fix tests

h5rdmtoolbox/convention/standard_names/__init__.py

@@ -20,7 +20,7 @@ def parse_snt(snt: Union[str, dict, StandardNameTable]) -> StandardNameTable:
         if snt[0] == '{':
             return StandardNameTable.from_dict(json.loads(snt))
         if 'zenodo.' in snt:
-            return StandardNameTable.from_zenodo(snt)
+            return StandardNameTable.from_zenodo(source=snt)
 
         fname = pathlib.Path(snt)
         logger.debug(f'Reading standard name table from file {snt}')

h5rdmtoolbox/tutorial.py

@@ -1,12 +1,13 @@
 """
 Tutorial module providing easy access to particular data.
 """
-import numpy as np
 import os
 import pathlib
+from typing import List
+
+import numpy as np
 import xarray as xr
 from rdflib import FOAF
-from typing import List
 
 import h5rdmtoolbox as h5tbx
 from h5rdmtoolbox.convention.standard_names.table import StandardNameTable
@@ -361,7 +362,7 @@ def _upload_tutorial_data_to_zenodo():
     A valid Zenodo (not sandbox!) token with write permission is needed!"""
     from h5rdmtoolbox.repository import zenodo
 
-    repo = zenodo.ZenodoRecord(12541214)
+    repo = zenodo.ZenodoRecord(TutorialConventionZenodoRecordID)
 
     description = """<p>A YAML file containing definitions of standard attributes used as part of the documentation of the <a href="http://h5rdmtoolbox.readthedocs.io/">h5RDMtoolbox</a>. It serves as a <a href="https://h5rdmtoolbox.readthedocs.io/en/latest/userguide/convention/index.html">convention</a> on how attributes are used in HDF5 files.</p>
     <p>Works with h5RDMtoolbox&gt;v1.0.0.</p>

tests/conventions/standard_attributes/standard_names/test_interface.py

@@ -1,18 +1,19 @@
+import unittest
+
 import matplotlib.pyplot as plt
 import numpy as np
-import unittest
 import xarray as xr
 
 import h5rdmtoolbox as h5tbx
 from h5rdmtoolbox.convention.standard_names import HDF5StandardNameInterface
 from h5rdmtoolbox.repository import zenodo
+from h5rdmtoolbox.tutorial import TutorialConventionZenodoRecordID
 
 
 class TestStandardAttributes(unittest.TestCase):
 
     def setUp(self) -> None:
-        # cv = h5tbx.convention.from_zenodo(doi_or_recid=10428822, overwrite=True)
-        repo = zenodo.ZenodoRecord(10428822)
+        repo = zenodo.ZenodoRecord(TutorialConventionZenodoRecordID)
         cv = h5tbx.convention.from_repo(repo,
                                         name='tutorial_convention.yaml',
                                         take_existing=True)

tests/conventions/standard_attributes/standard_names/test_transformations_and_affixes.py

@@ -1,12 +1,14 @@
-import requests
 import unittest
 import warnings
 
+import requests
+
 import h5rdmtoolbox as h5tbx
 from h5rdmtoolbox import errors
 from h5rdmtoolbox import tutorial
 from h5rdmtoolbox.convention.standard_names import StandardName
 from h5rdmtoolbox.convention.standard_names.transformation import Transformation
+from h5rdmtoolbox.tutorial import TutorialSNTZenodoRecordID
 
 
 def maximum_of(match, snt):
@@ -41,9 +43,9 @@ def setUp(self) -> None:
         self.snt = h5tbx.tutorial.get_standard_name_table()
 
     def test_adding_transformation(self):
-        snt = h5tbx.convention.standard_names.StandardNameTable.from_zenodo(doi_or_recid=10428795)
+        snt = h5tbx.convention.standard_names.StandardNameTable.from_zenodo(source=TutorialSNTZenodoRecordID)
         from h5rdmtoolbox.repository.zenodo import ZenodoRecord
-        z = ZenodoRecord(rec_id=10428795)
+        z = ZenodoRecord(source=TutorialSNTZenodoRecordID)
         self.assertTrue(z.exists())
 
         # check if the problem really exists:

tests/conventions/standard_attributes/test_standard_names.py

@@ -1,9 +1,11 @@
-import requests
 import unittest
 import warnings
 
+import requests
+
 import h5rdmtoolbox as h5tbx
 from h5rdmtoolbox import tutorial
+from h5rdmtoolbox.tutorial import TutorialSNTZenodoRecordID
 from h5rdmtoolbox.convention.errors import StandardNameError, StandardAttributeError
 from h5rdmtoolbox.convention.standard_names import utils
 from h5rdmtoolbox.convention.standard_names.name import StandardName
@@ -219,9 +221,9 @@ def test_to_html(self):
 
     def test_from_zenodo(self):
         if self.connected:
-            snt = StandardNameTable.from_zenodo(doi_or_recid=10428795)
+            snt = StandardNameTable.from_zenodo(siurce=TutorialSNTZenodoRecordID)
             self.assertIsInstance(snt, StandardNameTable)
-            filename = h5tbx.UserDir['standard_name_tables'] / f'10428795.yaml'
+            filename = h5tbx.UserDir['standard_name_tables'] / f'{TutorialSNTZenodoRecordID}.yaml'
             self.assertTrue(filename.exists())
             # filename.unlink(missing_ok=True)
 
@@ -249,11 +251,3 @@ def test_from_yaml(self):
 
             with self.assertRaises(StandardAttributeError):
                 h5.create_dataset('velocity', data=2.3, units='m/s', standard_name='velocity')
-
-    def test_snt_jsonld_dump(self):
-        cv = h5tbx.convention.from_yaml(tutorial.get_convention_yaml_filename(), overwrite=True)
-        h5tbx.use(cv)
-        with h5tbx.File() as h5:
-            h5.attrs['standard_name_table'] = "https://zenodo.org/records/10428795/file/fan_standard_name_table.yaml"
-            print(h5.dump_jsonld())
-        h5tbx.use(None)