diff --git a/tests/test_training_tutorial.py b/tests/test_training_tutorial.py index 60c33475e..cb17fde47 100644 --- a/tests/test_training_tutorial.py +++ b/tests/test_training_tutorial.py @@ -1,6 +1,7 @@ """Training:tutorial functions.""" import os import shutil +import unittest from planemo.engine import ( engine_context, @@ -41,6 +42,7 @@ training = Training(KWDS) +@unittest.skip("Debug") def test_get_galaxy_datatype(): """Test :func:`planemo.training.tutorial.get_galaxy_datatype`.""" assert get_galaxy_datatype("csv", datatype_fp) == "csv" @@ -48,6 +50,7 @@ def test_get_galaxy_datatype(): assert "# Please add" in get_galaxy_datatype("unknown", datatype_fp) +@unittest.skip("Debug") def test_get_zenodo_record(): """Test :func:`planemo.training.tutorial.get_zenodo_record`.""" z_record, req_res = get_zenodo_record(zenodo_link) @@ -71,6 +74,7 @@ def test_get_zenodo_record(): assert file_link_prefix in req_res['files'][0]['links']['self'] +@unittest.skip("Debug") def test_get_wf_inputs(): """Test :func:`planemo.training.tutorial.get_wf_inputs`.""" step_inp = { @@ -96,6 +100,7 @@ def test_get_wf_inputs(): assert 'tt' in step_inputs['add_to_database']['tab']['0'] +@unittest.skip("Debug") def test_get_wf_param_values(): """Test :func:`planemo.training.tutorial.get_wf_param_values`.""" wf_step = wf['steps']['3'] @@ -129,6 +134,7 @@ def test_get_hands_on_boxes_from_running_galaxy(): assert_body_contains(tuto_body, '## Sub-step with **Select first**') +@unittest.skip("Debug") def test_tutorial_init(): """Test :func:`planemo.training.tutorial.tutorial.init`.""" # with default parameter @@ -159,6 +165,7 @@ def test_tutorial_init(): assert "my_tuto" in tuto.dir +@unittest.skip("Debug") def test_tutorial_init_from_kwds(): """Test :func:`planemo.training.tutorial.tutorial.init_from_kwds`.""" kwds = { @@ -187,6 +194,7 @@ def test_tutorial_init_from_kwds(): assert "my_tuto" in tuto.dir +@unittest.skip("Debug") def test_tutorial_init_from_existing_tutorial(): """Test :func:`planemo.training.tutorial.tutorial.init_from_existing_tutorial`.""" tuto = Tutorial( @@ -207,6 +215,7 @@ def test_tutorial_init_from_existing_tutorial(): shutil.rmtree("topics") +@unittest.skip("Debug") def test_tutorial_init_data_lib(): """Test :func:`planemo.training.tutorial.tutorial.init_data_lib`.""" tuto = Tutorial( @@ -231,6 +240,7 @@ def test_tutorial_init_data_lib(): shutil.rmtree("topics") +@unittest.skip("Debug") def test_tutorial_get_tuto_metata(): """Test :func:`planemo.training.tutorial.tutorial.get_tuto_metata`.""" tuto = Tutorial( @@ -242,6 +252,7 @@ def test_tutorial_get_tuto_metata(): assert '- q1' in metadata +@unittest.skip("Debug") def test_tutorial_set_dir_name(): """Test :func:`planemo.training.tutorial.tutorial.set_dir_name`.""" tuto = Tutorial( @@ -257,6 +268,7 @@ def test_tutorial_set_dir_name(): assert tuto.name in tuto.wf_fp +@unittest.skip("Debug") def test_tutorial_exists(): """Test :func:`planemo.training.tutorial.tutorial.exists`.""" # default @@ -270,6 +282,7 @@ def test_tutorial_exists(): shutil.rmtree("topics") +@unittest.skip("Debug") def test_tutorial_has_workflow(): """Test :func:`planemo.training.tutorial.tutorial.has_workflow`.""" # default @@ -315,6 +328,7 @@ def test_tutorial_export_workflow_file(): shutil.rmtree("topics") +@unittest.skip("Debug") def test_tutorial_get_files_from_zenodo(): """Test :func:`planemo.training.tutorial.tutorial.get_files_from_zenodo`.""" tuto = Tutorial( @@ -335,6 +349,7 @@ def test_tutorial_get_files_from_zenodo(): assert files[1]['ext'] == 'csv' +@unittest.skip("Debug") def test_tutorial_prepare_data_library_from_zenodo(): """Test :func:`planemo.training.tutorial.tutorial.prepare_data_library_from_zenodo`.""" # without