WIP: New ontokit tool

ontopy/ontokit/setup.py

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+"""Module for the ontokit setup sub-command."""
+
+# pylint: disable=fixme
+
+import shutil
+from glob import glob
+from pathlib import Path
+from string import Template
+
+
+def setup_arguments(subparsers):
+    """Define arguments for the setup sub-command."""
+    parser = subparsers.add_parser(
+        "setup",
+        help=(
+            "Set up a repository with various github workflows, including "
+            "publishing of squashed and inferred ontologies, generation of "
+            "documentation, releases, etc..."
+        ),
+    )
+    parser.set_defaults(subcommand=setup_subcommand)
+    parser.add_argument(
+        "root",
+        metavar="PATH",
+        help="Root folder of repository to setup.",
+    )
+    parser.add_argument(
+        "--ontology-name",
+        "-n",
+        metavar="NAME",
+        help=(
+            "Name of the ontology.  By default it is inferred from the base "
+            "name of the `root` folder."
+        ),
+    )
+    parser.add_argument(
+        "--ontology-prefix",
+        "-p",
+        metavar="PREFIX",
+        help=(
+            "Prefix for the ontology.  By default it is inferred from the "
+            "turtle file `{ONTOLOGY_NAME}.ttl`."
+        ),
+    )
+    parser.add_argument(
+        "--ontology-iri",
+        "-i",
+        metavar="IRI",
+        help=(
+            "IRI for the ontology.  By default it is inferred from the "
+            "turtle file `{ONTOLOGY_NAME}.ttl`."
+        ),
+    )
+
+
+def setup_subcommand(args):
+    """Implements the setup sub-command."""
+
+    thisdir = Path(__file__).resolve().parent
+    srcdir = thisdir / "setup"
+
+    root = Path(args.root)
+    workflows_dir = root / ".github" / "workflows"
+    workflows_dir.mkdir(mode=0o755, parents=True, exist_ok=True)
+
+    # TODO: infer ONTOLOGY_PREFIX and ONTOLOGY_IRI
+    ontology_name = args.ontology_name if args.ontology_name else root.name
+    ontology_prefix = args.ontology_prefix
+    ontology_iri = args.ontology_iri
+
+    shutil.copy(srcdir / "emmocheck_conf.yml", root / ".github")
+
+    for fname in glob(str(srcdir / "workflows" / "*.yml")):
+        template = Template(Path(fname).read_text())
+        substituted = template.safe_substitute(
+            {
+                "ONTOLOGY_NAME": ontology_name,
+                "ONTOLOGY_PREFIX": ontology_prefix,
+                "ONTOLOGY_IRI": ontology_iri,
+            }
+        )
+        outfile = workflows_dir / Path(fname).name
+        outfile.write_text(substituted)

ontopy/ontokit/setup/emmocheck_conf.yml

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+# Configurations used when running emmocheck from the ci_emmocheck workflow
+
+test_namespace:
+  exceptions:
+    - manufacturing.EngineeredMaterial
+
+test_quantity_dimension:
+  exceptions:
+    - emmo.ModelledQuantitativeProperty
+    - emmo.MeasuredQuantitativeProperty
+    - emmo.ConventionalQuantitativeProperty
+    - emmo.QuantitativeProperty
+    - emmo.Quantity
+    - emmo.OrdinalQuantity
+    - emmo.BaseQuantity
+    - emmo.PhysicalConstant
+    - emmo.PhysicalQuantity
+    - emmo.ExactConstant
+    - emmo.MeasuredConstant
+    - emmo.DerivedQuantity
+    - emmo.ISQBaseQuantity
+    - emmo.InternationalSystemOfQuantity
+    - emmo.ISQDerivedQuantity
+    - emmo.SIExactConstant
+    - microstructure.PhysicalField
+    - microstructure.PhysicalScalarField
+    - microstructure.PhysicalDiscretisedField
+    - microstructure.VoxelField
+    - microstructure.PixelField
+    - microstructure.PhysicalTensorField
+    - microstructure.PhysicalVectorField
+    - microstructure.ConcentrationField
+    - microstructure.AverageQuantity
+    - microstructure.ReferenceFrame
+    - microstructure.GlobalReferenceFrame
+    - microstructure.LocalReferenceFrame
+    - microstructure.GeneralisedDensity
+    - microstructure.LengthDensity  # should not be ignored!!!
+    - microstructure.Orientation  # does this have a unit? LengthFractionUnit?
+    - microstructure.OrientationDistribution
+    - microstructure.StatisticalQuantity
+    - microstructure.MicrostructureQuantity
+
+test_unit_dimension:
+  exceptions:
+    - emmo.MultipleUnit
+    - emmo.SubMultipleUnit
+    - emmo.OffSystemUnit
+    - emmo.PrefixedUnit
+    - emmo.NonPrefixedUnit
+    - emmo.SpecialUnit
+    - emmo.DerivedUnit
+    - emmo.BaseUnit
+    - emmo.UnitSymbol
+    - emmo.SICoherentDerivedUnit
+    - emmo.SINonCoherentDerivedUnit
+    - emmo.SISpecialUnit
+    - emmo.SICoherentUnit
+    - emmo.SIPrefixedUnit
+    - emmo.SIBaseUnit
+    - emmo.SIUnitSymbol
+    - emmo.SIUnit
+
+test_description:
+  exceptions:
+    - electrochemistry.Electrolyte

