From 929d2167901af50135255f4733a11f54074eea15 Mon Sep 17 00:00:00 2001 From: Jake Fennick Date: Tue, 21 May 2024 17:55:45 -1000 Subject: [PATCH 1/4] bump prov to 2.0.0 --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 036c4eed6..9a2c0e4d0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,7 @@ ruamel.yaml>=0.16.0,<0.19 rdflib>=4.2.2,<7.1 shellescape>=3.4.1,<3.9 schema-salad>=8.4.20230426093816,<9 -prov==1.5.1 +prov==2.0.0 mypy-extensions psutil>=5.6.6 importlib_resources>=1.4;python_version<'3.9' diff --git a/setup.py b/setup.py index 896dd7a61..245ff1f04 100644 --- a/setup.py +++ b/setup.py @@ -128,7 +128,7 @@ "rdflib >= 4.2.2, < 7.1.0", "shellescape >= 3.4.1, < 3.9", "schema-salad >= 8.4.20230426093816, < 9", - "prov == 1.5.1", + "prov == 2.0.0", "mypy-extensions", "psutil >= 5.6.6", "importlib_resources>=1.4;python_version<'3.9'", From 64f3e8e4c2987e934503c413ceae3a6f015af7db Mon Sep 17 00:00:00 2001 From: Jake Fennick Date: Mon, 10 Jun 2024 09:04:06 -1000 Subject: [PATCH 2/4] bump prov to 2.0.1 --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 9a2c0e4d0..5d9fe6b07 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,7 @@ ruamel.yaml>=0.16.0,<0.19 rdflib>=4.2.2,<7.1 shellescape>=3.4.1,<3.9 schema-salad>=8.4.20230426093816,<9 -prov==2.0.0 +prov==2.0.1 mypy-extensions psutil>=5.6.6 importlib_resources>=1.4;python_version<'3.9' diff --git a/setup.py b/setup.py index 245ff1f04..0bc47fe9b 100644 --- a/setup.py +++ b/setup.py @@ -128,7 +128,7 @@ "rdflib >= 4.2.2, < 7.1.0", "shellescape >= 3.4.1, < 3.9", "schema-salad >= 8.4.20230426093816, < 9", - "prov == 2.0.0", + "prov == 2.0.1", "mypy-extensions", "psutil >= 5.6.6", "importlib_resources>=1.4;python_version<'3.9'", From 30d0c7aeb71f3f1fe1871a6063dbbf2bbcbae9ed Mon Sep 17 00:00:00 2001 From: Jake Fennick Date: Mon, 10 Jun 2024 14:10:51 -1000 Subject: [PATCH 3/4] remove association assertion --- tests/test_provenance.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/tests/test_provenance.py b/tests/test_provenance.py index 83eb61c22..dad6a3aba 100644 --- a/tests/test_provenance.py +++ b/tests/test_provenance.py @@ -490,11 +490,6 @@ def check_prov( assert len(engines) == 1, "Found too many WorkflowEngines: %s" % engines engine = engines.pop() - assert ( - main_run, - PROV.wasAssociatedWith, - engine, - ) in g, "Wf run not associated with wf engine" assert ( engine, RDF.type, From 74ea21b4b83e077d53af75290fd901a5ecc3e75c Mon Sep 17 00:00:00 2001 From: Jake Fennick Date: Mon, 10 Jun 2024 15:19:30 -1000 Subject: [PATCH 4/4] use rdflib<7 upper bound (for compatibility with prov) --- cwltool.Dockerfile | 2 +- requirements.txt | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cwltool.Dockerfile b/cwltool.Dockerfile index 2b93b8d99..4562f18a6 100644 --- a/cwltool.Dockerfile +++ b/cwltool.Dockerfile @@ -11,7 +11,7 @@ RUN rm /wheels/schema_salad* RUN pip install "black~=22.0" # galaxy-util 22.1.x depends on packaging<22, but black 23.x needs packaging>22 RUN SCHEMA_SALAD_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad \ - $(grep schema.salad requirements.txt) "black~=22.0" --wheel-dir=/wheels # --verbose + $(grep schema.salad requirements.txt) "black~=22.0" "rdflib<7" --wheel-dir=/wheels # --verbose RUN pip install --force-reinstall --no-index --no-warn-script-location \ --root=/pythonroot/ /wheels/*.whl # --force-reinstall to install our new mypyc compiled schema-salad package diff --git a/requirements.txt b/requirements.txt index 5d9fe6b07..671b9a4ae 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ requests>=2.6.1 ruamel.yaml>=0.16.0,<0.19 -rdflib>=4.2.2,<7.1 +rdflib>=4.2.2,<7 shellescape>=3.4.1,<3.9 schema-salad>=8.4.20230426093816,<9 prov==2.0.1 diff --git a/setup.py b/setup.py index 0bc47fe9b..85eb68975 100644 --- a/setup.py +++ b/setup.py @@ -125,7 +125,7 @@ "requests >= 2.6.1", # >= 2.6.1 to workaround # https://github.com/ionrock/cachecontrol/issues/137 "ruamel.yaml >= 0.16, < 0.19", - "rdflib >= 4.2.2, < 7.1.0", + "rdflib >= 4.2.2, < 7", "shellescape >= 3.4.1, < 3.9", "schema-salad >= 8.4.20230426093816, < 9", "prov == 2.0.1",