Upgrade base system to Ubuntu 24.04

Dockerfile

@@ -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

@@ -61,7 +61,7 @@ docs:
 	@ODK_IMAGE=odklite ./odk.sh python ./odk/schema_documentation.py
 
 # Building docker image
-VERSION = "v1.5"
+VERSION = "v1.6"
 IM=obolibrary/odkfull
 IMLITE=obolibrary/odklite
 ROB=obolibrary/robot
@@ -168,7 +168,7 @@ 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/*

constraints.txt

@@ -12,7 +12,6 @@ async-lru==2.0.4
 attrs==23.2.0
 Babel==2.15.0
 babelon==0.2.9
-backports.tarfile==1.2.0
 bcp47==0.1.0
 beautifulsoup4==4.12.3
 bidict==0.23.1
@@ -54,7 +53,6 @@ dosdp==0.1.10.dev1
 EditorConfig==0.12.4
 et-xmlfile==1.1.0
 eutils==0.6.0
-exceptiongroup==1.2.1
 executing==2.0.1
 fastjsonschema==2.20.0
 fastobo==0.12.3
@@ -292,12 +290,11 @@ sssom-schema==0.15.2
 stack-data==0.6.3
 stringcase==1.2.0
 tabulate==0.9.0
-tenacity==8.4.1
+tenacity==8.4.2
 termcolor==2.4.0
 terminado==0.18.1
 terminaltables==3.1.10
 tinycss2==1.3.0
-tomli==2.0.1
 tornado==6.4.1
 tox==4.15.1
 tqdm==4.66.4

docker/builder/Dockerfile

@@ -3,7 +3,7 @@
 # (typically because pre-compiled binaries don't exist for arm64) and
 # we don't want to build directly on the final image (to avoid
 # cluttering the image with build-time dependencies).
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 WORKDIR /build
 
 # Software versions
@@ -27,8 +27,7 @@ RUN apt-get update && \
         rustc \
         cargo \
         python3-dev \
-        python3-pip \
-        python3-virtualenv
+        python3-pip
 
 # Build the Python packages.
 # On x86_64, most if not all of these packages should be available as
@@ -45,6 +44,7 @@ COPY constraints.txt /build/constraints.txt
 RUN python3 -m pip install \
         -r /build/requirements.txt.lite \
         -c /build/constraints.txt \
+        --no-warn-script-location \
         --root /staging/lite
 # Then those needed by the odkfull image.
 # After installing those packages, we forcibly remove from the odkfull
@@ -54,6 +54,7 @@ RUN python3 -m pip install \
 RUN python3 -m pip install \
         -c /build/constraints.txt \
         -r /build/requirements.txt \
+        --no-warn-script-location \
         --root /staging/full && \
         cd /staging/lite && \
         find . -type f | while read f ; do rm -f /staging/full/$f ; done && \

docker/odklite/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 LABEL maintainer="[email protected]"
 
 ENV ROBOT_VERSION=1.9.6

docker/robot/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 LABEL maintainer="[email protected]" 
 
 WORKDIR /tools

odk/odk.py

@@ -778,7 +778,7 @@ class ExecutionContext(JsonSchemaMixin):
     project : Optional[OntologyProject] = None
     meta : str = ""
 
-    
+
 @dataclass
 class Generator(object):
     """
@@ -787,7 +787,7 @@ class Generator(object):
     """
 
     ## TODO: consider merging Generator and ExecutionContext?
-    context : ExecutionContext = ExecutionContext()
+    context : ExecutionContext = field(default_factory=ExecutionContext)
 
     def generate(self, input : str) -> str:
         """
@@ -1083,7 +1083,7 @@ def seed(config, clean, outdir, templatedir, dependencies, title, user, source,
         print(" 5. See the section under '…or push an existing repository from the command line'")
         print("    E.g.:")
         print("cd {}".format(outdir))
-        print("git remote add origin git\@github.com:{org}/{repo}.git".format(org=project.github_org, repo=project.repo))
+        print("git remote add origin [email protected]:{org}/{repo}.git".format(org=project.github_org, repo=project.repo))
         print("git branch -M {branch}\n".format(branch=project.git_main_branch))
         print("git push -u origin {branch}\n".format(branch=project.git_main_branch))
         print("BE BOLD: you can always delete your repo and start again\n")

update-constraints.sh

@@ -2,6 +2,11 @@
 
 set -e
 
+if [ "x$1" = x--install-virtualenv ]; then
+    apt-get update
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends python3-virtualenv
+fi
+
 virtualenv tmpdir
 . tmpdir/bin/activate
 python3 -m pip install -U pip