Merge branch 'main' into parallel_runs_docs

openfecli/tests/commands/test_gather.py

@@ -5,6 +5,7 @@
 import pathlib
 import pytest
 import pooch
+from ..utils import assert_click_success
 
 from openfecli.commands.gather import (
     gather, format_estimate_uncertainty, _get_column,
@@ -135,24 +136,24 @@ def test_get_column(val, col):
 """
 
 @pytest.fixture()
-def results_dir_serial(tmpdir):
+def results_dir_serial(tmpdir)->str:
     """Example output data, with replicates run in serial (3 replicates per results JSON)."""
     with tmpdir.as_cwd():
         with resources.files('openfecli.tests.data') as d:
-            t = tarfile.open(d / 'rbfe_results.tar.gz', mode='r')
-            t.extractall('.')
+            tar = tarfile.open(d / 'rbfe_results.tar.gz', mode='r')
+            tar.extractall('.')
 
-        return os.path.abspath(t.getnames()[0])
+        return os.path.abspath(tar.getnames()[0])
 
 @pytest.fixture()
-def results_dir_parallel(tmpdir):
+def results_dir_parallel(tmpdir)->str:
     """Example output data, with replicates run in serial (3 replicates per results JSON)."""
     with tmpdir.as_cwd():
         with resources.files('openfecli.tests.data') as d:
-            t = tarfile.open(d / 'rbfe_results_parallel.tar.gz', mode='r')
-            t.extractall('.')
+            tar = tarfile.open(d / 'rbfe_results_parallel.tar.gz', mode='r')
+            tar.extractall('.')
 
-        return os.path.abspath(t.getnames()[0])
+        return os.path.abspath(tar.getnames()[0])
 
 @pytest.mark.parametrize('data_fixture', ['results_dir_serial', 'results_dir_parallel'])
 @pytest.mark.parametrize('report', ["", "dg", "ddg", "raw"])
@@ -194,54 +195,39 @@ def test_generate_bad_legs_error_message(include):
     for string in expected:
         assert string in msg
 
+class TestGatherFailedEdges:
+    @pytest.fixture()
+    def results_dir_serial_missing_leg(self, tmpdir)->str:
+        """Example output data, with replicates run in serial and one deleted results JSON."""
+        with tmpdir.as_cwd():
+            with resources.files('openfecli.tests.data') as d:
+                tar = tarfile.open(d / 'rbfe_results.tar.gz', mode='r')
+                tar.extractall('.')
 
-@pytest.mark.xfail
-def test_missing_leg_error(results_dir_serial):
-    file_to_remove = "easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json"
-    (pathlib.Path("results") / file_to_remove).unlink()
+                results_dir_path = os.path.abspath(tar.getnames()[0])
+                file_to_remove = "easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json"
+                (pathlib.Path(results_dir_path)/ file_to_remove).unlink()
+        return results_dir_path
 
-    runner = CliRunner()
-    result = runner.invoke(gather, ['results'] + ['-o', '-'])
-    assert result.exit_code == 1
-    assert isinstance(result.exception, RuntimeError)
-    assert "Unable to determine" in str(result.exception)
-    assert "'lig_ejm_31'" in str(result.exception)
-    assert "'lig_ejm_42'" in str(result.exception)
+    def test_missing_leg_error(self, results_dir_serial_missing_leg: str):
+        runner = CliRunner()
+        result = runner.invoke(gather, [results_dir_serial_missing_leg] + ['-o', '-'])
 
+        assert result.exit_code == 1
+        assert isinstance(result.exception, RuntimeError)
+        assert "Unable to determine" in str(result.exception)
+        assert "'lig_ejm_31'" in str(result.exception)
+        assert "'lig_ejm_42'" in str(result.exception)
 
-@pytest.mark.xfail
-def test_missing_leg_allow_partial(results_dir_serial):
-    file_to_remove = "easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json"
-    (pathlib.Path("results") / file_to_remove).unlink()
 
-    runner = CliRunner()
-    result = runner.invoke(gather,
-                           ['results'] + ['--allow-partial', '-o', '-'])
-    assert result.exit_code == 0
+    def test_missing_leg_allow_partial(self, results_dir_serial_missing_leg: str):
+        runner = CliRunner()
+        result = runner.invoke(gather, [results_dir_serial_missing_leg] + ['--allow-partial', '-o', '-'])
 
+        assert_click_success(result)
 
 RBFE_RESULTS = pooch.create(
     pooch.os_cache('openfe'),
     base_url="doi:10.6084/m9.figshare.25148945",
     registry={"results.tar.gz": "bf27e728935b31360f95188f41807558156861f6d89b8a47854502a499481da3"},
 )
-
-
-@pytest.fixture
-def rbfe_results():
-    # fetches rbfe results from online
-    # untars into local directory and returns path to this
-    d = RBFE_RESULTS.fetch('results.tar.gz', processor=pooch.Untar())
-
-    return os.path.join(pooch.os_cache('openfe'), 'results.tar.gz.untar', 'results')
-
-
-@pytest.mark.download
-@pytest.mark.xfail
-def test_rbfe_results(rbfe_results):
-    runner = CliRunner()
-
-    result = runner.invoke(gather, ['--report', 'raw', rbfe_results])
-
-    assert result.exit_code == 0
-    assert result.stdout_bytes == _EXPECTED_RAW

openfecli/tests/utils.py

@@ -0,0 +1,15 @@
+"""Helper utilities for CLI tests"""
+
+import click
+import traceback
+
+
+def assert_click_success(result: click.testing.Result): # -no-cov-
+    """Pass through error message if a click test fails.
+    Taken from https://github.com/openpathsampling/openpathsampling-cli/blob/main/paths_cli/commands/pathsampling.py
+    """
+    if result.exit_code != 0:
+        print(result.output)
+        traceback.print_tb(result.exc_info[2])
+        print(result.exc_info[0], result.exc_info[1])
+    assert result.exit_code == 0