From 10833d65bfe99c7f72554a947b3e7e6defcd8053 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 12 Apr 2024 06:48:59 +0000 Subject: [PATCH 01/24] Update pytest-cov requirement from ~=4.1 to ~=5.0 (#738) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version.
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Sourced from pytest-cov's changelog.

5.0.0 (2024-03-24)

4.1.0 (2023-05-24)

4.0.0 (2022-09-28)

Note that this release drops support for multiprocessing.

... (truncated)

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--------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> Co-authored-by: francescalb --- requirements_dev.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index efed240da..db8dc8f5d 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -4,4 +4,5 @@ pylint~=2.17; python_version<"3.8" pylint~=3.1; python_version>="3.8" pytest~=7.4; python_version<"3.8" pytest~=8.1; python_version>="3.8" -pytest-cov~=4.1 +pytest-cov~=4.1; python_version<"3.8" +pytest-cov~=5.0; python_version>="3.8" From b82147d46c13c2cf5addcbffab964a89ea317c89 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 12 Apr 2024 06:54:23 +0000 Subject: [PATCH 02/24] Update mkdocstrings[python-legacy] requirement from ~=0.24.1 to ~=0.24.3 (#743) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [mkdocstrings[python-legacy]](https://github.com/mkdocstrings/mkdocstrings) to permit the latest version.
Release notes

Sourced from mkdocstrings[python-legacy]'s releases.

0.24.3

0.24.3 - 2024-04-05

Compare with 0.24.2

Bug Fixes

  • Support HTML toc labels with Python-Markdown 3.6+ (uncomment code...) (7fe3e5f by Timothée Mazzucotelli).
Changelog

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0.24.3 - 2024-04-05

Compare with 0.24.2

Bug Fixes

  • Support HTML toc labels with Python-Markdown 3.6+ (uncomment code...) (7fe3e5f by Timothée Mazzucotelli).

0.24.2 - 2024-04-02

Compare with 0.24.1

Bug Fixes

0.24.1 - 2024-02-27

Compare with 0.24.0

Code Refactoring

0.24.0 - 2023-11-14

Compare with 0.23.0

Features

Bug Fixes

Code Refactoring

0.23.0 - 2023-08-28

Compare with 0.22.0

Breaking Changes

  • Removed BaseCollector and BaseRenderer classes: they were merged into the BaseHandler class.
  • Removed the watch feature, as MkDocs now provides it natively.

... (truncated)

Commits
  • 828bd59 chore: Prepare release 0.24.3
  • 7fe3e5f fix: Support HTML toc labels with Python-Markdown 3.6+ (uncomment code...)
  • 7b9827c chore: Prepare release 0.24.2
  • 17bfc87 chore: Use PEP 440 versioning scheme for changelog
  • 024ac41 ci: Ignore mypy warning
  • c0d0090 fix: Support HTML toc labels with Python-Markdown 3.6+
  • ccbbbf1 chore: Template upgrade
  • 56cf7d5 docs: List VBA handler
  • 9e1bf62 docs: Fix link to Griffe extension
  • f071d5d chore: Switch to Copier UV template
  • Additional commits viewable in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_docs.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 5bda3e3ca..f88d5f517 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -3,5 +3,5 @@ mkdocs~=1.5 mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" mkdocs-material~=9.2; python_version<"3.8" -mkdocstrings[python-legacy]~=0.24.1; python_version>="3.8" +mkdocstrings[python-legacy]~=0.24.3; python_version>="3.8" mkdocstrings[python-legacy]~=0.22.0; python_version<"3.8" From efa396f4871dfe166fe137184c9e434d632797af Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Apr 2024 05:51:37 +0000 Subject: [PATCH 03/24] Update mkdocstrings[python-legacy] requirement from ~=0.24.3 to ~=0.25.0 (#754) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [mkdocstrings[python-legacy]](https://github.com/mkdocstrings/mkdocstrings) to permit the latest version.
Release notes

Sourced from mkdocstrings[python-legacy]'s releases.

0.25.0

0.25.0 - 2024-04-27

Compare with 0.24.3

Features

  • Support once parameter in logging methods, allowing to log a message only once with a given logger (1532b59 by Timothée Mazzucotelli).
  • Support blank line between ::: path and YAML options (d799d2f by Timothée Mazzucotelli). Issue-450

Code Refactoring

  • Allow specifying name of template loggers (c5b5f69 by Timothée Mazzucotelli).
Changelog

Sourced from mkdocstrings[python-legacy]'s changelog.

0.25.0 - 2024-04-27

Compare with 0.24.3

Features

  • Support once parameter in logging methods, allowing to log a message only once with a given logger (1532b59 by Timothée Mazzucotelli).
  • Support blank line between ::: path and YAML options (d799d2f by Timothée Mazzucotelli). Issue-450

Code Refactoring

  • Allow specifying name of template loggers (c5b5f69 by Timothée Mazzucotelli).

0.24.3 - 2024-04-05

Compare with 0.24.2

Bug Fixes

  • Support HTML toc labels with Python-Markdown 3.6+ (uncomment code...) (7fe3e5f by Timothée Mazzucotelli).

0.24.2 - 2024-04-02

Compare with 0.24.1

Bug Fixes

0.24.1 - 2024-02-27

Compare with 0.24.0

Code Refactoring

0.24.0 - 2023-11-14

Compare with 0.23.0

Features

Bug Fixes

... (truncated)

Commits
  • 87d8229 chore: Prepare release 0.25.0
  • c5b5f69 refactor: Allow specifying name of template loggers
  • 7ff1681 docs: Enable parameter headings
  • 253d215 docs: Load inventories for MkDocs and Markdown
  • 1532b59 feat: Support once parameter in logging methods, allowing to log a message ...
  • d799d2f feat: Support blank line between ::: path and YAML options
  • See full diff in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_docs.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index f88d5f517..16885acb3 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -3,5 +3,5 @@ mkdocs~=1.5 mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" mkdocs-material~=9.2; python_version<"3.8" -mkdocstrings[python-legacy]~=0.24.3; python_version>="3.8" +mkdocstrings[python-legacy]~=0.25.0; python_version>="3.8" mkdocstrings[python-legacy]~=0.22.0; python_version<"3.8" From 7e0bca14c82618d63795cd63ba294b92a43143b1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Apr 2024 05:56:50 +0000 Subject: [PATCH 04/24] Update pytest requirement from ~=8.1 to ~=8.2 (#753) Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
Release notes

Sourced from pytest's releases.

8.2.0

pytest 8.2.0 (2024-04-27)

Deprecations

  • #12069: A deprecation warning is now raised when implementations of one of the following hooks request a deprecated py.path.local parameter instead of the pathlib.Path parameter which replaced it:

    • pytest_ignore_collect{.interpreted-text role="hook"} - the path parameter - use collection_path instead.
    • pytest_collect_file{.interpreted-text role="hook"} - the path parameter - use file_path instead.
    • pytest_pycollect_makemodule{.interpreted-text role="hook"} - the path parameter - use module_path instead.
    • pytest_report_header{.interpreted-text role="hook"} - the startdir parameter - use start_path instead.
    • pytest_report_collectionfinish{.interpreted-text role="hook"} - the startdir parameter - use start_path instead.

    The replacement parameters are available since pytest 7.0.0. The old parameters will be removed in pytest 9.0.0.

    See legacy-path-hooks-deprecated{.interpreted-text role="ref"} for more details.

Features

  • #11871: Added support for reading command line arguments from a file using the prefix character @, like e.g.: pytest @tests.txt. The file must have one argument per line.

    See Read arguments from file <args-from-file>{.interpreted-text role="ref"} for details.

Improvements

  • #11523: pytest.importorskip{.interpreted-text role="func"} will now issue a warning if the module could be found, but raised ImportError{.interpreted-text role="class"} instead of ModuleNotFoundError{.interpreted-text role="class"}.

    The warning can be suppressed by passing exc_type=ImportError to pytest.importorskip{.interpreted-text role="func"}.

    See import-or-skip-import-error{.interpreted-text role="ref"} for details.

  • #11728: For unittest-based tests, exceptions during class cleanup (as raised by functions registered with TestCase.addClassCleanup <unittest.TestCase.addClassCleanup>{.interpreted-text role="meth"}) are now reported instead of silently failing.

