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Merge branch '1.0.0-rc1' into 286-fairify
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jesper-friis authored May 25, 2024
2 parents 30c537a + 03f78c6 commit 02b1ea3
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4 changes: 4 additions & 0 deletions .github/expected_redirections.yaml
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Expand Up @@ -83,3 +83,7 @@ redirections:
https://w3id.org/emmo/domain/domain-microstructure: https://emmo-repo.github.io/domain-microstructure/microstructure.ttl
https://w3id.org/emmo/domain/microstructure/source: https://raw.githubusercontent.com/emmo-repo/domain-microstructure/master/microstructure.ttl
https://w3id.org/emmo/domain/microstructure: https://emmo-repo.github.io/domain-microstructure/microstructure.ttl


# application-battmo
https://w3id.org/emmo/application/battmo/source: https://raw.githubusercontent.com/emmo-repo/application-battmo/master/battmo.ttl
6 changes: 3 additions & 3 deletions .github/scripts/makeversions.sh
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Expand Up @@ -93,14 +93,14 @@ while read version name; do
"$src" "$d/emmo.owl"
fi

# Generate inferred ontology
# Generate inferred ontology (may fail)
if $remake || [ ! -f "$d/emmo-inferred.ttl" ]; then
echo "Generate inferred ontology"
#ontoconvert -i HermiT -wsa "$d/emmo.ttl" "$d/emmo-inferred.ttl"
ontoconvert -w -i HermiT "$d/emmo.ttl" "$d/emmo-inferred.ttl"
ontoconvert -w -i HermiT "$d/emmo.ttl" "$d/emmo-inferred.ttl" || true
fi
if $remake || [ ! -f "$d/emmo-inferred.owl" ]; then
ontoconvert -w "$d/emmo-inferred.ttl" "$d/emmo-inferred.owl"
ontoconvert -w "$d/emmo-inferred.ttl" "$d/emmo-inferred.owl" || true
fi

# Generate renamed ontology
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108 changes: 85 additions & 23 deletions .github/workflows/cd_update_pages.yml
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Expand Up @@ -5,57 +5,119 @@ on:
branches:
- '[0-9]+.[0-9]+.[0-9]+'
- '[0-9]+.[0-9]+.[0-9]+-*'
- update_pages
- fix-github-workflow
- cd_update_pages

env:
GIT_USER_NAME: EMMO Developers
GIT_USER_EMAIL: "[email protected]"

jobs:

build:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v4
- name: Checkout repository
uses: actions/checkout@v4

- name: Setup git identity
- name: Debug info
run: |
git config --global user.email "[email protected]"
git config --global user.name "EMMO GitHub Action"
echo "GITHUB_REF_NAME=${GITHUB_REF_NAME}"
- name: Setup Python 3.11
uses: actions/setup-python@v5
with:
python-version: 3.11

- name: Debug info
- name: Install dependencies
run: |
echo "GITHUB_REF_NAME=${GITHUB_REF_NAME}"
pip install --upgrade pip
pip install sphinx sphinxcontrib-globalsubs sphinx_design nbsphinx pydata-sphinx-theme
pip install git+https://github.com/emmo-repo/EMMOntoPy.git@ontodoc2
#pip install sphinx EMMOntoPy
- name: Install EMMO-python
- name: Create and prepare build and public directories
run: |
pip install --upgrade pip
pip install EMMOntoPy
mkdir build public
if [ -d doc/_static ]; then cp -rf doc/_static/* build/. ; fi
- name: Install pandoc 2.1.2
- name: Create ontologies for publishing
run: |
#sudo apt-get install pandoc # we need v2.1.2
wget https://github.com/jgm/pandoc/releases/download/2.1.2/pandoc-2.1.2-1-amd64.deb
sudo apt-get install ./pandoc-2.1.2-1-amd64.deb
ontoconvert -sawe --base-iri="https://w3id.org/emmo#" --iri=https://w3id.org/emmo emmo.ttl public/emmo.ttl
ontoconvert public/emmo.ttl public/emmo.owl
- name: Install other dependencies
- name: Generate html documentation
run: |
sudo apt-get install graphviz
sudo apt-get install texlive-xetex
sudo apt-get install texlive-latex-extra
pip install semver
ontodoc --iri-regex=https://w3id.org/emmo --imported emmo.ttl build/emmo.rst
sphinx-build "build/" "public/"
- name: Checkout GitHub Pages for EMMO-repo
uses: actions/checkout@v4
with:
repository: emmo-repo/emmo-repo.github.io
path: ".github/pages"
path: pages
ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
ssh-strict: no

