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Using first version of ontokit for generating documentation.
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‎.github/emmocheck_conf.yml‎

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# Configurations used when running emmocheck from the ci_emmocheck workflow

‎.github/scripts/init_ghpages.sh‎

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#!/bin/bash
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#set -x
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help() {
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cat <<EOF
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Usage: init_ghpages.sh [OPTIONS]
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Initialise GitHub Pages branch.
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Options:
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-h, --help Print this help and exit.
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-g, --ghpages BRANCH Name of GitHub Pages branch. Default: gh-pages
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-n, --ontology-name NAME Name of ontology.
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-p, --ontology-prefix PREFIX Ontology prefix.
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-n, --ontology-iri IRI Ontology IRI.
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-r, --remote Remote git repository. Default: origin
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EOF
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}
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## Defaults
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GHPAGES=gh-pages
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ONTOLOGY_NAME=
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ONTOLOGY_PREFIX=
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ONTOLOGY_IRI=
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REMOTE=origin
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## Parse options
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TEMP=$(getopt -o hg: --long help,ghpages:,ontology: -- "$@")
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[ $? != 0 ] && exit 1
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eval set -- "$TEMP"
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while true; do
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case "$1" in
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-h|--help) help; exit 0;;
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-g|--ghpages) GHPAGES=$2; shift 2;;
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-n|--ontology-name) ONTOLOGY_NAME=$2; shift 2;;
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-p|--ontology-prefix) ONTOLOGY_PREFIX=$2; shift 2;;
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-i|--ontology-iri) ONTOLOGY_IRI=$2; shift 2;;
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-r|--remote) REMOTE=$2; shift 2;;
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--) shift; break;;
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esac
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done
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current_branch="$(git branch --show-current)"
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rootdir="$(git rev-parse --show-toplevel)"
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reponame="${rootdir##*/}"
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# Ensure that all changes are comitted
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if [ -n "$(git status --porcelain --untracked-files=no)" ]; then
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echo "There exist uncomitted changes"
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exit 1
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fi
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# Set defaults
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if [ -z "$ONTOLOGY_NAME" ]; then
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ONTOLOGY_NAME="$reponame"
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ONTOLOGY_NAME="${ONTOLOGY_NAME#domain-}"
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ONTOLOGY_NAME="${ONTOLOGY_NAME#application-}"
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fi
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if [ ! -f "$rootdir/${ONTOLOGY_NAME}.ttl" ]; then
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echo "Missing ontology file: $rootdir/${ONTOLOGY_NAME}.ttl"
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exit 1
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fi
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if [ -z "$ONTOLOGY_IRI" ]; then
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ONTOLOGY_IRI="$(sed -n 's/^@prefix : *<\([^>]*\)>.*/\1/p' $rootdir/${ONTOLOGY_NAME}.ttl)"
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ONTOLOGY_IRI=${ONTOLOGY_IRI%#}
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ONTOLOGY_IRI=${ONTOLOGY_IRI%/}
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fi
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if [ -z "${ONTOLOGY_IRI}" ]; then
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echo "Empty ONTOLOGY_IRI"
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exit 1
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fi
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if [ -z "$ONTOLOGY_PREFIX" ]; then
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ONTOLOGY_PREFIX="$(sed -n 's|^@prefix *\([^:]*\): *<${ONTOLOGY_IRI}>.*|\1|p' $rootdir/${ONTOLOGY_NAME}.ttl)"
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fi
