Renamed the dataset subpackage to datadoc (#298)

# Description
Renamed the dataset subpackage to datadoc

README.md

@@ -42,7 +42,7 @@ Sub-packages
 ------------
 Additional functionality beyond interfacing triplestore backends is provided by specialised sub-package:
 
-* [tripper.dataset]: An API for data documentation.
+* [tripper.datadoc]: An API for data documentation.
 * [tripper.mappings]: Traverse mappings stored in the triplestore and find possible mapping routes.
 * [tripper.convert]: Convert between RDF and other data representations.
 
@@ -106,7 +106,7 @@ We gratefully acknowledge the following projects for supporting the development
 
 
 [Tutorial]: https://emmc-asbl.github.io/tripper/latest/tutorial/
-[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/dataset/introduction/
+[tripper.datadoc]: https://emmc-asbl.github.io/tripper/latest/datadoc/introduction/
 [tripper.mappings]: https://emmc-asbl.github.io/tripper/latest/api_reference/mappings/mappings/
 [tripper.convert]: https://emmc-asbl.github.io/tripper/latest/api_reference/convert/convert/
 [Discovery of custom backends]: https://emmc-asbl.github.io/tripper/latest/backend_discovery/

docs/api_reference/datadoc/.pages

@@ -0,0 +1 @@
+title: "datadoc"

docs/api_reference/datadoc/clitool.md

@@ -0,0 +1,3 @@
+# clitool
+
+::: tripper.datadoc.clitool

docs/api_reference/datadoc/dataaccess.md

@@ -0,0 +1,3 @@
+# dataaccess
+
+::: tripper.datadoc.dataaccess

docs/api_reference/datadoc/dataset.md

@@ -0,0 +1,3 @@
+# dataset
+
+::: tripper.datadoc.dataset

docs/api_reference/datadoc/tabledoc.md

@@ -0,0 +1,3 @@
+# tabledoc
+
+::: tripper.datadoc.tabledoc

docs/dataset/customisation.md → docs/datadoc/customisation.md

@@ -172,7 +172,7 @@ You can save this context to a triplestore with
 
 ```python
 >>> from tripper import Triplestore
->>> from tripper.dataset import save_datadoc
+>>> from tripper.datadoc import save_datadoc
 >>>
 >>> ts = Triplestore("rdflib")
 >>> save_datadoc(  # doctest: +ELLIPSIS
@@ -242,9 +242,9 @@ Instead, the list of available resource types should be stored and retrieved fro
 [predefined prefixes]: prefixes.md
 [predefined keywords]: keywords.md
 [default context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
-[save_dict()]: ../api_reference/dataset/dataset.md#tripper.dataset.dataset.save_dict
-[as_jsonld()]: ../api_reference/dataset/dataset.md#tripper.dataset.dataset.as_jsonld
-[save_datadoc()]: ../api_reference/dataset/dataset.md#tripper.dataset.dataset.save_datadoc
-[TableDoc]: ../api_reference/dataset/tabledoc.md/#tripper.dataset.tabledoc.TableDoc
-[TableDoc.parse_csv()]: ../api_reference/dataset/tabledoc.md/#tripper.dataset.tabledoc.TableDoc.parse_csv
+[save_dict()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.save_dict
+[as_jsonld()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.as_jsonld
+[save_datadoc()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.save_datadoc
+[TableDoc]: ../api_reference/datadoc/tabledoc.md/#tripper.datadoc.tabledoc.TableDoc
+[TableDoc.parse_csv()]: ../api_reference/datadoc/tabledoc.md/#tripper.datadoc.tabledoc.TableDoc.parse_csv
 [default JSON-LD context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json

docs/dataset/documenting-a-resource.md → docs/datadoc/documenting-a-resource.md

@@ -1,6 +1,6 @@
 Documenting a resource
 ======================
-In the [tripper.dataset] sub-package are the documents documenting the resources internally represented as [JSON-LD] documents stored as Python dicts.
+In the [tripper.datadoc] sub-package are the documents documenting the resources internally represented as [JSON-LD] documents stored as Python dicts.
 However, the API tries to hide away the complexities of JSON-LD behind simple interfaces.
 To support different use cases, the sub-package provide several interfaces for data documentation, including Python dicts, YAML files and tables.
 These are further described below.
@@ -49,7 +49,7 @@ We therefore have to define them explicitly
 
     ```python
     >>> import json
-    >>> from tripper.dataset import as_jsonld
+    >>> from tripper.datadoc import as_jsonld
     >>> d = as_jsonld(dataset, prefixes=prefixes)
     >>> print(json.dumps(d, indent=2))
     {
@@ -76,7 +76,7 @@ Since the prefixes "sem" and "kb" are not included in the [Predefined prefixes],
 
