Changelog¶

v0.1.0 (2021-10-27)¶

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Implemented enhancements:

"Warning" Importing from collections #236

Fixed bugs:

Loading ontologies that do not import skos fails #261
Fix documentation build warnings #250
Fix images in documentation #233
Circular reference from Owlready2 #210

Closed issues:

Write up transfer from EMMOpython to EMMOntoPy i README.md #267
Add test to emmocheck for upcoming EMMO #257
Add packaging as dependency in requirements #255
Add CI check for building documentation #244
Add OpenModel as contributing project #237
Update public documentation to new framework #234
Automate documentation releases #232
Update name of EMMO to Elemental Multiperspective Material Ontology #230
Tidy up unittests #220
Remove importability of sub-factpluspluswrapper folders #213
Make function that automatically loads emmo #209
Require rdflib>5.0.0? #206
change package name #205
test_catalog fails because seraching for .owl in emmo/master #203
Consider using mike for versioned documentation #197
Add a test that checks that loading of non-EMMO based ontologies work - e.g. do not require skos:prefLabel #196
Setup Materials for MkDocs framework #195
Clean up demo, examples and docs #193
Formalize review process with checklists #190
funksjon ontology.add_class(label, parent) #183

Merged pull requests:

Reset version to 0.1.0 #271 (CasperWA)
Update README with PyPI and deprecation msgs #270 (CasperWA)
Added option: EMMObased = False in ontology.load() #262 (francescalb)
Update pyyaml requirement from \<6,>=5.4.1 to >=5.4.1,\<7 #260 (dependabot[bot])
Update owlready2 requirement from !=0.32,!=0.34,\<0.35,>=0.28 to >=0.28,!=0.32,!=0.34,\<0.36 #259 (dependabot[bot])
Added new test "test_physical_quantity_dimension" #258 (jesper-friis)
Add packaging to list of requirements #256 (CasperWA)
Fix MkDocs build warnings and CI job #254 (CasperWA)
Update mkdocstrings requirement from ~=0.16.1 to ~=0.16.2 #253 (dependabot[bot])
Update dependencies #252 (CasperWA)
Add OpenModel contributing project #247 (francescalb)
Automate documentation releases #242 (CasperWA)
Import from collections.abc when possible #240 (CasperWA)
Ensure all produced files from tests are in a temp dir #239 (CasperWA)
Changed EMMO to be acronym for Elemental Multiperspective Material Ontology #238 (francescalb)
Use width in img HTML #235 (CasperWA)
Update graphviz requirement from \<0.17,>=0.16 to >=0.16,\<0.18 #229 (dependabot[bot])
Added function to load the emmo (the ontology) directly #226 (francescalb)
Created pull request template #225 (francescalb)
Setup new documentation framework #222 (CasperWA)
Remove __init__.py files for FaCT++ wrapper (again) #221 (CasperWA)
Unskip test as #210 has been resolved #218 (CasperWA)
Remove sub-fact++ modules importability #217 (CasperWA)
Update requirements #216 (CasperWA)
Avoid using Owlready2 v0.34 #211 (CasperWA)
Update package names #208 (CasperWA)
Added function new_entitiy to ontology #207 (francescalb)
ttl standard for emmo #204 (francescalb)
Added choice for specifying namespace in get_by_label #202 (francescalb)

v1.0.1b (2021-07-01)¶

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Closed issues:

Correct updating of catalog in ontology.load #188

Merged pull requests:

Update version to 1.0.1 #189 (francescalb)

v1.0.1 (2021-07-01)¶

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Implemented enhancements:

Specify version ranges for dependencies #155

Fixed bugs:

Windows paths are not handled properly #147

Closed issues:

