pylode 3.5.0__tar.gz → 3.5.2__tar.gz

{pylode-3.5.0 → pylode-3.5.2}/PKG-INFO

@@ -1,13 +1,11 @@
 Metadata-Version: 2.4
 Name: pylode
-Version: 3.5.0
+Version: 3.5.2
 Summary: An OWL ontology documentation tool using Python, based on LODE.
 Author: Nicholas Car
 Author-email: Nicholas Car <nick@kurrawong.ai>
 License-Expression: BSD-3-Clause
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
@@ -38,25 +36,7 @@ An OWL ontology documentation tool using Python, based on LODE.
 
 In addition to making web page, human-readable forms of ontologies, pyLODE encourages ontology annotation *best practice* by only producing good results for well documented inputs! pyLODE defines what it considers “well documented” in sections below, e.g. [What pyLODE understands](#what-pylode-understands).
 
-**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` mode. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
-
----
-
-## A note on the v 3.x change
-
-This is pyLODE version 3.0.1 and it’s vastly different from pyLODE 2.x. It doesn’t yet handle all the various “profiles” that pyLODE 2.13.2 does, such as SKOS “vocabularies” & Profiles Vocabulary “profiles”, it only handles OWL “ontologies”, nor all the special data types, such as JSON literals.
-
-However, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it’s been made.
-
-v 3.x will eventually catch up to all of v 2.13.2’s features.
-
-To access v 2.13.2 of pyLODE, either:
-
-- [Download it from PyPI](https://pypi.org/project/pylode/2.13.2/)
-- [Check it out from GitHub](https://github.com/RDFLib/pyLODE/releases/tag/2.13.2)
-- Access it via the [online service](http://tools.kurrawong.ai/pylode)
-
----
+**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` & `vocpub` modes. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
 
 ## Contents
 
@@ -101,20 +81,23 @@ The tool can be used in multiple ways:
 ### Command line arguments
 
 ```text
-usage: cli.py [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] input
+usage: pylode [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] [-s] [-p {ontpub,vocpub,supermodel}] [-l {error,warning,info,debug}] input
 
 positional arguments:
-    input                 Input file location or URL
-
-optional arguments:
-    -h, --help            show this help message and exit
-    -v, --version         show program's version number and exit
-    -o OUTPUTFILE,
-    --outputfile OUTPUTFILE
-                          Output file name (postfixed with .html if needed)
-    -c {true,false},
-    --css {true,false}
-                          Include CSS in the output HTML
+  input                 Input file location or URL
+
+options:
+  -h, --help            show this help message and exit
+  -v, --version         show program's version number and exit
+  -o, --outputfile OUTPUTFILE
+                        A name you wish to assign to the output file. Will be postfixed with .html if not already added. If no output file is given, output will be printed to screen
+  -c, --css {true,false}
+                        Whether (true) or not (false) to include CSS within an output HTML file.
+  -s, --sort            Enables sorting of the subjects in the ontology in the output
+  -p, --profile {ontpub,vocpub,supermodel}
+                        Which profile to use to generate HTML. Must be one of 'ontpub' (https://linked.data.gov.au/def/ontpub) - for ontologies, 'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies, 'supermodel' - for profiles of profiles
+  -l, --loglevel {error,warning,info,debug}
+                        Set the logging level
 ```
 
 ### Basic Use
@@ -125,6 +108,12 @@ optional arguments:
 python pylode examples/ontpub/minimal.ttl -o minimal.html
 ```
 
+for a SKOS vocabulary, indicate the `vocpub` profile:
+
+```bash
+python pylode examples/vocpub/GeologicSpecimenMaterialTypes.ttl -o GeologicSpecimenMaterialTypes.html -p vocpub
+```
+
 #### As a Docker container
 
 ```bash
@@ -305,9 +294,6 @@ Older releases
 
 | Version | Date             | Description                                                                     |
 |---------|------------------|---------------------------------------------------------------------------------|
-| 3.0.5   | 27 April 2023    | Minor patching                                                                  |
-| 3.0.4   | 24 May 2022      | Use of Poetry                                                                   |
-| 3.0.2   | 24 May 2022      | Support for preformatted skos:example literals                                  |
 | 3.0.1   | 6 Jan 2022       | Direct HTML generation using dominate; easier to maintain and extend            |
 | 2.13.2  | 21 December 2021 | Updated RDFlib to 6.1.1, improved test to properly use pytest                   |
 | 2.10.0  | 24 May 2021      | Update Windows EXE build process, simplified versioning                         |
@@ -355,11 +341,11 @@ Nicholas Car
 2. pass all tests: `$ task test`
 3. increment version number in `pyproject.toml`
 4. commit all changes `$ git commit -a "..."`
-5. tag with version number: `$git tag ...`
+5. tag with version number: `$ git tag ...`
 6. push changes `$ git push`
 7. push version `git push --tags`
-8make a GitHub release
+8. make a GitHub release
     * PyPI release is automated from this in `pypi.yml`
 9. increment version number to next release alpha in `pyproject.toml`
 10. commit all changes `$ git commit -a "..."`
-1push changes `$ git push`
+11. push changes `$ git push`