  • #11777: Text is no longer truncated in the short test summary info section when -vv is given.

  • #12112: Improved namespace packages detection when consider_namespace_packages{.interpreted-text role="confval"} is enabled, covering more situations (like editable installs).

  • #9502: Added PYTEST_VERSION{.interpreted-text role="envvar"} environment variable which is defined at the start of the pytest session and undefined afterwards. It contains the value of pytest.__version__, and among other things can be used to easily check if code is running from within a pytest run.

Bug Fixes

  • #12065: Fixed a regression in pytest 8.0.0 where test classes containing setup_method and tests using @staticmethod or @classmethod would crash with AttributeError: 'NoneType' object has no attribute 'setup_method'.

    Now the request.instance <pytest.FixtureRequest.instance>{.interpreted-text role="attr"} attribute of tests using @staticmethod and @classmethod is no longer None, but a fresh instance of the class, like in non-static methods.

... (truncated)

Commits
  • 6bd3f31 Tweak changelog for 8.2.0
  • 9b6219b Prepare release version 8.2.0
  • 835765c Merge pull request #12130 from bluetech/fixtures-inline
  • 7e7503c unittest: report class cleanup exceptions (#12250)
  • 882c4da fixtures: inline fail_fixturefunc
  • 2e8fb9f fixtures: extract a _check_fixturedef method
  • acf2971 fixtures: inline _getnextfixturedef into _get_active_fixturedef
  • 3c77aec fixtures: move "request" check early
  • d217d68 fixtures: inline _compute_fixture_value
  • 530be28 fixtures: use early return in _get_active_fixturedef
  • Additional commits viewable in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index db8dc8f5d..a8fdb47f1 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -3,6 +3,6 @@ pre-commit~=3.7; python_version>="3.9" pylint~=2.17; python_version<"3.8" pylint~=3.1; python_version>="3.8" pytest~=7.4; python_version<"3.8" -pytest~=8.1; python_version>="3.8" +pytest~=8.2; python_version>="3.8" pytest-cov~=4.1; python_version<"3.8" pytest-cov~=5.0; python_version>="3.8" From 01ba5202163ee148d4ac98ccea01f30998450ca7 Mon Sep 17 00:00:00 2001 From: "TEAM 4.0[bot]" Date: Wed, 17 Apr 2024 09:58:32 +0200 Subject: [PATCH 05/24] [Auto-generated] Update dependencies (#748) Automatically created PR from [`ci/dependabot-updates`](https://github.com/emmo-repo/EMMOntoPy/tree/ci/dependabot-updates). The PR is based on the ['CI - Update dependencies PR' workflow](https://SINTEF.github.io/ci-cd/latest/workflows/ci_update_dependencies/) in [SINTEF/ci-cd](https://github.com/SINTEF/ci-cd). - [ ] Check that the diff is sensible, and that tests and builds pass with the new dependency versions. - [ ] Make sure that the PR is **squash** merged, with a sensible commit message. --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> Co-authored-by: francescalb --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0f3719470..8cac74b8c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,7 +17,7 @@ repos: args: [--markdown-linebreak-ext=md] - repo: https://github.com/ambv/black - rev: 24.3.0 + rev: 24.4.0 hooks: - id: black name: Blacken From 65e1bf910bb4d4596f86a24582c8a88d0121f844 Mon Sep 17 00:00:00 2001 From: "Francesca L. Bleken" <48128015+francescalb@users.noreply.github.com> Date: Fri, 26 Apr 2024 10:05:46 +0200 Subject: [PATCH 06/24] Added possibility for = in extra annotations defined in excelparser (#752) # Description For each annotation it is now allowed to have = in the string that is added. It is tested in the excel2onto test which checks that the created ontology is correct (small change in one of the annotations there). ## Type of change - [ ] Bug fix. - [ ] New feature. - [ ] Documentation update. - [ ] Test update. ## Checklist This checklist can be used as a help for the reviewer. - [ ] Is the code easy to read and understand? - [ ] Are comments for humans to read, not computers to disregard? - [ ] Does a new feature has an accompanying new test (in the CI or unit testing schemes)? - [ ] Has the documentation been updated as necessary? - [ ] Does this close the issue? - [ ] Is the change limited to the issue? - [ ] Are errors handled for all outcomes? - [ ] Does the new feature provide new restrictions on dependencies, and if so is this documented? ## Comments --- ontopy/excelparser.py | 2 +- tests/test_excelparser/onto.xlsx | Bin 24136 -> 24202 bytes .../result_ontology/fromexcelonto.ttl | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ontopy/excelparser.py b/ontopy/excelparser.py index 1462659aa..02cd9c49f 100755 --- a/ontopy/excelparser.py +++ b/ontopy/excelparser.py @@ -808,7 +808,7 @@ def _add_entities( or row["Other annotations"] == "nan" ): for annotation in row["Other annotations"].split(";"): - key, value = annotation.split("=") + key, value = annotation.split("=", 1) entity[key.strip(" ")] = english(value.strip(" ")) remaining_rows.difference_update(added_rows) diff --git a/tests/test_excelparser/onto.xlsx b/tests/test_excelparser/onto.xlsx index 3e7a07528cd284e449eb6ac9d8a1b09f38dbb9e3..0c926c48da40a7d3ebf89b938cd02cf605146d73 100644 GIT binary patch delta 9169 zcmZX4bx<8`^X0{YyItJfU4lCVcXtTx7Hn_}esKs8GFYVQ&TffPn|wzMmu5Rx?sMdAOaB!h=gfyAP^f82!sg&f&82}d|f>pEnQt5 z+5McIN_32pRs`{a&Fo*LcW;vgCCrOL<6w$pkDO+_R=Q<~g<`4J-H)qJ&z< zo;(J_3ah8BotPwz{ur6)W8u+Jtu3if_zWeO+SR}0(ojg~XL3%iJf#PKh?$KYB~U|) zWi^bh69yK}><3|*ojjOKskp)fm@1gJUP`>yWEUmt_i}v2mrIqU{o!bdQmz{qmTF!8 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zPZ#qEF@~BHHalDC!7qZHb;xaoLkNqsE&%<@ky_Sm#P32e20ugWh|k5X@t2*ie&ByW z6O(F#ouauTkv4Ypp4g_mkB{wSbsRJ8*hjE-2EE= ztVe=xzau^vuL7dk#O&W29j~!U&~Xm;FmwdR_eYPf;A$W+SS#8XW>28@DJrfoe2xny zS&w)0h_syh^)_IlD61&N!Ds$622>=ti?AE0n=A?;voc4Uc^{`YrD-kZ-_6XZp zrgn;e^8Y`5K(loeVdtQyI?`|q0H`P_2r8=!BKfz63(w}$@rO2PWCsSXPPdTRhA z`L`|jzs6k9KSmG&bX6Dl52%G+=z`!VNdMj-f|Bb2N&bTi$^PO&a`d5uZm-Iwn<)8%m Date: Fri, 26 Apr 2024 22:22:40 +0200 Subject: [PATCH 07/24] [Auto-generated] Update dependencies (#750) ### Update dependencies Automatically created PR from [`ci/dependabot-updates`](https://github.com/emmo-repo/EMMOntoPy/tree/ci/dependabot-updates). The PR is based on the ['CI - Update dependencies PR' workflow](https://SINTEF.github.io/ci-cd/latest/workflows/ci_update_dependencies/) in [SINTEF/ci-cd](https://github.com/SINTEF/ci-cd). #### To do - [ ] Check that the diff is sensible, and that tests and builds pass with the new dependency versions. - [ ] Make sure that the PR is **squash** merged, with a sensible commit message. --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> Co-authored-by: francescalb From 93044e57417f4aa5c5146947639ea292e3da138b Mon Sep 17 00:00:00 2001 From: Jesper Friis Date: Wed, 1 May 2024 15:48:11 +0200 Subject: [PATCH 08/24] Make it possible to run HermiT on EMMO (#740) # Description Make it possible to run HermiT on EMMO, by: * Add support for additional keyword arguments that `sync_reasoner()` may pass to the `save()` method. * Remove custom datatypes before running HermiT. Readd the removed data properties after HermiT completes. * Add `--java-executable` and `--java-memory` arguments to ontoconvert to control how to run java. ## Type of change - [x] Bug fix. - [ ] New feature. - [ ] Documentation update. - [ ] Test update. Co-authored-by: francescalb --- ontopy/ontology.py | 51 +++++++++++++++++++++++++++++++++++++++++++--- tools/ontoconvert | 18 +++++++++++++++- 2 files changed, 65 insertions(+), 4 deletions(-) diff --git a/ontopy/ontology.py b/ontopy/ontology.py index 47425c771..5eacec242 100644 --- a/ontopy/ontology.py +++ b/ontopy/ontology.py @@ -871,6 +871,7 @@ def save( write_catalog_file=False, append_catalog=False, catalog_file="catalog-v001.xml", + **kwargs, ) -> Path: """Writes the ontology to file. @@ -915,6 +916,7 @@ def save( # pylint: disable=redefined-builtin,too-many-arguments # pylint: disable=too-many-statements,too-many-branches # pylint: disable=too-many-locals,arguments-renamed,invalid-name + if not _validate_installed_version( package="rdflib", min_version="6.0.0" ) and format == FMAP.get("ttl", ""): @@ -940,7 +942,9 @@ def save( raise TypeError("`filename` and `format` cannot both be None.") else: file = filename - filepath = os.path.join(dir, file) + filepath = os.path.join( + dir, file if isinstance(file, (str, Path)) else file.name + ) returnpath = filepath dir = Path(filepath).resolve().parent @@ -980,6 +984,7 @@ def save( recursive=False, squash=False, write_catalog_file=False, + **kwargs, ) if write_catalog_file: @@ -1045,7 +1050,7 @@ def save( graph.serialize(destination=filepath, format=format) elif format in OWLREADY2_FORMATS: - super().save(file=filepath, format=fmt) + super().save(file=filepath, format=fmt, **kwargs) else: # The try-finally clause is needed for cleanup and because # we have to provide delete=False to NamedTemporaryFile @@ -1056,7 +1061,7 @@ def save( suffix=".owl", delete=False ) as handle: tmpfile = handle.name - super().save(tmpfile, format="ntriples") + super().save(tmpfile, format="ntriples", **kwargs) graph = rdflib.Graph() graph.parse(tmpfile, format="ntriples") graph.namespace_manager.bind( @@ -1331,12 +1336,46 @@ def sync_reasoner( Keyword arguments are passed to the underlying owlready2 function. """ + # pylint: disable=too-many-branches + + removed_equivalent = defaultdict(list) + removed_subclasses = defaultdict(list) + if reasoner == "FaCT++": sync = sync_reasoner_factpp elif reasoner == "Pellet": sync = owlready2.sync_reasoner_pellet elif reasoner == "HermiT": sync = owlready2.sync_reasoner_hermit + + # Remove custom data propertyes, otherwise HermiT will crash + datatype_iri = "http://www.w3.org/2000/01/rdf-schema#Datatype" + + for cls in self.classes(imported=include_imported): + remove_eq = [] + for i, r in enumerate(cls.equivalent_to): + if isinstance(r, owlready2.Restriction): + if ( + hasattr(r.value.