Merge branch 'main' of https://github.com/hubmapconsortium/hra-do-pro…

…cessor

Dockerfile

@@ -18,7 +18,7 @@ RUN apt-get update && \
 
 COPY scripts scripts
 COPY schemas schemas
-COPY requirements.txt package.json package-lock.json /build/
+COPY requirements.txt requirements-freeze.txt package.json package-lock.json /build/
 
 RUN ./scripts/setup-environment.sh /venv
 

requirements-freeze.txt

@@ -0,0 +1,108 @@
+annotated-types==0.6.0
+antlr4-python3-runtime==4.9.3
+argcomplete==3.1.6
+arrow==1.3.0
+attrs==23.1.0
+bcp47==0.0.4
+CacheControl==0.13.1
+cachetools==5.3.2
+certifi==2023.11.17
+CFGraph==0.2.1
+chardet==5.2.0
+charset-normalizer==3.3.2
+check-jsonschema==0.27.2
+click==8.1.7
+colorama==0.4.6
+coloredlogs==15.0.1
+curies==0.7.4
+cwl-upgrader==1.2.10
+cwl-utils==0.31
+cwltool==3.1.20231114134824
+Deprecated==1.2.14
+distlib==0.3.7
+et-xmlfile==1.1.0
+exceptiongroup==1.2.0
+filelock==3.13.1
+fqdn==1.5.1
+funowl==0.2.3
+graphviz==0.20.1
+greenlet==3.0.1
+hbreader==0.9.1
+humanfriendly==10.0
+idna==3.6
+importlib-resources==6.1.1
+iniconfig==2.0.0
+isodate==0.6.1
+isoduration==20.11.0
+Jinja2==3.1.2
+json-flattener==0.1.9
+jsonasobj==1.3.1
+jsonasobj2==1.0.4
+jsonpatch==1.33
+jsonpath-ng==1.6.0
+jsonpointer==2.4
+jsonschema==4.20.0
+jsonschema-specifications==2023.11.1
+linkml==1.6.3
+linkml-dataops==0.1.0
+linkml-runtime==1.6.2
+linkml_owl @ git+https://github.com/linkml/linkml-owl@3ea977a73d68624e4be94793e69acc79a2672c29
+lxml==4.9.3
+MarkupSafe==2.1.3
+mistune==2.0.5
+msgpack==1.0.7
+mypy-extensions==1.0.0
+networkx==3.2.1
+nodeenv==1.8.0
+openpyxl==3.1.2
+packaging==23.2
+parse==1.20.0
+platformdirs==4.0.0
+pluggy==1.3.0
+ply==3.11
+prefixcommons==0.1.12
+prefixmaps==0.2.0
+prov==1.5.1
+psutil==5.9.6
+pydantic==2.5.2
+pydantic_core==2.14.5
+pydot==1.4.2
+PyJSG==0.11.10
+pyparsing==3.1.1
+pyproject-api==1.6.1
+PyShEx==0.8.1
+PyShExC==0.9.1
+pytest==7.4.3
+pytest-logging==2015.11.4
+python-dateutil==2.8.2
+PyTrie==0.4.0
+PyYAML==6.0.1
+rdflib==7.0.0
+rdflib-jsonld==0.6.1
+rdflib-shim==1.0.3
+referencing==0.31.0
+regress==0.4.2
+requests==2.31.0
+rfc3339-validator==0.1.4
+rfc3987==1.3.8
+rpds-py==0.13.1
+ruamel.yaml==0.18.5
+ruamel.yaml.clib==0.2.8
+schema-salad==8.4.20231117150958
+shellescape==3.8.1
+ShExJSG==0.8.2
+six==1.16.0
+sortedcontainers==2.4.0
+sparqlslurper==0.5.1
+SPARQLWrapper==2.0.0
+SQLAlchemy==2.0.23
+tomli==2.0.1
+tox==4.11.4
+types-python-dateutil==2.8.19.14
+typing_extensions==4.8.0
+uri-template==1.3.0
+urllib3==2.1.0
+virtualenv==20.24.7
+watchdog==3.0.0
+webcolors==1.13
+wrapt==1.16.0

scripts/setup-environment.sh

@@ -33,8 +33,9 @@ if [ -e "$ENV/bin/activate" ]; then
   set -u
 
   # Install python deps
-  python -m pip install -r "$ROOT_DIR/requirements.txt"
+  python -m pip install -r "$ROOT_DIR/requirements-freeze.txt"
   python -m pip install "cwltool"
+  python -m pip cache purge
 
   # Install Robot
   if [ ! -e "$ENV/bin/robot" ]; then