{pylode-3.5.0 → pylode-3.5.2}/README.md

@@ -7,25 +7,7 @@ An OWL ontology documentation tool using Python, based on LODE.
 
 In addition to making web page, human-readable forms of ontologies, pyLODE encourages ontology annotation *best practice* by only producing good results for well documented inputs! pyLODE defines what it considers “well documented” in sections below, e.g. [What pyLODE understands](#what-pylode-understands).
 
-**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` mode. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
-
----
-
-## A note on the v 3.x change
-
-This is pyLODE version 3.0.1 and it’s vastly different from pyLODE 2.x. It doesn’t yet handle all the various “profiles” that pyLODE 2.13.2 does, such as SKOS “vocabularies” & Profiles Vocabulary “profiles”, it only handles OWL “ontologies”, nor all the special data types, such as JSON literals.
-
-However, it generates HTML in a much more straightforward manner and the code is both more efficient and much more maintainable, which is why it’s been made.
-
-v 3.x will eventually catch up to all of v 2.13.2’s features.
-
-To access v 2.13.2 of pyLODE, either:
-
-- [Download it from PyPI](https://pypi.org/project/pylode/2.13.2/)
-- [Check it out from GitHub](https://github.com/RDFLib/pyLODE/releases/tag/2.13.2)
-- Access it via the [online service](http://tools.kurrawong.ai/pylode)
-
----
+**New mode**: In v3.1.0, pyLODE now has a new mode called `supermodel`, in addition to the existing `ontpub` & `vocpub` modes. This new mode allows for documenting **profiles and modules** of multipart models. See [supermodel.md](supermodel.md) for more information.
 
 ## Contents
 
@@ -70,20 +52,23 @@ The tool can be used in multiple ways:
 ### Command line arguments
 
 ```text
-usage: cli.py [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] input
+usage: pylode [-h] [-v] [-o OUTPUTFILE] [-c {true,false}] [-s] [-p {ontpub,vocpub,supermodel}] [-l {error,warning,info,debug}] input
 
 positional arguments:
-    input                 Input file location or URL
-
-optional arguments:
-    -h, --help            show this help message and exit
-    -v, --version         show program's version number and exit
-    -o OUTPUTFILE,
-    --outputfile OUTPUTFILE
-                          Output file name (postfixed with .html if needed)
-    -c {true,false},
-    --css {true,false}
-                          Include CSS in the output HTML
+  input                 Input file location or URL
+
+options:
+  -h, --help            show this help message and exit
+  -v, --version         show program's version number and exit
+  -o, --outputfile OUTPUTFILE
+                        A name you wish to assign to the output file. Will be postfixed with .html if not already added. If no output file is given, output will be printed to screen
+  -c, --css {true,false}
+                        Whether (true) or not (false) to include CSS within an output HTML file.
+  -s, --sort            Enables sorting of the subjects in the ontology in the output
+  -p, --profile {ontpub,vocpub,supermodel}
+                        Which profile to use to generate HTML. Must be one of 'ontpub' (https://linked.data.gov.au/def/ontpub) - for ontologies, 'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies, 'supermodel' - for profiles of profiles
+  -l, --loglevel {error,warning,info,debug}
+                        Set the logging level
 ```
 
 ### Basic Use
@@ -94,6 +79,12 @@ optional arguments:
 python pylode examples/ontpub/minimal.ttl -o minimal.html
 ```
 
+for a SKOS vocabulary, indicate the `vocpub` profile:
+
+```bash
+python pylode examples/vocpub/GeologicSpecimenMaterialTypes.ttl -o GeologicSpecimenMaterialTypes.html -p vocpub
+```
+
 #### As a Docker container
 
