Merge pull request #891 from dwhswenson/bump-1.1.1

Bump version on master to 1.2.0.dev0

.coveragerc

@@ -5,6 +5,7 @@ omit =
     */openpathsampling/tests/*
     */mdtraj/*
     */setup.py
+    openpathsampling/version.py
 exclude_lines = 
     pragma: no cover
     def __repr__

.travis.yml

@@ -1,22 +1,34 @@
+version: ~> 1.0
+
 language: python
 filter_secrets: false   # https://github.com/travis-ci/travis-ci/issues/8934
 
+branches:
+  only:
+    - master
+    - stable
+    - docs_deploy  # used for experimenting with docs builds
+    - /^v\d+(\.\d+)+/
+
+
 notifications:
   webhooks: https://coveralls.io/webhook
 
 before_install:
   - deactivate  # virtual envs don't play nice with conda
   - export PYTHONUNBUFFERED=true  # immediately flush stdout to terminal
   - source devtools/ci/miniconda_install.sh
-  - conda install -y pyyaml
+  #- conda install -y pyyaml  # I don't think this is needed now...
 
 install:
   - export OPS_ENV="openpathsampling-py${CONDA_PY}"
   - if [ -z "$MINIMAL" ] ; then source devtools/conda_install_reqs.sh; else pip install -r devtools/minimal.txt -r devtools/minimal_testing.txt; fi
+  # for the first OPS install, we will run the ops_fixes autorelease branch
+  #- pip install git+https://github.com/dwhswenson/autorelease.git@v0.1.2
   - pip install autorelease
   - pip install --no-deps -e .
 
-before_script:
+before_script: 
   - python --version
   - python -c "import openpathsampling"
   - source devtools/ci/git_hash.sh
@@ -39,10 +51,10 @@ addons:
 env:
   global:
     - TWINE_USERNAME="dwhswenson"
-    # TWINE_PASSWORD
-    - secure: "zs/3PN46wXFzTDli8LE9jJmNov27xAy7REaTK4s3DV9Ocmf5grqIUbUfFfa7XyOvamr6C7TSHib1SqQvEbHv416AcOD9FWZm9iNj0MO2dBimyXrvR50TFKG/dcp0Qzlp54hYFM4bEzWJZUVN120xynIKgfy74YBOA8DQ6B7FlyY="
-    # AUTORELEASE_TOKEN
-    - secure: "r9u8xvXo3avaloOogrqIVF/oFDeMLSYvZbBYv3y3nBN17p3I9C2FhUbu/VpiRBA0kX6U2BsAHh5DF8ymRD254/f3s8L1BapanLfmoRjp9cXAJ95RZhZ8Cxw9W36VEGcIa+JG1G31oqabEBW4ozQmXsGPSYI3+wfFmhchJPpaDRE="
+    # TWINE_PASSWORD (set via web)
+    #- secure: "zs/3PN46wXFzTDli8LE9jJmNov27xAy7REaTK4s3DV9Ocmf5grqIUbUfFfa7XyOvamr6C7TSHib1SqQvEbHv416AcOD9FWZm9iNj0MO2dBimyXrvR50TFKG/dcp0Qzlp54hYFM4bEzWJZUVN120xynIKgfy74YBOA8DQ6B7FlyY="
+    # AUTORELEASE_TOKEN (set via web)
+    #- secure: "r9u8xvXo3avaloOogrqIVF/oFDeMLSYvZbBYv3y3nBN17p3I9C2FhUbu/VpiRBA0kX6U2BsAHh5DF8ymRD254/f3s8L1BapanLfmoRjp9cXAJ95RZhZ8Cxw9W36VEGcIa+JG1G31oqabEBW4ozQmXsGPSYI3+wfFmhchJPpaDRE="
     - secure: "NJvoSrLNd2ZR3HluJjEqI36gD5lsucwIvgnYjNmM4cwnnA77aLV9FRYTwlLRZn3XY9FL8KOzL5l0amNzMD7sQrf7bWwWv7iCUBddH549q9RSgiuOugtodYJ6VaXi76hk1rOgcJpDoCj9wTCIlMtWibPUzr1QHmdihfdM2iA2kkE="
     - secure: "l9NJkZDD0ALhkErUvhRrreLsrcWErd+CXpWv8dxHGtkjemNx6CwVtyL+a30jz/QwMANSZbKll/cPK5yJQvuwDaWxja6UPLLKVNGtma+CmwKcIC/wwTwbMoxcS62fyLJ3kS0qR8oCQz2nCPKiYyRGADtPLWVMZckY1SJfNYcKuCM="
     - secure: "kb37xmsSV3pEnESnINzwlW2Cju/UFzA/G+m+NsihAwO8RMPZwKCrZK/rptgkUDACXJxom5M690WEukQkHnOt+OTrWhu7WKZgYeVuWUs2++RohYv/m5npaOHMMn+uYmF328v4PvPmXxbD02zzg5Tgdn82x8oa6J8BKX8ohOQ6Xpg="
@@ -53,4 +65,4 @@ env:
     - CONDA_PY=3.7
 
 import:
-  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.0
+  - dwhswenson/autorelease:autorelease-travis.yml@v0.1.2

