Merge branch 'main' of github.com:openpathsampling/openpathsampling-cli into release-0.3

Author: dwhswenson

.github/workflows/test-suite.yml

@@ -24,12 +24,12 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
+          - "3.12"
           - "3.11"
           - "3.10"
-          - "3.9"
         INTEGRATIONS: [""]
         include:
-          - CONDA_PY: "3.11"
+          - CONDA_PY: "3.12"
             INTEGRATIONS: 'all-optionals'
 
     steps:

paths_cli/cli.py

@@ -95,6 +95,13 @@ def main(log):
         logging.config.fileConfig(log, disable_existing_loggers=False)
     # TODO: if log not given, check for logging.conf in .openpathsampling/
 
+    # TODO: remove when openmmtools doesn't trigger these warnings
+    silence_warnings = ['pymbar.mbar_solvers', 'pymbar.timeseries']
+    for lname in silence_warnings:
+        logger = logging.getLogger(lname)
+        logger.setLevel(logging.CRITICAL)
+
+
     logger = logging.getLogger(__name__)
     logger.debug("About to run command")  # TODO: maybe log invocation?
 

paths_cli/tests/compiling/test_root_compiler.py

@@ -247,8 +247,8 @@ def test_register_plugins_unit(foo_compiler_plugin, foo_baz_builder_plugin):
     with patch(BASE + "_register_builder_plugin", Mock()) as builder, \
             patch(BASE + "_register_compiler_plugin", Mock()) as compiler:
         register_plugins([foo_baz_builder_plugin, foo_compiler_plugin])
-        assert builder.called_once_with(foo_baz_builder_plugin)
-        assert compiler.called_once_with(foo_compiler_plugin)
+        builder.assert_called_once_with(foo_baz_builder_plugin)
+        compiler.assert_called_once_with(foo_compiler_plugin)
 
 
 def test_register_plugins_integration(foo_compiler_plugin,

paths_cli/tests/wizard/test_plugin_classes.py

@@ -38,7 +38,7 @@ def test_call(self):
         with mock.patch(patch_loc, mock_load):
             result = loader(wiz)
 
-        assert mock_load.called_once_with(wiz, "foos", "foo")
+        mock_load.assert_called_once_with(wiz, "foos", "foo")
         assert result == "some_object"