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Move file virtualization in toil-wdl-runner to task boundaries #5028

Merged
merged 56 commits into from
Oct 1, 2024
Merged

Move file virtualization in toil-wdl-runner to task boundaries #5028

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89c276a
Defer file virtualization to task boundaries and consolidate decl eva…
stxue1 Jul 19, 2024
c85f173
Implement support for importing relative URL paths; import files at s…
stxue1 Jul 24, 2024
230efa0
Fix possible invalid lookup and don't import raw URLs
stxue1 Jul 24, 2024
2955bc3
Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
stxue1 Jul 24, 2024
066f780
Get rid of sentinel value implementation + drop files before virtuali…
stxue1 Jul 24, 2024
d5365a2
Drop missing files during decl eval for outputs + Add a check for inv…
stxue1 Jul 25, 2024
bbb098d
Deal with mypy
stxue1 Jul 25, 2024
1b6bd02
Don't drop unnecesssarily
stxue1 Jul 25, 2024
f65d59c
Switch to setattr implementation
stxue1 Aug 20, 2024
be0203e
Fix overwriting files
stxue1 Aug 20, 2024
f60d475
Fix prototype implementation
stxue1 Aug 22, 2024
552ac74
Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
stxue1 Aug 23, 2024
8163c2c
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Aug 27, 2024
4bbe63d
Fix documentation
stxue1 Aug 23, 2024
05dc240
Merge branch 'issues/5004-wdl-virtualize-only-at-task-boundaries' of …
stxue1 Aug 27, 2024
a6b18c7
Resolve nested virtualize files issue by converting back to original …
stxue1 Aug 29, 2024
94da9af
Fix virtualization of URLs that aren't toil URIs
stxue1 Aug 29, 2024
644fd51
Mypy
stxue1 Aug 29, 2024
d5bedee
Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
stxue1 Aug 29, 2024
f8c0ef1
Remove documentation that no longer applies
stxue1 Aug 29, 2024
6365b34
Fix merge conflict issue
stxue1 Aug 29, 2024
0a35c53
Enable symlink conformance test
stxue1 Aug 29, 2024
ce21051
whitespace
stxue1 Aug 29, 2024
343d6d8
Fix virtualize/devirtualize_filename to be called only during command…
stxue1 Aug 31, 2024
f5f3eea
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 3, 2024
37efd55
Add documentation and make convert_files function import greedily
stxue1 Sep 6, 2024
491ba1b
Get rid of memoization as File is not hashable (I believe inside LRU)
stxue1 Sep 10, 2024
8569a81
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 10, 2024
731120d
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 10, 2024
b25c80d
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 12, 2024
ffb2e08
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 16, 2024
7f17413
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 16, 2024
82383ab
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 16, 2024
a7292be
Apply suggestions from code review
stxue1 Sep 17, 2024
e6718cd
Update src/toil/wdl/wdltoil.py
stxue1 Sep 18, 2024
2ad130f
Rename, add comments, remove unused code/comments
stxue1 Sep 18, 2024
cb8b230
Merge branch 'issues/5004-wdl-virtualize-only-at-task-boundaries' of …
stxue1 Sep 18, 2024
b0db027
Add comments and adjust wdl context usage
stxue1 Sep 18, 2024
8c24d8f
add namespace
stxue1 Sep 19, 2024
666aef5
integrate namespace into wdl_context
stxue1 Sep 19, 2024
0b6fb82
properly name wdl value bases
stxue1 Sep 19, 2024
4d5ecae
Remove irrelevant comment
stxue1 Sep 24, 2024
b43d256
Adjust docstring formatting to remove RST warnings
adamnovak Sep 24, 2024
7a36b59
Adjust comment grammar
adamnovak Sep 24, 2024
96cde22
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 24, 2024
8c42888
Remove disallowed backticks
adamnovak Sep 24, 2024
fec8663
Merge remote-tracking branch 'upstream/issues/5004-wdl-virtualize-onl…
adamnovak Sep 24, 2024
966d855
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 26, 2024
dcf2f27
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 26, 2024
a318208
Extract out the import function to add back memoization and resolve i…
stxue1 Sep 27, 2024
a545493
Merge remote-tracking branch 'origin/issues/5004-wdl-virtualize-only-…
stxue1 Sep 27, 2024
3ece42b
Merge branch 'master' of github.com:DataBiosphere/toil into issues/50…
stxue1 Sep 27, 2024
f9db076
change wdl_context to wdlcontext
stxue1 Sep 27, 2024
c16290f
also change typeddict
stxue1 Sep 27, 2024
cb0f986
Add some documentation for the WDLContext object
stxue1 Sep 27, 2024
c7c69eb
Merge master into issues/5004-wdl-virtualize-only-at-task-boundaries
github-actions[bot] Sep 30, 2024
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