diff --git a/.github/ABOUT.md b/.github/ABOUT.md index f74d3cbf..8a05690c 100644 --- a/.github/ABOUT.md +++ b/.github/ABOUT.md @@ -37,7 +37,7 @@ Directory content The format is simple - each line starts with a version number. Optionally it may be followed by label indicating the - status. Use either "unstable" or "latest" or leave it out as + status. Use either "development" or "stable" or leave it out as default. diff --git a/.github/expected_redirections.yaml b/.github/expected_redirections.yaml index 8706b7bd..15d1ebbe 100644 --- a/.github/expected_redirections.yaml +++ b/.github/expected_redirections.yaml @@ -10,30 +10,44 @@ redirections: # EMMO + https://w3id.org/emmo#EMMO_297999d6_c9e4_4262_9536_bd524d1c6e21: https://emmo-repo.github.io/emmo.ttl#EMMO_297999d6_c9e4_4262_9536_bd524d1c6e21 # ttl file because tests are not from a browser + https://w3id.org/emmo: https://emmo-repo.github.io/emmo.ttl # ttl file because tests are not from a browser https://w3id.org/emmo/inferred: https://emmo-repo.github.io/emmo-inferred.ttl - https://w3id.org/emmo/dev: https://emmo-repo.github.io/development/emmo.ttl - https://w3id.org/emmo/dev-inferred: https://emmo-repo.github.io/development/emmo-inferred.ttl https://w3id.org/emmo/1.0.0-beta4: https://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl https://w3id.org/emmo/1.0.0-beta4/inferred: https://emmo-repo.github.io/versions/1.0.0-beta4/emmo-inferred.ttl https://w3id.org/emmo/1.0.0-beta5: https://emmo-repo.github.io/versions/1.0.0-beta5/emmo.ttl - https://w3id.org/emmo/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl + #https://w3id.org/emmo/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl https://w3id.org/emmo/1.0.0-beta5/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/emmo.ttl https://w3id.org/emmo/1.0.0-beta5/mereocausality: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/mereocausality/mereocausality.ttl https://w3id.org/emmo/1.0.0-beta5/perspectives: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/perspectives.ttl https://w3id.org/emmo/1.0.0-beta5/multiperspective: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/multiperspective/multiperspective.ttl https://w3id.org/emmo/1.0.0-beta5/disciplines: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/disciplines.ttl - https://w3id.org/emmo/1.0.0-beta5/disciplines/units: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/disciplines/units.ttl - https://w3id.org/emmo/master: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl - https://w3id.org/emmo/master/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl + https://w3id.org/emmo/1.0.0-beta5/disciplines/units: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/units.ttl https://w3id.org/emmo/source: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl https://w3id.org/emmo/source/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl - https://w3id.org/emmo/perspectives/data: https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl - https://w3id.org/emmo/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl + https://w3id.org/emmo/latest: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl + https://w3id.org/emmo/latest/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl + #https://w3id.org/emmo/perspectives/data: https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl + #https://w3id.org/emmo/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/master/perspectives/data.ttl https://w3id.org/emmo/1.0.0-beta5/perspectives/data: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl - https://w3id.org/emmo/1.0.0-beta5/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl + #https://w3id.org/emmo/1.0.0-beta5/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl + + + # Electrochemistry + #https://w3id.org/emmo/domain/electrochemistry#electrochemistry_b6319c74_d2ce_48c0_a75a_63156776b302: https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl#electrochemistry_b6319c74_d2ce_48c0_a75a_63156776b302 + + #https://w3id.org/emmo/domain/electrochemistry: https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl + https://w3id.org/emmo/domain/electrochemistry/: https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry.ttl + # Battery - https://w3id.org/emmo/domain/battery#battery_50b911f7_c903_4700_9764_c308d8a95470: https://emmo-repo.github.io/domain-battery.ttl - https://w3id.org/emmo/domain/battery: https://emmo-repo.github.io/domain-battery.ttl + #https://w3id.org/emmo/domain/battery#battery_50b911f7_c903_4700_9764_c308d8a95470: https://emmo-repo.github.io/domain-battery/battery.ttl + + #https://w3id.org/emmo/domain/battery: https://emmo-repo.github.io/domain-battery.ttl + https://w3id.org/emmo/domain/battery/: https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl + https://w3id.org/emmo/domain/battery/source: https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl + https://w3id.org/emmo/domain/battery/source/: https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl + https://w3id.org/emmo/domain/battery/latest: https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl + https://w3id.org/emmo/domain/battery/latest/: https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl diff --git a/.github/pages-index.html.in b/.github/pages-index.html.in index 5c5a9236..336b1c37 100644 --- a/.github/pages-index.html.in +++ b/.github/pages-index.html.in @@ -18,7 +18,7 @@
-

Elementary Multiperspective Material Ontology (EMMO)

+

The Elementary Multiperspective Material Ontology (EMMO)

The Elementary Multiperspective Material Ontology (EMMO) is the result of a multidisciplinary effort within the EMMC, aimed at the development of a standard representational ontology framework based on current materials modelling and characterization knowledge. Instead of starting from general upper level concepts, as done by other ontologies, the EMMO development started from the very bottom level, using the actual picture of the physical world coming from applied sciences, and in particular from physics and material sciences. @@ -37,8 +37,8 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to - Compacted1 ontology - Inferred ontology (compacted1) + Compacted ontology1 + Inferred ontology2 Documentation @@ -54,11 +54,15 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to ${versions} -1. - With "compacted ontology", we here mean that all - the top and middle level modules are joint together into a single - file with no imports. - + +
+ 1 + Compacted ontology means that all modules have been squashed together into a single file with no imports. + Also, rdfs:isDefinedBy annotations referring to the original module IRI have been added. +
+ 2 + Inferred ontology is reasoned and compacted. + diff --git a/.github/scripts/makeindex.sh b/.github/scripts/makeindex.sh index ec38ef69..d5ec2e0b 100755 --- a/.github/scripts/makeindex.sh +++ b/.github/scripts/makeindex.sh @@ -61,8 +61,6 @@ while read version name; do tdlink $d/emmo.ttl $version $l/emmo.ttl >> "$tmpfile" tdlink $d/emmo-inferred.owl $version $l/emmo-inferred.owl >> "$tmpfile" tdlink $d/emmo-inferred.ttl $version $l/emmo-inferred.ttl >> "$tmpfile" - tdlink $d/emmo-renamed.owl $version $l/emmo-renamed.owl >> "$tmpfile" - tdlink $d/emmo-renamed.ttl $version $l/emmo-renamed.ttl >> "$tmpfile" tdlink $d/emmo.html $version $l/emmo.html >> "$tmpfile" tdlink $d/emmo.pdf $version $l/emmo.pdf >> "$tmpfile" echo " " >> "$tmpfile" diff --git a/.github/scripts/makeversions.sh b/.github/scripts/makeversions.sh index b3a0d006..3c36a62c 100755 --- a/.github/scripts/makeversions.sh +++ b/.github/scripts/makeversions.sh @@ -14,7 +14,7 @@ set -e rootdir="$(git rev-parse --show-toplevel)" -remote=$(git remote -v | awk '{print $2; exit}') +remote=$(git remote -v | awk '/^origin/ {print $2; exit}') ghdir="$rootdir/.github" pagesdir="$ghdir/pages" scriptsdir="$ghdir/scripts" @@ -83,44 +83,44 @@ while read version name; do else echo "missing source in EMMO $version" >&2; exit 1 fi - ontoconvert "$src" "$d/emmo.owl" -s -a - ontoconvert "$src" "$d/emmo.ttl" -s -a + ontoconvert -saw "$src" "$d/emmo.owl" + ontoconvert -saw "$src" "$d/emmo.ttl" fi # Generate inferred ontology - if $remake || [ ! -f "$d/emmo-inferred.owl" ]; then + if $remake || [ ! -f "$d/emmo-inferred.ttl" ]; then echo "Generate inferred ontology" - ontoconvert "$d/emmo.owl" "$d/emmo-inferred.owl" \ - -i HermiT -b http://emmo.info/emmo-inferred + #ontoconvert -i HermiT -wsa "$d/emmo.ttl" "$d/emmo-inferred.ttl" + ontoconvert -w -i HermiT "$d/emmo.ttl" "$d/emmo-inferred.ttl" fi - if $remake || [ ! -f "$d/emmo-inferred.ttl" ]; then - ontoconvert "$d/emmo-inferred.owl" "$d/emmo-inferred.ttl" + if $remake || [ ! -f "$d/emmo-inferred.owl" ]; then + ontoconvert -w "$d/emmo-inferred.ttl" "$d/emmo-inferred.owl" fi # Generate renamed