Failing tests when lodaing battinfo #185
Fix dependatbot to 'wider' #182
Change to get_label instead of asstring in ontograph, emmodoc, ontodoc, be careful #158
licence does not work with metadata #157
ontograph with several roots fails #153
fix redudant getlabel, get_preferred_label, get_label #152
add --no-catalog and default as in emmocheck for ontograph #150
make tests for checking upgrade of Owlready2 #137
Add periodic_table to examples #130
Add support for simple property-based ontology annotations like dcterms:license #129
Update documentation of tools re reasoner #123
Ontograph: Include multiple parents/inheritance #86

Merged pull requests:

Fixed updating of catalog in load #187 (francescalb)
Temporarily commented out loading ontologies with error in redirecting link on emmo.info #186 (francescalb)
Changed dependabot to widen #181 (francescalb)
Changed requirements to greater than #179 (francescalb)
Owread2-0.32 not accepted die to error in owlready2 triplelite #178 (francescalb)
Fixed import of defaultstyle in ontograph-tool #177 (francescalb)
Update pyyaml requirement from ~=5.4.0 to ~=5.4.1 #171 (dependabot[bot])
Updated pygments req to at least 2.7.4 because of high seq alert #168 (francescalb)
Owlready requirement >0.28 #167 (francescalb)
Bump actions/setup-python from 2 to 2.2.2 #166 (dependabot[bot])
Bump actions/checkout from 2 to 2.3.4 #165 (dependabot[bot])
Bump owlready2 from 0.30 to 0.31 #164 (dependabot[bot])
WIP: Ipycytoscape #163 (francescalb)
Made it possible to load other ontologies like foaf #162 (jesper-friis)
Added get_label instead of asstring #160 (francescalb)
Added write_catalog() #159 (jesper-friis)
Periodic table example #156 (francescalb)
Make one get label #154 (francescalb)
Issue150 ontograph cannotload emmo inferred directly #151 (francescalb)
Added Fact++ in tools documentation #149 (francescalb)
Bump owlready2 from 0.29 to 0.30 #148 (dependabot[bot])
Improved issue reporting in emmocheck #146 (jesper-friis)

v1.0.0 (2021-03-25)¶

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Closed issues:

Use rdflib in Ontology.save() to support more file formats #143
Tool for publishing domain ontologies #140

Merged pull requests:

Save to turtle and ontology annotations (via the metadata attribute) #144 (jesper-friis)
Corrected configuration of exceptions for test_class_label test. #142 (jesper-friis)

v1.0.0-alpha-30 (2021-03-18)¶

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Merged pull requests:

Load ontology #141 (jesper-friis)

v1.0.0-alpha-29 (2021-03-16)¶

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Implemented enhancements:

Add Wu&Palmer measure #134

Closed issues:

Convert-imported update in utils #138

Merged pull requests:

Fixed reading xml as 'rdfxml' #139 (francescalb)
Bump owlready2 from 0.28 to 0.29 #136 (dependabot[bot])
Added wu_palmer_measure for semantic similarity #135 (francescalb)

v1.0.0-alpha-28 (2021-03-09)¶

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Closed issues:

Also use the catalog file to map web URLs, not only local files. #109
Check Error with Owlready2-0.26 #81

Merged pull requests:

Version updated for rel of v0.28 #133 (francescalb)
Bump owlready2 from 0.27 to 0.28 #132 (dependabot[bot])
Load ontology #131 (jesper-friis)
Optimised label lookup in ontology and dir listing. It is now much faster #127 (jesper-friis)
Use catalog by default #126 (jesper-friis)

v1.0.0-alpha-27 (2021-02-27)¶

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Merged pull requests:

Ontodoc #125 (jesper-friis)

v1.0.0-alpha-26 (2021-02-26)¶

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Closed issues:

Make fact++ reasoner available and default in tools #122
Use PyPI token in publish workflow #118
Update publish workflow #115
do something #108

Merged pull requests:

