Merge branch 'master' into importskip

SINTEF · Dec 14, 2024 · 225b9e7 · 225b9e7
2 parents 3a0e299 + 9890759
commit 225b9e7
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diff --git a/.github/workflows/cd_release.yml b/.github/workflows/cd_release.yml
@@ -80,55 +80,31 @@ jobs:
           - os: ubuntu-20.04
             system_type: ["manylinux", "_2_34"]
             arch: x86_64
-            py_minors: 8,9,10,11,12
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2014"]
-          #  arch: x86_64
-          #  py_minors: 8,9,10,11,12
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2010"]
-          #  arch: x86_64
-          #  py_minors: 8,9
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "_2_28"]
-          #  arch: x86_64
-          #  py_minors: 8,9,10,11,12
+            py_minors: 8,9,10,11,12,13
 
           # 64-bit musllinux
           - os: ubuntu-20.04
             system_type: ["musllinux", "_1_2"]
             arch: x86_64
-            py_minors: 8,9,10,11
-          #- os: ubuntu-20.04
-          #  system_type: ["musllinux", "_1_1"]
-          #  arch: x86_64
-          #  py_minors: 8,9,10,11
+            py_minors: 8,9,10,11,12,13
 
           # 32-bit manylinux
           - os: ubuntu-20.04
             system_type: ["manylinux", "2014"]
             arch: i686
-            py_minors: 10,11
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2014"]
-          #  arch: i686
-          #  py_minors: 8,9,10,11
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2010"]
-          #  arch: i686
-          #  py_minors: 8,9
+            py_minors: 10,11,12,13
 
           # 32-bit musllinux
           - os: ubuntu-20.04
             system_type: ["musllinux", "_1_2"]
             arch: i686
-            py_minors: 8,9,10,11
+            py_minors: 9,10,11
 
           # 64-bit Windows
           - os: windows-2019
             system_type: ["win", ""]
             arch: amd64
-            py_minors: '8,9,10,11,12'
+            py_minors: '8,9,10,11,12,13'
 
           # 32-bit Windows
 

diff --git a/.github/workflows/ci_build_wheels.yml b/.github/workflows/ci_build_wheels.yml
@@ -22,68 +22,41 @@ jobs:
           - os: ubuntu-20.04
             system_type: ["manylinux", "_2_34"]
             arch: x86_64
-            py_minors: 8,12
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "_2_28"]
-          #  arch: x86_64
-          #  py_minors: 8,12
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2014"]
-          #  arch: x86_64
-          #  py_minors: 8,12
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2010"]
-          #  arch: x86_64
-          #  py_minors: 8,9
+            py_minors: 8,13
 
           # 64-bit musllinux
           - os: ubuntu-20.04
             system_type: ["musllinux", "_1_2"]
             arch: x86_64
-            py_minors: 8,11
-          # Python 3.12 fails since cibuildwheel still depends on distutils
-          # for musllinux
-          #- os: ubuntu-20.04
-          #  system_type: ["musllinux", "_1_1"]
-          #  arch: x86_64
-          #  py_minors: 8,11
+            py_minors: 8,13
 
           # 32-bit manylinux
+          # Python 3.8 does not have numpy2
           - os: ubuntu-20.04
             system_type: ["manylinux", "2014"]
             arch: i686
-            py_minors: 10,12
-          # Python 3.12 fails since cibuildwheel still depends on distutils
-          # for musllinux
-          #- os: ubuntu-20.04
-          #  system_type: ["manylinux", "2010"]
-          #  arch: i686
-          #  py_minors: 8,9
+            py_minors: 10,13
 
           # 32-bit musllinux
+          # Python 3.8 does not have numpy2
+          # Python 3.12 fails since cibuildwheel still depends on distutils
           - os: ubuntu-20.04
             system_type: ["musllinux", "_1_2"]
             arch: i686
-            py_minors: 8,11
-          # Python 3.12 fails since cibuildwheel still depends on distutils
-          # for musllinux
-          #- os: ubuntu-20.04
-          #  system_type: ["musllinux", "_1_1"]
-          #  arch: i686
-          #  py_minors: 8,11
+            py_minors: 9,11
 