ontopy/ontokit/setup/workflows/cd_ghpages.yml

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+name: Deploy on GitHub Pages
+on: push
+#on:
+#  push:
+#    branches: [master]
+
+env:
+  ONTOLOGY_NAME: $ONTOLOGY_NAME
+  ONTOLOGY_PREFIX: $ONTOLOGY_PREFIX
+  ONTOLOGY_IRI: $ONTOLOGY_IRI
+
+permissions:
+  contents: write
+
+
+jobs:
+  deploy-on-ghpages:
+    #concurrency: ci-${{ github.ref }}  # Recommended if you intend to make multiple deployments in quick succession.
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+
+    - name: Install EMMOntoPy
+      run: |
+        pip install --upgrade pip
+        #pip install EMMOntoPy
+        pip install -U git+https://github.com/emmo-repo/EMMOntoPy.git@annotating
+
+    - name: Install temgo and tripper
+      run: |
+        pip install .
+        #pip install tripper[datadoc]
+        #pip install -U git+https://github.com/EMMC-ASBL/tripper.git@master
+        pip install -U git+https://github.com/EMMC-ASBL/tripper.git@datadoc-redefine-option
+
+    - name: Install ROBOT
+      run: |
+        mkdir bin
+        wget -nv https://github.com/ontodev/robot/releases/download/v1.9.6/robot.jar
+        mv robot.jar bin/.
+        curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot > bin/robot
+        chmod +x bin/robot
+        ls -l bin/
+
+    - name: Download Widoco
+      run: |
+        wget --quiet https://github.com/dgarijo/Widoco/releases/download/v1.4.25/widoco-1.4.25-jar-with-dependencies_JDK-17.jar
+
+    - name: Create squashed ontology
+      run: |
+        mkdir build
+        cp README.md LICENSE build/.
+
+        ontoconvert \
+            -saw \
+            --namespace="emmo:https://w3id.org/emmo#" \
+            --namespace="${ONTOLOGY_PREFIX}:${ONTOLOGY_IRI}#" \
+            ${ONTOLOGY_NAME}-dependencies.ttl \
+            build/${ONTOLOGY_NAME}-dependencies.ttl
+
+        ontoconvert \
+            -sawe \
+            --namespace="emmo:https://w3id.org/emmo#" \
+            --namespace="${ONTOLOGY_PREFIX}:${ONTOLOGY_IRI}#" \
+            --base-iri="${ONTOLOGY_IRI}#" \
+            --iri="${ONTOLOGY_IRI}" \
+            ${ONTOLOGY_NAME}.ttl \
+            build/${ONTOLOGY_NAME}.ttl
+
+        ontoconvert \
+            -awe \
+            --namespace="emmo:https://w3id.org/emmo#" \
+            --namespace="${ONTOLOGY_PREFIX}:${ONTOLOGY_IRI}#" \
+            --base-iri="${ONTOLOGY_IRI}#" \
+            --iri="${ONTOLOGY_IRI}" \
+            --copy-annotation="elucidation-->http://purl.org/dc/terms/description" \
+            --copy-annotation="prefLabel-->http://www.w3.org/2000/01/rdf-schema#label" \
+            ${ONTOLOGY_NAME}.ttl \
+            build/${ONTOLOGY_NAME}-doc.ttl
+
+    - name: Create inferred ontology
+      run: |
+        # Running HermiT via ontoconvert fails with custom datatypes.
+        # Use ROBOT instead.
+        #
+        #ontoconvert \
+        #    -sawe \
+        #    --base-iri="${ONTOLOGY_IRI}#" \
+        #    --iri="${ONTOLOGY_IRI}" \
+        #    --infer=HermiT \
+        #    ${ONTOLOGY_NAME}.ttl \
+        #    build/${ONTOLOGY_NAME}-inferred.ttl
+        #
+        bin/robot reason \
+            --reasoner HermiT \
+            --input build/${ONTOLOGY_NAME}.ttl \
+            --output build/${ONTOLOGY_NAME}-inferred.ttl
+
+    - name: Generate markdown documentation of all keywords
+      run: |
+        keywords -i build/${ONTOLOGY_NAME}-doc.ttl --keywords build/${ONTOLOGY_NAME}.md --namespace-filter=${ONTOLOGY_IRI} --redefine=allow
+
+    - name: Generate Widoco documentation
+      run: |
+        java -jar widoco-1.4.25-jar-with-dependencies_JDK-17.jar \
+            -ontFile build/${ONTOLOGY_NAME}-doc.ttl \
+            -outFolder build/widoco \
+            -getOntologyMetadata \
+            -oops \
+            -rewriteAll \
+            -saveConfig build/widoco/widoco.conf \
+            - webVowl \
+            -licensius \
+            -includeAnnotationProperties
+
+
+
+    - name: Deploy to GitHub Pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        folder: build
+        branch: gh-pages

