move test data to zenodo

openfecli/tests/commands/test_gather.py

@@ -1,3 +1,4 @@
+from typing import Callable
 from click.testing import CliRunner
 from importlib import resources
 import tarfile
@@ -6,10 +7,10 @@
 import pytest
 import pooch
 from ..utils import assert_click_success
+from ..conftest import HAS_INTERNET
 
 from openfecli.commands.gather import (
     gather, format_estimate_uncertainty, _get_column,
-    _generate_bad_legs_error_message,
 )
 
 @pytest.mark.parametrize('est,unc,unc_prec,est_str,unc_str', [
@@ -134,30 +135,29 @@ def test_get_column(val, col):
 solvent	lig_ejm_46	lig_jmc_28	23.3	0.8
 solvent	lig_ejm_46	lig_jmc_28	23.4	0.8
 """
-
-@pytest.fixture()
-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:
-            tar = tarfile.open(d / 'rbfe_results.tar.gz', mode='r')
-            tar.extractall('.')
-
-        return os.path.abspath(tar.getnames()[0])
-
-@pytest.fixture()
-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:
-            tar = tarfile.open(d / 'rbfe_results_parallel.tar.gz', mode='r')
-            tar.extractall('.')
-
-        return os.path.abspath(tar.getnames()[0])
-
-@pytest.mark.parametrize('data_fixture', ['results_dir_serial', 'results_dir_parallel'])
+POOCH_CACHE = pooch.os_cache('openfe')
+ZENODO_RBFE_DATA = pooch.create(
+        path = POOCH_CACHE,
+        base_url="doi:10.5281/zenodo.14884797",
+        registry={
+            "rbfe_results_serial_repeats.tar.gz": "md5:d7c5e04786d03e1280a74639c2981546",
+            "rbfe_results_parallel_repeats.tar.gz": "md5:cc54afe32b56232339a9315f4c3d6d91"},
+    )
+
+@pytest.fixture
+def rbfe_result_dir()->pathlib.Path:
+    def _rbfe_result_dir(dataset)->str:
+        ZENODO_RBFE_DATA.fetch(f'{dataset}.tar.gz', processor=pooch.Untar())
+        cache_dir = pathlib.Path(pooch.os_cache('openfe'))/f'{dataset}.tar.gz.untar/{dataset}/'
+        return  cache_dir
+
+    return _rbfe_result_dir
+
+@pytest.mark.skipif(not os.path.exists(POOCH_CACHE) and not HAS_INTERNET,reason="Internet seems to be unavailable and test data is not cached locally.")
+@pytest.mark.parametrize('dataset', ['rbfe_results_serial_repeats', 'rbfe_results_parallel_repeats'])
 @pytest.mark.parametrize('report', ["", "dg", "ddg", "raw"])
-def test_gather(request, data_fixture, report):
+def test_gather(rbfe_result_dir, dataset, report):
+
     expected = {
         "": _EXPECTED_DG,
         "dg": _EXPECTED_DG,
@@ -171,30 +171,30 @@ def test_gather(request, data_fixture, report):
     else:
         args = []
 
-    results_dir = request.getfixturevalue(data_fixture)
-    result = runner.invoke(gather, [results_dir] + args + ['-o', '-'])
+    results_dir = rbfe_result_dir(dataset)
+    result = runner.invoke(gather, [str(results_dir)] + args + ['-o', '-'])
 
     assert_click_success(result)
 
     actual_lines = set(result.stdout_bytes.split(b'\n'))
     assert set(expected.split(b'\n')) == actual_lines
 
+@pytest.mark.skipif(not os.path.exists(POOCH_CACHE) and not HAS_INTERNET,reason="Internet seems to be unavailable and test data is not cached locally.")
 class TestGatherFailedEdges:
     @pytest.fixture()
-    def results_dir_serial_missing_legs(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('.')
-
-                results_dir_path = os.path.abspath(tar.getnames()[0])
-                files_to_remove = ["rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json",
-                                   "rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json"
-                                   ]
-                for fname in files_to_remove:
-                    (pathlib.Path(results_dir_path)/ fname).unlink()
-        return results_dir_path
+    def results_dir_serial_missing_legs(self, rbfe_result_dir, tmpdir)->str:
+        """Example output data, with replicates run in serial and two missing results JSONs."""
+        # TODO: update to return a list of paths without doing this symlink mess, when gather supports it.
+        rbfe_result_dir = rbfe_result_dir('rbfe_results_serial_repeats')
+        tmp_results_dir =  tmpdir
+        files_to_skip = ["rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json",
+                         "rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json"
+                            ]
+        for item in os.listdir(rbfe_result_dir):
+            if item not in files_to_skip:
+                os.symlink(rbfe_result_dir/item, tmp_results_dir/item)
+
+        return str(tmp_results_dir)
 
     def test_missing_leg_error(self, results_dir_serial_missing_legs: str):
         runner = CliRunner()
@@ -213,9 +213,3 @@ def test_missing_leg_allow_partial(self, results_dir_serial_missing_legs: str):
         result = runner.invoke(gather, [results_dir_serial_missing_legs] + ['--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"},
-)

openfecli/tests/test_fetchables.py

@@ -23,11 +23,11 @@ def fetchable_test(fetchable):
             assert (pathlib.Path("output-dir") / path).exists()
 
 
-def test_rhfe_tutorial():
+def test_rbfe_tutorial():
     fetchable_test(RBFE_TUTORIAL)
 
-def test_rhfe_tutorial_results():
+def test_rbfe_tutorial_results():
     fetchable_test(RBFE_TUTORIAL_RESULTS)
 
-def test_rhfe_showcase():
+def test_rbfe_showcase():
     fetchable_test(RBFE_SHOWCASE)