Added functionality to document domain ontologies #124 (jesper-friis)
Bump owlready2 from 0.25 to 0.27 #121 (dependabot[bot])
Made ontoconvert and ontograph tools executable in linux #120 (jesper-friis)
Update CI #119 (CasperWA)
Update publish workflow + add dependabot #116 (CasperWA)

v1.0.0-alpha-25 (2021-01-17)¶

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Closed issues:

Update Dockerfile to install correct pandoc #99
Correct turtle serialisation #97

Merged pull requests:

Update emmocheck exceptions #113 (jesper-friis)
Fix recursion in graph #112 (jesper-friis)
Avoid unnessesary/infinite recursion in get_imported_ontologies() #111 (jesper-friis)
Break recursion error in get_by_label() #110 (jesper-friis)
Updated the Ontology.sync_attributes() method. #107 (jesper-friis)
Updated pandoc req in Dockerfile #106 (francescalb)

v1.0.0-alpha-24 (2021-01-04)¶

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Merged pull requests:

Bumped version number up to 1.0.0-alpha-24 #105 (jesper-friis)

v1.0.0-alpha-23 (2021-01-04)¶

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Closed issues:

Fix loading imported ttl from web such that emmocheck works for crystallography.ttl #98
Add reasoning with FaCT++ #95
Correctly load ontologies like crystallography that imports both local and online sub-ontologies #91
Fix flake8 errors #88
Remove the .ttl namespace when loading domain-crystallography in EMMO-python #83
Add option of documenting imported ontologies in ontodoc and ontograph #82
Emmocheck fails if Physicaluantities and MeaurementsUnits are not imported from emmo. Make sure that it does not fail if whole of EMMO is not imported. #80
Ontograph: Make default root #79
Ontodoc: PDF is not generated, produces error. #76
AttributeError from ontodoc #70
Import emmo .ttl from emmo-repo.github.io #69
Unable to use the vertical interoperability demo .py files #66

Merged pull requests:

Release 1.0.0-alpha-23 #104 (jesper-friis)
Allow to load turtle ontologies without catalog file. #102 (jesper-friis)
Bump junit from 4.11 to 4.13.1 in /emmo/factpluspluswrapper/java #101 (dependabot[bot])
Updated README file #100 (jesper-friis)
Changed the sync_reasoner() method to use FaCT++ as the default reasoner #94 (jesper-friis)
Add reasoning #93 (jesper-friis)
Improve load ontologies #92 (jesper-friis)
Remove the '.ttl' in namespace names by monkey patching owlready2.Namespace #90 (jesper-friis)
Fix flake8 warnings #89 (jesper-friis)
Ontodoc pdf #87 (jesper-friis)
Automatically find roots in ontograph #85 (francescalb)
Automatic import of ttl from GitHub emmo-repo.io #84 (francescalb)
Fixes needed for access ontologies #77 (jesper-friis)

v1.0.0-alpha-22 (2020-12-21)¶

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Merged pull requests:

Loading ttl both locally and importing from iri #75 (francescalb)
Added sync_python_names() and corrected handling of individuals in sync_attributes() #73 (jesper-friis)
Add preflabel to individuals declared in python #72 (jesper-friis)

v1.0.0-alpha-21b (2020-12-13)¶

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Merged pull requests:

Fix bug introduced in ontoconvert #71 (jesper-friis)

v1.0.0-alpha-21 (2020-12-11)¶

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Merged pull requests:

Use rdflib to load non-supported formats. #68 (jesper-friis)
Added a quick fix for vertical demo. #67 (jesper-friis)
Updated emmocheck to new 1.0.0-beta. Old version should still work. #65 (jesper-friis)
Added ontoconvert tool #64 (jesper-friis)
Improved error messages for classes that doesn't define prefLabel #63 (jesper-friis)

v1.0.0-alpha-20b (2020-11-04)¶

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Merged pull requests:

Version1.0.0 alpha20 #62 (francescalb)

v1.0.0-alpha-20 (2020-11-04)¶

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Merged pull requests:

