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Rename existing modules #135

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emdupre opened this issue Oct 3, 2018 · 3 comments
Closed

Rename existing modules #135

emdupre opened this issue Oct 3, 2018 · 3 comments
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enhancement issues describing possible enhancements to the project
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transparent and r...

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@emdupre
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emdupre commented Oct 3, 2018

In discussing #131, we seemed to reach a consensus on renaming and reorganizing a few of the existing modules for clarity. Specifically:

  • renaming model.monoexponential to decay
  • renaming model.combine to combine
  • reorganizing io and utils into separate modules such that:
    - io holds functions for handling reading and writing data, including consolidating components into relevant time series, and
    - utils holds miscellaneous utility functions supporting the general package (e.g., new_nii_like(), filewrite(), load_data())

A clipped version of the tree would thus look like:

tedana/
...
├── combine.py
├── decay.py
├── io.py
└── utils.py

If this does not match your understanding, @ everyone, please let us know here !
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
rename model.monoexponential to decay
d80387e 
 - tedana.model.fit_decay => tedana.decay.fit_decay
 - tedana.model.fit_decay_ts => tedana.decay.fit_decay_ts

ref: ME-ICA#135
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
rename model.combine to combine
675e647 
breaks:

   tedana.model.make_optcom

not sure if this should first be depricated

ref: ME-ICA#135
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
move io and utils into separate modules
98253d2 
ref: ME-ICA#135
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
move utils.new_nii_like to io.new_nii_like
1befb25 
ref: ME-ICA#135
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
move utils.filewrite to io.filewrite
316653a 
ref: ME-ICA#135
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
move utils.load_data to io.load_data
4c2091e 
ref: ME-ICA#135
frodeaa added a commit to frodeaa/tedana that referenced this issue Oct 4, 2018
@frodeaa
move utils.load_data to io.load_data
a5cbacb 
ref: ME-ICA#135
@frodeaa frodeaa mentioned this issue Oct 4, 2018
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@tsalo
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tsalo commented Oct 4, 2018

I think the proposed module names are good, although filewrite and load_data probably belong in io, right?

@frodeaa
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frodeaa commented Oct 4, 2018

they are moved from utils into io by #136

@KirstieJane KirstieJane added the enhancement issues describing possible enhancements to the project label Oct 31, 2018
@tsalo
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tsalo commented Nov 11, 2018

This was handled in #136, so I think we can close this now.

@tsalo tsalo closed this as completed Nov 11, 2018
emdupre pushed a commit to emdupre/tedana that referenced this issue Nov 15, 2018
@tsalo @emdupre
Fix mmix dimensions. (#17)
8f6b833 
* Use pandas for component tables.

* Write out MEPCA component maps.

* Fix.

* Update.

* Fix tedpca selection.

* Re-add duplication.

* More cleanup.

* Add decision information to ICA compatible.

* Add metrics to PCA component table.

* Undo some refactoring.

* Edit test failed file.

* Undo refactor.

* Fix style issues.

* Add pandas to requirements.

* Update requirements.

* Fix tests.

* Update test just to test a thing.

* Fix how writeresults is called.

* Add orphans to ignored and revert integration test.

* Clean up MEICA component table.

* Address review comments and track reasons to ignore components.

* midkreg --> midkrej. Whoops!

* Address some review comments.

- Add docstring for comptable output in selcomps.
- “variance explained 2 (normalized)” —> “normalized variance explained”
- “variance explained (normalized)” —> “normalized variance explained”

* Split PCA off into a separate function and rename some variables

* Remove writect function.

* Remove writect from init file too.

* Remove unused import.

* Rename run_pca to run_svd and improve documentation.

* Add MLEPCA citation.

* Remove mlepca flag and consolidate SVD functions.

* Change markdown to rst and add figures.

* Update file name.

* Update file name.

* Update documentation.

* Update outputs file.

* Document derivatives.

* Fix some RST formatting issues in README.

* rename model.monoexponential to decay

 - tedana.model.fit_decay => tedana.decay.fit_decay
 - tedana.model.fit_decay_ts => tedana.decay.fit_decay_ts

ref: ME-ICA#135

* rename model.combine to combine

breaks:

   tedana.model.make_optcom

not sure if this should first be depricated

ref: ME-ICA#135

* move io and utils into separate modules

ref: ME-ICA#135

* move utils.new_nii_like to io.new_nii_like

ref: ME-ICA#135

* move utils.filewrite to io.filewrite

ref: ME-ICA#135

* move utils.load_data to io.load_data

ref: ME-ICA#135

* revert docs/api.rts to a534c1e

the changes did not work correctly,

  Failed to import 'tedana.io': no module named tedana.io

* fix: remove duplicate imports

* Add notebooks and figures for pipeline description page.

* Fix some formatting.

* move io.gscontrol_mmix to utils

suggested by @tsalo

* update api with the changes

* fix test failure circular dependency

circular dependency between io and utils
after gscontrol_mmix move to utils

ref: 5889135

* Revert "fix test failure circular dependency"

This reverts commit 2200cd8.

* Revert "move io.gscontrol_mmix to utils"

This reverts commit 5889135.

* add io.gscontrol_mmix  to api.rst

* Update multi-echo.rst

* Update multi-echo.rst

* Update figures in walkthrough.

* Add yellow_heart emoji to README.

* Split README into rst (for site) and md (for GitHub).

* Update requirements.

* Fix updated requirements.

* Revert changes.

* Try changing the tests a bit.

* Wow... I had the files switched.

* Fix test.

* Fix test again.

* Revert changes to tests.

* Update README.md

Added notes for creating a conda environment for use with tedana
Added links to dependencies

* [FIX] Logging in tedana and t2smap

Closes: ME-ICA#127

Changes proposed in this pull request:

 - use logging.basicConfig to fix logging level
   for tedana and t2smap

see: https://docs.python.org/3.7/howto/logging.html#logging-from-multiple-modules

* Update list of workflow outputs on RTD site.

* Fix docstrings.

* Add note!!!

* Fix MMIX dimensions.

* Remove unused import.

* Re-run workflow and re-make figures.

- Change example voxel to one more affected by T1c-GSR.
- Use SVD+decision tree for TEDPCA instead of MLEPCA (because MLEPCA
doesn’t whiten this dataset).
- Turn off GSR.

* Change precision of floats in output tables and change midk to rejected.

* Address review comments

* Remove verbose output table

* Update filenames in workflow docstring.

* Change component table float precision from %g to %.6f.

* Link workflow to outputs page.

* Add Support and Communication page to docs.

* Update line lengths, remove sys admin information

* Fix old link.

* [DOC] Remove getting started section

* fix style errors

 - E127 continuation line over-indented for
   visual indent
 - E128 continuation line under-indented for
   visual indent

* fix filewrite call

filewriter is moved to io

* Hackily "fix" bugs in component selection and model fitting.

* Use tables in v2.5 component selection.

* Remove unused import.

* Revert TEDICA reindexing.

I’d prefer to sort by variance explained, but Kappa is good too.

* Clean up how metrics are added to ICA compatible.
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@frodeaa @KirstieJane @tsalo @emdupre