zenodo link @@ -355,6 +370,7 @@ def test_tutorial_prepare_data_library_from_zenodo(): shutil.rmtree("topics") +@unittest.skip("Debug") def test_tutorial_write_hands_on_tutorial(): """Test :func:`planemo.training.tutorial.tutorial.write_hands_on_tutorial`.""" tuto = Tutorial( diff --git a/tests/test_training_utils.py b/tests/test_training_utils.py index ca89ab01a..4ce895869 100644 --- a/tests/test_training_utils.py +++ b/tests/test_training_utils.py @@ -1,5 +1,6 @@ """Training:utils functions.""" import os +import unittest from planemo.training.utils import ( load_yaml, @@ -11,6 +12,7 @@ metadata_fp = os.path.join(TEST_DATA_DIR, "training_metadata.yaml") +@unittest.skip("Debug") def test_load_yaml(): """Test :func:`planemo.training.utils.load_yaml`.""" metadata = load_yaml(metadata_fp) @@ -20,6 +22,7 @@ def test_load_yaml(): assert metadata['maintainers'][0] == 'maintainer1' +@unittest.skip("Debug") def test_save_to_yaml(): """Test :func:`planemo.training.utils.save_to_yaml`.""" metadata = load_yaml(metadata_fp) @@ -29,6 +32,7 @@ def test_save_to_yaml(): os.remove(new_metadata_fp) +@unittest.skip("Debug") def test_requirement_init(): """Test :func:`planemo.training.utils.Requirement.init`.""" # test requirement with default parameter @@ -43,6 +47,7 @@ def test_requirement_init(): assert req.link == "URL" +@unittest.skip("Debug") def test_requirement_init_from_dict(): """Test :func:`planemo.training.utils.Requirement.init_from_dict`.""" req = Requirement() @@ -56,6 +61,7 @@ def test_requirement_init_from_dict(): assert req.link == "http://URL" +@unittest.skip("Debug") def test_requirement_export_to_ordered_dict(): """Test :func:`planemo.training.utils.Requirement.export_to_ordered_dict`.""" req = Requirement() diff --git a/tests/test_validation.py b/tests/test_validation.py index ae13e1fe5..e4eed7172 100644 --- a/tests/test_validation.py +++ b/tests/test_validation.py @@ -1,4 +1,5 @@ import os +import unittest from galaxy.util import unicodify @@ -11,18 +12,21 @@ ) +@unittest.skip("Debug") @skip_unless_module("lxml") def test_lxml_validation(): lxml_xsd_validator = validation.LxmlValidator() _check_validator(lxml_xsd_validator) +@unittest.skip("Debug") @skip_unless_executable("xmllint") def test_xmllint_validation(): xmllint_xsd_validator = validation.XmllintValidator() _check_validator(xmllint_xsd_validator) +@unittest.skip("Debug") def test_tool_dependencies_validation(): _assert_validates(shed_lint.TOOL_DEPENDENCIES_XSD, _path("tool_dependencies_good_1.xml")) @@ -30,6 +34,7 @@ def test_tool_dependencies_validation(): _path("tool_dependencies_good_2.xml")) +@unittest.skip("Debug") def test_repository_dependencies_validation(): _assert_validates(shed_lint.REPO_DEPENDENCIES_XSD, _path("repository_dependencies.xml")) diff --git a/tests/test_workflow_lint.py b/tests/test_workflow_lint.py index bed860178..04dad0955 100644 --- a/tests/test_workflow_lint.py +++ b/tests/test_workflow_lint.py @@ -1,4 +1,5 @@ import os +import unittest from planemo.workflow_lint import input_labels from .test_utils import ( @@ -6,6 +7,7 @@ ) +@unittest.skip("Debug") def test_input_labels(): wf_example_1 = os.path.join(TEST_DATA_DIR, "wf_repos", "basic_format2_ok", "basic_format2.gxwf.yml") labels = input_labels(wf_example_1) diff --git a/tests/test_xml_diff.py b/tests/test_xml_diff.py index 8b3549746..c71be3156 100644 --- a/tests/test_xml_diff.py +++ b/tests/test_xml_diff.py @@ -1,11 +1,13 @@ import os import sys +import unittest from xml.etree import ElementTree from planemo.xml.diff import diff from .test_utils import TEST_DIR +@unittest.skip("Debug") def test_diff(): # Check with and without reporter. _check(sys.stdout.write)