Merge pull request #13 from eccenca/feature/templateUpdate

update copier template and dependencies

.copier-answers.yml

@@ -1,10 +1,10 @@
 # Changes here will be overwritten by Copier
-_commit: v6.3.1
+_commit: v6.4.0
 _src_path: gh:eccenca/cmem-plugin-template
-author_mail: info@eccenca.com
+author_mail: cmempy-developer@eccenca.com
 author_name: eccenca GmbH
 github_page: https://github.com/eccenca/cmem-plugin-reason
-project_description: Reasoning with Robot
+project_description: Perform reasoning tasks and validate OWL consistency.
 project_slug: reason
-pypi: false
+pypi: true
 

.github/workflows/check.yml

@@ -23,11 +23,11 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install Task
-        uses: arduino/setup-task@v1
+        uses: arduino/setup-task@v2
 
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 

.github/workflows/publish.yml

@@ -20,11 +20,11 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install Task
-        uses: arduino/setup-task@v1
+        uses: arduino/setup-task@v2
 
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 

README-public.md

@@ -1,6 +1,6 @@
 # cmem-plugin-reason
 
-This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin bundle contains plugins performing reasoning (Reason) andontology consistency checking (Validate) using [ROBOT](http://robot.obolibrary.org/).
+Perform reasoning tasks and validate OWL consistency.
 
 ROBOT is published under the [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/).
 Copyright © 2015, the authors. All rights reserved.

README.md

@@ -1,10 +1,18 @@
+# cmem-plugin-reason
 
+Perform reasoning tasks and validate OWL consistency.
 
-# cmem-plugin-reason
+[![eccenca Corporate Memory](https://img.shields.io/badge/eccenca-Corporate%20Memory-orange)](https://documentation.eccenca.com) [![workflow](https://github.com/eccenca/cmem-plugin-reason/actions/workflows/check.yml/badge.svg)](https://github.com/eccenca/cmem-plugin-reason/actions) [![pypi version](https://img.shields.io/pypi/v/cmem-plugin-reason)](https://pypi.org/project/reason) [![license](https://img.shields.io/pypi/l/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reason)
 
-This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin bundle contains plugins performing reasoning (Reason) and ontology consistency checking (Validate) using [ROBOT](http://robot.obolibrary.org/).
+## Development
 
-[![eccenca Corporate Memory](https://img.shields.io/badge/eccenca-Corporate%20Memory-orange)](https://documentation.eccenca.com) [![workflow](https://github.com/eccenca/cmem-plugin-pyshacl/actions/workflows/check.yml/badge.svg)](https://github.com/eccenca/cmem-plugin-pyshacl/actions) [![pypi version](https://img.shields.io/pypi/v/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reason/) [![license](https://img.shields.io/pypi/l/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reasom)
+- Run [task](https://taskfile.dev/) to see all major development tasks.
+- Use [pre-commit](https://pre-commit.com/) to avoid errors before commit.
+- This repository was created with [this copier template](https://github.com/eccenca/cmem-plugin-template).
+
+## Robot
+
+This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) plugin contains workflow tasks to perform reasoning (Reason) and ontology consistency checking (Validate) using [ROBOT](http://robot.obolibrary.org/).
 
