Merge pull request #1113 from INCATools/prepare-odk-1.5.3

Prepare ODK 1.5.3

CHANGELOG.md

@@ -1,3 +1,22 @@
+# v1.5.3
+
+- Updates:
+    - Base image updated to Ubuntu 24.04
+    - Python updated to version 3.12
+    - Several Python packages updated, including:
+        - `oaklib` (OAK) 0.6.18
+        - `linkml` 1.8.5 and `linkml-runtime` 1.8.3
+        - `sssom-schema` 1.0.0 and `sssom` 0.4.12
+    - KGCL plugin for ROBOT updated to version 0.5.0
+    - SSSOM command-line tool and plugin
+- Bugfixes:
+    - Fix permission issue on macOS when seeding ([#1105](https://github.com/INCATools/ontology-development-kit/issues/1105))
+    - Fix permission on the SSH socket ([#1096](https://github.com/INCATools/ontology-development-kit/issues/1096))
+    - Fix lack of robustness of the odk.py script ([#1097](https://github.com/INCATools/ontology-development-kit/issues/1097))
+
+BREAKING CHANGE: [J2cli](https://github.com/kolypto/j2cli), which is no longer maintained, has been removed and replaced with [Jinjanator](https://github.com/kpfleming/jinjanator). Standard ODK-generated workflows never used that tool, but if you have custom workflows that are using the `j2` command, you will need to update them to make them use `jinjanate` instead.
+
+
 # v1.5.2
 
 This version updates the Ontology Access Kit (`oaklib`) to improve
@@ -16,6 +35,7 @@ compatibility with the OWLAPI version 4.5.29 used in ROBOT 1.9.6.
     - Added back `class-count-by-prefix.sparql` ([https://github.com/INCATools/ontology-development-kit/issues/1030](#1030))
     - Disabled `table-reader` mkdocs plygin ([https://github.com/INCATools/ontology-development-kit/issues/1028](#1028))
 
+
 # v1.5
 
 For more detailed changes see:

Dockerfile

@@ -11,8 +11,8 @@ ENV ODK_VERSION $ODK_VERSION
 
 # Software versions
 ENV JENA_VERSION=4.9.0
-ENV KGCL_JAVA_VERSION=0.4.0
-ENV SSSOM_JAVA_VERSION=0.7.7
+ENV KGCL_JAVA_VERSION=0.5.0
+ENV SSSOM_JAVA_VERSION=0.9.0
 
 # Avoid repeated downloads of script dependencies by mounting the local coursier cache:
 # docker run -v $HOME/.coursier/cache/v1:/tools/.coursier-cache ...
@@ -40,9 +40,11 @@ RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-i
     xlsx2csv \
     gh \
     nodejs \
+    npm \
     graphviz \
     python3-psycopg2 \
-    swi-prolog
+    swi-prolog \
+    libpcre3
 
 # Install run-time dependencies for Soufflé.
 RUN DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends \
@@ -95,7 +97,7 @@ COPY scripts/obodash /tools
 RUN chmod +x /tools/obodash && \
     git clone --depth 1 https://github.com/OBOFoundry/OBO-Dashboard.git && \
     cd OBO-Dashboard && \
-    python3 -m pip install -r requirements.txt && \
+    python3 -m pip install -r requirements.txt --break-system-packages && \
     echo " " >> Makefile && \
     echo "build/robot.jar:" >> Makefile && \
     echo "	echo 'skipped ROBOT jar download.....' && touch \$@" >> Makefile && \

Makefile

@@ -35,6 +35,7 @@ test_odklite_programs:
 	@./tests/test-program.sh DOSDP-TOOLS dosdp-tools -v
 	@./tests/test-program.sh OWLTOOLS owltools --version
 	@./tests/test-program.sh AMMONITE sh amm --help
+	@./tests/test-program.sh JINJANATOR jinjanate --version
 	@./tests/test-program.sh ODK odk.py
 
 test_odkfull_programs: test_odklite_programs
@@ -61,7 +62,7 @@ docs:
 	@ODK_IMAGE=odklite ./odk.sh python ./odk/schema_documentation.py
 
 # Building docker image
-VERSION = "v1.5.2"
+VERSION = "v1.5.3"
 IM=obolibrary/odkfull
 IMLITE=obolibrary/odklite
 ROB=obolibrary/robot
@@ -168,7 +169,7 @@ publish-multiarch-dev:
 		.
 
 constraints.txt: requirements.txt.full
-	docker run -v $$PWD:/work -w /work --rm -ti obolibrary/odkbuild:latest /work/update-constraints.sh
+	docker run -v $$PWD:/work -w /work --rm -ti obolibrary/odkbuild:latest /work/update-constraints.sh --install-virtualenv
 
 clean-tests:
 	rm -rf target/*