EMMC-ASBL · jesper-friis · May 7, 2025 · Apr 23, 2025 · Apr 23, 2025 · Apr 23, 2025
diff --git a/docs/datadoc/customisation.md b/docs/datadoc/customisation.md
@@ -177,9 +177,9 @@ You can save this context to a triplestore with
 >>> ts = Triplestore("rdflib")
 >>> save_datadoc(  # doctest: +ELLIPSIS
 ...     ts,
-...      "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/custom_context.yaml",
+...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/custom_context.yaml",
 ... )
-AttrDict(...)
+{'@context': [...]}
 
 ```
 

diff --git a/docs/datadoc/documenting-a-resource.md b/docs/datadoc/documenting-a-resource.md
@@ -37,7 +37,7 @@ We therefore have to define them explicitly
 
 ```python
 >>> prefixes = {
-...     "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+...     "sem": "https://w3id.org/emmo/domain/sem/0.1#",
 ...     "kb": "http://example.com/kb/"
 ... }
 
@@ -60,7 +60,7 @@ We therefore have to define them explicitly
     {
         "@context": "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.3/context.json",
         "@id": "http://example.com/kb/image1",
-        "@type": "https://w3id.com/emmo/domain/sem/0.1#SEMImage",
+        "@type": "https://w3id.org/emmo/domain/sem/0.1#SEMImage",
         "creator": {
             "@type": [
                 "http://xmlns.com/foaf/0.1/Agent",
@@ -104,7 +104,7 @@ You can use `ts.serialize()` to list the content of the triplestore (defaults to
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix kb: <http://example.com/kb/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix sem: <https://w3id.com/emmo/domain/sem/0.1#> .
+@prefix sem: <https://w3id.org/emmo/domain/sem/0.1#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 kb:image1 a sem:SEMImage ;
@@ -145,11 +145,11 @@ Saving [semdata.yaml] to a triplestore can e.g. be done with
 
 ```python
 >>> from tripper.datadoc import save_datadoc
->>> save_datadoc(  # doctest: +ELLIPSIS
+>>> save_datadoc(  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
 ...    ts,
 ...    "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml"
 ... )
-AttrDict(...)
+{'@graph': [...], ...}
 
 ```
 
@@ -186,7 +186,7 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 >>> td = TableDoc.parse_csv(
 ...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv",
 ...     prefixes={
-...         "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+...         "sem": "https://w3id.org/emmo/domain/sem/0.1#",
 ...         "semdata": "https://he-matchmaker.eu/data/sem/",
 ...         "sample": "https://he-matchmaker.eu/sample/",
 ...         "mat": "https://he-matchmaker.eu/material/",

diff --git a/docs/session.md b/docs/session.md
@@ -57,7 +57,11 @@ you can now do:
 ```python
 >>> from tripper import Literal, Session
 
->>> session = Session()
+# Normally you will call Session with no arguments
+>>> session = Session()  # doctest: +SKIP
+
+# ...but it is also possible to specify the config file explicitly
+>>> session = Session("tests/input/session.yaml")
 >>> ts = session.get_triplestore("FusekiTest")
 >>> EX = ts.bind("ex", "http://example.com#")
 

diff --git a/docs/tutorial.md b/docs/tutorial.md
@@ -137,8 +137,7 @@ The `check=True` enables checking for existing IRIs.
 >>> EMMO.invalid_name  # doctest: +ELLIPSIS
 Traceback (most recent call last):
     ...
-tripper.errors.NoSuchIRIError: https://w3id.org/emmo#invalid_name
-Maybe you have to remove the cache file: ...
+tripper.errors.NoSuchIRIError: https://w3id.org/emmo#invalid_name...
 
 ```
 
@@ -167,8 +166,7 @@ For example:
 >>> FOOD.Hamburger  # doctest: +ELLIPSIS
 Traceback (most recent call last):
     ...
-tripper.errors.NoSuchIRIError: http://onto-ns.com/ontologies/examples/food#Hamburger
-...
+tripper.errors.NoSuchIRIError: http://onto-ns.com/ontologies/examples/food#Hamburger...
 
 # Add Hamburger to known labels
 >>> extend_namespace(FOOD, {"Hamburger": FOOD + "Hamburger"})
@@ -179,8 +177,7 @@ True
 >>> FOOD.Fish  # doctest: +ELLIPSIS
 Traceback (most recent call last):
     ...
-tripper.errors.NoSuchIRIError: http://onto-ns.com/ontologies/examples/food#Fish
-...
+tripper.errors.NoSuchIRIError: http://onto-ns.com/ontologies/examples/food#Fish...
 