 ROBOT is published under the [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/).
 Copyright © 2015, the authors. All rights reserved.
@@ -27,227 +35,3 @@ Alternatively, the _build_ and _installation_ process can be initiated with the
 ➜ task deploy
 ```
 
-## Development
-
-- Run [task](https://taskfile.dev/) to see all major development tasks.
-- Use [pre-commit](https://pre-commit.com/) to avoid errors before commit.
-- This repository was created with [this copier template](https://github.com/eccenca/cmem-plugin-template).
-
-# Reason
-## Options
-
-### Data graph IRI
-
-The IRI of the input data graph. The graph IRI is selected from a list of graphs of types `di:Dataset`, `void:Dataset`
-and `owl:Ontology`.
-
-### Ontology graph IRI
-
-The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
-
-### Output graph IRI
-
-The IRI of the output graph for the reasoning result.
-
-⚠️ Existing graphs will be overwritten.
-
-### Reasoner
-
-The following reasoner options are supported: 
-- [ELK](https://code.google.com/p/elk-reasoner/) (elk)
-- [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
-- [HermiT](http://www.hermit-reasoner.com/) (hermit)
-- [JFact](http://jfact.sourceforge.net/) (jfact)
-- [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
-- [Whelk](https://github.com/balhoff/whelk) (whelk)
-
-### Generated Axioms
-
-The plugin provides the following parameters to include inferred axiom generators:
-
-#### Class axiom generators
-- **Class inclusion (rdfs:subClassOf)**  
-The reasoner will infer assertions about the hierarchy of classes, i.e.
-`SubClassOf:` statements.  
-If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
-Student, Professor` holds, the reasoner will infer `Student SubClassOf: Person`.  
-
-
-- **Class equivalence (owl:equivalentClass)**  
-The reasoner will infer assertions about the equivalence of classes, i.e.
-`EquivalentTo:` statements.  
-If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
-Student, Professor` holds, the reasoner will infer `Person EquivalentTo: Student and Professor`.
-
-
-- **Class disjointness (owl:disjointWith)**  
-The reasoner will infer assertions about the disjointness of classes, i.e.
-`DisjointClasses:` statements.  
-If there are classes `Person`, `Student` and `Professor`, such that `Person DisjointUnionOf:
-Student, Professor` holds, the reasoner will infer `DisjointClasses: Student, Professor`.
-
-
-- **Data property equivalence (owl:equivalentProperty)**  
-The reasoner will infer axioms about the equivalence of data properties,
- i.e. `EquivalentProperties` statements.  
-If there are data properties `identifier` and `enrollmentNumber`, such that `enrollmentNumber
-SubPropertyOf: identifier` and `identifier SubPropertyOf: enrollmentNumber` holds, the reasoner
-will infer `Student EquivalentProperties: identifier, enrollmentNumber`.
-
-
-- **Data property inclusion (rdfs:subPropertyOf)**  
-The reasoner will infer axioms about the hierarchy of data properties,
-i.e. `SubPropertyOf:` statements.  
-If there are data properties `identifier`, `studentIdentifier` and `enrollmentNumber`, such that
-`studentIdentifier SubPropertyOf: identifier` and `enrollmentNumber SubPropertyOf:
-studentIdentifier` holds, the reasoner will infer `enrollmentNumber SubPropertyOf: identifier`.
-
-
-#### Individual axiom generators
-- **Individual class assertions (rdf:type)**  
-The reasoner will infer assertions about the classes of individuals, i.e.
-`Types:` statements.  
-Assume, there are classes `Person`, `Student` and `University` as well as the property
-`enrolledIn`, such that `Student EquivalentTo: Person and enrolledIn some University` holds. For
-the individual `John` with the assertions `John Types: Person; Facts: enrolledIn
-LeipzigUniversity`, the reasoner will infer `John Types: Student`.
-
-
-- **Individual property assertions**  
-The reasoner will infer assertions about the properties of individuals,
-i.e. `Facts:` statements.  
-Assume, there are properties `enrolledIn` and `offers`, such that `enrolled SubPropertyChain:
-enrolledIn o inverse (offers)` holds. For the individuals `John`and `LeipzigUniversity` with the
-assertions `John Facts: enrolledIn KnowledgeRepresentation` and `LeipzigUniversity Facts: offers
-KnowledgeRepresentation`,  the reasoner will infer `John Facts: enrolledIn LeipzigUniversity`.
-
-
-#### Object property axiom generators
-- **Object property equivalence (owl:equivalentProperty)**  
-The reasoner will infer assertions about the equivalence of object
-properties, i.e. `EquivalentTo:` statements.  
-If there are object properties `hasAlternativeLecture` and `hasSameTopicAs`, such that
-`hasAlternativeLecture Characteristics: Symmetric` and `hasSameTopicAs InverseOf:
-hasAlternativeLecture` holds, the reasoner will infer `EquivalentProperties: hasAlternativeLecture,
-hasSameTopicAs`.
-
-
-- **Object property inversion (owl:inverseOf)**  