__class__, "iri") + and r.value.__class__.iri == datatype_iri + ): + remove_eq.append(i) + removed_equivalent[cls].append(r) + for i in reversed(remove_eq): + del cls.equivalent_to[i] + + remove_subcls = [] + for i, r in enumerate(cls.is_a): + if isinstance(r, owlready2.Restriction): + if ( + hasattr(r.value.__class__, "iri") + and r.value.__class__.iri == datatype_iri + ): + remove_subcls.append(i) + removed_subclasses[cls].append(r) + for i in reversed(remove_subcls): + del cls.is_a[i] + else: raise ValueError( f"Unknown reasoner '{reasoner}'. Supported reasoners " @@ -1353,6 +1392,12 @@ def sync_reasoner( else: sync(self, **kwargs) + # Restore removed custom data properties + for cls, eqs in removed_equivalent.items(): + cls.extend(eqs) + for cls, subcls in removed_subclasses.items(): + cls.extend(subcls) + def sync_attributes( # pylint: disable=too-many-branches self, name_policy=None, diff --git a/tools/ontoconvert b/tools/ontoconvert index 4e06cdf79..d97123bd9 100755 --- a/tools/ontoconvert +++ b/tools/ontoconvert @@ -9,6 +9,9 @@ from rdflib.util import guess_format from ontopy import get_ontology from ontopy.utils import annotate_source, rename_iris, copy_annotation +import owlready2 # pylint: disable=wrong-import-order +import owlready2.reasoning # pylint: disable=wrong-import-order + def main(argv: list = None): """Main run function. @@ -116,7 +119,14 @@ def main(argv: list = None): action="store_true", help="Do not infer imported ontologies.", ) - # To be implemented... + parser.add_argument( + "--java-executable", + help="Path to Java executable to use. Default is `java`.", + ) + parser.add_argument( + "--java-memory", + help="Maximum memory allocated to Java in MB. Default is 2000.", + ) parser.add_argument( "--iri", "-I", @@ -218,6 +228,12 @@ def main(argv: list = None): if not output_format: output_format = "xml" + # Settings for running Java + if args.java_executable: + owlready2.JAVA_EXE = args.java_executable + if args.java_memory: + owlready2.reasoning.JAVA_MEMORY = int(args.java_memory) + # Annotations to copy with --copy-emmo-annotations if args.copy_emmo_annotations: args.copy_annotation.extend( From a98ee512d4e4085cb777234a203417d4136ee965 Mon Sep 17 00:00:00 2001 From: Jesper Friis Date: Thu, 2 May 2024 09:55:36 +0200 Subject: [PATCH 09/24] Added minor fixes for ontoconvert (#739) # Description Minor fixes for ontoconvert option help. Also included `emmo:comment` to the set of annotations included in the `--copy-emmo-annotations` option. **Note**: Builds on top of PR https://github.com/emmo-repo/EMMOntoPy/pull/756. Merge that PR first! ## Type of change - [x] Bug fix. - [ ] New feature. - [ ] Documentation update. - [ ] Test update. ## Checklist This checklist can be used as a help for the reviewer. - [ ] Is the code easy to read and understand? - [ ] Are comments for humans to read, not computers to disregard? - [ ] Does a new feature has an accompanying new test (in the CI or unit testing schemes)? - [ ] Has the documentation been updated as necessary? - [ ] Does this close the issue? - [ ] Is the change limited to the issue? - [ ] Are errors handled for all outcomes? - [ ] Does the new feature provide new restrictions on dependencies, and if so is this documented? ## Comments --------- Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> --- tests/testonto/domainonto.ttl | 5 +++++ tools/ontoconvert | 7 +++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/tests/testonto/domainonto.ttl b/tests/testonto/domainonto.ttl index f7e5bf71e..545bcd20b 100644 --- a/tests/testonto/domainonto.ttl +++ b/tests/testonto/domainonto.ttl @@ -43,6 +43,11 @@ emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 a owl:AnnotationProperty ; skos:prefLabel "elucidation"@en ; rdfs:comment "Short enlightening explanation aimed to facilitate the user in drawing the connection (interpretation) between a OWL entity and the real world object(s) for which it stands."@en . +emmo:EMMO_c7b62dd7_063a_4c2a_8504_42f7264ba83f a owl:AnnotationProperty ; + rdfs:subPropertyOf rdfs:comment ; + skos:prefLabel "comment"@en ; + rdfs:comment "A text that add some information about the entity."@en . + :EMMO_70fe84ff_99b6_4206_a9fc_9a8931836d84 a owl:AnnotationProperty ; rdfs:subPropertyOf rdfs:comment ; skos:prefLabel "definition"@en ; diff --git a/tools/ontoconvert b/tools/ontoconvert index d97123bd9..3e1e6a6fb 100755 --- a/tools/ontoconvert +++ b/tools/ontoconvert @@ -87,8 +87,10 @@ def main(argv: list = None): "http://www.w3.org/2004/02/skos/core#prefLabel" "-->http://www.w3.org/2000/01/rdf-schema#label " "--copy-annotation=elucidation" - "-->http://www.w3.org/2000/01/rdf-schema#comment`" + "-->http://www.w3.org/2000/01/rdf-schema#comment` " "--copy-annotation=definition" + "-->http://www.w3.org/2000/01/rdf-schema#comment` " + "--copy-annotation=comment" "-->http://www.w3.org/2000/01/rdf-schema#comment`" ), ) @@ -110,7 +112,7 @@ def main(argv: list = None): metavar="NAME", help=( "Add additional relations inferred by the reasoner. Supported " - 'reasoners are "FaCT++" (default), "HermiT" and "Pellet".' + 'reasoners are "HermiT" (default), "Pellet" and "FaCT++".' ), ) parser.add_argument( @@ -242,6 +244,7 @@ def main(argv: list = None): "-->http://www.w3.org/2000/01/rdf-schema#label", "elucidation-->http://www.w3.org/2000/01/rdf-schema#comment", "definition-->http://www.w3.org/2000/01/rdf-schema#comment", + "comment-->http://www.w3.org/2000/01/rdf-schema#comment", ] ) From ebdb53e868b8816c05eebb8a054c4baadccad3c4 Mon Sep 17 00:00:00 2001 From: "TEAM 4.0[bot]" Date: Fri, 3 May 2024 11:22:38 +0200 Subject: [PATCH 10/24] [Auto-generated] Update dependencies (#755) ### Update dependencies Automatically created PR from [`ci/dependabot-updates`](https://github.com/emmo-repo/EMMOntoPy/tree/ci/dependabot-updates). The PR is based on the ['CI - Update dependencies PR' workflow](https://SINTEF.github.io/ci-cd/latest/workflows/ci_update_dependencies/) in [SINTEF/ci-cd](https://github.com/SINTEF/ci-cd). #### To do - [ ] Check that the diff is sensible, and that tests and builds pass with the new dependency versions. - [ ] Make sure that the PR is **squash** merged, with a sensible commit message. --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> Co-authored-by: francescalb --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8cac74b8c..8d02b5ef8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,7 +17,7 @@ repos: args: [--markdown-linebreak-ext=md] - repo: https://github.com/ambv/black - rev: 24.4.0 + rev: 24.4.2 hooks: - id: black name: Blacken From f418dd39de734401aebc6166c204c986d377ea73 Mon Sep 17 00:00:00 2001 From: "TEAM 4.0[bot]" Date: Wed, 8 May 2024 13:27:01 +0200 Subject: [PATCH 11/24] [Auto-generated] Update dependencies (#760) ### Update dependencies Automatically created PR from [`ci/dependabot-updates`](https://github.com/emmo-repo/EMMOntoPy/tree/ci/dependabot-updates). The PR is based on the ['CI - Update dependencies PR' workflow](https://SINTEF.github.io/ci-cd/latest/workflows/ci_update_dependencies/) in [SINTEF/ci-cd](https://github.com/SINTEF/ci-cd). #### To do - [ ] Check that the diff is sensible, and that tests and builds pass with the new dependency versions. - [ ] Make sure that the PR is **squash** merged, with a sensible commit message. --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> Co-authored-by: francescalb From 01e8617e9c8c2da4ffe09dc7603dc48dd4a7f37a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 May 2024 11:43:48 +0000 Subject: [PATCH 12/24] Update mike requirement from ~=2.0 to ~=2.1 (#758) Updates the requirements on [mike](https://github.com/jimporter/mike) to permit the latest version.
Release notes