 ```bash
@@ -274,9 +265,6 @@ Older releases
 
 | Version | Date             | Description                                                                     |
 |---------|------------------|---------------------------------------------------------------------------------|
-| 3.0.5   | 27 April 2023    | Minor patching                                                                  |
-| 3.0.4   | 24 May 2022      | Use of Poetry                                                                   |
-| 3.0.2   | 24 May 2022      | Support for preformatted skos:example literals                                  |
 | 3.0.1   | 6 Jan 2022       | Direct HTML generation using dominate; easier to maintain and extend            |
 | 2.13.2  | 21 December 2021 | Updated RDFlib to 6.1.1, improved test to properly use pytest                   |
 | 2.10.0  | 24 May 2021      | Update Windows EXE build process, simplified versioning                         |
@@ -324,11 +312,11 @@ Nicholas Car
 2. pass all tests: `$ task test`
 3. increment version number in `pyproject.toml`
 4. commit all changes `$ git commit -a "..."`
-5. tag with version number: `$git tag ...`
+5. tag with version number: `$ git tag ...`
 6. push changes `$ git push`
 7. push version `git push --tags`
-8make a GitHub release
+8. make a GitHub release
     * PyPI release is automated from this in `pypi.yml`
 9. increment version number to next release alpha in `pyproject.toml`
 10. commit all changes `$ git commit -a "..."`
-1push changes `$ git push`
+11. push changes `$ git push`

{pylode-3.5.0 → pylode-3.5.2}/pylode/__init__.py

@@ -1,4 +1,4 @@
-from .profiles import OntPub, Supermodel, VocPub
+from .profiles import OntPub, Supermodel, ValPub, VocPub
 from .rdf_elements import *
 from .utils import *
 from .utils import PylodeError

{pylode-3.5.0 → pylode-3.5.2}/pylode/cli.py

@@ -4,7 +4,7 @@ import sys
 from pathlib import Path
 
 sys.path.insert(0, str(Path(__file__).absolute().parent.parent))
-from pylode import OntPub, PylodeError, Supermodel, VocPub, __version__
+from pylode import OntPub, PylodeError, Supermodel, ValPub, VocPub, __version__
 
 parser = argparse.ArgumentParser()
 
@@ -46,9 +46,10 @@ parser.add_argument(
     "--profile",
     help="Which profile to use to generate HTML. Must be one of "
     "'ontpub' (https://linked.data.gov.au/def/ontpub) - for ontologies, "
-    "'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies"
+    "'valpub' (https://linked.data.gov.au/def/valpub) - for SHACL Shapes Graphs, "
+    "'vocpub' (https://linked.data.gov.au/def/vocpub) - for SKOS vocabularies, "
     "'supermodel' - for profiles of profiles",
-    choices=["ontpub", "vocpub", "supermodel"],
+    choices=["ontpub", "valpub", "vocpub", "supermodel"],
     default="ontpub",
 )
 
@@ -79,6 +80,8 @@ def main():
         sort_subjects = args.sort
         if args.profile == "ontpub":
             html = OntPub(args.input, sort_subjects=sort_subjects)
+        elif args.profile == "valpub":
+            html = ValPub(args.input, sort_subjects=sort_subjects)
         elif args.profile == "vocpub":
             html = VocPub(args.input, sort_subjects=sort_subjects)
         elif args.profile == "supermodel":

{pylode-3.5.0 → pylode-3.5.2}/pylode/profiles/__init__.py

@@ -1,3 +1,4 @@
 from .ontpub import OntPub
 from .supermodel import Supermodel
+from .valpub import ValPub
 from .vocpub import VocPub

{pylode-3.5.0 → pylode-3.5.2}/pylode/profiles/ontpub.py

@@ -1,82 +1,18 @@
-import shutil
-from collections import defaultdict
-from itertools import chain
-from pathlib import Path
-from typing import Dict, Union
-
-import dominate
-from dominate.tags import (
-    a,
-    code,
-    dd,
-    div,
-    dl,
-    dt,
-    h1,
-    h2,
-    h3,
-    h4,
-    h5,
-    li,
-    link,
-    meta,
-    script,
-    section,
-    strong,
-    style,
-    sup,
-    table,
-    td,
-    tr,
-    ul,
-)
-from dominate.util import raw
-from rdflib import Graph, Literal
-from rdflib.namespace import (
-    DC,
-    DCTERMS,
-    FOAF,
-    ORG,
-    OWL,
-    PROF,
-    PROV,
-    RDF,
-    RDFS,
-    SDO,
-    SKOS,
-)
-
-from ..rdf_elements import AGENT_PROPS, CLASS_PROPS, ONT_PROPS, ONTDOC, PROP_PROPS
-from ..utils import (
-    PylodeError,
-    back_onts_label_props,
-    get_ns,
-    load_background_onts,
-    load_background_onts_titles,
-    load_ontology,
-    make_pylode_logo,
-    prop_obj_pair_html,
-    section_html,
-    sort_ontology,
-)
-from ..version import __version__
-
-RDF_FOLDER = Path(__file__).parent / "rdf"
+from pylode.utils import *
 
 
 class OntPub:
-    """Ontology Document class used to create HTML documentation
-    from OWL Ontologies.
+    """Used to create HTML documentation from OWL Ontologies.
 
