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Dataset documentation improvements #3012

Merged
merged 39 commits into from
Jan 9, 2025
Merged

Dataset documentation improvements #3012

merged 39 commits into from
Jan 9, 2025

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nicholascar
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Summary of changes

Minor improvements in Dataset class documentation:

  • improved printout of results in examples/datasets.py

Checklist

  • Checked that there aren't other open pull requests for
    the same change.
  • Checked that all tests and type checking passes.
  • If the change adds new features or changes the RDFLib public API:
    • N/A
  • If the change has a potential impact on users of this project:
    • N/A
  • Considered granting push permissions to the PR branch,
    so maintainers can fix minor issues and keep your PR up to date.

@nicholascar nicholascar marked this pull request as draft December 18, 2024 10:21
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coveralls commented Dec 18, 2024 •
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Coverage Status

coverage: 90.282%. remained the same
when pulling 4baaf4f on dataset-docco
into 54b3bb6 on main.

@nicholascar nicholascar marked this pull request as ready for review January 6, 2025 04:42
recalcitrantsupplant
recalcitrantsupplant approved these changes Jan 9, 2025
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Approved - will make a small commit to address my comments

examples/datasets.py Outdated Show resolved Hide resolved
rdflib/graph.py Show resolved Hide resolved
@nicholascar nicholascar merged commit 97ff668 into main Jan 9, 2025
21 of 22 checks passed
@nicholascar nicholascar deleted the dataset-docco branch January 9, 2025 05:17
edmondchuc pushed a commit that referenced this pull request Jan 15, 2025
@nicholascar @edmondchuc
Dataset documentation improvements (#3012)
8542e1d 
* example printout improvements

* added BN graph creation

* updated tests var names & added one subtest

* typos & improved formatting

* updated Graph & Dataset docco

* typo fix

* fix code-in-comment syntax

* fix code-in-comment syntax 2

* fix code-in-comment syntax - ellipses

* fix code-in-comment syntax - sort print loop output

* blacked

* ruff fixes

* Poetry 2.0.0 pyproject.toml file

* move to PEP621 (Poetry 2.0.0) pyproject.toml

* require poetry 2.0.0

* require poetry 2.0.0

* add in requirement for poetry-plugin-export

* change from --sync to sync command

* further pyproject.toml format updates

* add poetry plugin to requirements-poetry.in

* fix pre-commit poetry version to 2.0.0

* remove testing artifact

* update license to 2025

* add me to contributors

* remove outdated --check arg

* typo

* test add back in precommit args

* test remove precommit args

* match ruff version to pre-commit autoupdate PR #3026; add back in --check

* re-remove --check

* add David to CONTRIBUTORS

* ruff in pyproject.toml to match pre-commit

* updates for David's comments

* fix Dataset docc ReST formatting
edmondchuc pushed a commit that referenced this pull request Jan 15, 2025
@nicholascar @edmondchuc
Dataset documentation improvements (#3012)
cfc2501 
* example printout improvements

* added BN graph creation

* updated tests var names & added one subtest

* typos & improved formatting

* updated Graph & Dataset docco

* typo fix

* fix code-in-comment syntax

* fix code-in-comment syntax 2

* fix code-in-comment syntax - ellipses

* fix code-in-comment syntax - sort print loop output

* blacked

* ruff fixes

* Poetry 2.0.0 pyproject.toml file

* move to PEP621 (Poetry 2.0.0) pyproject.toml

* require poetry 2.0.0

* require poetry 2.0.0

* add in requirement for poetry-plugin-export

* change from --sync to sync command

* further pyproject.toml format updates

* add poetry plugin to requirements-poetry.in

* fix pre-commit poetry version to 2.0.0

* remove testing artifact

* update license to 2025

* add me to contributors

* remove outdated --check arg

* typo

* test add back in precommit args

* test remove precommit args

* match ruff version to pre-commit autoupdate PR #3026; add back in --check

* re-remove --check

* add David to CONTRIBUTORS

* ruff in pyproject.toml to match pre-commit

* updates for David's comments

* fix Dataset docc ReST formatting
edmondchuc pushed a commit that referenced this pull request Jan 15, 2025
@nicholascar @edmondchuc
Dataset documentation improvements (#3012)
b2ceae6 
* example printout improvements