Sourced from mike's releases.

v2.1.1

Bug fixes

  • Support using environment variables for INHERIT when injecting the mike plugin into mkdocs.yml
Changelog

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v2.1.1 (2024-05-03)

Bug fixes

  • Support using environment variables for INHERIT when injecting the mike plugin into mkdocs.yml

v2.1.0 (2024-05-01)

New features

  • When calling set-default, you can now pass --allow-undefined to set the default to a version that doesn't exist yet
  • Add global-level -q / --quiet option to suppress warning messages
  • Add support for handling !relative in mkdocs.yml

Bug fixes

  • When loading an MkDocs config, mike now runs the startup and shutdown events

v2.0.0 (2023-11-02)

New features

  • Add support for applying arbitrary properties to documentation versions
  • Add support for hiding specific versions from the selector when using the default themes
  • Deploy aliases using symbolic links by default; this can be configured via --alias-type on the command line or alias_type in the mike MkDocs plugin
  • Avoid creating empty commits by default; if you want empty commits, pass --allow-empty
  • Look for both mkdocs.yml and mkdocs.yaml configuration files
  • Support GIT_COMMITTER_(NAME|EMAIL|DATE) when generating commits
  • Allow specifying alias_type, redirect_template, and deploy_prefix in the mike MkDocs plugin
  • Add a --debug flag to help diagnose bugs with mike
  • Port number is now optional for --dev-addr in mike serve, defaulting to 8000

Breaking changes

  • --prefix is now --deploy-prefix
  • --no-redirect is now --alias-type=copy
  • --ignore is now --ignore-remote-status
  • -f / --force is no longer supported on subcommands that can push (this option was too error-prone, and users who really need to force-push can use Git directly)
  • --rebase is no longer supported (instead of using this, it's better to use

... (truncated)

Commits
  • 0bdfe24 Update version to 2.1.1
  • 3351d5f Expand environment variables when injecting the mike plugin; resolves #217
  • e4d83ed Update version to 2.2.0.dev0
  • 6e6cfbb Update version to 2.1.0
  • 5773be9 Fix CI
  • 7904925 Further tests for deserializing Python objects during inject_plugin
  • 01219bd Allow arbitrary Python object in YAML config
  • ac7b240 Handle !relative (and any future constructors) in mkdocs.yml; resolves #199
  • fdcc912 Add --quiet option; resolves #210
  • a39ea73 Add set-default --allow-undefined; see #210
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> --- requirements_docs.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 16885acb3..57a9c428a 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -1,4 +1,4 @@ -mike~=2.0 +mike~=2.1 mkdocs~=1.5 mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" From 45850ac6cf20a348e835a9e2727699989555106c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 May 2024 11:51:50 +0000 Subject: [PATCH 13/24] Update mkdocstrings[python-legacy] requirement from ~=0.25.0 to ~=0.25.1 (#757) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [mkdocstrings[python-legacy]](https://github.com/mkdocstrings/mkdocstrings) to permit the latest version.
Release notes

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0.25.1

0.25.1 - 2024-05-05

Compare with 0.25.0

Bug Fixes

Changelog

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0.25.1 - 2024-05-05

Compare with 0.25.0

Bug Fixes

0.25.0 - 2024-04-27

Compare with 0.24.3

Features

  • Support once parameter in logging methods, allowing to log a message only once with a given logger (1532b59 by Timothée Mazzucotelli).
  • Support blank line between ::: path and YAML options (d799d2f by Timothée Mazzucotelli). Issue-450

Code Refactoring

  • Allow specifying name of template loggers (c5b5f69 by Timothée Mazzucotelli).

0.24.3 - 2024-04-05

Compare with 0.24.2

Bug Fixes

  • Support HTML toc labels with Python-Markdown 3.6+ (uncomment code...) (7fe3e5f by Timothée Mazzucotelli).

0.24.2 - 2024-04-02

Compare with 0.24.1

Bug Fixes

0.24.1 - 2024-02-27

Compare with 0.24.0

Code Refactoring

0.24.0 - 2023-11-14

Compare with 0.23.0

... (truncated)

Commits
  • e135869 chore: Prepare release 0.25.1
  • cb86e08 fix: Always descend into sub-headings when re-applying their label
  • a86ca7d docs: Customize parameters color in ToC
  • bc25b6a docs: Remove requirements link in readme
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francesca L. Bleken <48128015+francescalb@users.noreply.github.com> --- requirements_docs.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 57a9c428a..10cfca2b5 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -3,5 +3,5 @@ mkdocs~=1.5 mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" mkdocs-material~=9.2; python_version<"3.8" -mkdocstrings[python-legacy]~=0.25.0; python_version>="3.8" +mkdocstrings[python-legacy]~=0.25.1; python_version>="3.8" mkdocstrings[python-legacy]~=0.22.0; python_version<"3.8" From 5bc93179100ce5f27e6ccc07832d80b2aeab7f96 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 May 2024 13:51:43 +0000 Subject: [PATCH 14/24] Update mkdocs requirement from ~=1.5 to ~=1.6 (#749) Updates the requirements on [mkdocs](https://github.com/mkdocs/mkdocs) to permit the latest version.
Release notes

Sourced from mkdocs's releases.

