fix updated PROV-JSONLD via specific serializer for JSON-LD

[fmigneault]

Description

Replace the previous manual RDF-graph-patching workaround (vendored prov-jsonld-context.json + rdflib json-ld compaction) with a direct call to ProvDocument.serialize(format="jsonld"), now that prov>=3.1.0 implements the PROV-JSONLD submission natively and produces a proper {"@context": [...], "@graph": [...]} document.

• Bump prov==3.1.0 prov==3.2.2 dependency (requirements.txt, setup.py).
  • Removes the need for the typing stubs.
  • Thanks to the quick fix Typing needs refinement for additional attributes trungdong/prov#474, type cast are not needed anymore e5ae375 (this PR)
  • Patches a bool represenetation:
    prov:value="1" %% xsd:boolean becomes the more appropriate prov:value="true" %% xsd:boolean
• Keep emitting the direct prov:wasAssociatedWith shortcut triple in RDF-based serializations (ttl/nt/jsonld): prov 3.1.0's RDF serializer only emits it for associations with no extra qualifying attributes, so add an unqualified association alongside the plan-qualified one.
• Replace mentionOf/Mention (unsupported by the PROV-JSONLD submission) with an equivalent
  specializationOf plus a plain prov:asInBundle attribute, valid across all serializations.
• Bump CWLPROV_VERSION to 0.7.0 (breaking change to the emitted provenance graph shape for associations/directory mentions).
• Add more test coverage for CWL prov under certain code paths that were not evaluted.

References

• Closes Proper PROV JSON-LD structure #2345
• Relates to 2026-09-01 context/schema revision openprov/prov-jsonld#3
• Relates to Modernisation roadmap — tracking & feedback trungdong/prov#181

[codecov]

Codecov Report

❌ Patch coverage is 90.62500% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.56%. Comparing base (2655097) to head (8d62110).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
cwltool/cwlprov/provenance_profile.py	90.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2349      +/-   ##
==========================================
+ Coverage   85.27%   85.56%   +0.29%     
==========================================
  Files          46       46              
  Lines        8629     8640      +11     
  Branches     2022     2022              
==========================================
+ Hits         7358     7393      +35     
+ Misses        806      783      -23     
+ Partials      465      464       -1     

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[fmigneault]

@mr-c
What do you think of this update? It aligns with latest W3C PROV JSON-LD. Current contents are generated in a way that are not proper representations.

@stain
Would you be interested in back-porting this as cwlprov==0.7.0 since the reference will not exist otherwise.

[mr-c]

@fmigneault Can you open a draft PR to https://github.com/common-workflow-language/cwlprov/ for your proposed 0.7.0 version?

[mr-c]

@fmigneault Here is a patch to fix the Python 3.15 build; I guess you didn't check the "Allow edits from maintainers" box?

From c70987670773866adb7025be1e77ab1a4544710c Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Sat, 12 Sep 2026 11:43:29 +0200
Subject: [PATCH] adjust requirements to match
 https://prov.readthedocs.io/en/latest/upgrading-3.0.html

---
 requirements.txt | 4 ++--
 setup.py         | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index b4efc578..e837cabb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,8 +1,8 @@
 requests>=2.32.2
 ruamel.yaml>=0.16.0,<0.20
-rdflib>=4.2.2,<7.7
+rdflib>=7,<7.7
 schema-salad>=8.10,<9
-prov==3.1.0
+prov[xml,rdf]>=3.1.0,<3.2
 mypy-extensions
 psutil>=5.6.6
 coloredlogs
diff --git a/setup.py b/setup.py
index 58ed3e48..7023ed6d 100644
--- a/setup.py
+++ b/setup.py
@@ -151,9 +151,9 @@ setup(
         "requests >= 2.6.1",  # >= 2.6.1 to workaround
         # https://github.com/ionrock/cachecontrol/issues/137
         "ruamel.yaml >= 0.16, < 0.20",
-        "rdflib >= 4.2.2, < 7.7.0",
+        "rdflib >= 7, < 7.7.0",
         "schema-salad >= 8.10, < 9",
-        "prov == 3.1.0",
+        "prov[xml,rdf] >= 3.1.0, < 3.2",
         "mypy-extensions",
         "psutil >= 5.6.6",
         "coloredlogs",
-- 
2.47.3

[fmigneault]

I guess you didn't check the "Allow edits from maintainers" box?

The option is not there. Maybe because it is in draft?

[mr-c]

I guess you didn't check the "Allow edits from maintainers" box?

The option is not there. Maybe because it is in draft?

As @CGuichard discovered, that option isn't available when your fork is from an organization.

Can you apply the changes from #2349 (comment) and merge/rebase with the latest from main?

[fmigneault]

@mr-c
Ready for re-review.
I've opened corresponding:

• Prepare CWLPROV 0.7.0 (impl) cwlprov-py#49
• Prepare CWLPROV 0.7.0 (doc) cwlprov#5

Let me know if anything else needs adjustment.

[fmigneault]

@mr-c
I've added some extra coverage tests for the CWL PROV module. There is 1 failing job in the CI that I am not sure if it is a sporadic docker pull problem or another actual problem to address. Can you check?