From 929d2167901af50135255f4733a11f54074eea15 Mon Sep 17 00:00:00 2001
From: Jake Fennick <jake.fennick@axleinfo.com>
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 <jake.fennick@axleinfo.com>
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 <jake.fennick@axleinfo.com>
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 <jake.fennick@axleinfo.com>
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",