 ```python
 >>> from tripper import Triplestore
->>> from tripper.dataset import save_dict
+>>> from tripper.datadoc import save_dict
 >>> ts = Triplestore(backend="rdflib")
 >>> save_dict(ts, dataset, prefixes=prefixes)  # doctest: +ELLIPSIS
 AttrDict(...)
@@ -135,7 +135,7 @@ The [save_datadoc()] function allow to save a [YAML] file in [multi-resource](#m
 Saving [semdata.yaml] to a triplestore can e.g. be done with
 
 ```python
->>> from tripper.dataset import save_datadoc
+>>> from tripper.datadoc import save_datadoc
 >>> save_datadoc(  # doctest: +ELLIPSIS
 ...    ts,
 ...    "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml"
@@ -172,7 +172,7 @@ correspond to the following turtle representation:
 The below example shows how to save all datasets listed in the CSV file [semdata.csv] to a triplestore.
 
 ```python
->>> from tripper.dataset import TableDoc
+>>> from tripper.datadoc import TableDoc
 
 >>> td = TableDoc.parse_csv(
 ...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv",
@@ -191,7 +191,7 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 ```
 
 
-[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset
+[tripper.datadoc]: https://emmc-asbl.github.io/tripper/latest/datadoc/introduction
 [DCAT vocabulary]: https://www.w3.org/TR/vocab-dcat-3/
 [DLite]: https://github.com/SINTEF/dlite
 [YAML]: https://yaml.org/
@@ -206,10 +206,10 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
-[save_dict()]: ../api_reference/dataset/dataset.md/#tripper.dataset.dataset.save_dict
-[as_jsonld()]: ../api_reference/dataset/dataset.md/#tripper.dataset.dataset.as_jsonld
+[save_dict()]: ../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.save_dict
+[as_jsonld()]: ../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.as_jsonld
 [save_datadoc()]:
-../api_reference/dataset/dataset.md/#tripper.dataset.dataset.save_datadoc
+../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.save_datadoc
+[TableDoc]: ../api_reference/datadoc/tabledoc.md/#tripper.datadoc.tabledoc.TableDoc
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
 [semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv
-[TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc

docs/dataset/introduction.md → docs/datadoc/introduction.md

@@ -9,10 +9,10 @@ The data documentation is based on small [JSON-LD documents], each documenting a
 Examples of resources can be a dataset, an instrument, a sample, etc.
 All resources are uniquely identified by their IRI.
 
-The primary focus of the [tripper.dataset] module is to document datasets such that they are consistent with the [DCAT vocabulary], but at the same time easily extended additional semantic meaning provided by other ontologies.
+The primary focus of the [tripper.datadoc] module is to document datasets such that they are consistent with the [DCAT vocabulary], but at the same time easily extended additional semantic meaning provided by other ontologies.
 It is also easy to add and relate the datasets to other types of documents, like people, instruments and samples.
 
-The [tripper.dataset] module provides a Python API for documenting resources at all four levels of data documentation, including:
+The [tripper.datadoc] module provides a Python API for documenting resources at all four levels of data documentation, including:
 
 - **Cataloguing**: Storing and accessing *documents* based on their IRI and data properties.
   (Addressed FAIR aspects: *findability* and *accessibility*).
@@ -30,7 +30,7 @@ The figure below shows illustrates how a dataset is documented in a triplestore.
 
 Resource types
 --------------
-The [tripper.dataset] module include the following set of predefined resource types:
+The [tripper.datadoc] module include the following set of predefined resource types:
 
 - **dataset**: Individual of [dcat:Dataset] and [emmo:DataSet].
 - **distribution**: Individual of [dcat:Distribution].
@@ -43,7 +43,7 @@ Future releases will support adding custom resource types.
 
 
 
-[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset
+[tripper.datadoc]: https://emmc-asbl.github.io/tripper/latest/datadoc/introduction
 [DCAT vocabulary]: https://www.w3.org/TR/vocab-dcat-3/
 [DLite]: https://github.com/SINTEF/dlite
 [YAML]: https://yaml.org/
@@ -58,10 +58,10 @@ Future releases will support adding custom resource types.
 [emmo:DataSet]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
-[save_dict()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_dict
-[as_jsonld()]: ../../api_reference/dataset/dataset/#tripper.dataset.dataset.as_jsonld
+[save_dict()]: ../../api_reference/datadoc/dataset/#tripper.datadoc.dataset.save_dict
+[as_jsonld()]: ../../api_reference/datadoc/dataset/#tripper.datadoc.dataset.as_jsonld
 [save_datadoc()]:
-../../api_reference/dataset/dataset/#tripper.dataset.dataset.save_datadoc
+../../api_reference/datadoc/dataset/#tripper.datadoc.dataset.save_datadoc
 [semdata.yaml]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml
-[semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/tabledoc-csv/tests/input/semdata.csv
-[TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/dataset/dataset/#tripper.dataset.tabledoc.TableDoc
+[semdata.csv]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv
+[TableDoc]: https://emmc-asbl.github.io/tripper/latest/api_reference/datadoc/tabledoc/#tripper.datadoc.tabledoc.TableDoc