ontopy/ontokit/setup/workflows/cd_release.yml

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+name: Release new version
+
+on:
+  release:
+    types: [published]
+
+env:
+  ONTOLOGY_NAME: $ONTOLOGY_NAME
+  TAG: ${{ github.ref_name }}
+
+permissions:
+  contents: write
+
+jobs:
+  release_version:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout gh-pages
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+
+      - name: Create and copy generated files to versions/
+        run: |
+          mkdir -p versions/${TAG#v}
+          cp -f \
+              README.md \
+              ${ONTOLOGY_NAME}.ttl \
+              ${ONTOLOGY_NAME}-dependencies.ttl \
+              ${ONTOLOGY_NAME}-inferred.ttl \
+              versions/${TAG#v}/.
+
+      - name: Push to gh-pages
+        run: |
+          git config --global user.email "${ONTOLOGY_NAME}@emmc.eu"
+          git config --global user.name "${ONTOLOGY_NAME}"
+          git add versions/${TAG#v}
+          git commit -m "Release version ${TAG#v}"
+          git push origin gh-pages

ontopy/ontokit/setup/workflows/ci_tests.yml

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+name: CI tests
+on: [push]
+
+env:
+  ONTOLOGY_NAME: $ONTOLOGY_NAME
+
+jobs:
+  ci_testing:
+    concurrency: ci-${{ github.ref }}  # Recommended if you intend to make multiple deployments in quick succession.
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+
+    - name: Install EMMOntoPy
+      run: |
+        pip install --upgrade pip
+        pip install EMMOntoPy
+
+    - name: Test
+      run: |
+        emmocheck --configfile=.github/emmocheck_conf.yml ${ONTOLOGY_NAME}.ttl

tools/ontokit

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+#!/usr/bin/env python
+"""General toolkit for managing ontologies."""
+import argparse
+from ontopy.ontokit.setup import setup_arguments
+
+
+def main(argv: "list" = None):
+    """Main function.
+
+    Arguments:
+        argv: List of arguments, similar to `sys.argv[1:]`.
+            Mainly for testing purposes, since it allows one to invoke the tool
+            manually / through Python.
+
+    """
+    # General options
+    parser = argparse.ArgumentParser(
+        description=__doc__,
+        # usage="ontokit [GENERAL_OPTIONS] SUBCOMMAND [SUBCOMMAND_OPTIONS]"
+    )
+    parser.add_argument(
+        "--debug", action="store_true", help="Show Python traceback on error."
+    )
+
+    # Add sub-command arguments
+    subparsers = parser.add_subparsers(required=True, help="Subcommands:")
+    setup_arguments(subparsers)
+
+    args = parser.parse_args(argv)
+
+    # Call the subcommand handler
+    try:
+        return args.subcommand(args)
+    except Exception as exc:  # pylint: disable=broad-exception-caught
+        if args.debug:
+            raise
+        print(f"{exc.__class__.__name__}: {exc}")
+        return exc
+
+
+if __name__ == "__main__":
+    main()