convert convertxfm.py

[yibeichan]

hello, I manually converted convertxfm.py, hope it's correct and can pass the test

[codecov-commenter]

Codecov Report

Merging #33 (cca0b1f) into master (094cec2) will decrease coverage by 0.41%.
The diff coverage is 0.00%.

@@            Coverage Diff            @@
##           master     #33      +/-   ##
=========================================
- Coverage    0.87%   0.45%   -0.42%     
=========================================
  Files          25      33       +8     
  Lines         343     656     +313     
  Branches       43     126      +83     
=========================================
  Hits            3       3              
- Misses        340     653     +313     

Impacted Files	Coverage Δ
pydra/tasks/fsl/model/cluster.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/model/feat.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/model/featmodel.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/model/filmgls.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/model/flameo.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/model/glm.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/model/melodic.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/utils/complex.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/utils/convertxfm.py	0.00% <0.00%> (ø)
pydra/tasks/fsl/utils/filterregressor.py	0.00% <ø> (ø)

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[yibeichan]

okay... I'll stop creating more failed test reports. @djarecka I'll see you in your office hour tomorrow morning around 7am (your 10 am).

[djarecka]

@yibeichan - the tests were failing even before, it's not your fault. We should fix it.

Also, tomorrow I can also be around 11:30 ET if that works better for you

[yibeichan]

@djarecka finally!!! I passed all tests, except the docker one. I had some issues with doctest.
FSL generates tmp outputs and have them in the cmdline. This causes the difference between my input cmdline and doctest generated cmdline. Only two model/cluster.py and model/glm.py have this issue. So I add #doctest: +SKIP for those two files.
After merge this pr, I'll work on

1. make converter.py more specific
2. write pydra tasks for interfaces which don't have _cmdline

[yibeichan]

@djarecka as we just discussed, I changed settings in related to bet.py, cluster.py, and flameo.py and they passed the test locally but still failed the docker here.
Also, this time the docker test has 17 failures, I'm pretty sure I didn't change other files.
the errors are the same Error: short read, file may be truncated

[yibeichan]

@djarecka I changed ty.Any to ty.Union[bool, str] and set the default value as False in cluster.py https://github.com/yibeichan/pydra-fsl/blob/cca0b1f96a38fed6cbaad2b48a3391f63413e486/pydra/tasks/fsl/model/cluster.py#L32
The test has failed. Similar errors as other failed tests which don't need ty.Union[bool, str]

E               stderr:
E               terminate called after throwing an instance of 'NiftiIO::NiftiException'
E                 what():  Error: short read, file may be truncated

We can talk about this tomorrow 10am (EST)/7am (PST), via jit.si

[djarecka]

that is interesting, we can look at this tomorrow.

I've change the FNIRT interface/test, but still not passing, trying to figure out what I misunderstood how the interface works

[yibeichan]

@djarecka hello, just one more thing I noticed. Remember that I have FSL installed on my Mac so I don't need to use docker to do testing, and I passed all tests locally but failed checks here. So, I pulled your docker image, followed the workflow here, and ran all tests in the docker. The same working branch, same pydra version, I passed all tests locally...
Maybe there are also some issues with the docker test online? We can talk tomorrow morning!

[djarecka]

@yibeichan - let fix the issues with test in docker in a separate PR, will merge it now! Great work, thank you!

[djarecka]

wait, I forgot that we figured this out and I can see that you opened another PR...