Merge branch 'master' into annotations

.github/emmocheck_conf.yml

@@ -0,0 +1,60 @@
+# 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.
+    - microstructure.
+
+
+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

.github/workflows/cd_ghpages.yml

@@ -0,0 +1,39 @@
+name: Deploy on GitHub Pages
+on:
+  push:
+    branches: [master]
+
+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
+
+    - name: Create squashed and inferred ontology
+      run: |
+        mkdir build
+        ontoconvert -saw --base-iri="https://w3id.org/emmo/domain/microstructure#" --iri="https://w3id.org/emmo/domain/microstructure" microstructure.ttl build/microstructure.ttl
+        #ontoconvert -saw --base-iri="https://w3id.org/emmo/domain/microstructure#" --iri="https://w3id.org/emmo/domain/microstructure" microstructure.ttl build/microstructure-inferred.ttl --infer=HermiT
+
+    - name: Deploy to GitHub Pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        folder: build
+        branch: gh-pages

.github/workflows/ci_tests.yml

@@ -0,0 +1,25 @@
+name: CI tests
+on: [push]
+
+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 microstructure.ttl

.gitignore

@@ -0,0 +1,2 @@
+*~
+build

README.md

@@ -1,11 +1,13 @@
-[![pipeline status](https://gitlab.com/sfi-physmet/platform/physmetontology/badges/master/pipeline.svg)](https://gitlab.com/sfi-physmet/platform/physmetontology/pipelines/latest)
+[![DOI](https://zenodo.org/badge/348298817.svg)](https://zenodo.org/badge/latestdoi/348298817)
 
 
-First draft of an EMMO-based ontology for physical metallurgy
-=============================================================
-This is intended to be a domain ontology for physical metallurgy.  The
-intension is to cover all relevant aspect of metallic microstructures,
-including
+Microstructure Domain Ontology
+==============================
+This is work in progress.
+
+The Microstructure Domain Ontology is intended to be a domain ontology
+for physical metallurgy.  The intension is to cover all relevant
+aspect of metallic microstructures, including:
   - composition
   - particles, both stable (primary) and metastable (precipitates)
   - grains
@@ -23,7 +25,7 @@ For modelling, we will distinguish between
     succession of states) and
   - property models (that relates a microstructure state to a property).
 
-It should support describing same concept at different spacial
+It should support describing same concept at different spatial
 resolutions, like mean field, 1D, 2D and 3D.
 
 For mean field descriptions (what about spatially resolved), it should
@@ -57,30 +59,38 @@ compatibilies:
 
 | Imported Ontologies  | Version           |
 | -------------------- | ----------------- |
-| [EMMO][1]            | 1.0.0-alpha2      |
+| [EMMO][1]            | 1.0.0-rc1         |
 | [crystallography][2] | 0.0.1             |
 
 
-Obtaining PhysMetOntology
--------------------------
-This repository include the correct version of the crystallography and
-mechanics domain ontologies as a git submodules.  Hence, use the
-following command when cloning this repository:
+Obtaining the Microstructure Domain Ontology
+--------------------------------------------
+The Microstructure Domain Ontology can be access or opened in Protege
+using the following url
+
+    https://w3id.org/emmo/domain/microstructure/source
+
+It can also be cloned from its [GitHub repository][3] using the `git`
+command:
+
+    git clone https://github.com/emmo-repo/domain-microstructure.git
 
-    git clone --recurse-submodules --shallow-submodules git@gitlab.com:sfi-physmet/platform/physmetontology.git
 
 
 Attributions and credits
 ------------------------
 ### Authors
-- Jesper Friis, SINTEF
-- Tomas Manik, NTNU
-- Sylvain Gouttenbroze, SINTEF
-- Astrid Marthinsen, SINTEF
+- Jesper Friis, SINTEF, Norway
+- Tomas Manik, NTNU, Norway
+- Sylvain Gouttenbroze, SINTEF, Norway
+- Astrid Marthinsen, SINTEF, Norway
+- Georg Schmitz, ACCESS, Germany
+- Ulrike Cihak-Bayr, AC2T, Austria
+
 
 ### Projects
 - Demystify ontologies - Internal project at [SINTEF](www.sintef.no)
-- SFI PhysMet
+- [SFI PhysMet](https://www.ntnu.edu/physmet)
 
 
 License
@@ -93,3 +103,6 @@ license (CC BY 4.0).
 
 [1]: https://github.com/emmo-repo/EMMO
 [2]: https://github.com/emmo-repo/domain-crystallography
+[3]: https://github.com/emmo-repo/domain-microstructure
+[github]: https://github.com/
+[github-ssh]: https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent

catalog-v001.xml

@@ -1,8 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
-    <uri id="Imports Wizard Entry" name="https://emmo-repo.github.io/versions/1.0.0-beta/emmo-inferred-chemistry/1.0.0-beta" uri="https://emmo-repo.github.io/versions/1.0.0-beta/emmo-inferred-chemistry2.ttl"/>
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
-        <uri name="http://emmo.info/physmet/0.0.1/physmet" uri="./physmet.ttl"/>
-        <uri name="http://emmo.info/crystallography/0.0.1/crystallography" uri="./crystallography/crystallography.ttl"/>
+        <uri name="https://w3id.org/emmo/domain/microstructure/0.3"            uri="./microstructure.ttl"/>
     </group>
 </catalog>