funowl - npm Package Compare versions

Comparing version 0.1.10 to 0.1.11

tests/test_issues/test_issue_24.py

+import os
+import unittest
+from contextlib import redirect_stderr
+from io import StringIO
+
+from funowl.converters.functional_converter import to_python
+from tests import datadir, SKIP_LONG_TESTS
+
+
+class OBILangTagTestCase(unittest.TestCase):
+
+    @unittest.skipIf(SKIP_LONG_TESTS, "obi image must be present to run this")
+    def test_obi_issue(self):
+        # To run this test:
+        #   a) Download an image of https://bioportal.bioontology.org/ontologies/OBI from the owl link
+        #   b) Use protege to load the downloaded image (ext.owl) and save it in OWL functional syntax (obi.owlf.owl)
+        #   c) Save the output in tests/data/obi.owlf
+        txt = StringIO()
+        with redirect_stderr(txt):
+            with open(os.path.join(datadir, 'obi.owlf')) as f:
+                owl = to_python(f.read())
+        print(str(owl)[-1024:])
+
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_issues/test_issue_33.py

+import sys
+import unittest
+
+from rdflib import Namespace
+
+from funowl import EquivalentObjectProperties, Axiom
+from funowl.terminals.TypingHelper import isinstance_
+
+EX = Namespace("https://example.org/ex#")
+
+
+class AxiomInstanceTestCase(unittest.TestCase):
+
+    def test_axiom_instance(self):
+        """ Test axiom instance problem """
+        x = EquivalentObjectProperties(EX.foo, EX.bar)
+        self.assertTrue(isinstance_(x, Axiom) if sys.version_info < (3, 10, 0) else isinstance(x, Axiom))
+
+
+if __name__ == '__main__':
+    unittest.main()

.github/workflows/main.yaml

@@ -5,3 +5,3 @@ name: Build
   push:
-    branches: [ master ]
+    branches: [ main ]
 
@@ -39,3 +39,3 @@ jobs:
       matrix:
-        python-version: [ 3.8, 3.9 ]
+        python-version: [ 3.8, 3.9, "3.10" ]
 
@@ -42,0 +42,0 @@ steps:

AUTHORS

@@ -1,1 +0,1 @@
-hsolbrig <[e-mail]>
+Harold Solbrig <[e-mail]>

funowl.egg-info/PKG-INFO

 Metadata-Version: 1.2
 Name: funowl
-Version: 0.1.10
+Version: 0.1.11
 Summary: Python rendering of the OWL Functional syntax
@@ -5,0 +5,0 @@ Home-page: http://biolink.github.io/hsolbrig

funowl.egg-info/requires.txt

 bcp47
 pyjsg>=0.11.6
-rdflib>=5.0.0,~=5.0
+rdflib-shim
+rdflib!=6.1.*,>=5.0.0
 rfc3987

funowl/__init__.py

@@ -39,2 +39,8 @@ import sys
 
+# Use the rdflib shim
+from rdflib_shim import RDFLIB_SHIM
+x = RDFLIB_SHIM                 # Force import to stay put
+# from rdflib.plugins.serializers.turtle import RecursiveSerializer
+# RecursiveSerializer.roundtrip_prefixes = True
+
 # TODO: Run coverage and test or toss anything that isn't executed
@@ -41,0 +47,0 @@ # TODO: Consider removing the streaming IO feature -- it doesn't seem to do a lot for performance and makes things compicated

funowl/base/cast_function.py

 import logging
-from collections import Iterable, UserList
+from collections.abc import Iterable
+from collections import UserList
 from copy import copy
@@ -4,0 +5,0 @@ from dataclasses import Field, MISSING, field

funowl/base/list_support.py

@@ -1,2 +0,3 @@
-from collections import UserList, Iterable
+from collections.abc import Iterable
+from collections import UserList
 from copy import copy
@@ -3,0 +4,0 @@ from dataclasses import field

Pipfile

@@ -10,5 +10,6 @@ [[source]]
 [packages]
-rdflib = "~=5.0, >=5.0.0"
+rdflib = ">=5.0.0, !=6.1.*"
+rdflib-shim = "*"
 pyjsg = ">=0.11.6"
 rfc3987 = "*"
 bcp47 = "*"