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have_deps=$([ -f "${rootdir}/${ONTOLOGY_NAME}-dependencies.ttl" ] && echo true || echo false)
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# Show settings
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echo "-- Settings:"
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echo " - current_branch=$current_branch"
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echo " - rootdir=$rootdir"
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echo " - reponame=$reponame"
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echo " - have_deps=$have_deps"
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echo " - GHPAGES=$GHPAGES"
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echo " - ONTOLOGY_NAME=$ONTOLOGY_NAME"
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echo " - ONTOLOGY_PREFIX=$ONTOLOGY_PREFIX"
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echo " - ONTOLOGY_IRI=$ONTOLOGY_IRI"
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echo " - REMOTE=$REMOTE"
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# Squashed ontology
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echo -n "-- Checking for squashed ${ONTOLOGY_NAME}.ttl "
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if git show "${GHPAGES}:${ONTOLOGY_NAME}.ttl" > "/tmp/${ONTOLOGY_NAME}.ttl" 2>/dev/null; then
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echo "- exists"
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else
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echo "- creating"
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ontoconvert \
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-sawe \
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--namespace="emmo:https://w3id.org/emmo#" \
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--namespace="${ONTOLOGY_PREFIX}:${ONTOLOGY_IRI}#" \
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--base-iri="${ONTOLOGY_IRI}#" \
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--iri="${ONTOLOGY_IRI}" \
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"$rootdir/${ONTOLOGY_NAME}.ttl" \
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"/tmp/${ONTOLOGY_NAME}.ttl"
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fi
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# Squashed dependencies
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echo -n "-- Checking for dependencies "
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if $have_deps; then
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if git show "${GHPAGES}:${ONTOLOGY_NAME}-dependencies.ttl" >"/tmp/${ONTOLOGY_NAME}-dependencies.ttl" 2>/dev/null; then
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echo "- exists"
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else
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echo "- creating"
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ontoconvert \
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-saw \
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--namespace="emmo:https://w3id.org/emmo#" \
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--namespace="${ONTOLOGY_PREFIX}:${ONTOLOGY_IRI}#" \
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"${ONTOLOGY_NAME}-dependencies.ttl" \
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"/tmp/${ONTOLOGY_NAME}-dependencies.ttl"
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fi
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else
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echo "- missing ${ONTOLOGY_NAME}-dependencies.ttl (skipping)"
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fi
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# Switch to gh-pages branch (creating it if it doesn't exists)
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if [ -z $(git branch --list "$GHPAGES") ]; then
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git switch --orphan "$GHPAGES"
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else
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git switch "$GHPAGES"
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fi
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# Pull from remote
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git pull $REMOTE $GHPAGES 2>/dev/null
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# Add generated files to gh-pages branch
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mv -f "/tmp/${ONTOLOGY_NAME}.ttl" "$rootdir/."
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git add "$rootdir/${ONTOLOGY_NAME}.ttl"
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if $have_deps; then
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mv -f "/tmp/${ONTOLOGY_NAME}-dependencies.ttl" "$rootdir/."
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git add "$rootdir/${ONTOLOGY_NAME}-dependencies.ttl"
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fi
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# Commit gh-pages branch (if needed)
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if [ -n "$(git status --porcelain --untracked-files=no)" ]; then
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git commit -m "Added squashed ontology and dependencies"
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fi
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# Push to remote repository
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git push $REMOTE $GHPAGES || exit 1
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# Change back to original branch
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git checkout "$current_branch"