1.6.0

Local preview

  • mkdocs serve no longer locks up the browser when more than 5 tabs are open. This is achieved by closing the polling connection whenever a tab becomes inactive. Background tabs will no longer auto-reload either - that will instead happen as soon the tab is opened again. Context: #3391

  • New flag serve --open to open the site in a browser.
    After the first build is finished, this flag will cause the default OS Web browser to be opened at the home page of the local site.
    Context: #3500

Drafts

[!warning] Changed from version 1.5:

The exclude_docs config was split up into two separate concepts.

The exclude_docs config no longer has any special behavior for mkdocs serve - it now always completely excludes the listed documents from the site.

If you wish to use the "drafts" functionality like the exclude_docs key used to do in MkDocs 1.5, please switch to the new config key draft_docs.

See documentation.

Other changes:

  • Reduce warning levels when a "draft" page has a link to a non-existent file. Context: #3449

Update to deduction of page titles

MkDocs 1.5 had a change in behavior in deducing the page titles from the first heading. Unfortunately this could cause unescaped HTML tags or entities to appear in edge cases.

Now tags are always fully sanitized from the title. Though it still remains the case that Page.title is expected to contain HTML entities and is passed directly to the themes.

Images (notably, emojis in some extensions) get preserved in the title only through their alt attribute's value.

Context: #3564, #3578

Themes

  • Built-in themes now also support Polish language (#3613)

"readthedocs" theme

  • Fix: "readthedocs" theme can now correctly handle deeply nested nav configurations (over 2 levels deep), without confusedly expanding all sections and jumping around vertically. (#3464)

  • Fix: "readthedocs" theme now shows a link to the repository (with a generic logo) even when isn't one of the 3 known hosters. (#3435)

  • "readthedocs" theme now also has translation for the word "theme" in the footer that mistakenly always remained in English. (#3613, #3625)

"mkdocs" theme

... (truncated)

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--------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: francescalb --- requirements_docs.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 10cfca2b5..48a2c3b5a 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -1,5 +1,6 @@ mike~=2.1 -mkdocs~=1.5 +mkdocs~=1.5; python_version<"3.8" +mkdocs~=1.6; python_version>="3.8" mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" mkdocs-material~=9.2; python_version<"3.8" From 8949b1dfc94b1c32ae79275bcef15a20bb1ad98f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 29 May 2024 13:06:42 +0000 Subject: [PATCH 15/24] Update pylint requirement from ~=3.1 to ~=3.2 (#765) Updates the requirements on [pylint](https://github.com/pylint-dev/pylint) to permit the latest version.
Commits
  • 9223172 Bump pylint to 3.2.1, update changelog
  • 926547b [trailing-comma-tuple] Fix enabling with message control locally when disable...
  • 1498675 Fix linterstats.get_module_message_count() (#9146) (#9648)
  • aed496a Fix FP for possibly-used-before-assignment with assert_never() (#9645) (#...
  • 9dae975 [Backport maintenance/3.2.x] Add --prefer-stubs=y option (#9646)
  • a03ceae Add --prefer-stubs=y option (#9632)
  • b2ea316 [Backport maintenance/3.2.x] Don't emit incorrect-variance for type parameter...
  • cdcc509 Don't emit incorrect-variance for type parameters (PEP 695) (#9638)
  • ee6b62f Fix a false negative for --ignore-patterns (#9630) (#9636)
  • 08359be [possibly-used-before-assignment] Fix FP for sys.exit() (#9634) (#9635)
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--------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: francescalb --- ontopy/excelparser.py | 1 + ontopy/ontology.py | 6 +++--- requirements_dev.txt | 2 +- tools/excel2onto | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/ontopy/excelparser.py b/ontopy/excelparser.py index 02cd9c49f..243fec14a 100755 --- a/ontopy/excelparser.py +++ b/ontopy/excelparser.py @@ -643,6 +643,7 @@ def _add_entities( if not altlabel == "nan": labels.update(altlabel.split(";")) # Find column name depending on entitytype + rowheader = "entity_type_not_set" if entitytype is owlready2.ThingClass: rowheader = "subClassOf" # If entitytype is a subclass of owlready2.PropertyClass diff --git a/ontopy/ontology.py b/ontopy/ontology.py index 5eacec242..c69da1662 100644 --- a/ontopy/ontology.py +++ b/ontopy/ontology.py @@ -1112,15 +1112,15 @@ def get_imported_ontologies(self, recursive=False): are also returned. """ - def rec_imported(onto): + def rec_imported(onto, imported): for ontology in onto.imported_ontologies: if ontology not in imported: imported.add(ontology) - rec_imported(ontology) + rec_imported(ontology, imported) if recursive: imported = set() - rec_imported(self) + rec_imported(self, imported) return list(imported) return self.imported_ontologies diff --git a/requirements_dev.txt b/requirements_dev.txt index a8fdb47f1..c278c9e39 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,7 +1,7 @@ pre-commit>=2.21.0,<3; python_version<"3.9" pre-commit~=3.7; python_version>="3.9" pylint~=2.17; python_version<"3.8" -pylint~=3.1; python_version>="3.8" +pylint~=3.2; python_version>="3.8" pytest~=7.4; python_version<"3.8" pytest~=8.2; python_version>="3.8" pytest-cov~=4.1; python_version<"3.8" diff --git a/tools/excel2onto b/tools/excel2onto index 8b144d1a1..a86e68c89 100755 --- a/tools/excel2onto +++ b/tools/excel2onto @@ -71,6 +71,7 @@ def main(argv: list = None): except SystemExit as exc: sys.exit(exc.code) # Exit without traceback on invalid arguments + input_ontology = None if args.update: try: if args.input_ontology: @@ -83,7 +84,6 @@ def main(argv: list = None): "Did not find the output ontology to be updated, " "will fully generate a new one." ) - input_ontology = None else: raise FileNotFoundError( "The output ontology to be updated " From bdeab6bcd1876d66388815548602096e000d8e7e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 21 Jun 2024 21:12:54 +0000 Subject: [PATCH 16/24] Update numpy requirement from <2,>=1.19.5 to >=1.19.5,<3 (#771) Updates the requirements on [numpy](https://github.com/numpy/numpy) to permit the latest version.
Release notes

Sourced from numpy's releases.

v2.0.0

NumPy 2.0.0 Release Notes

NumPy 2.0.0 is the first major release since 2006. It is the result of 11 months of development since the last feature release and is the work of 212 contributors spread over 1078 pull requests. It contains a large number of exciting new features as well as changes to both the Python and C APIs.

This major release includes breaking changes that could not happen in a regular minor (feature) release - including an ABI break, changes to type promotion rules, and API changes which may not have been emitting deprecation warnings in 1.26.x. Key documents related to how to adapt to changes in NumPy 2.0, in addition to these release notes, include:

Highlights

Highlights of this release include:

  • New features:
    • A new variable-length string dtype, numpy.dtypes.StringDType and a new numpy.strings namespace with performant ufuncs for string operations,
    • Support for float32 and longdouble in all numpy.fft functions,
    • Support for the array API standard in the main numpy namespace.
  • Performance improvements:
    • Sorting functions sort, argsort, partition, argpartition have been accelerated through the use of the Intel x86-simd-sort and Google Highway libraries, and may see large (hardware-specific) speedups,
    • macOS Accelerate support and binary wheels for macOS >=14, with significant performance improvements for linear algebra operations on macOS, and wheels that are about 3 times smaller,
    • numpy.char fixed-length string operations have been accelerated by implementing ufuncs that also support numpy.dtypes.StringDType in addition to the fixed-length string dtypes,
    • A new tracing and introspection API, numpy.lib.introspect.opt_func_info, to determine which hardware-specific kernels are available and will be dispatched to.
    • numpy.save now uses pickle protocol version 4 for saving arrays with object dtype, which allows for pickle objects larger than 4GB and improves saving speed by about 5% for large arrays.
  • Python API improvements:

