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update docs #241

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2 changes: 1 addition & 1 deletion CITATION
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Expand Up @@ -3,6 +3,6 @@
title = {{kglab: a simple abstraction layer in Python for building knowledge graphs}},
year = 2020,
publisher = {Derwen},
doi = {10.5281/zenodo.4602403},
doi = {10.5281/zenodo.6360664},
url = {https://github.com/DerwenAI/kglab}
}
4 changes: 2 additions & 2 deletions README.md
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@@ -1,6 +1,6 @@
# kglab

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4717287.svg)](https://doi.org/10.5281/zenodo.4717287)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6360664.svg)](https://doi.org/10.5281/zenodo.6360664)
![Licence](https://img.shields.io/github/license/DerwenAI/kglab)
![Repo size](https://img.shields.io/github/repo-size/DerwenAI/kglab)
![GitHub commit activity](https://img.shields.io/github/commit-activity/w/DerwenAI/kglab?style=plastic)
Expand Down Expand Up @@ -187,7 +187,7 @@ this library.
title = {{kglab: a simple abstraction layer in Python for building knowledge graphs}},
year = 2020,
publisher = {Derwen},
doi = {10.5281/zenodo.4717287},
doi = {10.5281/zenodo.6360664},
url = {https://github.com/DerwenAI/kglab}
}
```
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9 changes: 8 additions & 1 deletion changelog.txt
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@@ -1,8 +1,15 @@
# `kglab` changelog

## 0.5.?

2022-03-?

* ?


## 0.5.2

2022-03-??
2022-03-15

* bump up versions of dependencies to fit Py 3.7+
* improve testing based on pytest; kudos @Mec-iS
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4 changes: 2 additions & 2 deletions docs/ack.md
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Expand Up @@ -93,12 +93,12 @@ it in your research or software:
title = {{kglab: a simple abstraction layer in Python for building knowledge graphs}},
year = 2020,
publisher = {Derwen},
doi = {10.5281/zenodo.4717287},
doi = {10.5281/zenodo.6360664},
url = {https://github.com/DerwenAI/kglab}
}
```

**DOI:** <https://doi.org/10.5281/zenodo.4717287>
**DOI:** <https://doi.org/10.5281/zenodo.6360664>


## License and Copyright
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82 changes: 48 additions & 34 deletions docs/ref.md
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Expand Up @@ -16,10 +16,10 @@ Core feature areas include:

---
#### [`__init__` method](#kglab.KnowledgeGraph.__init__)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L81)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L77)

```python
__init__(name="generic", base_uri=None, language="en", use_gpus=True, import_graph=None, namespaces=None)
__init__(name="generic", base_uri=None, language="en", store=None, use_gpus=True, import_graph=None, namespaces=None)
```
Constructor for a `KnowledgeGraph` object.

Expand All @@ -32,6 +32,9 @@ the default [*base URI*](https://tools.ietf.org/html/rfc3986#section-5.1) for th
* `language` : `str`
the default [*language tag*](https://www.w3.org/TR/rdf11-concepts/#dfn-language-tag), e.g., used for [*language indexing*](https://www.w3.org/TR/json-ld11/#language-indexing)

* `store` : `str`
optionally, string representing an `rdflib.Store` plugin to use.

* `use_gpus` : `bool`
optionally, use the NVidia GPU devices with [RAPIDS](https://rapids.ai/) if these libraries have been installed and the devices are available; defaults to `True`

Expand All @@ -43,9 +46,20 @@ a dictionary of [*namespace*](https://rdflib.readthedocs.io/en/stable/apidocs/rd



---
#### [`build_blank_graph` method](#kglab.KnowledgeGraph.build_blank_graph)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L141)

```python
build_blank_graph()
```
Build a new `rdflib.Graph` object, based on storage plugin configuration.



---
#### [`rdf_graph` method](#kglab.KnowledgeGraph.rdf_graph)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L140)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L155)

```python
rdf_graph()
Expand All @@ -59,7 +73,7 @@ the [`rdflib.Graph`](https://rdflib.readthedocs.io/en/stable/apidocs/rdflib.html

---
#### [`add_ns` method](#kglab.KnowledgeGraph.add_ns)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L165)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L180)

```python
add_ns(prefix, iri, override=True, replace=False)
Expand All @@ -84,7 +98,7 @@ replace any existing prefix with the new namespace

---
#### [`get_ns` method](#kglab.KnowledgeGraph.get_ns)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L209)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L224)

```python
get_ns(prefix)
Expand All @@ -101,7 +115,7 @@ the RDFlib [`Namespace`](https://rdflib.readthedocs.io/en/stable/apidocs/rdflib.

---
#### [`get_ns_dict` method](#kglab.KnowledgeGraph.get_ns_dict)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L225)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L240)