‎.github/workflows/cd_ghpages.yml‎

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name: Deploy on GitHub Pages
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# Only run this workflow on push to a release branch or master
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#on: push
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on:
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push:
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branches:
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- '[0-9]+.[0-9]+.[0-9]+'
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- '[0-9]+.[0-9]+.[0-9]+-*'
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- master
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- main
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- flb/test_ontokit
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env:
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ONTOLOGY_NAME: atomistic
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ONTOLOGY_PREFIX: at
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ONTOLOGY_IRI: https://w3id.org/emmo/domain/atomistic
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GITHUB_REPOSITORY: emmo-repo/domain-atomistic
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permissions:
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contents: write
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jobs:
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deploy-on-ghpages:
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#concurrency: ci-${{ github.ref }} # Recommended if you intend to make multiple deployments in quick succession.
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.14
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- name: Install EMMOntoPy and tripper
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run: |
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pip install --upgrade pip
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pip install \
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"EMMOntoPy[ontokit] @ git+https://github.com/emmo-repo/EMMOntoPy.git@master" \
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"tripper[datadoc] @ git+https://github.com/EMMC-ASBL/tripper.git@master"
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#- name: Install current ontology for keywords tool
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# run: |
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# pip install -U git+
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- name: Install ROBOT
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run: |
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mkdir bin
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wget -nv https://github.com/ontodev/robot/releases/download/v1.9.6/robot.jar
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mv robot.jar bin/.
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curl https://raw.githubusercontent.com/ontodev/robot/master/bin/robot > bin/robot
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chmod +x bin/robot
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ls -l bin/
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- name: Download Widoco
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run: |
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wget --quiet https://github.com/dgarijo/Widoco/releases/download/v1.4.25/widoco-1.4.25-jar-with-dependencies_JDK-17.jar
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- name: Copy readme and license files to gh-pages
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run: |
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mkdir build
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cp README.md LICENSE build/.
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- name: Create dependencies on gh-pages
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run: |
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ontoconvert \
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-saw \
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--namespace="emmo:https://w3id.org/emmo#" \
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--namespace="at:https://w3id.org/emmo/domain/atomistic#" \
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atomistic-dependencies.ttl \
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build/atomistic-dependencies.ttl
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- name: Create squashed ontology
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run: |
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ontoconvert \
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-sawe \
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--namespace="emmo:https://w3id.org/emmo#" \
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--namespace="at:https://w3id.org/emmo/domain/atomistic#" \
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--base-iri="https://w3id.org/emmo/domain/atomistic#" \
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--iri="https://w3id.org/emmo/domain/atomistic" \
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atomistic.ttl \
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build/atomistic.ttl
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- name: Create ontology for used later for generating documentation
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run: |
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ontoconvert \
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-awe \
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--namespace="emmo:https://w3id.org/emmo#" \
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--namespace="at:https://w3id.org/emmo/domain/atomistic#" \
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--base-iri="https://w3id.org/emmo/domain/atomistic#" \
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--iri="https://w3id.org/emmo/domain/atomistic" \
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--copy-annotation="elucidation-->http://purl.org/dc/terms/description" \
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--copy-annotation="prefLabel-->http://www.w3.org/2000/01/rdf-schema#label" \
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atomistic.ttl \
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build/atomistic-doc.ttl
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- name: Create inferred ontology
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run: |
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bin/robot reason \
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--reasoner HermiT \
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--remove-redundant-subclass-axioms true \
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--preserve-annotated-axioms true \
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--exclude-owl-thing true \
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--exclude-duplicate-axioms true \
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--input build/atomistic.ttl \
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--output atomistic-inferred.ttl
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ontoconvert --iri=https://w3id.org/emmo/domain/atomistic/inferred atomistic-inferred.ttl build/atomistic-inferred.ttl
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- name: Generate markdown documentation of all keywords
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run: |
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keywords -i build/atomistic-doc.ttl --write-kw-md build/atomistic_kw.md --namespace-filter=https://w3id.org/emmo/domain/atomistic# --redefine=allow
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- name: Generate Widoco documentation
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run: |
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java -jar widoco-1.4.25-jar-with-dependencies_JDK-17.jar \
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-ontFile build/atomistic-doc.ttl \
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-outFolder build/widoco \
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-getOntologyMetadata \
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-oops \
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-rewriteAll \
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-saveConfig build/widoco/widoco.conf \
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-webVowl \
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-licensius \
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-includeAnnotationProperties
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- name: Generate Ontokit documentation to public
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run: ontokit docs --iri-regex=https://w3id.org/emmo/domain/atomistic . && touch public/.nojekyll
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# Copy turtle files from build to public
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- name: Copy ontologies to public
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run: cp build/*ttl public/
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# Copy widoco documentation to public, what to do with it is not yet decided.
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- name: Copy widoco documentation to public
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run: cp -r build/widoco public
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- name: Deploy to GitHub Pages
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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folder: public
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branch: gh-pages
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clean: false
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single-commit: true

‎.github/workflows/cd_release.yml‎

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

‎.github/workflows/ci_tests.yml‎

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

‎README.md‎

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|---------|--------------|-------------------|-------------|
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| 0.0.1 | 1.0.0-alpha1 | 0.0.1 | 0.0.1 |
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| 0.0.2 | 1.0.1 | 0.0.1 | 0.0.1 |
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| 0.0.3 | 1.0.1 | 0.0.1 | 0.0.1 |
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| 0.0.3 | 1.0.1 | N/A | N/A |
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Obtaining domain-atomistic
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--------------------------
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This repository include the correct version of the crystallography and
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mechanics domain ontologies as a git submodules. Hence, use the
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following command when cloning this repository:
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Use the following command when cloning this repository:
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git clone --recurse-submodules --shallow-submodules git@github.com:emmo-repo/domain-atomistic.git
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git clone git@github.com:emmo-repo/domain-atomistic.git
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