... (truncated)

Commits
  • 1d49c7f Merge pull request #26698 from charris/prepare-2.0.0
  • 2103511 DOC: Remove duplicate in author list.
  • db8030e BUG: Change cibuildwheel version [wheel build]
  • 1a68264 REL: Prepare for the NumPy 2.0.0 release [wheel build]
  • c8665ba Merge pull request #26696 from charris/backport-26582
  • 103f4dd Merge pull request #26697 from charris/backport-25963
  • c193dcd Merge pull request #26695 from charris/backport-26667
  • 8fa8191 BUG: Fix bug in numpy.pad() (#25963)
  • ece3559 BUG: weighted nanpercentile, nanquantile and multi-dim q (#26582)
  • b31e195 BUG: Adds asanyarray to start of linalg.cross (#26667)
  • Additional commits viewable in compare view

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--------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: francescalb --- .github/workflows/ci_workflow.yml | 19 +++++++++++-------- requirements.txt | 2 +- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci_workflow.yml b/.github/workflows/ci_workflow.yml index 7ed2a9890..435f55a73 100644 --- a/.github/workflows/ci_workflow.yml +++ b/.github/workflows/ci_workflow.yml @@ -26,19 +26,22 @@ jobs: pylint_options: "--rcfile=pyproject.toml" pylint_targets: "*.py tools emmopy ontopy" - # safety - # Ignore ID 44715 for now. - # See this NumPy issue for more information: https://github.com/numpy/numpy/issues/19038 - # Also ignore IDs 44716 and 44717 as they are not deemed to be as severe as it is - # laid out in the CVE. - # Remove ignoring 48547 as soon as RDFLib/rdflib#1844 has been fixed and the fix - # has been released. + + # safety-specific settings run_safety: true + # 48547: RDFLib vulnerability: https://pyup.io/vulnerabilities/PVE-2022-48547/48547/ + # 44715-44717: NumPy vulnerabilities: + # https://pyup.io/vulnerabilities/CVE-2021-41495/44715/ + # https://pyup.io/vulnerabilities/CVE-2021-41496/44716/ + # https://pyup.io/vulnerabilities/CVE-2021-34141/44717/ + # 70612: Jinja2 vulnerability. Only used as subdependency for mkdocs++ in tripper. + # https://data.safetycli.com/v/70612/97c/ safety_options: | + --ignore=48547 --ignore=44715 --ignore=44716 --ignore=44717 - --ignore=48547 + --ignore=70612 # Build distribution run_build_package: true diff --git a/requirements.txt b/requirements.txt index 8980a005c..0d97d1d20 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ blessings>=1.7,<2 Cython>=0.29.21,<3.1 defusedxml>=0.7.1,<1 graphviz>=0.16,<0.21 -numpy>=1.19.5,<2 +numpy>=1.19.5,<3 openpyxl>=3.0.9,<3.2 Owlready2>=0.28,!=0.32,!=0.34,<0.44 packaging>=21.0,<25 From 7ee6d0256e4f259910fa286faa78ac0b0734cb4f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jul 2024 06:54:34 +0000 Subject: [PATCH 17/24] Update pytest requirement from ~=8.2 to ~=8.3 (#774) Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
Release notes

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8.3.1

pytest 8.3.1 (2024-07-20)

The 8.3.0 release failed to include the change notes and docs for the release. This patch release remedies this. There are no other changes.

Commits
  • de98446 Prepare release version 8.3.1
  • bd0a042 Merge pull request #12636 from pytest-dev/update-release-notes
  • 664325b doc/changelog: update 8.3.0 notes
  • 19d225d Merge pull request #12635 from pytest-dev/release-8.3.0
  • bc33028 Prepare release version 8.3.0
  • a7d5a8e Merge pull request #12557 from x612skm/maintainence/11771-pypy-3.9-bump
  • ced7072 Add a change note for PR #11771
  • d42b76d Adjust test_errors_in_xfail_skip_expressions for PyPy
  • 9eee45a Bump PyPy runtime to v3.9 @ GHA
  • d489247 Fix caching of parameterized fixtures (#12600)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index c278c9e39..3390bdb8c 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -3,6 +3,6 @@ pre-commit~=3.7; python_version>="3.9" pylint~=2.17; python_version<"3.8" pylint~=3.2; python_version>="3.8" pytest~=7.4; python_version<"3.8" -pytest~=8.2; python_version>="3.8" +pytest~=8.3; python_version>="3.8" pytest-cov~=4.1; python_version<"3.8" pytest-cov~=5.0; python_version>="3.8" From ca647255d9f29b9a614e784f283fe2577ad24286 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Jul 2024 05:32:35 +0000 Subject: [PATCH 18/24] Update pre-commit requirement from ~=3.7 to ~=3.8 (#775) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [pre-commit](https://github.com/pre-commit/pre-commit) to permit the latest version.
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Features

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3.7.1 - 2024-05-10

Fixes

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  • Use a tty for docker and docker_image hooks when --color is specified.

Fixes

Updating

  • The per-hook behaviour of fail_fast was fixed. If you want the pre-3.7.0 behaviour, add fail_fast: true to all hooks before the last fail_fast hook.

3.6.2 - 2024-02-18

Fixes

3.6.1 - 2024-02-10

Fixes

  • Remove PYTHONEXECUTABLE from environment when running.
  • Handle staged-files-only with only a crlf diff.

... (truncated)

Commits
  • d46423f v3.8.0
  • 8133abd Merge pull request #3265 from lorenzwalthert/issue-3206
  • da0c1d0 implement health check for language:r
  • f641f6a Merge pull request #3264 from pre-commit/pre-commit-ci-update-config
  • a68a19d fixes for mypy 1.11
  • 88317dd [pre-commit.ci] pre-commit autoupdate
  • faa6f8c Merge pull request #3244 from pre-commit/pre-commit-ci-update-config
  • f632459 [pre-commit.ci] pre-commit autoupdate
  • 0252908 Merge pull request #3240 from pre-commit/pre-commit-ci-update-config
  • 69b5dce [pre-commit.ci] pre-commit autoupdate
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index 3390bdb8c..e789bdf72 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,5 +1,5 @@ pre-commit>=2.21.0,<3; python_version<"3.9" -pre-commit~=3.7; python_version>="3.9" +pre-commit~=3.8; python_version>="3.9" pylint~=2.17; python_version<"3.8" pylint~=3.2; python_version>="3.8" pytest~=7.4; python_version<"3.8" From f1c2e5a5137e89e2c97daec924a326fb8388cc58 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Jul 2024 05:38:27 +0000 Subject: [PATCH 19/24] Update mkdocstrings[python-legacy] requirement from ~=0.25.1 to ~=0.25.2 (#776) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [mkdocstrings[python-legacy]](https://github.com/mkdocstrings/mkdocstrings) to permit the latest version.
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0.25.2

0.25.2 - 2024-07-25

Compare with 0.25.1

Code Refactoring

  • Give precedence to Markdown heading level (##) (2e5f89e by Timothée Mazzucotelli).
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0.25.2 - 2024-07-25

Compare with 0.25.1

Code Refactoring

  • Give precedence to Markdown heading level (##) (2e5f89e by Timothée Mazzucotelli).

0.25.1 - 2024-05-05

Compare with 0.25.0

Bug Fixes

0.25.0 - 2024-04-27

Compare with 0.24.3

Features

  • Support once parameter in logging methods, allowing to log a message only once with a given logger (1532b59 by Timothée Mazzucotelli).
  • Support blank line between ::: path and YAML options (d799d2f by Timothée Mazzucotelli). Issue-450

Code Refactoring

  • Allow specifying name of template loggers (c5b5f69 by Timothée Mazzucotelli).

0.24.3 - 2024-04-05

Compare with 0.24.2

Bug Fixes

  • Support HTML toc labels with Python-Markdown 3.6+ (uncomment code...) (7fe3e5f by Timothée Mazzucotelli).

