Detect pathmapper name conflicts.

[tetron]

No description provided.

[codecov]

Codecov Report

Merging #805 into master will decrease coverage by <.01%.
The diff coverage is 100%.

@@ Coverage Diff @@ ## master #805 +/- ## ========================================== - Coverage 68.69% 68.69% -0.01%  ========================================== Files 33 33 Lines 5300 5306 +6 Branches 1408 1411 +3 ========================================== + Hits 3641 3645 +4  - Misses 1293 1294 +1  - Partials 366 367 +1

Impacted Files	Coverage Δ
cwltool/pathmapper.py	87.23% <100%> (+0.42%)	⬆️
cwltool/executors.py	70.27% <0%> (-2.71%)	⬇️
cwltool/workflow.py	81.3% <0%> (-0.37%)	⬇️
cwltool/main.py	38.77% <0%> (+0.76%)	⬆️

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[mr-c]

Some conformance tests are failing

Test [111/132] Test that nameroot and nameext are generated from basename at execution time by the runner Test failed: /home/jenkins/workspace/cwltool-pr-conformance-multiver/version/v1.0/cwltool_with_cov --outdir=/tmp/tmp2O_5aD --quiet v1.0/basename-fields-test.cwl v1.0/basename-fields-job.yml Test that nameroot and nameext are generated from basename at execution time by the runner Returned non-zero Workflow checker warning: v1.0/basename-fields-test.cwl:22:7: 'tool' is not an input parameter of file:///home/jenkins/workspace/cwltool-pr-conformance-multiver/version/v1.0/common-workflow-language-master/v1.0/v1.0/echo-file-tool.cwl, expected in v1.0/basename-fields-test.cwl:29:7: 'tool' is not an input parameter of file:///home/jenkins/workspace/cwltool-pr-conformance-multiver/version/v1.0/common-workflow-language-master/v1.0/v1.0/echo-file-tool.cwl, expected in Input object failed validation: Name conflict: both file:///tmp/tmp2iFvx1/d89b855ec592203974172af5cae00aa5dc04ce78 and file:///tmp/tmpUTsh9f/d89b855ec592203974172af5cae00aa5dc04ce78 have been assigned to target /tmp/tmp2O_5aD/d89b855ec592203974172af5cae00aa5dc04ce78 

[tetron]

It seems like the main reason this hasn't been merged is this failing conformance test....