Pipfile.lock

 {
     "_meta": {
         "hash": {
-            "sha256": "5aad704633b1f3aeea78dd70bd24b31643957398e6f75662f26a1904a87e30e2"
+            "sha256": "00d611f86cf6fb72afd7bc90b90680e2d83fbfe33450779eae90abdc20b87253"
         },
@@ -19,5 +19,5 @@ "pipfile-spec": 6,
             "hashes": [
-                "sha256:31f5abdc7faf16a1a6e9bf2eb31565d004359b821b09944436a34361929ae85a"
+                "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"
             ],
-            "version": "==4.9.2"
+            "version": "==4.9.3"
         },
@@ -34,6 +34,6 @@ "bcp47": {
             "hashes": [
-                "sha256:2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8",
-                "sha256:aa4d33c06640f5352aca96e4b81afd8ab3b47337cc12089822d6f322ac772c81"
+                "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96",
+                "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"
             ],
-            "version": "==0.6.0"
+            "version": "==0.6.1"
         },
@@ -49,24 +49,39 @@ "jsonasobj": {
             "hashes": [
-                "sha256:08d9a80f6996af8862e8a2a4e2d90049af695c4ccd84187e7d7a48f600d37952",
-                "sha256:3c98d3153a2e4ca8ae8942a4bb213477c68519b145ca2d973648bcb9495208e7"
+                "sha256:8679a81c00e2ccb12618adcc2ce5e9a7bef542f4f940ef18e5b7751f5c5a42a4",
+                "sha256:b9bf406c87aab4ff62f9372e38b4fcda5cffc0c12385c46a4b01eb83dafd7850"
             ],
             "index": "pypi",
-            "version": "==0.11.6"
+            "version": "==0.11.9"
         },
         "pyparsing": {
             "hashes": [
-                "sha256:9e3511118010f112a4b4b435ae50e1eaa610cda191acb9e421d60cf5fde83455",
-                "sha256:f8d3fe9fc404576c5164f0f0c4e382c96b85265e023c409c43d48f65da9d60d0"
+                "sha256:04ff808a5b90911829c55c4e26f75fa5ca8a2f5f36aa3a51f68e27033341d3e4",
+                "sha256:d9bdec0013ef1eb5a84ab39a3b3868911598afa494f5faa038647101504e2b81"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==3.0.3"
+            "version": "==3.0.6"
         },
         "rdflib": {
             "hashes": [
-                "sha256:78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155",
-                "sha256:88208ea971a87886d60ae2b1a4b2cdc263527af0454c422118d43fe64b357877"
+                "sha256:6136ae056001474ee2aff5fc5b956e62a11c3a9c66bb0f3d9c0aaa5fbb56854e",
+                "sha256:b7642daac8cdad1ba157fecb236f5d1b2aa1de64e714dcee80d65e2b794d88a6"
             ],
             "index": "pypi",
-            "version": "==5.0.0"
+            "version": "==6.0.2"
         },
+        "rdflib-jsonld": {
+            "hashes": [
+                "sha256:bcf84317e947a661bae0a3f2aee1eced697075fc4ac4db6065a3340ea0f10fc2",
+                "sha256:eda5a42a2e09f80d4da78e32b5c684bccdf275368f1541e6b7bcddfb1382a0e0"
+            ],
+            "version": "==0.6.1"
+        },
+        "rdflib-shim": {
+            "hashes": [
+                "sha256:7a853e7750ef1e9bf4e35dea27d54e02d4ed087de5a9e0c329c4a6d82d647081",
+                "sha256:d955d11e2986aab42b6830ca56ac6bc9c893abd1d049a161c6de2f1b99d4fc0d"
+            ],
+            "index": "pypi",
+            "version": "==1.0.3"
+        },
         "rfc3987": {
@@ -80,2 +95,10 @@ "hashes": [
         },
+        "setuptools": {
+            "hashes": [
+                "sha256:2404879cda71495fc4d5cbc445ed52fdaddf352b36e40be8dcc63147cb4edabe",
+                "sha256:68eb94073fc486091447fcb0501efd6560a0e5a1839ba249e5ff3c4c93f05f90"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==60.5.0"
+        },
         "six": {
@@ -100,7 +123,7 @@ "hashes": [
             "hashes": [
-                "sha256:e019de665e2bcf9c2b64e2e5aa025fa991da8720daa3c1138cadd2fd1856aed0",
-                "sha256:f7af805c321bfa1ce6714c51f254e0d5bb5e5834039bc17db7ebe3a4cec9492b"
+                "sha256:876d180e9d7432c5d1dfd4c5d26b72f099d503e8fcc0feb7532c9289be60fcbd",
+                "sha256:cb957888737fc0bbcd78e3df769addb41fd1ff8cf950dc9e7ad7793f1bf44455"
             ],
             "markers": "python_version >= '3'",
-            "version": "==2.0.7"
+            "version": "==2.0.10"
         },
@@ -117,17 +140,17 @@ "idna": {
             "hashes": [
-                "sha256:6c1246513ecd5ecd4528a0906f910e8f0f9c6b8ec72030dc9fd154dc1a6efd24",
-                "sha256:b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7"
+                "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61",
+                "sha256:f22fa1e554c9ddfd16e6e41ac79759e17be9e492b3587efa038054674760e72d"
             ],
             "index": "pypi",
-            "version": "==2.26.0"
+            "version": "==2.27.1"
         },
         "urllib3": {
             "hashes": [
-                "sha256:4987c65554f7a2dbf30c18fd48778ef124af6fab771a377103da0585e2336ece",
-                "sha256:c4fdf4019605b6e5423637e01bc9fe4daef873709a7973e195ceba0a62bbc844"
+                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
+                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.7"
+            "version": "==1.26.8"
         }
     }
 }