* added BN graph creation

* updated tests var names & added one subtest

* typos & improved formatting

* updated Graph & Dataset docco

* typo fix

* fix code-in-comment syntax

* fix code-in-comment syntax 2

* fix code-in-comment syntax - ellipses

* fix code-in-comment syntax - sort print loop output

* blacked

* ruff fixes

* Poetry 2.0.0 pyproject.toml file

* move to PEP621 (Poetry 2.0.0) pyproject.toml

* require poetry 2.0.0

* require poetry 2.0.0

* add in requirement for poetry-plugin-export

* change from --sync to sync command

* further pyproject.toml format updates

* add poetry plugin to requirements-poetry.in

* fix pre-commit poetry version to 2.0.0

* remove testing artifact

* update license to 2025

* add me to contributors

* remove outdated --check arg

* typo

* test add back in precommit args

* test remove precommit args

* match ruff version to pre-commit autoupdate PR #3026; add back in --check

* re-remove --check

* add David to CONTRIBUTORS

* ruff in pyproject.toml to match pre-commit

* updates for David's comments

* fix Dataset docc ReST formatting
edmondchuc pushed a commit that referenced this pull request Jan 16, 2025
@nicholascar @edmondchuc
Dataset documentation improvements (#3012)
42b7aaf 
* example printout improvements

* added BN graph creation

* updated tests var names & added one subtest

* typos & improved formatting

* updated Graph & Dataset docco

* typo fix

* fix code-in-comment syntax

* fix code-in-comment syntax 2

* fix code-in-comment syntax - ellipses

* fix code-in-comment syntax - sort print loop output

* blacked

* ruff fixes

* Poetry 2.0.0 pyproject.toml file

* move to PEP621 (Poetry 2.0.0) pyproject.toml

* require poetry 2.0.0

* require poetry 2.0.0

* add in requirement for poetry-plugin-export

* change from --sync to sync command

* further pyproject.toml format updates

* add poetry plugin to requirements-poetry.in

* fix pre-commit poetry version to 2.0.0

* remove testing artifact

* update license to 2025

* add me to contributors

* remove outdated --check arg

* typo

* test add back in precommit args

* test remove precommit args

* match ruff version to pre-commit autoupdate PR #3026; add back in --check

* re-remove --check

* add David to CONTRIBUTORS

* ruff in pyproject.toml to match pre-commit

* updates for David's comments

* fix Dataset docc ReST formatting
edmondchuc pushed a commit that referenced this pull request Jan 16, 2025
@nicholascar @edmondchuc
Dataset documentation improvements (#3012)
551654b 
* example printout improvements

* added BN graph creation

* updated tests var names & added one subtest

* typos & improved formatting

* updated Graph & Dataset docco

* typo fix

* fix code-in-comment syntax

* fix code-in-comment syntax 2

* fix code-in-comment syntax - ellipses

* fix code-in-comment syntax - sort print loop output

* blacked

* ruff fixes

* Poetry 2.0.0 pyproject.toml file

* move to PEP621 (Poetry 2.0.0) pyproject.toml

* require poetry 2.0.0

* require poetry 2.0.0

* add in requirement for poetry-plugin-export

* change from --sync to sync command

* further pyproject.toml format updates

* add poetry plugin to requirements-poetry.in

* fix pre-commit poetry version to 2.0.0

* remove testing artifact

* update license to 2025

* add me to contributors

* remove outdated --check arg

* typo

* test add back in precommit args

* test remove precommit args

* match ruff version to pre-commit autoupdate PR #3026; add back in --check

* re-remove --check

* add David to CONTRIBUTORS

* ruff in pyproject.toml to match pre-commit

* updates for David's comments

* fix Dataset docc ReST formatting
nicholascar added a commit that referenced this pull request Jan 16, 2025
@edmondchuc @nicholascar
@ashleysommer @dependabot @ajnelson-nist @joecrowleygaia @progval @jcbiddle @sandervd @mgberg
7.1.3 prep (#3036)
76a870c 
* 7.1.1 post release (#2953)

* Fix Black formatting in ./admin/get_merged_prs.py (#2954)

* build(deps-dev): bump ruff from 0.7.0 to 0.7.1 (#2955)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.0 to 0.7.1.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.7.0...0.7.1)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Ashley Sommer <ashleysommer@gmail.com>

* Fix defined namespace warnings (#2964)

* Fix defined namespace warnings

Current docs-generation tests are polluted by lots of warnings that occur when Sphinx tries to read various parts of DefinedNamespace.

