ENH: Allow Nipype configuration directory to be specified with NIPYPE_CONFIG_DIR environment variable

[stilley2]

Summary

Allow overwriting default location of nipype.cfg (~/.nipype) with the environment variable NIPYPECONFDIR. This is potentially useful for containerized pipelines which require a default nipype.cfg.

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[codecov]

Codecov Report

Merging #3073 into master will increase coverage by 0.18%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #3073      +/-   ##
==========================================
+ Coverage   67.86%   68.05%   +0.18%     
==========================================
  Files         295      295              
  Lines       39260    39747     +487     
  Branches     5171     5293     +122     
==========================================
+ Hits        26644    27050     +406     
- Misses      11911    11979      +68     
- Partials      705      718      +13

Flag	Coverage Δ
#smoketests	49.55% <100%> (-1.68%)	⬇️
#unittests	67.75% <100%> (+2.66%)	⬆️

Impacted Files	Coverage Δ
nipype/utils/config.py	65.19% <100%> (ø)	⬆️
nipype/pipeline/plugins/legacymultiproc.py	63.31% <0%> (+0.5%)	⬆️
nipype/interfaces/fsl/preprocess.py	83.88% <0%> (+2.16%)	⬆️
nipype/interfaces/spm/model.py	47.11% <0%> (+4.84%)	⬆️

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[oesteban]

Could we test this updating the circleci jobs?

[stilley2]

Sorry @oesteban , I'm not sure exactly what you mean. Do you want me to add some tests for this?

[effigies]

I'm not sure what a good test would be. I guess you could mock the environment and validate that the expected contents are loaded when the variable is set or not set.

In any event, you should add a note about the environment variable to, once this is merged: https://github.com/miykael/nipype_tutorial/blob/master/notebooks/basic_execution_configuration.ipynb

[effigies]

Hi @stilley2, this PR is also affected by our recent merges. Could you re-apply these changes on the latest master? You'll want to re-run make specs entirely, and we're now using the Black formatter. You can run it manually, or use pre-commit to have it automatically run every time you commit.

Please let me know if you need any help or clarifications.

[effigies]

There are two cases of NIPYPE* environment variables:

nipype/tools/run_examples.py

Lines 21 to 22 in 1a86999

	if plugin == "MultiProc":
	plugin_args["n_procs"] = int(os.getenv("NIPYPE_NUMBER_OF_CPUS", cpu_count()))

nipype/nipype/interfaces/spm/base.py

Lines 258 to 259 in 1a86999

	if "NIPYPE_NO_MATLAB" in os.environ or Info.version() is None:
	return True

Both have the form with underscores separating words, so let's do something in that direction.

Thanks for your patience, btw.

[effigies]

Hi @stilley2, do you have a couple minutes to consider the above proposal?

[stilley2]

Sorry last week was pretty busy. Change looks good!

[effigies]

Thanks for your patience.