     Use:
         # initialise
-        od = OntDoc(ontology="some-ontology-file.ttl")
+        x = OntPub(ontology="some-ontology-file.ttl")
 
         # produce HTML
-        html = od.make_html()
+        html = x.make_html()
 
         # or save HTML to a file
-        od.make_html(destination="some-resulting-html-file.html")
+        x.make_html(destination="some-resulting-html-file.html")
     """
 
     def __init__(self, ontology: Union[Graph, Path, str], sort_subjects: bool = False):
@@ -134,6 +70,9 @@ class OntPub:
         for s_ in g.subjects(RDF.type, OWL.Class):
             g.add((s_, RDF.type, RDFS.Class))
 
+        for s_ in g.subjects(RDF.type, RDFS.Class):
+            g.add((s_, RDF.type, OWL.Class))
+
         # # property types
         # for s_ in chain(
         #     g.subjects(RDF.type, OWL.ObjectProperty),
@@ -183,25 +122,25 @@ class OntPub:
         # we do these next few so we only need to loop through
         # Class & Property properties once: single subject
         for s_, o in g.subject_objects(RDFS.subClassOf):
-            g.add((o, ONTDOC.superClassOf, s_))
+            g.add((o, ONTPUB.superClassOf, s_))
 
         for s_, o in g.subject_objects(RDFS.subPropertyOf):
-            g.add((o, ONTDOC.superPropertyOf, s_))
+            g.add((o, ONTPUB.superPropertyOf, s_))
 
         for s_, o in g.subject_objects(RDFS.domain):
-            g.add((o, ONTDOC.inDomainOf, s_))
+            g.add((o, ONTPUB.inDomainOf, s_))
 
         for s_, o in g.subject_objects(SDO.domainIncludes):
-            g.add((o, ONTDOC.inDomainIncludesOf, s_))
+            g.add((o, ONTPUB.inDomainIncludesOf, s_))
 
         for s_, o in g.subject_objects(RDFS.range):
-            g.add((o, ONTDOC.inRangeOf, s_))
+            g.add((o, ONTPUB.inRangeOf, s_))
 
         for s_, o in g.subject_objects(SDO.rangeIncludes):
-            g.add((o, ONTDOC.inRangeIncludesOf, s_))
+            g.add((o, ONTPUB.inRangeIncludesOf, s_))
 
         for s_, o in g.subject_objects(RDF.type):
-            g.add((o, ONTDOC.hasMember, s_))
+            g.add((o, ONTPUB.hasMember, s_))
 
         #
         #   Agents
@@ -295,9 +234,7 @@ class OntPub:
         """Helper function for make_html(). Makes <body>???</body> content.
 
         Just calls other helper functions in order"""
-        make_pylode_logo(
-            self.doc, __version__, "OntPub", "https://linked.data.gov.au/def/ontpub"
-        )
+        make_pylode_logo(self.doc, "OntPub", "https://linked.data.gov.au/def/ontpub")
         self._make_metadata()
         self._make_main_sections()
         self._make_namespaces()
@@ -314,14 +251,14 @@ class OntPub:
         ):
             iri = s_
             for p_, o in self.ont.predicate_objects(s_):
-                if p_ in ONT_PROPS:
+                if p_ in ONTOLOGY_PROPS:
                     this_onts_props[p_].append(o)
 
         # make HTML for all props in order of ONT_PROPS
         sec = div(h1(this_onts_props[DCTERMS.title]), id="metadata", _class="section")
         sec.appendChild(h2("Metadata"))
         d = dl(div(dt(strong("IRI")), dd(code(str(iri)))))
-        for prop in ONT_PROPS:
+        for prop in ONTOLOGY_PROPS:
             if prop in this_onts_props.keys():
                 d.appendChild(
                     prop_obj_pair_html(
@@ -605,7 +542,7 @@ class OntPub:
                                 )
                             )
                             with ul(_class="second"):
-                                for c in self.toc["classes"]:
+                                for c in sorted(self.toc["classes"]):
                                     li(a(c[1], href=c[0]), style="margin-left:10px;")
 