0.24.2 - 2024-04-02

Compare with 0.24.1

Bug Fixes

0.24.1 - 2024-02-27

Compare with 0.24.0

Code Refactoring

... (truncated)

Commits
  • afb2a2f chore: Prepare release 0.25.2
  • e7c8abd tests: Ignore deprecation warnings for now
  • 924ecd8 chore: Template upgrade
  • da216b0 ci: Ignore unused arg
  • 80ab498 chore: Clean up pytest warning filters
  • 2e5f89e refactor: Give precedence to Markdown heading level (##)
  • fb194d8 chore: Clean up get_anchors
  • 64c5ff6 chore: Improve code comments
  • 8013be4 chore: Clean up unused condition
  • See full diff in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_docs.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 48a2c3b5a..66ff4858b 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -4,5 +4,5 @@ mkdocs~=1.6; python_version>="3.8" mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" mkdocs-material~=9.2; python_version<"3.8" -mkdocstrings[python-legacy]~=0.25.1; python_version>="3.8" +mkdocstrings[python-legacy]~=0.25.2; python_version>="3.8" mkdocstrings[python-legacy]~=0.22.0; python_version<"3.8" From 9dbfbf90768fe795af52652734b6a9f240cb87bc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 30 Jul 2024 05:20:12 +0000 Subject: [PATCH 20/24] Bump SINTEF/ci-cd from 2.7.4 to 2.8.0 (#778) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [SINTEF/ci-cd](https://github.com/sintef/ci-cd) from 2.7.4 to 2.8.0.
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v2.8.0

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v2.8.0 (2024-07-29)

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Support Trusted Publishers from PyPI

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Support Trusted Publishers from PyPI

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Breaking change: This is not a "true" breaking change - but it may cause certain workflows to fail that uses the callable workflow CD - Release: The parameter publish_on_pypi has become required, meaning one must provide it in the with section of the calling workflow. For more information, see the documentation page for the CD - Release workflow.

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cd_publish.yml | 2 +- .github/workflows/ci_automerge_dependabot.yml | 2 +- .github/workflows/ci_cd_updated_master.yml | 2 +- .github/workflows/ci_dependabot.yml | 2 +- .github/workflows/ci_workflow.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/cd_publish.yml b/.github/workflows/cd_publish.yml index fe675a707..b1f566000 100644 --- a/.github/workflows/cd_publish.yml +++ b/.github/workflows/cd_publish.yml @@ -7,7 +7,7 @@ on: jobs: publish: name: External - uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.7.4 + uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.0 if: github.repository == 'emmo-repo/EMMOntoPy' && startsWith(github.ref, 'refs/tags/v') with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_automerge_dependabot.yml b/.github/workflows/ci_automerge_dependabot.yml index 69faf0bb6..c15774334 100644 --- a/.github/workflows/ci_automerge_dependabot.yml +++ b/.github/workflows/ci_automerge_dependabot.yml @@ -7,7 +7,7 @@ on: jobs: update-dependabot-branch: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.7.4 + uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.8.0 if: github.repository_owner == 'emmo-repo' && startsWith(github.event.pull_request.head.ref, 'dependabot/') && github.actor == 'dependabot[bot]' secrets: PAT: ${{ secrets.RELEASE_PAT }} diff --git a/.github/workflows/ci_cd_updated_master.yml b/.github/workflows/ci_cd_updated_master.yml index ba58a14d5..41473492d 100644 --- a/.github/workflows/ci_cd_updated_master.yml +++ b/.github/workflows/ci_cd_updated_master.yml @@ -7,7 +7,7 @@ on: jobs: updates-to-master: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.7.4 + uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.8.0 if: github.repository_owner == 'emmo-repo' with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_dependabot.yml b/.github/workflows/ci_dependabot.yml index 3b9e53dd8..987676116 100644 --- a/.github/workflows/ci_dependabot.yml +++ b/.github/workflows/ci_dependabot.yml @@ -11,7 +11,7 @@ on: jobs: create-collected-pr: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.7.4 + uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.8.0 if: github.repository_owner == 'emmo-repo' with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_workflow.yml b/.github/workflows/ci_workflow.yml index 435f55a73..95de5d909 100644 --- a/.github/workflows/ci_workflow.yml +++ b/.github/workflows/ci_workflow.yml @@ -10,7 +10,7 @@ on: jobs: tests: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.7.4 + uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.0 with: # General install_extras: "[dev,docs]" From def69b3c8e369c1148f424bcefa8b979c1dee3b1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 22 Aug 2024 05:24:32 +0000 Subject: [PATCH 21/24] Bump SINTEF/ci-cd from 2.8.0 to 2.8.1 (#781) Bumps [SINTEF/ci-cd](https://github.com/sintef/ci-cd) from 2.8.0 to 2.8.1.
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Sourced from SINTEF/ci-cd's changelog.

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Unreleased

Full Changelog

Support Trusted Publishers from PyPI

Trusted Publishers from PyPI is now supported via uploading the distribution(s) as artifacts (for more information about GitHub Actions artifacts, see the GitHub Docs).

Breaking change: This is not a "true" breaking change - but it may cause certain workflows to fail that uses the callable workflow CD - Release: The parameter publish_on_pypi has become required, meaning one must provide it in the with section of the calling workflow. For more information, see the documentation page for the CD - Release workflow.

DX updates

Several fixes from the development tools have been implemented into the code base.

Commits

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=SINTEF/ci-cd&package-manager=github_actions&previous-version=2.8.0&new-version=2.8.1)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cd_publish.yml | 2 +- .github/workflows/ci_automerge_dependabot.yml | 2 +- .github/workflows/ci_cd_updated_master.yml | 2 +- .github/workflows/ci_dependabot.yml | 2 +- .github/workflows/ci_workflow.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/cd_publish.yml b/.github/workflows/cd_publish.yml index b1f566000..6bc519240 100644 --- a/.github/workflows/cd_publish.yml +++ b/.github/workflows/cd_publish.yml @@ -7,7 +7,7 @@ on: jobs: publish: name: External - uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.0 + uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.1 if: github.repository == 'emmo-repo/EMMOntoPy' && startsWith(github.ref, 'refs/tags/v') with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_automerge_dependabot.yml b/.github/workflows/ci_automerge_dependabot.yml index c15774334..2bbdce65f 100644 --- a/.github/workflows/ci_automerge_dependabot.yml +++ b/.github/workflows/ci_automerge_dependabot.yml @@ -7,7 +7,7 @@ on: jobs: update-dependabot-branch: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.8.0 + uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.8.1 if: github.repository_owner == 'emmo-repo' && startsWith(github.event.pull_request.head.ref, 'dependabot/') && github.actor == 'dependabot[bot]' secrets: PAT: ${{ secrets.RELEASE_PAT }} diff --git a/.github/workflows/ci_cd_updated_master.yml b/.github/workflows/ci_cd_updated_master.yml index 41473492d..e011b39b9 100644 --- a/.github/workflows/ci_cd_updated_master.yml +++ b/.github/workflows/ci_cd_updated_master.yml @@ -7,7 +7,7 @@ on: jobs: updates-to-master: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.8.0 + uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.8.1 if: github.repository_owner == 'emmo-repo' with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_dependabot.yml b/.github/workflows/ci_dependabot.yml index 987676116..60439c0ed 100644 --- a/.github/workflows/ci_dependabot.yml +++ b/.github/workflows/ci_dependabot.yml @@ -11,7 +11,7 @@ on: jobs: create-collected-pr: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.8.0 + uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.8.1 if: github.repository_owner == 'emmo-repo' with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_workflow.yml b/.github/workflows/ci_workflow.yml index 95de5d909..c8758bf4b 100644 --- a/.github/workflows/ci_workflow.yml +++ b/.github/workflows/ci_workflow.yml @@ -10,7 +10,7 @@ on: jobs: tests: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.0 + uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.1 with: # General install_extras: "[dev,docs]" From d5e97144c16e7990ad03d836e11c3b15d9f42efd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 23 Aug 2024 06:03:58 +0000 Subject: [PATCH 22/24] Bump SINTEF/ci-cd from 2.8.1 to 2.8.2 (#782) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [SINTEF/ci-cd](https://github.com/sintef/ci-cd) from 2.8.1 to 2.8.2.
Release notes

Sourced from SINTEF/ci-cd's releases.

v2.8.2

Changelog

v2.8.2 (2024-08-22)

Full Changelog

Support self-hosted runners

The runs-on key can not be specified via the runner input, which is available for all callable workflows. This means one can use the callable workflows with self-hosted runners, for example.