docs/index.md

@@ -42,7 +42,7 @@ Sub-packages
 ------------
 Additional functionality beyond interfacing triplestore backends is provided by specialised sub-package:
 
-* [tripper.dataset]: An API for data documentation.
+* [tripper.datadoc]: An API for data documentation.
 * [tripper.mappings]: Traverse mappings stored in the triplestore and find possible mapping routes.
 * [tripper.convert]: Convert between RDF and other data representations.
 
@@ -106,7 +106,7 @@ We gratefully acknowledge the following projects for supporting the development
 
 
 [Tutorial]: https://emmc-asbl.github.io/tripper/latest/tutorial/
-[tripper.dataset]: https://emmc-asbl.github.io/tripper/latest/dataset/introduction/
+[tripper.datadoc]: https://emmc-asbl.github.io/tripper/latest/datadoc/introduction/
 [tripper.mappings]: https://emmc-asbl.github.io/tripper/latest/api_reference/mappings/mappings/
 [tripper.convert]: https://emmc-asbl.github.io/tripper/latest/api_reference/convert/convert/
 [Discovery of custom backends]: https://emmc-asbl.github.io/tripper/latest/backend_discovery/

docs/tools/datadoc.md

@@ -422,4 +422,4 @@ The `--output` option allows to write the dataset to a local file.
 
 
 
-[resource types]: ../dataset/introduction.md/#resource-types
+[resource types]: ../datadoc/introduction.md/#resource-types

mkdocs.yml

@@ -51,7 +51,7 @@ markdown_extensions:
       permalink: true
 
 exclude_docs: |
-  ../dataset/datadoc.py
+  ../datadoc/datadoc.py
 
 
 plugins:
@@ -89,11 +89,11 @@ nav:
   - Tools:
     - datadoc: tools/datadoc.md
   - Data documentation:
-    - Introduction: dataset/introduction.md
-    - Documenting a resource: dataset/documenting-a-resource.md
-    - Customisation: dataset/customisation.md
-    - Predefined prefixes: dataset/prefixes.md
-    - Predefined keywords: dataset/keywords.md
+    - Introduction: datadoc/introduction.md
+    - Documenting a resource: datadoc/documenting-a-resource.md
+    - Customisation: datadoc/customisation.md
+    - Predefined prefixes: datadoc/prefixes.md
+    - Predefined keywords: datadoc/keywords.md
   - ... | api_reference/**
   - Known issues: known-issues.md
   - For developers: developers.md

pyproject.toml

@@ -38,7 +38,7 @@ mappings = [
     "pint>=0.16.1,<0.25",
     "rdflib>=6.3.0,<7.0.0",
 ]
-dataset = [
+datadoc = [
     "tripper[mappings]",
     "PyYaml>=3.0.0,<6.0.3",  # todo: check lower version
     "requests>=2.0.0,<3.4.1",  # todo: check lower version
@@ -52,7 +52,7 @@ testing-core = [
     "pytest-cov==4.1.0",
 ]
 testing = [
-    "tripper[testing-core,mappings,dataset]",
+    "tripper[testing-core,mappings,datadoc]",
     "dlite-python>=0.5.23,<0.5.27; python_version>='3.8' and python_version<'3.13'",
     "dlite-python>=0.5.25,<0.5.27; python_version>='3.13'",
     "emmontopy>=0.5.0,<0.7.1; python_version<'3.13'",
@@ -84,7 +84,7 @@ Changelog = "https://github.com/EMMC-ASBL/tripper/blob/master/CHANGELOG.md"
 Package = "https://pypi.org/project/tripper"
 
 [project.scripts]
-datadoc = "tripper.dataset.datadoc:main"
+datadoc = "tripper.datadoc.clitool:main"
 
