Fix factory.py

[suecharo]

I have modified factory.py to be the same as when executed from the command line.
It has been fixed to be the same runtimeContext and loadingContext as when executed from the command line.
As it uses argparse, we can pass command line runtime options to factory.py.
It has passed the conformance test.
Adapt this pull request, we can use factory.py as follows:

import cwltool.factory
from pprint import pprint

def main():
    argsl = [
        "--outdir",
        "/home/suecharo/tmp/test/test_output",
    ]
    fac = cwltool.factory.Factory(argsl)
    workflow = fac.make(
        "https://github.com/suecharo/test-workflow/raw/master/workflow/bwa_mapping_pe.cwl")
    result = workflow(
        nthreads=2,
        fastq1_url="https://github.com/suecharo/test-workflow/raw/master/data/small.ERR034597_1.fastq",
        fastq2_url="https://github.com/suecharo/test-workflow/raw/master/data/small.ERR034597_2.fastq",
        fasta_url="https://github.com/suecharo/test-workflow/raw/master/data/small.chr22.fa",
    )
    pprint(result)


if __name__ == "__main__":
    main()

[cwl-bot]

Can one of the admins verify this patch?

[mr-c]

Jenkins, okay to test

[codecov]

Codecov Report

Merging #1099 into master will decrease coverage by 23.65%.
The diff coverage is 0%.

@@             Coverage Diff             @@
##           master    #1099       +/-   ##
===========================================
- Coverage   79.92%   56.26%   -23.66%     
===========================================
  Files          30       30               
  Lines        6152     6176       +24     
  Branches     1537     1543        +6     
===========================================
- Hits         4917     3475     -1442     
- Misses        854     2349     +1495     
+ Partials      381      352       -29

Impacted Files	Coverage Δ
cwltool/factory.py	0% <0%> (-92.69%)	⬇️
cwltool/pack.py	10.55% <0%> (-73.3%)	⬇️
cwltool/subgraph.py	16.19% <0%> (-67.62%)	⬇️
cwltool/provenance.py	14.6% <0%> (-65.85%)	⬇️
cwltool/singularity.py	23.52% <0%> (-51.64%)	⬇️
cwltool/secrets.py	40.47% <0%> (-42.86%)	⬇️
cwltool/resolver.py	34.42% <0%> (-42.63%)	⬇️
cwltool/cwlrdf.py	15.73% <0%> (-32.59%)	⬇️
cwltool/load_tool.py	57.94% <0%> (-25.71%)	⬇️
cwltool/sandboxjs.py	46.55% <0%> (-22.85%)	⬇️
... and 18 more

---

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[codecov]

Codecov Report

Attention: Patch coverage is 0% with 41 lines in your changes missing coverage. Please review.

Project coverage is 54.46%. Comparing base (4a31f2a) to head (cc95907).
Report is 953 commits behind head on main.

Files with missing lines	Patch %	Lines
cwltool/factory.py	0.00%	41 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (4a31f2a) and HEAD (cc95907). Click for more details.

HEAD has 4 uploads less than BASE

Flag	BASE (4a31f2a)	HEAD (cc95907)
	8	4

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #1099       +/-   ##
===========================================
- Coverage   73.22%   54.46%   -18.77%     
===========================================
  Files          34       34               
  Lines        6858     6885       +27     
  Branches     1743     1749        +6     
===========================================
- Hits         5022     3750     -1272     
- Misses       1301     2705     +1404     
+ Partials      535      430      -105     

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[mr-c]

tests/util.py:35 may also need updating

[mr-c]

Hello @suecharo , this looks really useful! I made some review comments based upon the unit tests and the type checking.

[mr-c]

Resurrected as #2060