release version different from internal version; circleci tests failing because nipype printing out a message

[satra]

@binarybottle - your release versions (see github releases for mindboggle) are different from internal versions. so etelemetry is getting misleading info from the source code and github.

et.get_project('nipy/mindboggle')                                                                               
Out[2]: {'version': '1.2.4_thickinthehead_revision'}

where as internally it says: 1.3.6/7 now

[binarybottle]

Okay -- just added a github v1.3.7 release:

https://github.com/nipy/mindboggle/releases/tag/v1.3.7

Does that take care of things?

[satra]

that should help. there is an error that is cropping up in doctests because nipype is printing out a message. this could be avoided by importing nipype earlier. but i have to think if this is indeed a change we want to make in how nipype reports the version change.

[binarybottle]

When do you suggest I import nipype, or should I wait for your change in nipype?

[binarybottle]

@satra --

Why would I get a doctest error when the command in question is returning something (area_file)?

Failed example: area_file = area(command, surface_file, verbose) Expected nothing Got: 190924-17:46:53,790 nipype.utils INFO: Running nipype version 1.2.3 (latest: 1.2.3)

[binarybottle]

@satra -- I moved nipype installation to earlier in the conda install line of neurodocker.sh, but circleci tests are still failing:

FAIL: Doctest: mindboggle.shapes.surface_shapes.area

Traceback (most recent call last): File "/opt/conda/envs/mindboggle-env/lib/python3.6/doctest.py", line 2199, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for mindboggle.shapes.surface_shapes.area File "/opt/conda/envs/mindboggle-env/lib/python3.6/site-packages/mindboggle/shapes/surface_shapes.py", line 14, in area

---

File "/opt/conda/envs/mindboggle-env/lib/python3.6/site-packages/mindboggle/shapes/surface_shapes.py", line 45, in mindboggle.shapes.surface_shapes.area Failed example: area_file = area(command, surface_file, verbose) Expected nothing Got: 191105-03:33:17,962 nipype.utils INFO: Running nipype version 1.3.0-rc1 (latest: 1.2.3)

[satra]

this is because the first time nipype is imported in a terminal interaction setting, it will try to check if you are running the latest version. this results in a stdout which you are seeing. one way to avoid the issue is to add another dummy line after that doctest.

we will have to figure out how best to change nipype behavior, but for now we are keeping this.

[binarybottle]

By "dummy line after that doctest", do you mean an empty line ">>> " after the line: area_file = area(command, surface_file, verbose) or after the last line of the docstring?