It is worth noting that the workflows are built with Linux/Unix systems in mind, hence specifying windows-latest may lead to issues with certain workflows. This is also true if the self-hosted runner is not Linux/Unix-based.

Implemented enhancements:

  • Support self-hosted runners #279

Merged pull requests:

* This Changelog was automatically generated by github_changelog_generator

Changelog

Sourced from SINTEF/ci-cd's changelog.

v2.8.2 (2024-08-22)

Full Changelog

Support self-hosted runners

The runs-on key can not be specified via the runner input, which is available for all callable workflows. This means one can use the callable workflows with self-hosted runners, for example.

It is worth noting that the workflows are built with Linux/Unix systems in mind, hence specifying windows-latest may lead to issues with certain workflows. This is also true if the self-hosted runner is not Linux/Unix-based.

Merged pull requests:

  • Add runner input for all callable workflows #280 (CasperWA)
Commits

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=SINTEF/ci-cd&package-manager=github_actions&previous-version=2.8.1&new-version=2.8.2)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cd_publish.yml | 2 +- .github/workflows/ci_automerge_dependabot.yml | 2 +- .github/workflows/ci_cd_updated_master.yml | 2 +- .github/workflows/ci_dependabot.yml | 2 +- .github/workflows/ci_workflow.yml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/cd_publish.yml b/.github/workflows/cd_publish.yml index 6bc519240..746cde3f8 100644 --- a/.github/workflows/cd_publish.yml +++ b/.github/workflows/cd_publish.yml @@ -7,7 +7,7 @@ on: jobs: publish: name: External - uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.1 + uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v2.8.2 if: github.repository == 'emmo-repo/EMMOntoPy' && startsWith(github.ref, 'refs/tags/v') with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_automerge_dependabot.yml b/.github/workflows/ci_automerge_dependabot.yml index 2bbdce65f..60a4de915 100644 --- a/.github/workflows/ci_automerge_dependabot.yml +++ b/.github/workflows/ci_automerge_dependabot.yml @@ -7,7 +7,7 @@ on: jobs: update-dependabot-branch: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.8.1 + uses: SINTEF/ci-cd/.github/workflows/ci_automerge_prs.yml@v2.8.2 if: github.repository_owner == 'emmo-repo' && startsWith(github.event.pull_request.head.ref, 'dependabot/') && github.actor == 'dependabot[bot]' secrets: PAT: ${{ secrets.RELEASE_PAT }} diff --git a/.github/workflows/ci_cd_updated_master.yml b/.github/workflows/ci_cd_updated_master.yml index e011b39b9..32bdd8b11 100644 --- a/.github/workflows/ci_cd_updated_master.yml +++ b/.github/workflows/ci_cd_updated_master.yml @@ -7,7 +7,7 @@ on: jobs: updates-to-master: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.8.1 + uses: SINTEF/ci-cd/.github/workflows/ci_cd_updated_default_branch.yml@v2.8.2 if: github.repository_owner == 'emmo-repo' with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_dependabot.yml b/.github/workflows/ci_dependabot.yml index 60439c0ed..612289651 100644 --- a/.github/workflows/ci_dependabot.yml +++ b/.github/workflows/ci_dependabot.yml @@ -11,7 +11,7 @@ on: jobs: create-collected-pr: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.8.1 + uses: SINTEF/ci-cd/.github/workflows/ci_update_dependencies.yml@v2.8.2 if: github.repository_owner == 'emmo-repo' with: git_username: EMMOntoPy Developers diff --git a/.github/workflows/ci_workflow.yml b/.github/workflows/ci_workflow.yml index c8758bf4b..17927d22b 100644 --- a/.github/workflows/ci_workflow.yml +++ b/.github/workflows/ci_workflow.yml @@ -10,7 +10,7 @@ on: jobs: tests: name: External - uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.1 + uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.2 with: # General install_extras: "[dev,docs]" From 277053e3c44cffafae78b09919868e33cf054a67 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Sep 2024 05:08:43 +0000 Subject: [PATCH 23/24] Update mkdocstrings[python-legacy] requirement from ~=0.25.2 to ~=0.26.1 (#784) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updates the requirements on [mkdocstrings[python-legacy]](https://github.com/mkdocstrings/mkdocstrings) to permit the latest version.
Release notes

Sourced from mkdocstrings[python-legacy]'s releases.

0.26.1

0.26.1 - 2024-09-06

Compare with 0.26.0

Bug Fixes

  • Instantiate config of the autorefs plugin when it is not enabled by the user (db2ab34 by Timothée Mazzucotelli). Issue-autorefs#57
Changelog

Sourced from mkdocstrings[python-legacy]'s changelog.

0.26.1 - 2024-09-06

Compare with 0.26.0

Bug Fixes

  • Instantiate config of the autorefs plugin when it is not enabled by the user (db2ab34 by Timothée Mazzucotelli). Issue-autorefs#57

0.26.0 - 2024-09-02

Compare with 0.25.2

Build

  • Upgrade Python-Markdown lower bound to 3.6 (28565f9 by Timothée Mazzucotelli).

Dependencies

  • Depend on mkdocs-autorefs v1 (33aa573 by Timothée Mazzucotelli).

Features

0.25.2 - 2024-07-25

Compare with 0.25.1

Code Refactoring

  • Give precedence to Markdown heading level (##) (2e5f89e by Timothée Mazzucotelli).

0.25.1 - 2024-05-05

Compare with 0.25.0

Bug Fixes

0.25.0 - 2024-04-27

Compare with 0.24.3

Features

  • Support once parameter in logging methods, allowing to log a message only once with a given logger (1532b59 by Timothée Mazzucotelli).
  • Support blank line between ::: path and YAML options (d799d2f by Timothée Mazzucotelli). Issue-450

Code Refactoring

... (truncated)

Commits
  • 651d176 chore: Prepare release 0.26.1
  • db2ab34 fix: Instantiate config of the autorefs plugin when it is not enabled by the ...
  • a65035a docs: Clarify that Installation section
  • b1aa042 chore: Prepare release 0.26.0
  • b63e726 feat: Allow hooking into autorefs when converting Markdown docstrings
  • 3c878b7 chore: Upgrade mkdocs-redirects lower bound to avoid deprecation warning
  • 28565f9 build: Upgrade Python-Markdown lower bound to 3.6
  • 52fad11 style: Format
  • c6ca522 docs: Fix dead link
  • 8041ef3 docs: Update code highlight lines
  • Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- requirements_docs.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_docs.txt b/requirements_docs.txt index 66ff4858b..80e18f894 100644 --- a/requirements_docs.txt +++ b/requirements_docs.txt @@ -4,5 +4,5 @@ mkdocs~=1.6; python_version>="3.8" mkdocs-awesome-pages-plugin~=2.9 mkdocs-material~=9.5; python_version>="3.8" mkdocs-material~=9.2; python_version<"3.8" -mkdocstrings[python-legacy]~=0.25.2; python_version>="3.8" +mkdocstrings[python-legacy]~=0.26.1; python_version>="3.8" mkdocstrings[python-legacy]~=0.22.0; python_version<"3.8" From 4aaf2d5aeb3ec37198464ac11cb349346fda2253 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 23 Sep 2024 05:53:12 +0000 Subject: [PATCH 24/24] Update pylint requirement from ~=3.2 to ~=3.3 Updates the requirements on [pylint](https://github.com/pylint-dev/pylint) to permit the latest version. - [Release notes](https://github.com/pylint-dev/pylint/releases) - [Commits](https://github.com/pylint-dev/pylint/compare/v3.2.0...v3.3.0) --- updated-dependencies: - dependency-name: pylint dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_dev.txt b/requirements_dev.txt index e789bdf72..4cc663095 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,7 +1,7 @@ pre-commit>=2.21.0,<3; python_version<"3.9" pre-commit~=3.8; python_version>="3.9" pylint~=2.17; python_version<"3.8" -pylint~=3.2; python_version>="3.8" +pylint~=3.3; python_version>="3.8" pytest~=7.4; python_version<"3.8" pytest~=8.3; python_version>="3.8" pytest-cov~=4.1; python_version<"3.8"