           # 64-bit Windows
           - os: windows-2019
             system_type: ["win", ""]
             arch: amd64
-            py_minors: 8,12
+            py_minors: 8,13
 
           # 32-bit Windows
           # See issue #220: https://github.com/SINTEF/dlite/issues/220
           # - os: windows-2019
           #   system_type: ["win32", ""]
           #   arch: ""
-          #   py_minors: 7,10
+          #   py_minors: 8,13
 
           # 64-bit (Intel) macOS
           # See issue #221: https://github.com/SINTEF/dlite/issues/221

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@
 cmake_minimum_required(VERSION 3.14)
 
 project(dlite
-  VERSION 0.5.24
+  VERSION 0.5.26
   DESCRIPTION "Lightweight data-centric framework for semantic interoperability"
   HOMEPAGE_URL "https://github.com/SINTEF/dlite"
   LANGUAGES C

diff --git a/bindings/python/dataset.py b/bindings/python/dataset.py
@@ -27,7 +27,7 @@
 
 # XXX TODO - Make a local cache of EMMO such that we only download it once
 TS_EMMO = Triplestore("rdflib")
-TS_EMMO.parse("https://w3id.org/emmo/1.0.0-rc1")
+TS_EMMO.parse("https://w3id.org/emmo/1.0.0-rc3")
 
 EMMO_VERSIONIRI = TS_EMMO.value("https://w3id.org/emmo", OWL.versionIRI)
 
@@ -38,6 +38,15 @@
     triplestore=TS_EMMO,
 )
 
+# XXX TODO: Switch to EMMO.hasDimension when this relation is in EMMO.
+#           Please don't change the IRI when adding it.
+#Dimension = EMMO.Dimension
+Dimension = "https://w3id.org/emmo#EMMO_b4c97fa0_d82c_406a_bda7_597d6e190654"
+#hasDimension = EMMO.hasDimension
+hasDimension = "https://w3id.org/emmo#EMMO_0a9ae0cb_526d_4377_9a11_63d1ce5b3499"
+#hasScalarData = EMMO.hasScalarData
+hasScalarData = "https://w3id.org/emmo#EMMO_e5a34647_a955_40bc_8d81_9b784f0ac527"
+
 EMMO_TYPES = {
     "blob": "BinaryData",
     "bool": "BooleanData",
@@ -133,7 +142,7 @@ def get_shape(ts, dimiri, dimensions=None, mappings=None, uri=None):
                 label = str(obj)
             elif pred == EMMO.elucidation:
                 descr = str(obj)
-            elif pred == RDF.type and obj not in (EMMO.Dimension,):
+            elif pred == RDF.type and obj not in (Dimension,):
                 mapsto.append(obj)
         if not label:
             raise KBError("dimension has no prefLabel:", dimiri)
@@ -160,7 +169,7 @@ def get_unit_symbol(iri):
     symbol = TS_EMMO.value(iri, EMMO.unitSymbol)
     if symbol:
         return str(symbol)
-    for r in TS_EMMO.restrictions(iri, EMMO.hasSymbolValue, type="value"):
+    for r in TS_EMMO.restrictions(iri, EMMO.unitSymbolValue, type="value"):
         symbol = r["value"]
         if symbol:
             return str(symbol)
@@ -189,7 +198,7 @@ def get_unit_iri(unit):
         for r, _, o in ts.triples(predicate=OWL.hasValue):
             if (
                     ts.has(r, RDF.type, OWL.Restriction) and
-                    ts.has(r, OWL.onProperty, EMMO.hasSymbolValue)
+                    ts.has(r, OWL.onProperty, EMMO.unitSymbolValue)
             ):
                 s = ts.value(predicate=RDFS.subClassOf, object=r)
                 unit_cache[o.value] = s
@@ -289,7 +298,7 @@ def addmap(uri, iri):
             triples.extend([
                 (prop_iri, RDFS.subClassOf, restriction_iri),
                 (restriction_iri, RDF.type, OWL.Restriction),
-                (restriction_iri, OWL.onProperty, EMMO.hasScalarData),
+                (restriction_iri, OWL.onProperty, hasScalarData),
                 (restriction_iri, OWL.someValuesFrom, EMMO[emmotype]),
             ])
         else:
@@ -304,13 +313,13 @@ def addmap(uri, iri):
                 (prop_iri, RDFS.subClassOf, EMMO.Array),
                 (prop_iri, RDFS.subClassOf, restriction_iri),
                 (restriction_iri, RDF.type, OWL.Restriction),
-                (restriction_iri, OWL.onProperty, EMMO.hasDimension),
+                (restriction_iri, OWL.onProperty, hasDimension),
             ])
             for i, dim in enumerate(prop.shape):
                 dim_iri = f"{iri}#{prop.name}_dimension{i}"
                 addmap(f"{meta.uri}#{dim}", dim_iri)
                 triples.extend([
-                    (dim_iri, RDF.type, EMMO.Dimension),
+                    (dim_iri, RDF.type, Dimension),
                     (dim_iri, EMMO.hasSymbolValue,
                      Literal(dim, datatype=XSD.string)),
                     (dim_iri, EMMO.elucidation, en(dim_descr[dim])),
@@ -448,9 +457,9 @@ def get_dataset(
                         someval = po.get(OWL.someValuesFrom)
                         if onprop == EMMO.hasMeasurementUnit:
                             unit = get_unit_symbol(oncls)
-                        elif onprop == EMMO.hasScalarData:
+                        elif onprop == hasScalarData:
                             emmotype = emmotypes[someval]
-                        elif onprop == EMMO.hasDimension:
+                        elif onprop == hasDimension:
                             shape = get_shape(
                                 ts, onval, dimensions, mappings, uri
                             )