 # Extend FOOD from an online turtle file
 >>> extend_namespace(

diff --git a/docs/units/units.md b/docs/units/units.md
@@ -49,8 +49,8 @@ Item access creates a subclass of a Pint quantity representation (see [Working w
 >>> ureg["Pa"]
 <Quantity(1, 'Pascal')>
 
->>> ureg["N⋅m²"]
-<Quantity(1, 'Newton * Metre ** 2')>
+>>> ureg["A/m²"]
+<Quantity(1.0, 'Ampere / Metre ** 2')>
 
 ```
 

diff --git a/tests/input/semdata-context.json b/tests/input/semdata-context.json
@@ -1,13 +1,13 @@
 {
   "@context": {
-    "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+    "sem": "https://w3id.org/emmo/domain/sem/0.1#",
     "semdata": "https://he-matchmaker.eu/data/sem/",
     "sample": "https://he-matchmaker.eu/sample/",
     "mat": "https://he-matchmaker.eu/material/",
     "dm": "http://onto-ns.com/meta/characterisation/0.1/SEMImage#",
     "parser": "http://sintef.no/dlite/parser#",
     "gen": "http://sintef.no/dlite/generator#",
-    "micro": "https://w3id.com/emmo/domain/microstructure/0.3#"
+    "micro": "https://w3id.org/emmo/domain/microstructure/0.3#"
   },
 
   "fromSample": {

diff --git a/tests/test_markdown_doctest.py b/tests/test_markdown_doctest.py
@@ -30,4 +30,10 @@ def test_markdown_doctest():
             path = os.path.join(dirpath, filename)
             relpath = os.path.relpath(dirpath, str(rootdir))
             print(f"-- doctest {relpath}/{filename}")
-            doctest.testfile(str(path), module_relative=False)
+            result = doctest.testfile(str(path), module_relative=False)
+            if result.failed:
+                raise RuntimeError(
+                    f"failing doctest: {relpath}/{filename}\n"
+                    "To debug, please run:\n\n"
+                    f"    python -m doctest {relpath}/{filename}\n"
+                )
diff --git a/tripper/datadoc/dataset.py b/tripper/datadoc/dataset.py
@@ -236,11 +236,6 @@ def addsuperclasses(d, cls):
                 logging.info(
                     f"Class not in keywords: {', '.join(missing)}",
                 )
-                # warnings.warn(
-                #     "No superclass info. Not in keywords file: "
-                #     + ", ".join(missing),
-                #     category=MissingKeywordsClassWarning,
-                # )
 
     if isinstance(descr, str):
         return descr
@@ -276,10 +271,6 @@ def addsuperclasses(d, cls):
         if not k.startswith("@") and k not in keywords:
             # pylint: disable=logging-fstring-interpolation
             logging.info(f"Property not in keywords: {k}")
-            # warnings.warn(
-            #     f"No range info. Not in keywords file: {k}",
-            #     UnknownKeywordWarning,
-            # )
         if k in ("@context", "@id", "@type"):
             pass
         elif k == "@graph":
@@ -367,11 +358,6 @@ def save_dict(
     context.sync_prefixes(ts)
 
     add(d, "@context", context.get_context_dict())
-    # if "@context" in d:
-    #     context.add_context(d["@context"])
-    #     d = jsonld.compact(d, context.get_context_dict())
-    # else:
-    #    d["@context"] = context.get_context_dict()
 
     # Validate
     # TODO: reenable validation
@@ -1252,7 +1238,7 @@ def delete(
     flags: "Optional[str]" = None,
     keywords: "Optional[Keywords]" = None,
 ) -> None:
-    """Delete matching resources. See `search_iris()` for a description of arguments."""
+    """Delete matching resources. See `search()` for argument descriptions."""
     iris = search_iris(
         ts=ts,
         type=type,

diff --git a/tripper/units/units.py b/tripper/units/units.py
@@ -1030,6 +1030,29 @@ def asint(x):
     def to_ontology_units(self) -> "Quantity":
         """Return new quantity rescale to a unit with the same
         dimensionality that exists in the ontology.
+
+        Notes:
+            This function tries to select the "simplest" unit among all the
+            units with compatible physical dimensionality in the ontology.
+
+            This is done according to the following heuristics:
+
+            1. Find units with compatible physical dimensionality in the
+               ontology.
+            2. Among these units, select the unit that minimises the absolute
+               value of the sum of the powers of each unit component.
+
+               Example: among the units
+
+                   Pa = Pa^1       -> sum=1
+                   J/m^3 = J^1/m^3 -> sum=1+3=4
+                   N/m^2 = N^1/m^2 -> sum=1+2=3
+
+               Pa will be selected.
+            3. If two units have the same sum, the unit that minimises
+               `log10(magnitude/5)` is selected, where `magnitude` is the
+               magnitude of the quantity when expressed in SI base units.
+
         """
         # pylint: disable=protected-access
         ureg = self._REGISTRY