MANIFEST.in

@@ -1,3 +1,4 @@
 # include visualization .css files
+LICENSE
 graft openpathsampling
-include openpathsampling/resources/*.css
+include openpathsampling/resources/*.css

devtools/conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
-  name: openpathsampling-dev
-  version: "1.1.0.dev0"
+  name: openpathsampling
+  version: "1.2.0.dev0"
 
 source:
   path: ../../

openpathsampling/engines/openmm/topology.py

@@ -1,7 +1,6 @@
 import mdtraj as md
 import numpy as np
 import pandas as pd
-from simtk.openmm import XmlSerializer
 
 from openpathsampling.engines import Topology
 

openpathsampling/netcdfplus/netcdfplus.py

@@ -385,8 +385,12 @@ def file_size_str(self):
     @staticmethod
     def _cmp_version(v1, v2):
         # we only look at x.y.z parts
-        q1 = v1.split('.')[:3]
-        q2 = v2.split('.')[:3]
+        def version_parts(v):
+            return v.split('-')[0].split('+')[0].split('.')[:3]
+        q1 = version_parts(v1)
+        q2 = version_parts(v2)
+        # q1 = v1.split('.')[:3]
+        # q2 = v2.split('.')[:3]
         # q1 = v1.split('-')[0].split('.')
         # q2 = v2.split('-')[0].split('.')
         for v1, v2 in zip(q1, q2):

openpathsampling/netcdfplus/version.py

@@ -1,5 +1,5 @@
-short_version = '1.1.0.dev0'
-version = '1.1.0.dev0'
-full_version = '1.1.0.dev0'
+short_version = '1.2.0.dev0'
+version = '1.2.0.dev0'
+full_version = '1.2.0.dev0'
 git_revision = 'alpha'
 release = False

openpathsampling/tests/test_attribute.py

@@ -3,6 +3,7 @@
 """
 
 from .test_helpers import data_filename, assert_close_unit, make_1d_traj, md
+import pytest
 
 from nose.plugins.skip import SkipTest
 
@@ -18,6 +19,7 @@ def setup(self):
         if not md:
             raise SkipTest("mdtraj not installed")
         self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
+        pytest.importorskip("simtk.unit")
         self.traj_topology = peng.trajectory_from_mdtraj(self.mdtraj)
         self.traj_simple = peng.trajectory_from_mdtraj(
             self.mdtraj,

openpathsampling/tests/test_collectivevariable.py

@@ -7,6 +7,7 @@
 from builtins import object
 from .test_helpers import data_filename, assert_close_unit, md
 
+import pytest
 from nose.plugins.skip import SkipTest
 
 import numpy as np
@@ -32,6 +33,7 @@ def setup(self):
         if not md:
             raise SkipTest("mdtraj not installed")
         self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
+        _ = pytest.importorskip('simtk.unit')
         self.traj_topology = peng.trajectory_from_mdtraj(self.mdtraj)
         self.traj_simple = peng.trajectory_from_mdtraj(
             self.mdtraj,

openpathsampling/tests/test_mdtraj_support.py

@@ -2,6 +2,8 @@
 from builtins import object
 import logging
 
+import pytest
+
 from nose.tools import (
     assert_equal, assert_not_equal, raises
 )
@@ -29,6 +31,7 @@ def setup(self):
         if not md:
             raise SkipTest("mdtraj not installed")
         self.md_trajectory = md.load(data_filename("ala_small_traj.pdb"))
+        _ = pytest.importorskip("simtk.unit")
         self.ops_trajectory = trajectory_from_mdtraj(self.md_trajectory)
         self.md_topology = self.ops_trajectory.topology.mdtraj
 

openpathsampling/tests/test_openmm_tools.py

@@ -89,6 +89,8 @@ def test_reduced_box_vectors():
     else:
         raise AssertionError("Box already reduced")
 
+    if not HAS_OPENMM:
+        pytest.skip()
     snap = mock_snapshot_with_box_vector(box * nm)
     reduced_box = reduced_box_vectors(snap).value_in_unit(nm)
     check_reduced_box_vectors(reduced_box)
@@ -122,7 +124,7 @@ def test_reduce_trajectory_box_vectors():
 
 
 def test_load_trr_with_velocities():
-    if not HAS_MDTRAJ:
+    if not (HAS_MDTRAJ and HAS_OPENMM):
         pytest.skip()
     box_vect_dir = "reduce_box_vects"
     gro = data_filename(box_vect_dir + "/dna.gro")
@@ -134,7 +136,7 @@ def test_load_trr_with_velocities():
 
 
 def test_load_trr_no_velocities():
-    if not HAS_MDTRAJ:
+    if not (HAS_MDTRAJ and HAS_OPENMM):
         pytest.skip()
     box_vect_dir = "reduce_box_vects"
     gro = data_filename(box_vect_dir + "/dna.gro")

openpathsampling/tests/test_storage.py

@@ -8,6 +8,8 @@
 from builtins import object
 import os
 
+import pytest
+
 from nose.tools import (assert_equal)
 
 import openpathsampling as paths
@@ -28,6 +30,7 @@ def setup(self):
         if not md:
             raise SkipTest("mdtraj not installed")
         self.mdtraj = md.load(data_filename("ala_small_traj.pdb"))
+        _ = pytest.importorskip('simtk.unit')
         self.traj = peng.trajectory_from_mdtraj(
             self.mdtraj, simple_topology=True)
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = openpathsampling
-version = 1.1.0.dev0
+version = 1.2.0.dev0
 description = A Python package for path sampling simulations
 long_description = file: README.md
 long_description_content_type = text/markdown