ontology - if $remake || [ ! -f "$d/emmo-renamed.owl" ]; then - echo "Generate renamed ontology" - ontoconvert "$d/emmo-inferred.owl" "$d/emmo-renamed.owl" \ - -s -a -R -b http://emmo.info/emmo-renamed || true - fi - if $remake || [ ! -f "$d/emmo-renamed.ttl" ]; then - ontoconvert "$d/emmo-inferred.owl" "$d/emmo-renamed.ttl" \ - -s -a -R -b http://emmo.info/emmo-renamed || true - fi + #if $remake || [ ! -f "$d/emmo-renamed.owl" ]; then + # echo "Generate renamed ontology" + # ontoconvert "$d/emmo-inferred.ttl" "$d/emmo-renamed.owl" \ + # -w -R -b http://emmo.info/emmo-renamed || true + #fi + #if $remake || [ ! -f "$d/emmo-renamed.ttl" ]; then + # ontoconvert "$d/emmo-inferred.ttl" "$d/emmo-renamed.ttl" \ + # -w -R -b http://emmo.info/emmo-renamed || true + #fi # Generate documentation if $remake || [ ! -f "$d/emmo.html" ]; then echo "Generate documentation" - "$scriptsdir/makedoc.sh" "$d/emmo-inferred.owl" $version "$d" \ + "$scriptsdir/makedoc.sh" "$d/emmo-inferred.ttl" $version "$d" \ || true fi - # Create symlinks + # Create stable versions cd "$pagesdir" - if [ ! -z "$name" ]; then - rm -f $name - ln -sf versions/$version $name + if [ "$name" = "stable" ]; then + cp $d/*.ttl $d/*.owl . fi + done < "$ghdir/versions.txt" @@ -130,5 +130,5 @@ if [ -d "$tmpdir" ]; then fi -# Make sure that we exit with non-zero +# Make sure that we exit with zero on success exit 0 diff --git a/.github/versions.txt b/.github/versions.txt index 76b49fa5..07cf01a3 100644 --- a/.github/versions.txt +++ b/.github/versions.txt @@ -1,5 +1,5 @@ 1.0.0-beta5 development -1.0.0-beta4 +1.0.0-beta4 stable 1.0.0-beta3 1.0.0-beta2 1.0.0-beta diff --git a/.github/workflows/ci_emmocheck.yml b/.github/workflows/ci_emmocheck.yml index 515307d7..114e35d7 100644 --- a/.github/workflows/ci_emmocheck.yml +++ b/.github/workflows/ci_emmocheck.yml @@ -4,24 +4,24 @@ on: [push] jobs: build: - runs-on: ubuntu-18.04 + runs-on: ubuntu-latest strategy: max-parallel: 1 matrix: - python-version: [3.7] + python-version: [3.11] steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install EMMO-python + - name: Install EMMOntoPy run: | pip install --upgrade pip - pip install EMMO + pip install EMMOntoPy - name: Check EMMO run: | diff --git a/.github/workflows/ci_redirectioncheck.yml b/.github/workflows/ci_redirectioncheck.yml new file mode 100644 index 00000000..b3a35f72 --- /dev/null +++ b/.github/workflows/ci_redirectioncheck.yml @@ -0,0 +1,24 @@ +name: Check redirections +on: [push] + +jobs: + + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Setup Python 3.11 + uses: actions/setup-python@v5 + with: + python-version: 3.11 + + - name: Install EMMOntoPy + run: | + pip install --upgrade pip + pip install EMMOntoPy + + - name: Check redirections + run: | + redirectioncheck .github/expected_redirections.yaml diff --git a/.github/workflows/update_pages.yml b/.github/workflows/update_pages.yml index 555dfded..0c56ee3f 100644 --- a/.github/workflows/update_pages.yml +++ b/.github/workflows/update_pages.yml @@ -6,6 +6,7 @@ on: - '[0-9]+.[0-9]+.[0-9]+' - '[0-9]+.[0-9]+.[0-9]+-*' - update_pages + - fix-github-workflow jobs: @@ -13,17 +14,21 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Setup git identity run: | git config --global user.email "emmo.github.action@github.com" git config --global user.name "EMMO GitHub Action" - - name: Setup Python 3.7 - uses: actions/setup-python@v1 + - name: Setup Python 3.11 + uses: actions/setup-python@v5 with: - python-version: 3.7 + python-version: 3.11 + + - name: Debug info + run: | + echo "GITHUB_REF_NAME=${GITHUB_REF_NAME}" - name: Install EMMO-python run: | @@ -44,7 +49,7 @@ jobs: pip install semver - name: Checkout GitHub Pages for EMMO-repo - uses: actions/checkout@v2 + uses: actions/checkout@v4 with: repository: emmo-repo/emmo-repo.github.io path: ".github/pages" diff --git a/doc/emmodoc/classes.md b/doc/emmodoc/classes.md index 853c5706..c9c9f843 100644 --- a/doc/emmodoc/classes.md +++ b/doc/emmodoc/classes.md @@ -74,7 +74,7 @@ branch of mereotopology. -%BRANCHDOC PhysicalDimension rankdir=RL +%% %BRANCHDOC PhysicalDimension rankdir=RL %BRANCHDOC PhysicalQuantity %BRANCHDOC StandardizedPhysicalQuantity %BRANCHDOC CategorizedPhysicalQuantity @@ -92,7 +92,7 @@ branch of mereotopology. %BRANCHDOC Process -%BRANCHDOC Physicalistic +%% %BRANCHDOC Physicalistic %BRANCHDOC ElementaryParticle %BRANCHDOC Matter %BRANCHDOC Fluid