-The reasoner will infer axioms about the inversion about object
-properties, i.e. `InverseOf:` statements.  
-If there is a object property `hasAlternativeLecture`, such that `hasAlternativeLecture
-Characteristics: Symmetric` holds, the reasoner will infer `hasAlternativeLecture InverseOf:
-hasAlternativeLecture`.
-
-
-- **Object property inclusion (rdfs:subPropertyOf)**  
-The reasoner will infer axioms about the inclusion of object properties,
-i.e. `SubPropertyOf:` statements.  
-If there are object properties `enrolledIn`, `studentOf` and `hasStudent`, such that `enrolledIn
-SubPropertyOf: studentOf` and `enrolledIn InverseOf: hasStudent` holds, the reasoner will infer
-`hasStudent SubPropertyOf: inverse (studentOf)`.
-
-
-- **Object property ranges (rdfs:range)**  
-The reasoner will infer axioms about the ranges of object properties,
-i.e. `Range:` statements.  
-If there are classes `Student` and `Lecture` as wells as object properties `hasStudent` and
-`enrolledIn`, such that `hasStudent Range: Student and enrolledIn some Lecture` holds, the
-reasoner will infer `hasStudent Range: Student`.
-
-
-- **Object property domains (rdfs:domain)**  
-The reasoner will infer axioms about the domains of object
-properties, i.e. `Domain:` statements.  
-If there are classes `Person`, `Student` and `Professor` as wells as the object property
-`hasRoleIn`, such that `Professor SubClassOf: Person`, `Student SubClassOf: Person` and
-`hasRoleIn Domain: Professor or Student` holds, the reasoner will infer `hasRoleIn Domain: Person`.
-
-### Validate OWL2 profiles
-
-Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph. 
-
-### Process valid OWL profiles from input
-
-If enabled along with the "Validate OWL2 profiles" parameter, the valid profiles, ontology IRI and reasoner option is
-taken from the config port input (parameters "valid_profiles", "ontology_graph_iri" and "reasoner") and the OWL2
-profiles validation is not done in the plugin. The valid profiles input is a comma-separated string (e.g. "Full,DL").
-
-### Add ontology graph import to result graph
-
-Add the triple `<output_graph_iri> owl:imports <ontology_graph_iri>` to the output graph.
-
-### Add result graph import to ontology graph
-
-Add the triple `<ontology_graph_iri> owl:imports <output_graph_iri>` to the ontology graph
-
-### Maximum RAM Percentage
-
-Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
-
-⚠️ Setting the percentage too high may result in an out of memory error.
-
-# Validate
-
-The plugin outputs the explanation as text in Markdown format on the path "markdown",
-the ontology IRI on the path "ontology_graph_iri", and (if enabled) the valid OWL2 profiles on the path "valid_profiles" as 
-a comma-separated string.
-
-## Options
-
-### Ontology graph IRI
-
-The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
-
-### Reasoner
-
-The following reasoner options are supported: 
-- [ELK](https://code.google.com/p/elk-reasoner/) (elk)
-- [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
-- [HermiT](http://www.hermit-reasoner.com/) (hermit)
-- [JFact](http://jfact.sourceforge.net/) (jfact)
-- [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
-- [Whelk](https://github.com/balhoff/whelk) (whelk)
-
-### Produce output graph
-
-If enabled, an explanation graph is created.
-
-### Output graph IRI
-
-The IRI of the output graph for the reasoning result.
-
-⚠️ Existing graphs will be overwritten.
-
-### Write markdown explanation file
-
-If enabled, an explanation markdown file is written to the project.
-
-### Output filename
-
-The filename of the Markdown file with the explanation of inconsistencies.
-
-⚠️ Existing files will be overwritten.
-
-### Stop at inconsistencies
-Raise an error if inconsistencies are found. If enabled, the plugin does not output entities.
-
-### Mode
-Mode _inconsistency_ generates an explanation for an inconsistent ontology.  
-Mode _unsatisfiability_ generates explanations for many unsatisfiable classes at once.
-
-### Validate OWL2 profiles
-
-Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph.
-
-### Output entities
-
-Output entities. The plugin outputs the explanation as text in Markdown format on the path "markdown", the ontology IRI
-on the path "ontology_graph_iri", the reasoner option on the path "reasoner", and, if enabled, the valid OWL2 profiles
-on the path "valid_profiles".
-
-### Maximum RAM Percentage
-
-Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
-
-⚠️ Setting the percentage too high may result in an out of memory error.

Taskfile.yaml

@@ -147,7 +147,7 @@ tasks:
     <<: *preparation
     cmds:
       - poetry run ruff check --exit-zero tests {{.PACKAGE}} {{.XML_PARAMS}}
-      - poetry run ruff check --show-source tests {{.PACKAGE}}
+      - poetry run ruff check --output-format=concise tests {{.PACKAGE}}
       - poetry run ruff format --check tests {{.PACKAGE}}
     vars:
       JUNIT_FILE: ./{{.DIST_DIR}}/junit-ruff.xml