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Prepare for version 2.5.0 release (#550)
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| vmImage: $(imageName) | ||
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| steps: | ||
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| - checkout: self | ||
| submodules: true | ||
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| # pinned dependencies to reproduce an entire development environment to use HDMF, run HDMF tests, check code style, | ||
| # compute coverage, and create test environments | ||
| codecov==2.1.10 | ||
| coverage==5.3 | ||
| flake8==3.8.4 | ||
| codecov==2.1.11 | ||
| coverage==5.5 | ||
| flake8==3.9.1 | ||
| flake8-debugger==4.0.0 | ||
| flake8-print==4.0.0 | ||
| importlib-metadata<2 | ||
| importlib-metadata==4.0.1 | ||
| python-dateutil==2.8.1 | ||
| tox==3.20.1 | ||
| tox==3.23.0 |
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Submodule hdmf-common-schema
updated
5 files
| +2 −3 | .github/PULL_REQUEST_TEMPLATE/release.md | |
| +1 −1 | common/namespace.yaml | |
| +1 −1 | docs/source/conf.py | |
| +2 −2 | docs/source/format_release_notes.rst | |
| +16 −17 | docs/source/software_process.rst |
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| from h5py import File | ||
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| from hdmf.backends.hdf5 import HDF5IO | ||
| from hdmf.common import Container, get_manager | ||
| from hdmf.spec import NamespaceCatalog | ||
| from hdmf.testing import TestCase, remove_test_file | ||
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| from tests.unit.utils import get_temp_filepath | ||
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| class TestCacheSpec(TestCase): | ||
| """Test caching spec specifically with the namespaces provided by hdmf.common. | ||
| See also TestCacheSpec in tests/unit/test_io_hdf5_h5tools.py. | ||
| """ | ||
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| def setUp(self): | ||
| self.manager = get_manager() | ||
| self.path = get_temp_filepath() | ||
| self.container = Container('dummy') | ||
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| def tearDown(self): | ||
| remove_test_file(self.path) | ||
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| def test_write_no_cache_spec(self): | ||
| """Roundtrip test for not writing spec.""" | ||
| with HDF5IO(self.path, manager=self.manager, mode="a") as io: | ||
| io.write(self.container, cache_spec=False) | ||
| with File(self.path, 'r') as f: | ||
| self.assertNotIn('specifications', f) | ||
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| def test_write_cache_spec(self): | ||
| """Roundtrip test for writing spec and reading it back in.""" | ||
| with HDF5IO(self.path, manager=self.manager, mode="a") as io: | ||
| io.write(self.container) | ||
| with File(self.path, 'r') as f: | ||
| self.assertIn('specifications', f) | ||
| self._check_spec() | ||
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| def test_write_cache_spec_injected(self): | ||
| """Roundtrip test for writing spec and reading it back in when HDF5IO is passed an open h5py.File.""" | ||
| with File(self.path, 'w') as fil: | ||
| with HDF5IO(self.path, manager=self.manager, file=fil, mode='a') as io: | ||
| io.write(self.container) | ||
| with File(self.path, 'r') as f: | ||
| self.assertIn('specifications', f) | ||
| self._check_spec() | ||
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| def _check_spec(self): | ||
| ns_catalog = NamespaceCatalog() | ||
| HDF5IO.load_namespaces(ns_catalog, self.path) | ||
| self.maxDiff = None | ||
| for namespace in self.manager.namespace_catalog.namespaces: | ||
| with self.subTest(namespace=namespace): | ||
| original_ns = self.manager.namespace_catalog.get_namespace(namespace) | ||
| cached_ns = ns_catalog.get_namespace(namespace) | ||
| ns_fields_to_check = list(original_ns.keys()) | ||
| ns_fields_to_check.remove('schema') # schema fields will not match, so reset | ||
| for ns_field in ns_fields_to_check: | ||
| with self.subTest(namespace_field=ns_field): | ||
| self.assertEqual(original_ns[ns_field], cached_ns[ns_field]) | ||
| for dt in original_ns.get_registered_types(): | ||
| with self.subTest(data_type=dt): | ||
| original_spec = original_ns.get_spec(dt) | ||
| cached_spec = cached_ns.get_spec(dt) | ||
| with self.subTest('Data type spec is read back in'): | ||
| self.assertIsNotNone(cached_spec) | ||
| with self.subTest('Cached spec matches original spec'): | ||
| self.assertDictEqual(original_spec, cached_spec) |
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