diff --git a/bindings/python/dlite-entity-python.i b/bindings/python/dlite-entity-python.i
@@ -183,7 +183,7 @@ def get_instance(
                 if "meta" not in d or d["meta"] == dlite.ENTITY_SCHEMA:
                     if "dimensions" not in d:
                         d["dimensions"] = {}
-            inst = Instance.from_dict(d)
+                inst = Instance.from_dict(d)
 
     if inst is None:
         raise _dlite.DLiteMissingInstanceError(f"no such instance: {id}")

diff --git a/bindings/python/tests/test_dataset1_save.py b/bindings/python/tests/test_dataset1_save.py
@@ -62,7 +62,7 @@
     (FLUID.LJPotential,      EMMO.isDescriptionFor, EMMO.MolecularEntity),
     (FLUID.TemperatureField, MAP.mapsTo, EMMO.ThermodynamicTemperature),
     (FLUID.ntimes,           MAP.mapsTo, EMMO.Time),
-    (FLUID.npositions,       MAP.mapsTo, EMMO.Position),
+    (FLUID.npositions,       MAP.mapsTo, EMMO.PositionVector),
 ]
 #add_dataset(ts, chem.meta, base_iri=base_iri)
 add_dataset(ts, Fluid, iri=EX.FluidData, mappings=mappings)

diff --git a/bindings/python/tests/test_dataset2_load.py b/bindings/python/tests/test_dataset2_load.py
@@ -44,7 +44,7 @@
     (FLUID.LJPotential,      EMMO.isDescriptionFor, EMMO.MolecularEntity),
     (FLUID.TemperatureField, MAP.mapsTo, EMMO.ThermodynamicTemperature),
     (FLUID.ntimes,           MAP.mapsTo, EMMO.Time),
-    (FLUID.npositions,       MAP.mapsTo, EMMO.Position),
+    (FLUID.npositions,       MAP.mapsTo, EMMO.PositionVector),
 }
 
 

diff --git a/doc/getting_started/installation.md b/doc/getting_started/installation.md
@@ -32,14 +32,13 @@ DLite uses [cibuildwheel] for providing binary releases for Linux and
 Windows on various platforms and versions of Python.  The provided
 wheels are shown in the following table.
 