 [tool.isort]
 line_length = 79  # PEP8

tests/dataset/test_dataaccess.py → tests/datadoc/test_dataaccess.py

@@ -16,7 +16,7 @@ def test_save_and_load():
     from dataset_paths import outdir  # pylint: disable=import-error
 
     from tripper import DCAT, DCTERMS, EMMO, Triplestore
-    from tripper.dataset import load, load_dict, save, save_dict
+    from tripper.datadoc import load, load_dict, save, save_dict
 
     pytest.importorskip("dlite")
     pytest.importorskip("rdflib")

tests/dataset/test_dataset.py → tests/datadoc/test_dataset.py

@@ -10,8 +10,8 @@
 
 def test_get_jsonld_context():
     """Test get_jsonld_context()."""
-    from tripper.dataset import get_jsonld_context
-    from tripper.dataset.dataset import CONTEXT_URL
+    from tripper.datadoc import get_jsonld_context
+    from tripper.datadoc.dataset import CONTEXT_URL
 
     context = get_jsonld_context()
     assert isinstance(context, dict)
@@ -42,7 +42,7 @@ def test_get_jsonld_context():
 
 def test_get_prefixes():
     """Test get_prefixes()."""
-    from tripper.dataset import get_prefixes
+    from tripper.datadoc import get_prefixes
 
     prefixes = get_prefixes()
     assert prefixes["dcat"] == "http://www.w3.org/ns/dcat#"
@@ -56,7 +56,7 @@ def test_get_prefixes():
 def test_get_shortnames():
     """Test get_shortnames()."""
     from tripper import DCTERMS
-    from tripper.dataset.dataset import get_shortnames
+    from tripper.datadoc.dataset import get_shortnames
 
     # Short names that are not equal to the last component of the IRI
     exceptions = (
@@ -85,7 +85,7 @@ def test_get_shortnames():
 
 def test_add():
     """Test help-function add()."""
-    from tripper.dataset.dataset import add
+    from tripper.datadoc.dataset import add
 
     d = {}
     add(d, "a", "1")
@@ -99,7 +99,7 @@ def test_add():
 
 def test_addnested():
     """Test help-function addnested()."""
-    from tripper.dataset.dataset import addnested
+    from tripper.datadoc.dataset import addnested
     from tripper.utils import AttrDict
 
     d = AttrDict()
@@ -117,7 +117,7 @@ def test_addnested():
 
 def test_get():
     """Test help-function get()."""
-    from tripper.dataset.dataset import get
+    from tripper.datadoc.dataset import get
 
     d = {"a": [1, 2], "b": 1}
     assert get(d, "a") == [1, 2]
@@ -132,7 +132,7 @@ def test_get():
 def test_expand_iri():
     """Test help-function expand_iri()."""
     from tripper import CHAMEO, DCTERMS, OTEIO, RDF
-    from tripper.dataset.dataset import expand_iri, get_prefixes
+    from tripper.datadoc.dataset import expand_iri, get_prefixes
 
     prefixes = get_prefixes()
     assert expand_iri("chameo:Sample", prefixes) == CHAMEO.Sample
@@ -147,8 +147,8 @@ def test_expand_iri():
 def test_as_jsonld():
     """Test as_jsonld()."""
     from tripper import DCAT, EMMO, OWL, Namespace
-    from tripper.dataset import as_jsonld
-    from tripper.dataset.dataset import CONTEXT_URL
+    from tripper.datadoc import as_jsonld
+    from tripper.datadoc.dataset import CONTEXT_URL
 
     with pytest.raises(ValueError):
         as_jsonld({})
@@ -196,7 +196,7 @@ def test_datadoc():
     from dataset_paths import indir  # pylint: disable=import-error
 
     from tripper import CHAMEO, DCAT, EMMO, OTEIO, Triplestore
-    from tripper.dataset import load_dict, save_datadoc, save_dict, search_iris
+    from tripper.datadoc import load_dict, save_datadoc, save_dict, search_iris
 
     pytest.importorskip("dlite")
     pytest.importorskip("rdflib")
@@ -291,7 +291,7 @@ def test_custom_context():
     from dataset_paths import indir  # pylint: disable=import-error
 
     from tripper import Triplestore
-    from tripper.dataset import save_datadoc
+    from tripper.datadoc import save_datadoc
 
     ts = Triplestore("rdflib")
     d = save_datadoc(ts, indir / "custom_context.yaml")
@@ -321,7 +321,7 @@ def test_pipeline():
     otelib = pytest.importorskip("otelib")
     from dataset_paths import indir  # pylint: disable=import-error
 
-    from tripper.dataset import get_partial_pipeline, save_datadoc
+    from tripper.datadoc import get_partial_pipeline, save_datadoc
 
     # Prepare triplestore
     ts = Triplestore("rdflib")