Merge pull request #233 from Becksteinlab/release082

release 0.8.3

Author: orbeckst

.github/workflows/ci.yaml

@@ -6,10 +6,10 @@ on:
     - cron: "44 4 * * 0"
   push:
     branches:
-      - "master"
+      - "main"
   pull_request:
     branches:
-      - "master"
+      - "main"
 
 concurrency:
   group: "${{ github.ref }}-${{ github.head_ref }}"
@@ -22,34 +22,41 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macOS-latest]
-        python-version: [2.7, 3.6, 3.7, 3.8, 3.9]
+        python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
         gromacs-version: ["2021.1"]
         # Test other GROMACS versions selectively on a recent Python.
         # On macOS only test one GROMACS version and two Python versions
         # to keep the testing matrix manageable.
         exclude:
           - os: macOS-latest
-            python-version: 3.6
+            python-version: "3.6"
           - os: macOS-latest
-            python-version: 3.7
+            python-version: "3.7"
           - os: macOS-latest
-            python-version: 3.9
+            python-version: "3.8"
+          - os: macOS-latest
+            python-version: "3.9"
+          - os: macOS-latest
+            python-version: "3.10"
         include:
           - os: ubuntu-latest
-            python-version: 2.7
+            python-version: "2.7"
             gromacs-version: "4.6.5"	
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             gromacs-version: "4.6.5"
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             gromacs-version: "2018.6"
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             gromacs-version: "2019.1"
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             gromacs-version: "2020.6"
+          - os: ubuntu-latest
+            python-version: "3.10"
+            gromacs-version: "2022.4"
 
     env:
       MPLBACKEND: agg

CHANGES

@@ -2,6 +2,16 @@
  CHANGELOG for GromacsWrapper
 ==============================
 
+2023-03-09      0.8.3
+orbeckst
+
+* confirmed support for GROMACS 4.6.5, 2018, 2019, 2020, 2021, 2022 on
+  Python 2.7 and 3.6--3.11 on Linux and macOS  
+* replaced deprecated logger.warn() with logger.warning() (#229)
+* replaced deprecated numpy.bool with bool in a test (#234)
+* fixed use of moved collections.Iterable in test (#235)
+
+
 2021-09-09     0.8.2
 orbeckst, simonbray
 

gromacs/fileformats/xvg.py

@@ -1200,7 +1200,7 @@ def break_array(a, threshold=numpy.pi, other=None):
     b = numpy.empty((len(a) + m))
     # calculate new indices for breaks in b, taking previous insertions into account
     b_breaks = breaks + numpy.arange(m)
-    mask =  numpy.zeros_like(b, dtype=numpy.bool)
+    mask =  numpy.zeros_like(b, dtype=bool)
     mask[b_breaks] = True
     b[~mask] = a
     b[mask] = numpy.NAN

tests/fileformats/top/test_amber03star.py

@@ -7,11 +7,13 @@
 
 import pytest
 
-from gromacs.exceptions import GromacsError
+import gromacs
 
 from .top import TopologyTest
 from ...datafiles import datafile
 
+@pytest.mark.xfail(gromacs.release().startswith("2022"),
+                   reason="issue https://github.com/Becksteinlab/GromacsWrapper/issues/236")
 class TestAmber03star(TopologyTest):
         processed = datafile('fileformats/top/amber03star/processed.top')
         conf = datafile('fileformats/top/amber03star/conf.gro')

tests/fileformats/top/test_amber03w.py

@@ -7,11 +7,13 @@
 
 import pytest
 
-from gromacs.exceptions import GromacsError
+import gromacs
 
 from .top import TopologyTest
 from ...datafiles import datafile
 
+@pytest.mark.xfail(gromacs.release().startswith("2022"),
+                   reason="issue https://github.com/Becksteinlab/GromacsWrapper/issues/236")
 class TestAmber03w(TopologyTest):
         processed = datafile('fileformats/top/amber03w/processed.top')
         conf = datafile('fileformats/top/amber03w/conf.gro')

tests/test_tools.py

@@ -49,7 +49,8 @@ def test_failure_ignore():
         raise AssertionError("Should have ignored exception {}".format(err))
 
 class TestRelease(object):
-    major_releases = ('4', '5', '2016', '2018', '2019', '2020', '2021')
+    # add tested releases here
+    major_releases = ('4', '5', '2016', '2018', '2019', '2020', '2021', '2022')
 
     def test_release(self):
         assert gromacs.release().startswith(self.major_releases)

tests/test_utilities.py

@@ -9,7 +9,7 @@
 import pytest
 from six.moves import cPickle as pickle
 from six.moves import StringIO
-from collections import Iterable
+from six.moves.collections_abc import Iterable
 
 import numpy as np