```python
get_ns_dict()
Expand All @@ -115,7 +129,7 @@ a `dict` describing the namespaces in this RDF graph

---
#### [`describe_ns` method](#kglab.KnowledgeGraph.describe_ns)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L247)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L262)

```python
describe_ns()
Expand All @@ -129,7 +143,7 @@ a [`pandas.DataFrame`](https://pandas.pydata.org/pandas-docs/stable/reference/ap

---
#### [`get_context` method](#kglab.KnowledgeGraph.get_context)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L274)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L289)

```python
get_context()
Expand All @@ -144,7 +158,7 @@ context needed for JSON-LD serialization

---
#### [`encode_date` method](#kglab.KnowledgeGraph.encode_date)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L293)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L308)

```python
encode_date(dt, tzinfos)
Expand All @@ -164,7 +178,7 @@ timezones as a dict, used by

---
#### [`add` method](#kglab.KnowledgeGraph.add)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L315)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L330)

```python
add(s, p, o)
Expand All @@ -187,7 +201,7 @@ To prepare for upcoming **kglab** features, **this is the preferred method for a

---
#### [`remove` method](#kglab.KnowledgeGraph.remove)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L349)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L364)

```python
remove(s, p, o)
Expand Down Expand Up @@ -237,7 +251,7 @@ this `KnowledgeGraph` object – used for method chaining

---
#### [`load_rdf_text` method](#kglab.KnowledgeGraph.load_rdf_text)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L541)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L558)

```python
load_rdf_text(data, format="ttl", base=None, **args)
Expand All @@ -263,7 +277,7 @@ this `KnowledgeGraph` object – used for method chaining

---
#### [`save_rdf` method](#kglab.KnowledgeGraph.save_rdf)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L584)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L601)

```python
save_rdf(path, format="ttl", base=None, encoding="utf-8", **args)
Expand All @@ -287,7 +301,7 @@ optional text encoding value, defaults to `"utf-8"`, must be in the [Python code

---
#### [`save_rdf_text` method](#kglab.KnowledgeGraph.save_rdf_text)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L649)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L666)

```python
save_rdf_text(format="ttl", base=None, encoding="utf-8", **args)
Expand Down Expand Up @@ -333,7 +347,7 @@ this `KnowledgeGraph` object – used for method chaining

---
#### [`save_jsonld` method](#kglab.KnowledgeGraph.save_jsonld)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L736)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L753)

```python
save_jsonld(path, encoding="utf-8", **args)
Expand Down Expand Up @@ -373,7 +387,7 @@ this `KnowledgeGraph` object – used for method chaining

---
#### [`save_parquet` method](#kglab.KnowledgeGraph.save_parquet)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L825)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L842)

```python
save_parquet(path, compression="snappy", storage_options=None, **kwargs)
Expand All @@ -396,7 +410,7 @@ extra options parsed by [`fsspec`](https://github.com/intake/filesystem_spec) fo

---
#### [`load_csv` method](#kglab.KnowledgeGraph.load_csv)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L870)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L887)

```python
load_csv(url)
Expand All @@ -413,7 +427,7 @@ this `KnowledgeGraph` object – used for method chaining

---
#### [`materialize` method](#kglab.KnowledgeGraph.materialize)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L891)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L908)

```python
materialize(config)
Expand Down Expand Up @@ -458,7 +472,7 @@ a list of identifiers for the top-level nodes added from the Roam Research graph

---
#### [`query` method](#kglab.KnowledgeGraph.query)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1021)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1038)

```python
query(sparql, bindings=None)
Expand All @@ -478,7 +492,7 @@ initial variable bindings

---
#### [`query_as_df` method](#kglab.KnowledgeGraph.query_as_df)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1049)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1066)

```python
query_as_df(sparql, bindings=None, simplify=True, pythonify=True)
Expand All @@ -504,7 +518,7 @@ the query result set represented as a [`pandas.DataFrame`](https://pandas.pydata

---
#### [`visualize_query` method](#kglab.KnowledgeGraph.visualize_query)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1093)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1110)

```python
visualize_query(sparql, notebook=False)
Expand All @@ -524,7 +538,7 @@ PyVis network object, to be rendered

---
#### [`n3fy` method](#kglab.KnowledgeGraph.n3fy)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1114)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1131)

```python
n3fy(node, pythonify=True)
Expand All @@ -544,7 +558,7 @@ text (or Python objects) for the serialized node

---
#### [`n3fy_row` method](#kglab.KnowledgeGraph.n3fy_row)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1140)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1157)

```python
n3fy_row(row_dict, pythonify=True)
Expand All @@ -564,7 +578,7 @@ a dictionary of serialized row bindings

---
#### [`validate` method](#kglab.KnowledgeGraph.validate)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1169)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1186)