* Fix tests that no longer need incorrect exceptions handled.

* fix black formatting in test file

* Undo typing changes, so this works on current pre-3.9 branch

* better handling for any/all double-underscore properties

* Don't include __slots__ in dir().

* test: earl test passing

* Annotate Serializer.serialize and descendants (#2970)

This patch aligns the type signatures on `Serializer` subclasses,
including renaming the arbitrary-keywords dictionary to always be
`**kwargs`.  This is in part to prepare for the possibility of adding
`*args` as a positional-argument delimiter.

References:
* #1890 (comment)

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

* build(deps): bump orjson from 3.10.10 to 3.10.11 (#2966)

Bumps [orjson](https://github.com/ijl/orjson) from 3.10.10 to 3.10.11.
- [Release notes](https://github.com/ijl/orjson/releases)
- [Changelog](https://github.com/ijl/orjson/blob/master/CHANGELOG.md)
- [Commits](ijl/orjson@3.10.10...3.10.11)

---
updated-dependencies:
- dependency-name: orjson
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump ruff from 0.7.1 to 0.7.2 (#2969)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.1 to 0.7.2.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.7.1...0.7.2)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump ruff from 0.7.2 to 0.7.3 (#2979)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.2 to 0.7.3.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.7.2...0.7.3)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump ruff from 0.7.3 to 0.8.0 (#2994)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.3 to 0.8.0.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.7.3...0.8.0)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps): bump orjson from 3.10.11 to 3.10.12 (#2991)

Bumps [orjson](https://github.com/ijl/orjson) from 3.10.11 to 3.10.12.
- [Release notes](https://github.com/ijl/orjson/releases)
- [Changelog](https://github.com/ijl/orjson/blob/master/CHANGELOG.md)
- [Commits](ijl/orjson@3.10.11...3.10.12)

---
updated-dependencies:
- dependency-name: orjson
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* added Node as an exported name from the root package location. Updated linting commands section in the developer section to use ruff check. (#2981)

* build(deps-dev): bump wheel from 0.45.0 to 0.45.1 (#2992)

Bumps [wheel](https://github.com/pypa/wheel) from 0.45.0 to 0.45.1.
- [Release notes](https://github.com/pypa/wheel/releases)
- [Changelog](https://github.com/pypa/wheel/blob/main/docs/news.rst)
- [Commits](pypa/wheel@0.45.0...0.45.1)

---
updated-dependencies:
- dependency-name: wheel
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nicholas Car <nick@kurrawong.net>

* feat: sort longturtle blank nodes (#2997)

* feat: sort longturtle blank nodes in the object position by their cbd string

* fix: #2767

* build(deps-dev): bump pytest from 8.3.3 to 8.3.4 (#2999)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.3.3 to 8.3.4.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.3...8.3.4)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump poetry from 1.8.4 to 1.8.5 (#3001)

Bumps [poetry](https://github.com/python-poetry/poetry) from 1.8.4 to 1.8.5.
- [Release notes](https://github.com/python-poetry/poetry/releases)
- [Changelog](https://github.com/python-poetry/poetry/blob/1.8.5/CHANGELOG.md)
- [Commits](python-poetry/poetry@1.8.4...1.8.5)

---
updated-dependencies:
- dependency-name: poetry
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump ruff from 0.8.0 to 0.8.2 (#3003)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.8.0 to 0.8.2.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.0...0.8.2)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump ruff from 0.8.2 to 0.8.3 (#3010)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.8.2 to 0.8.3.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.2...0.8.3)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps): bump berkeleydb from 18.1.11 to 18.1.12 (#3009)

Bumps [berkeleydb](https://www.jcea.es/programacion/pybsddb.htm) from 18.1.11 to 18.1.12.

