Merge pull request #74 from dwhswenson/back-to-green

Fix CI problems

Author: dwhswenson

.github/workflows/test-suite.yml

@@ -24,12 +24,12 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - 3.9
-          - 3.8
-          - 3.7
+          - "3.11"
+          - "3.10"
+          - "3.9"
         INTEGRATIONS: [""]
         include:
-          - CONDA_PY: 3.9
+          - CONDA_PY: "3.11"
             INTEGRATIONS: 'all-optionals'
 
     steps:
@@ -70,6 +70,8 @@ jobs:
         run: |
           python -c "import paths_cli"
           py.test -vv --cov --cov-report xml:cov.xml
-      - uses: codecov/codecov-action@v2
+      - uses: codecov/codecov-action@v4
         with:
           files: ./cov.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

paths_cli/tests/commands/test_md.py

@@ -12,7 +12,7 @@
         make_1d_traj, CalvinistDynamics
 
 class TestProgressReporter(object):
-    def setup(self):
+    def setup_method(self):
         self.progress = ProgressReporter(timestep=None, update_freq=5)
 
     @pytest.mark.parametrize('timestep', [None, 0.1])
@@ -38,7 +38,7 @@ def test_report_progress(self, n_steps, force, capsys):
             assert out == ""
 
 class TestEnsembleSatisfiedContinueConditions(object):
-    def setup(self):
+    def setup_method(self):
         cv = paths.CoordinateFunctionCV('x', lambda x: x.xyz[0][0])
         vol_A = paths.CVDefinedVolume(cv, float("-inf"), 0.0)
         vol_B = paths.CVDefinedVolume(cv, 1.0, float("inf"))

paths_cli/tests/compiling/_gendocs/test_docs_generator.py

@@ -9,7 +9,7 @@
 from paths_cli.compiling.core import CategoryCompiler
 
 class TestDocsGenerator:
-    def setup(self):
+    def setup_method(self):
         self.required_parameter = Parameter(
             name="req_param",
             loader=None,

paths_cli/tests/compiling/test_core.py

@@ -25,7 +25,7 @@ def mock_named_object_factory(dct):
 
 
 class TestParameter:
-    def setup(self):
+    def setup_method(self):
         self.loader = Mock(
             return_value='foo',
             json_type='string',
@@ -131,7 +131,7 @@ class TestInstanceCompilerPlugin:
     def _builder(req_param, opt_default=10, opt_override=100):
         return f"{req_param}, {opt_default}, {opt_override}"
 
-    def setup(self):
+    def setup_method(self):
         identity = lambda x: x
         self.parameters = [
             Parameter('req_param', identity, json_type="string"),
@@ -227,7 +227,7 @@ def test_call(self):
 
 
 class TestCategoryCompiler:
-    def setup(self):
+    def setup_method(self):
         self.compiler = CategoryCompiler(
             {'foo': mock_named_object_factory},
             'foo_compiler'

paths_cli/tests/compiling/test_cvs.py

@@ -15,7 +15,7 @@
 
 
 class TestMDTrajFunctionCV:
-    def setup(self):
+    def setup_method(self):
         self.ad_pdb = data_filename("ala_small_traj.pdb")
         self.yml = "\n".join([
             "name: phi", "type: mdtraj", "topology: " + self.ad_pdb,

paths_cli/tests/compiling/test_engines.py

@@ -12,15 +12,15 @@
 import mdtraj as md
 
 class TestOpenMMEngineBuilder(object):
-    def setup(self):
+    def setup_method(self):
         self.cwd = os.getcwd()
         self.yml = "\n".join([
             "type: openmm", "name: engine", "system: system.xml",
             "integrator: integrator.xml", "topology: ad.pdb",
             "n_steps_per_frame: 10", "n_frames_max: 10000"
         ])
 
-    def teardown(self):
+    def teardown_method(self):
         os.chdir(self.cwd)
 
     def _create_files(self, tmpdir):

paths_cli/tests/compiling/test_plugins.py

@@ -3,7 +3,7 @@
 from unittest.mock import Mock
 
 class TestCompilerPlugin:
-    def setup(self):
+    def setup_method(self):
         self.plugin_class = Mock(category='foo')
         self.plugin = CategoryPlugin(self.plugin_class)
         self.aliased_plugin = CategoryPlugin(self.plugin_class,

paths_cli/tests/compiling/test_root_compiler.py

@@ -58,7 +58,7 @@ def test_canonical_name(input_name):
 
 
 class TestCategoryCompilerProxy:
-    def setup(self):
+    def setup_method(self):
         self.compiler = CategoryCompiler(None, "foo")
         self.compiler.named_objs['bar'] = 'baz'
         self.proxy = _CategoryCompilerProxy('foo')

paths_cli/tests/compiling/test_volumes.py

@@ -14,7 +14,7 @@
 from paths_cli.compiling.volumes import *
 
 class TestBuildCVVolume:
-    def setup(self):
+    def setup_method(self):
         self.yml = "\n".join(["type: cv-volume", "cv: {func}",
                               "lambda_min: 0", "lambda_max: 1"])
 
@@ -90,7 +90,7 @@ def test_build_cv_volume(self, inline, periodic):
 
 
 class TestBuildCombinationVolume:
-    def setup(self):
+    def setup_method(self):
         from  openpathsampling.experimental.storage.collective_variables \
                 import CollectiveVariable
         self.cv = CollectiveVariable(lambda s: s.xyz[0][0]).named('foo')

paths_cli/tests/test_cli.py

@@ -7,7 +7,7 @@
 
 
 class TestOpenPathSamplingCLI(object):
-    def setup(self):
+    def setup_method(self):
         def make_mock(name, helpless=False, return_val=None):
             if return_val is None:
                 return_val = name