Add mover_name="score"/>
</PROTOCOLS>
<MOVERS>
<FastRelax name="score" repeats="1" />
</MOVERS>
<PROTOCOLS>
<Add mover_name="score"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
""")

return protocol(test_pose)


import concurrent.futures
with concurrent.futures.ThreadPoolExecutor(max_workers=3) as p:
result = list(p.map(run_task, ["TEST"] * 3))
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100 changes: 63 additions & 37 deletions source/src/python/PyRosetta/src/pyrosetta/tests/distributed/test_dask.py
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Original file line number Diff line number Diff line change
@@ -1,64 +1,90 @@
import logging
# :noTabs=true:
#
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org.
# (c) Questions about this can be addressed to University of Washington CoMotion, email: [email protected].

import argparse
import unittest

import dask.distributed
import logging
import tempfile
import unittest

import pyrosetta.distributed.io as io
import pyrosetta.distributed.packed_pose as packed_pose
import pyrosetta.distributed.tasks.rosetta_scripts as rosetta_scripts


class TestDaskDistribution(unittest.TestCase):

_dask_scheduler = None

with tempfile.TemporaryDirectory() as workdir:

def setUp(self, local_dir=workdir):
if not self._dask_scheduler:
self.local_cluster = dask.distributed.LocalCluster(
n_workers=2, threads_per_worker=2, diagnostics_port=None, local_dir=local_dir
)
cluster = self.local_cluster
else:
self.local_cluster = None
cluster = self._dask_scheduler

def setUp(self):
if not self._dask_scheduler:
self.local_cluster = dask.distributed.LocalCluster(n_workers=2, threads_per_worker=2)
cluster = self.local_cluster
else:
self.local_cluster = None
cluster = self._dask_scheduler
self.client = dask.distributed.Client(cluster)

self.client = dask.distributed.Client(cluster)
def tearDown(self):
self.client.close()
def tearDown(self):
self.client.close()

if self.local_cluster:
self.local_cluster.close()

if self.local_cluster:
self.local_cluster.close()
def test_rosetta_scripts(self):
test_protocol = """
<ROSETTASCRIPTS>
<TASKOPERATIONS>
<RestrictToRepacking name="repack"/>
</TASKOPERATIONS>
<MOVERS>
<PackRotamersMover name="pack" task_operations="repack"/>
</MOVERS>
<PROTOCOLS>
<Add mover="pack"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
"""

def test_rosetta_scripts(self):
test_protocol = """
<ROSETTASCRIPTS>
<MOVERS>
<PackRotamersMover name="pack"/>
</MOVERS>
<PROTOCOLS>
<Add mover="pack" />
</PROTOCOLS>
</ROSETTASCRIPTS>
"""
test_pose = io.pose_from_sequence("TEST")
test_task = rosetta_scripts.SingleoutputRosettaScriptsTask(test_protocol)

test_pose = io.pose_from_sequence("TESTTESTTEST")
test_task = rosetta_scripts.SingleoutputRosettaScriptsTask(test_protocol)
logging.info("dask client: %s", self.client)
task = self.client.submit(test_task, test_pose)
result = task.result()
self.assertEqual(
packed_pose.to_pose(result).sequence(),
packed_pose.to_pose(test_pose).sequence()
)

logging.info("dask client: %s", self.client)
task = self.client.submit(test_task, test_pose)
result = task.result()
def test_basic(self):
logging.info("dask client: %s", self.client)
task = self.client.submit(lambda a: a + 1, 1)
self.assertEqual(task.result(), 2)

def test_basic(self):
logging.info("dask client: %s", self.client)
task = self.client.submit(lambda a: a + 1, 1)
self.assertEqual(task.result(), 2)

if __name__ == "__main__":

logging.basicConfig(
level=logging.INFO,
format="%(asctime)s.%(msecs).03d %(name)s %(message)s",
datefmt='%Y-%m-%dT%H:%M:%S'
)

parser = argparse.ArgumentParser(description='Run initial pyrosetta.distributed smoke test over given scheduler.')
parser.add_argument('scheduler', type=str, nargs='?', help='Target scheduler endpoint for test.')
parser = argparse.ArgumentParser(
description="Run initial pyrosetta.distributed smoke test over given scheduler."
)
parser.add_argument("scheduler", type=str, nargs="?", help="Target scheduler endpoint for test.")
args = parser.parse_args()

TestDaskDistribution._dask_scheduler = args.scheduler
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