---
updated-dependencies:
- dependency-name: berkeleydb
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
# Conflicts:
#	poetry.lock

* build(deps): bump orjson from 3.10.12 to 3.10.13 (#3018)

Bumps [orjson](https://github.com/ijl/orjson) from 3.10.12 to 3.10.13.
- [Release notes](https://github.com/ijl/orjson/releases)
- [Changelog](https://github.com/ijl/orjson/blob/master/CHANGELOG.md)
- [Commits](ijl/orjson@3.10.12...3.10.13)

---
updated-dependencies:
- dependency-name: orjson
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* build(deps-dev): bump ruff from 0.8.4 to 0.8.6 (#3025)

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.8.4 to 0.8.6.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.4...0.8.6)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* feat: deterministic longturtle serialisation using RDF canonicalization + n-triples sort (#3008)

* feat: use the RGDA1 canonicalization algorithm + lexical n-triples sort to produce deterministic longturtle serialisation

* chore: normalise usage of format

* chore: apply black

* fix: double up of semicolons when subject is a blank node

* fix: lint

* jsonld: Do not merge nodes with different invalid URIs (#3011)

When parsing JSON-LD with invalid URIs in the `@id`, the
`generalized_rdf: True` option allows parsing these nodes as blank nodes
instead of outright rejecting the document.

However, all nodes with invalid URIs were mapped to the same blank node,
resulting in incorrect data. For example, without this patch, the new test
fails with:

```
AssertionError: Expected:
@Prefix schema: <https://schema.org/> .

<https://example.org/root-object> schema:author [ schema:familyName "Doe" ;
            schema:givenName "Jane" ;
            schema:name "Jane Doe" ],
        [ schema:familyName "Doe" ;
            schema:givenName "John" ;
            schema:name "John Doe" ] .

Got:
@Prefix schema: <https://schema.org/> .

<https://example.org/root-object> schema:author <> .

<> schema:familyName "Doe" ;
    schema:givenName "Jane",
        "John" ;
    schema:name "Jane Doe",
        "John Doe" .
```

* Fixed incorrect ASK behaviour for dataset with one element (#2989)

* Pass base uri to serializer when writing to file. (#2977)

Co-authored-by: Nicholas Car <nick@kurrawong.net>

* Dataset documentation improvements (#3012)

* example printout improvements

* added BN graph creation

* updated tests var names & added one subtest

* typos & improved formatting

* updated Graph & Dataset docco

* typo fix

* fix code-in-comment syntax

* fix code-in-comment syntax 2

* fix code-in-comment syntax - ellipses

* fix code-in-comment syntax - sort print loop output

* blacked

* ruff fixes

* Poetry 2.0.0 pyproject.toml file

* move to PEP621 (Poetry 2.0.0) pyproject.toml

* require poetry 2.0.0

* require poetry 2.0.0

* add in requirement for poetry-plugin-export

* change from --sync to sync command

* further pyproject.toml format updates

* add poetry plugin to requirements-poetry.in

* fix pre-commit poetry version to 2.0.0

* remove testing artifact

* update license to 2025

* add me to contributors

* remove outdated --check arg

* typo

* test add back in precommit args

* test remove precommit args

* match ruff version to pre-commit autoupdate PR #3026; add back in --check

* re-remove --check

* add David to CONTRIBUTORS

* ruff in pyproject.toml to match pre-commit

* updates for David's comments

* fix Dataset docc ReST formatting

* remove ConjunctiveGraph example; add Dataset example; add JSON-LS serialization example

* Add RDFLib Path to SHACL path utility and corresponding tests (#2990)

* shacl path parser: Add additional test case

* shacl utilities: Add new SHACL path building utility with corresponding tests

---------

Co-authored-by: Nicholas Car <nick@kurrawong.net>
# Conflicts:
#	rdflib/extras/shacl.py

* fix: typing and import issues

* fix: line length as int

* fix: ruff version conflict

* fix: berkeleydb pin to 18.1.10 for python 3.8 compatibility

* 3a not 2a

---------

Signed-off-by: dependabot[bot] <support@github.com>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Co-authored-by: Nicholas Car <nick@kurrawong.net>
Co-authored-by: Ashley Sommer <ashleysommer@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Alex Nelson <alexander.nelson@nist.gov>
Co-authored-by: joecrowleygaia <142864129+joecrowleygaia@users.noreply.github.com>
Co-authored-by: Val Lorentz <vlorentz@softwareheritage.org>
Co-authored-by: jcbiddle <114963309+jcbiddle@users.noreply.github.com>
Co-authored-by: Sander Van Dooren <sandervd@users.noreply.github.com>
Co-authored-by: Nicholas Car <nick@kurrawong.ai>
Co-authored-by: Matt Goldberg <59745812+mgberg@users.noreply.github.com>
# for free to join this conversation on GitHub. Already have an account? # to comment
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@nicholascar @coveralls @recalcitrantsupplant