```python
validate(shacl_graph=None, shacl_graph_format=None, ont_graph=None, ont_graph_format=None, advanced=False, inference=None, inplace=True, abort_on_first=None, **kwargs)
Expand Down Expand Up @@ -601,7 +615,7 @@ a tuple of `conforms` (RDF graph passes the validation rules) + `report_graph` (

---
#### [`infer_owlrl_closure` method](#kglab.KnowledgeGraph.infer_owlrl_closure)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1247)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1264)

```python
infer_owlrl_closure()
Expand All @@ -614,7 +628,7 @@ See <https://wiki.uib.no/info216/index.php/Python_Examples#RDFS_inference_with_R

---
#### [`infer_rdfs_closure` method](#kglab.KnowledgeGraph.infer_rdfs_closure)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1260)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1277)

```python
infer_rdfs_closure()
Expand All @@ -627,7 +641,7 @@ See <https://wiki.uib.no/info216/index.php/Python_Examples#RDFS_inference_with_R

---
#### [`infer_rdfs_properties` method](#kglab.KnowledgeGraph.infer_rdfs_properties)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1273)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1290)

```python
infer_rdfs_properties()
Expand All @@ -640,7 +654,7 @@ Adapted from [`skosify`](https://github.com/NatLibFi/Skosify) which wasn't being

---
#### [`infer_rdfs_classes` method](#kglab.KnowledgeGraph.infer_rdfs_classes)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1301)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1318)

```python
infer_rdfs_classes()
Expand All @@ -653,7 +667,7 @@ Adapted from [`skosify`](https://github.com/NatLibFi/Skosify) which wasn't being

---
#### [`infer_skos_related` method](#kglab.KnowledgeGraph.infer_skos_related)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1334)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1351)

```python
infer_skos_related()
Expand All @@ -667,7 +681,7 @@ Adapted from [`skosify`](https://github.com/NatLibFi/Skosify) which wasn't being

---
#### [`infer_skos_concept` method](#kglab.KnowledgeGraph.infer_skos_concept)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1349)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1366)

```python
infer_skos_concept()
Expand All @@ -684,7 +698,7 @@ Adapted from [`skosify`](https://github.com/NatLibFi/Skosify) which wasn't being

---
#### [`infer_skos_hierarchical` method](#kglab.KnowledgeGraph.infer_skos_hierarchical)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1373)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1390)

```python
infer_skos_hierarchical(narrower=True)
Expand All @@ -701,7 +715,7 @@ if false, `skos:narrower` will be removed instead of added

---
#### [`infer_skos_transitive` method](#kglab.KnowledgeGraph.infer_skos_transitive)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1400)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1417)

```python
infer_skos_transitive(narrower=True)
Expand All @@ -722,7 +736,7 @@ also infer transitive closure for `skos:narrowerTransitive`

---
#### [`infer_skos_symmetric_mappings` method](#kglab.KnowledgeGraph.infer_skos_symmetric_mappings)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1429)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1446)

```python
infer_skos_symmetric_mappings(related=True)
Expand All @@ -739,7 +753,7 @@ infer the `skos:related` super-property for all `skos:relatedMatch` relations

---
#### [`infer_skos_hierarchical_mappings` method](#kglab.KnowledgeGraph.infer_skos_hierarchical_mappings)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1460)
[*\[source\]*](https://github.com/DerwenAI/kglab/blob/main/kglab/kglab.py#L1477)

```python
infer_skos_hierarchical_mappings(narrower=True)
Expand Down
10 changes: 5 additions & 5 deletions setup.py
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Expand Up @@ -113,13 +113,13 @@ def parse_requirements_file (

url = "https://derwen.ai/docs/kgl/",
project_urls = {
"Source Code": "https://github.com/DerwenAI/kglab",
"Issue Tracker": "https://github.com/DerwenAI/kglab/issues",
"Hands-on Tutorial": "https://derwen.ai/docs/kgl/tutorial/",
"DOI": "https://doi.org/10.5281/zenodo.6360664",
"Community Survey": "https://forms.gle/FMHgtmxHYWocprMn6",
"Discussion Forum": "https://www.linkedin.com/groups/6725785/",
"DockerHub": "https://hub.docker.com/r/derwenai/kglab",
"Community Survey": "https://forms.gle/FMHgtmxHYWocprMn6",
"DOI": "https://doi.org/10.5281/zenodo.4717287",
"Hands-on Tutorial": "https://derwen.ai/docs/kgl/tutorial/",
"Issue Tracker": "https://github.com/DerwenAI/kglab/issues",
"Source Code": "https://github.com/DerwenAI/kglab",
},

entry_points = {
Expand Down