Improve support for imported ontologies #61 (jesper-friis)

v1.0.0-alpha-19 (2020-11-02)¶

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Merged pull requests:

Added --ignore-namespace to emmocheck #60 (francescalb)

v1.0.0-alpha-18 (2020-10-29)¶

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Merged pull requests:

Bumped up version number to 1.0.0-alpha-18 #59 (jesper-friis)
Added option url_from_catalog to ontology.load() #58 (jesper-friis)
Added get_preferred_label() method to classes, properties and individuals #57 (jesper-friis)
Correct default IRI to inferred ontology #56 (jesper-friis)

v1.0.0-alpha-17 (2020-10-21)¶

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Merged pull requests:

Added materials.EngineeredMaterial to namespace exception in emmocheck #55 (francescalb)

v1.0.0-alpha-16 (2020-10-20)¶

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Closed issues:

Include all annotations in .get_annotations() #50

Merged pull requests:

Update to v1.0.0-alpha-16 for new release #54 (francescalb)
Update dimensionality checks #53 (jesper-friis)
Updated to say that pypi realese is automatic in docs #52 (francescalb)

v1.0.0-alpha-15 (2020-09-25)¶

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Merged pull requests:

Added all labels in get_class_annotations in emmo/patch.py including #51 (francescalb)
Support use of skos:prefLabel instead of rdfs:label #49 (jesper-friis)
v1.0.0-alpha-14 #48 (jesper-friis)
Fix emmocheck to not fail upon use of dcterms and skos #47 (jesper-friis)

v1.0.0-alpha-13 (2020-09-19)¶

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Closed issues:

Not immediately installable with pip #45

Merged pull requests:

Fix setup #46 (jesper-friis)
Make emmo package pip installable in fresh env #44 (CasperWA)
Update emmodoc to latest version of emmo-alpha2 #43 (jesper-friis)
Ensure that emmocheck exit with non-zero return value if a test is faing #42 (jesper-friis)
Installed missing dependencies in pythonpublish deployment workflow #41 (jesper-friis)

v1.0.0-alpha-11 (2020-08-12)¶

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Merged pull requests:

Add skip option to emmocheck #40 (jesper-friis)

v1.0.0-alpha-10 (2020-04-27)¶

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Merged pull requests:

Added exceptions to emmocheck "test_number_of_labels" #39 (jesper-friis)

v1.0.0-alpha-9 (2020-04-13)¶

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Closed issues:

Enhance ontology.sync_attributes() to also update class names #10
Add support for the FaCT++ reasoner #9

Merged pull requests:

Set new release version 1.0.0-alpha-9 #38 (francescalb)
Added get_version() and set_version() methods to emmo.Ontology. #37 (jesper-friis)
Updated example in README file to current version of EMMO. #36 (jesper-friis)
Update tools #35 (jesper-friis)
Updated simplifed demo_vertical in compliance with EMMO-1.0.0alpha2 as of 202… #34 (francescalb)
Fixed PyPI badge in README #33 (jesper-friis)
Update emmocheck #32 (jesper-friis)
Sync attributes #31 (jesper-friis)
Cleanup ci workflow #28 (jesper-friis)
Added ontoversion tool #27 (jesper-friis)
Update emmodoc #25 (jesper-friis)

v1.0.0-alpha-8 (2020-03-22)¶

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Merged pull requests:

1.0.0 alpha 8 #30 (jesper-friis)
Updated requirements such that "pip install EMMO" works #24 (jesper-friis)

v1.0.0-alpha-5 (2020-03-18)¶

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Implemented enhancements:

Make EMMO-python available on pypi (installable with pip) #7

Merged pull requests:

Bumbed up version to 1.0.0-alpha-5 #23 (jesper-friis)
Emmocheck #22 (jesper-friis)
Reworked the generation of graphs - using the graphviz Python package #21 (jesper-friis)
1.0.0 #19 (jesper-friis)