                     if (
@@ -615,7 +552,7 @@ class OntPub:
                         with li():
                             h4(a("Properties", href="#properties"))
                             with ul(_class="second"):
-                                for c in self.toc["properties"]:
+                                for c in sorted(self.toc["properties"]):
                                     li(a(c[1], href=c[0]))
 
                     if (
@@ -639,7 +576,7 @@ class OntPub:
                                 )
                             )
                             with ul(_class="second"):
-                                for c in self.toc["objectproperties"]:
+                                for c in sorted(self.toc["objectproperties"]):
                                     li(a(c[1], href=c[0]), style="margin-left:10px;")
 
                     if (
@@ -649,7 +586,7 @@ class OntPub:
                         with li():
                             h4(a("Datatype Properties", href="#datatypeproperties"))
                             with ul(_class="second"):
-                                for c in self.toc["datatypeproperties"]:
+                                for c in sorted(self.toc["datatypeproperties"]):
                                     li(a(c[1], href=c[0]))
 
                     if (
@@ -659,7 +596,7 @@ class OntPub:
                         with li():
                             h4(a("Annotation Properties", href="#annotationproperties"))
                             with ul(_class="second"):
-                                for c in self.toc["annotationproperties"]:
+                                for c in sorted(self.toc["annotationproperties"]):
                                     li(a(c[1], href=c[0]))
 
                     if (
@@ -669,7 +606,7 @@ class OntPub:
                         with li():
                             h4(a("Functional Properties", href="#functionalproperties"))
                             with ul(_class="second"):
-                                for c in self.toc["functionalproperties"]:
+                                for c in sorted(self.toc["functionalproperties"]):
                                     li(a(c[1], href=c[0]))
 
                     if (
@@ -679,7 +616,7 @@ class OntPub:
                         with li():
                             h4(a("Custom Datatypes", href="#datatypes"))
                             with ul(_class="second"):
-                                for c in self.toc["datatypes"]:
+                                for c in sorted(self.toc["datatypes"]):
                                     li(a(c[1], href=c[0]))
 
                     with li():

{pylode-3.5.0 → pylode-3.5.2}/pylode/profiles/supermodel/query/__init__.py

@@ -50,7 +50,7 @@ from pylode.profiles.supermodel.query.common import (
     get_values,
 )
 from pylode.profiles.supermodel.query.property_shape import get_class_properties_by_sh
-from pylode.rdf_elements import AGENT_PROPS, ONT_PROPS, ONTDOC
+from pylode.rdf_elements import AGENT_PROPS, ONTOLOGY_PROPS, ONTPUB
 from pylode.utils import (
     back_onts_label_props,
     load_background_onts,
@@ -493,7 +493,7 @@ class Query:
         this_onts_props = defaultdict(list)
         for s_ in self.graph.subjects(predicate=RDF.type, object=PROF.Profile):
             for p_, o in self.graph.predicate_objects(s_):
-                if p_ in ONT_PROPS:
+                if p_ in ONTOLOGY_PROPS:
                     this_onts_props[p_].append(o)
 
         return this_onts_props
@@ -569,25 +569,25 @@ class Query:
         # we do these next few so we only need to loop through
         # Class & Property properties once: single subject
         for s_, o in g.subject_objects(RDFS.subClassOf):
-            g.add((o, ONTDOC.superClassOf, s_))
+            g.add((o, ONTPUB.superClassOf, s_))
 
         for s_, o in g.subject_objects(RDFS.subPropertyOf):
-            g.add((o, ONTDOC.superPropertyOf, s_))
+            g.add((o, ONTPUB.superPropertyOf, s_))
 
         for s_, o in g.subject_objects(RDFS.domain):
-            g.add((o, ONTDOC.inDomainOf, s_))
+            g.add((o, ONTPUB.inDomainOf, s_))
 
         for s_, o in g.subject_objects(SDO.domainIncludes):
-            g.add((o, ONTDOC.inDomainIncludesOf, s_))
+            g.add((o, ONTPUB.inDomainIncludesOf, s_))
 
         for s_, o in g.subject_objects(RDFS.range):
-            g.add((o, ONTDOC.inRangeOf, s_))
+            g.add((o, ONTPUB.inRangeOf, s_))
 
         for s_, o in g.subject_objects(SDO.rangeIncludes):
-            g.add((o, ONTDOC.inRangeIncludesOf, s_))
+            g.add((o, ONTPUB.inRangeIncludesOf, s_))
 
         for s_, o in g.subject_objects(RDF.type):
-            g.add((o, ONTDOC.hasMember, s_))
+            g.add((o, ONTPUB.hasMember, s_))
 
         #
         #   Agents