- name: Update GitHub Pages
- name: Copy to GitHub Pages
run: |
.github/scripts/update_pages.sh -v -V ${GITHUB_REF_NAME}
# Do not overwrite index.html
rm public/index.html
cp -rf public/* pages/.
# Tell GitHub that this site is not generated with jekyll
touch public/.nojekyll
# Domain repositories can use peaceiris/actions-gh-pages@v3.
# However, since EMMO for historical reasons uses a separate repo
# for its GitHub Pages, it is easier to use git directly.
- name: Push to GitHub Pages
run: |
cd pages
git config --global user.email "[email protected]"
git config --global user.name "EMMO Developer"
git add --all
if [ -n "$(git status --porcelain -uno)" ]; then \
git commit -m 'Updated releasetable'; \
git pull origin master; \
git push origin master; \
fi
#- name: Publish
# uses: peaceiris/actions-gh-pages@v3
# if: github.ref == 'refs/heads/master'
# with:
# github_token: ${{ secrets.GITHUB_TOKEN }}
# publish_dir: ./public
# #keep_files: true
# #external_repository: emmo-repo emmo-repo.github.io
#
# #publish_branch: master
# #force_orphan: true



# - name: Install pandoc 2.1.2
# run: |
# #sudo apt-get install pandoc # we need v2.1.2
# wget https://github.com/jgm/pandoc/releases/download/2.1.2/pandoc-2.1.2-1-amd64.deb
# sudo apt-get install ./pandoc-2.1.2-1-amd64.deb
#
# - name: Install other dependencies
# run: |
# sudo apt-get install graphviz
# sudo apt-get install texlive-xetex
# sudo apt-get install texlive-latex-extra
# pip install semver
#
# - name: Checkout GitHub Pages for EMMO-repo
# uses: actions/checkout@v4
# with:
# repository: emmo-repo/emmo-repo.github.io
# path: ".github/pages"
# ssh-key: ${{ secrets.SSH_PRIVATE_KEY }}
# ssh-strict: no
#
# - name: Update GitHub Pages
# run: |
# .github/scripts/update_pages.sh -v -V ${GITHUB_REF_NAME}
3 changes: 3 additions & 0 deletions catalog-v001.xml
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Expand Up @@ -20,6 +20,7 @@
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/symbolic" uri="./multiperspective/symbolic.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/information" uri="./multiperspective/information.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/workflow" uri="./multiperspective/workflow.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/dataset" uri="./multiperspective/dataset.ttl"/>

<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines" uri="./disciplines/disciplines.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/chemistry" uri="./disciplines/chemistry.ttl"/>
Expand All @@ -29,6 +30,8 @@
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/math" uri="./disciplines/math.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/models" uri="./disciplines/models.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/periodictable" uri="./disciplines/periodictable.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/perceptual" uri="./disciplines/perceptual.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/geometrical" uri="./disciplines/geometrical.ttl"/>

<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/metrology" uri="./disciplines/metrology.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/isq" uri="./disciplines/isq.ttl"/>
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5 changes: 4 additions & 1 deletion disciplines/catalog-v001.xml
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Expand Up @@ -12,7 +12,7 @@
<uri name="https://w3id.org/emmo/1.0.0-rc1/perspectives/persistence" uri="../perspectives/persistence.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/perspectives/physicalistic" uri="../perspectives/physicalistic.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/perspectives/standardmodel" uri="../perspectives/standardmodel.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/perspectives/standardmodel-full" uri="../perspectives/standardmodel-full.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/perspectives/standardmodel-full" uri="../perspectives/standardmodel-full.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/perspectives/data" uri="../perspectives/data.ttl"/>

<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective" uri="../multiperspective/multiperspective.ttl"/>
Expand All @@ -21,6 +21,7 @@
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/symbolic" uri="../multiperspective/symbolic.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/information" uri="../multiperspective/information.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/workflow" uri="../multiperspective/workflow.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/multiperspective/dataset" uri="../multiperspective/dataset.ttl"/>

<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines" uri="../disciplines/disciplines.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/chemistry" uri="../disciplines/chemistry.ttl"/>
Expand All @@ -29,6 +30,8 @@
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/materials" uri="../disciplines/materials.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/math" uri="../disciplines/math.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/models" uri="../disciplines/models.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/perceptual" uri="../disciplines/perceptual.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/geometrical" uri="../disciplines/geometrical.ttl"/>
<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/periodictable" uri="../disciplines/periodictable.ttl"/>

<uri name="https://w3id.org/emmo/1.0.0-rc1/disciplines/metrology" uri="../disciplines/metrology.ttl"/>
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