-
-| Platform         | Arch   | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 |
-|------------------|--------|-----|-----|------|------|------|
-| [manylinux_2_34] | x86_64 | x   | x   | x    | x    | x    |
-| [manylinux2014]  | i686   |     |     | x    | x    | x    |
-| [musllinux_1_2]  | x86_64 | x   | x   | x    | x    | x    |
-| [musllinux_1_2]  | i686   |     | x   | x    | x    |      |
-| windows          | x86_64 | x   | x   | x    | x    | x    |
+| Platform         | Arch   | 3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 |
+|------------------|--------|-----|-----|------|------|------|------|
+| [manylinux_2_34] | x86_64 | x   | x   | x    | x    | x    | x    |
+| [manylinux2014]  | i686   |     |     | x    | x    | x    | x    |
+| [musllinux_1_2]  | x86_64 | x   | x   | x    | x    | x    | x    |
+| [musllinux_1_2]  | i686   |     | x   | x    | x    |      |      |
+| windows          | x86_64 | x   | x   | x    | x    | x    | x    |
 
 
 Development installation

diff --git a/python/pyproject.toml b/python/pyproject.toml
@@ -1,23 +1,13 @@
 [build-system]
 requires = [
-  "setuptools>=58",
-  "wheel>=0.37",
   "numpy>=1.14.5,<2.1.3",
+  "swig==4.3.0",
   "cmake==3.31.1",
-  "swig==4.1.1",
+  #"setuptools==57.5.0; python_version<'3.9'",
+  #"setuptools==75.3.0; python_version>='3.9'",
+  "setuptools==75.3.0",
+  "wheel==0.41.3",
 ]
-
-
-#requires = [
-#  #"setuptools>=58; python_version<'3.12'",
-#  #"wheel>=0.37; python_version<'3.12'",
-#  "setuptools==67.6.1; python_version<'3.9'",
-#  "setuptools>=68.2.1; python_version>='3.9'",
-#  "wheel>=0.37",
-#  "numpy>=1.14.5,<2.1.3",
-#  "cmake==3.31.1",
-#  "swig==4.1.1",
-#]
 build-backend = "setuptools.build_meta"
 
 [tool.cibuildwheel]
@@ -31,12 +21,10 @@ test-command = "python {package}\\..\\bindings\\python\\tests\\test_python_bindi
 [tool.cibuildwheel.linux]
 environment-pass = ["CI_BUILD_CMAKE_ARGS", "CI_PIP_CACHE_DIR"]
 before-build = [
-  #"python -m pip install --cache-dir /ci/pip_cache --prefer-binary -r {project}/requirements.txt -r {project}/requirements_dev.txt",
   "rm -rf {project}/python/build/temp*",
   "export PYVER=$(python -c \"import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')\")",
   "export ABITAG=$(python -c \"import sys; cp=f'cp{sys.version_info.major}{sys.version_info.minor}'; print(f'{cp}-{cp}{sys.abiflags}')\")",
 ]
-before-test = "python -m pip install --cache-dir /ci/pip_cache --prefer-binary -r {project}/requirements.txt"
 test-command = "python {package}/../bindings/python/tests/test_python_bindings.py"
 
 [tool.cibuildwheel.linux.environment]

diff --git a/python/setup.py b/python/setup.py
@@ -215,6 +215,7 @@ def run(self):
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
         "Topic :: Software Development :: Libraries :: Python Modules",
     ],
     build_requires=requirements_dev,

diff --git a/requirements_dev.txt b/requirements_dev.txt
@@ -1,8 +1,10 @@
 # Requirements building
 swig==4.3.0
 cmake==3.31.1
-setuptools==67.6.1; python_version<"3.9"
-setuptools>=68.2.1; python_version>="3.9"
+#setuptools==67.5.0; python_version<"3.9"
+#setuptools==75.3.0; python_version>="3.9"
+setuptools==75.3.0
+wheel==0.41.3
 
 # Requirements for running tests
-mongomock>=4.1.2,<5
+mongomock==4.2.0.post1