PKG-INFO

 Metadata-Version: 1.2
 Name: funowl
-Version: 0.1.10
+Version: 0.1.11
 Summary: Python rendering of the OWL Functional syntax
@@ -5,0 +5,0 @@ Home-page: http://biolink.github.io/hsolbrig

requirements.txt

@@ -15,3 +15,4 @@ ################################################################################
 pyjsg>=0.11.6
-rdflib~=5.0, >=5.0.0
+rdflib-shim
+rdflib>=5.0.0, !=6.1.*
 rfc3987

tests/__init__.py

@@ -8,2 +8,5 @@ import logging
 cwd = os.path.abspath(os.path.dirname(__file__))
-datadir = os.path.join(cwd, 'data')
+datadir = os.path.join(cwd, 'data')
+
+# Set this to False if you want to make sure some of the big inputs work
+SKIP_LONG_TESTS = True

tests/test_issues/test_issue_27.py

@@ -9,7 +9,4 @@ import os
 
-from tests import datadir
+from tests import datadir, SKIP_LONG_TESTS
 
-# Set this to False if you want to make sure some of the big inputs work
-SKIP_LONG_TESTS = True
-
 OWL_1 = """
@@ -80,5 +77,2 @@ Prefix(:=<http://www.biopax.org/release/biopax-level3.owl#>)
 
-        # TO Complete -- redirect the part of the stdout that kicks out the errors on URI's
-        #  Verify that we don't have an error message in it
-        #  Look up a bit of the OWL that has a PMID in it and make sure that it prints correctly
         txt = StringIO()
@@ -85,0 +79,0 @@ with redirect_stderr(txt):

tests/test_issues/test_issue_28.py

 import unittest
-from contextlib import redirect_stderr
 from io import StringIO
 
 from funowl.converters.functional_converter import to_python
-import requests
 
@@ -8,0 +6,0 @@ OWL_1 = """

tests/test_owl2_test_suite/test_owl2.py

@@ -103,3 +103,3 @@ import logging
         expected_rdf = Graph()
-        expected_rdf.load(fileloc.replace('.func', '.ttl'), format="turtle")
+        expected_rdf.parse(fileloc.replace('.func', '.ttl'), format="turtle")
         actual_rdf_graph = Graph()
@@ -106,0 +106,0 @@ actual_rdf_graph.add = lambda t: add(actual_rdf_graph, t)

funowl.egg-info/pbr.json

-{"git_version": "0929156", "is_release": false}

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Improved metrics

Total package byte prevSize

50516923

442.65%

Number of package files

2188

0.18%

Lines of code

5203

0.7%