Merge branch 'dev' into f-extend-yaml-model

.gitlab-ci.yml

@@ -64,6 +64,7 @@ test:
       - rc=`cat .docker/result`  
       - exit $rc
   dependencies: [cert]
+  needs: [cert]
   artifacts:
     paths:
       - caosdb_log.txt
@@ -95,6 +96,7 @@ cert:
   tags: [docker]
   stage: cert
   image: $CI_REGISTRY_IMAGE
+  needs: [build-testenv]
   artifacts:
     paths:
       - .docker/cert/
@@ -106,6 +108,7 @@ style:
   tags: [docker]
   stage: style
   image: $CI_REGISTRY_IMAGE
+  needs: []
   script:
       - make style
   allow_failure: true
@@ -114,6 +117,7 @@ unittest:
   tags: [docker]
   stage: unittest
   image: $CI_REGISTRY_IMAGE
+  needs: []
   script:
       - tox
 

README_SETUP.md

@@ -48,7 +48,8 @@ Optional h5-crawler:
    `integrationtest/extroot/` directory.
 
 ## Code Formatting
-`autopep8 -i -r ./`
+
+`make style`
 
 ## Documentation #
 

integrationtests/test_assure_functions.py

@@ -32,26 +32,25 @@ from caosadvancedtools.cfood import (assure_object_is_in_list)
 from caosadvancedtools.guard import (global_guard, RETRIEVE, UPDATE)
 
 
-def setup_module():
+def setup():
     """Delete all test entities."""
     db.execute_query("FIND Test*").delete(raise_exception_on_error=False)
 
 
-def setup():
+def setup_module():
     """Allow all updates and delete test data"""
     global_guard.level = UPDATE
-    setup_module()
+    setup()
 
 
-def teardown():
+def teardown_module():
     """Reset guard level and delete test data."""
     global_guard.level = RETRIEVE
-    setup_module()
+    setup()
 
 
 def test_assure_list_in_place():
     """Test an in-place update with `assure_object_is_in_list`."""
-
     int_list_prop = db.Property(name="TestIntListProperty",
                                 datatype=db.LIST(db.INTEGER)).insert()
     rt1 = db.RecordType(name="TestType1").add_property(

integrationtests/test_base_table_exporter_integration.py

@@ -23,6 +23,7 @@
 # ** end header
 #
 import caosdb as db
+import pytest
 from caosadvancedtools import table_export as te
 
 
@@ -85,8 +86,11 @@ def setup_module():
         pass
 
 
+@pytest.fixture(autouse=True)
 def setup():
-    """No further setup"""
+    """Same as module setup."""
+    setup_module()
+    yield None
     setup_module()
 
 

integrationtests/test_crawl_with_datamodel_problems.py

@@ -20,10 +20,11 @@
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 #
 # ** end header
-"""Test whether the crawler correctly identifies the data model
-problems caused by a faulty model.
+
+"""Test whether the crawler correctly identifies the data model problems caused by a faulty model.
 
 """
+
 import caosdb as db
 from caosadvancedtools import loadFiles
 from caosadvancedtools.cfood import fileguide

integrationtests/test_datamodel_problems.py

@@ -44,12 +44,15 @@ def setup_module():
         print(delete_exc)
 
 
+@pytest.fixture(autouse=True)
 def setup():
-    """No further setup"""
+    """Same as module setup."""
+    setup_module()
+    yield None
     setup_module()
 
 
-def teardown():
+def teardown_module():
     """Clear and delete again."""
     setup_module()
 

setup.py

@@ -154,10 +154,10 @@ def setup_package():
         long_description_content_type="text/markdown",
         author='Henrik tom Wörden',
         author_email='h.tomwoerden@indiscale.com',
-        install_requires=["caosdb>=0.6.0",
+        install_requires=["caosdb>=0.7.0",
+                          "numpy>=1.17.3",
                           "openpyxl>=3.0.0",
                           "pandas>=1.2.0",
-                          "numpy>=1.17.3",
                           "xlrd>=2.0",
                           ],
         extras_require={"h5-crawler": ["h5py>=3.3.0", ],

src/caosadvancedtools/cfood.py

@@ -391,7 +391,7 @@ class AbstractFileCFood(AbstractCFood):
 def assure_object_is_in_list(obj, containing_object, property_name,
                              to_be_updated=None, datatype=None):
     """Checks whether `obj` is one of the values in the list property
-    `property_name` of the supplied entity  containing_object`.
+    `property_name` of the supplied entity `containing_object`.
 
     If this is the case this function returns. Otherwise the entity is
     added to the property `property_name` and the entity