[REF] Modularize io

.gitignore

@@ -108,4 +108,7 @@ ENV/
 
 # jupyter notebooks
 .ipynb_checkpoints/
-*.ipynb
+*.ipynb
+
+# vim swap files
+*.swp

.zenodo.json

@@ -33,6 +33,11 @@
             "affiliation": "Montreal Neurological Institute, McGill University",
             "orcid": "0000-0003-1358-196X"
         },
+        {
+            "name": "Gonzalez-Castillo, Javier",
+            "affiliation": "National Institutes of Health",
+            "orcid": "0000-0002-6520-5125"
+        },
         {
             "name": "Handwerker, Dan",
             "affiliation": "National Institutes of Health",

CODE_OF_CONDUCT.md

@@ -49,19 +49,25 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting Elizabeth DuPre at <elizabeth.dupre@mail.mcgill.ca>.
+reported by contacting our
+[Code of Conduct Enforcement Team](https://tedana.readthedocs.io/en/stable/governance.html#leadership):
+[Elizabeth Dupre](https://github.com/emdupre),
+[Dan Handwerker](https://github.com/handwerkerd),
+and [Stefano Moia](https://github.com/smoia).
 Confidentiality will be respected in reporting.
-
-As the first interim [Benevolent Dictator for Life (BDFL)](https://en.wikipedia.org/wiki/Benevolent_dictator_for_life),
-Elizabeth DuPre can take any action she deems appropriate
-for the safety of the `tedana` community, including but not limited to:
+The Code of Conduct Enforcement Team any take any action they deem
+necessary for the safety of the `tedana` community, including but not 
+limited to:
 
 * facilitating a conversation between the two parties involved in the violation of the code of conduct
 * requesting a contributor apologize for their behaviour
 * asking a contributor or multiple contributors to enter a cooling off period that puts a
   time-limited pause on a particular discussion topic
 * asking a contributor to no longer participate in the development of `tedana`
 
+For more details on the enforcement process, please see our documentation
+on [governance](https://tedana.readthedocs.io/en/stable/governance.html).
+
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,

CONTRIBUTING.md

@@ -306,6 +306,9 @@ You can see a list of current contributors in the README
 (kept up to date by the [all contributors bot][link_all-contributors-bot]).
 You can see [here][link_all-contributors-bot-usage] for instructions on
 how to use the bot.
+We encourage all contributors to write a brief statement and self-describe how they feel they've
+contributed, showcased [here][contributions.md].
+Thanks to all of our wonderful contributors!
 
 ## Thank you!
 

tedana/__init__.py

@@ -11,7 +11,6 @@
     __version__,
     __author__,
     __copyright__,
-    __credits__,
     __license__,
     __maintainer__,
     __email__,

tedana/decomposition/pca.py

@@ -245,7 +245,7 @@ def tedpca(data_cat, data_oc, combmode, mask, adaptive_mask, t2sG,
 
     # write component maps to 4D image
     comp_maps = utils.unmask(computefeats2(data_oc, comp_ts, mask), mask)
-    io.filewrite(comp_maps, op.join(out_dir, 'desc-PCA_stat-z_components.nii.gz'), ref_img)
+    io.filewrite(comp_maps, 'z-scored PCA components', ref_img)
 
     # Select components using decision tree
     if algorithm == 'kundu':

tedana/gscontrol.py

@@ -81,7 +81,7 @@ def gscontrol_raw(catd, optcom, n_echos, ref_img, out_dir='.', dtrank=4):
     sphis -= sphis.mean()
     io.filewrite(
         utils.unmask(sphis, Gmask),
-        op.join(out_dir, 'desc-globalSignal_map.nii.gz'),
+        'gs map',
         ref_img
     )
 
@@ -102,13 +102,13 @@ def gscontrol_raw(catd, optcom, n_echos, ref_img, out_dir='.', dtrank=4):
 
     io.filewrite(
         optcom,
-        op.join(out_dir, 'desc-optcomWithGlobalSignal_bold.nii.gz'),
+        'has gs combined',
         ref_img
     )
     dm_optcom = utils.unmask(tsoc_nogs, Gmask)
     io.filewrite(
         dm_optcom,
-        op.join(out_dir, 'desc-optcomNoGlobalSignal_bold.nii.gz'),
+        'removed gs combined',
         ref_img
     )
 
@@ -219,7 +219,9 @@ def minimum_image_regression(optcom_ts, mmix, mask, comptable, ref_img, out_dir=
     t1_map = mehk_ts.min(axis=-1)  # map of T1-like effect
     t1_map -= t1_map.mean()
     io.filewrite(
-        utils.unmask(t1_map, mask), op.join(out_dir, "desc-T1likeEffect_min.nii.gz"), ref_img
+        utils.unmask(t1_map, mask),
+        't1 like',
+        ref_img
     )
     t1_map = t1_map[:, np.newaxis]
 
@@ -233,15 +235,15 @@ def minimum_image_regression(optcom_ts, mmix, mask, comptable, ref_img, out_dir=
     hik_ts = mehk_noT1gs * optcom_std  # rescale
     io.filewrite(
         utils.unmask(hik_ts, mask),
-        op.join(out_dir, "desc-optcomAcceptedMIRDenoised_bold.nii.gz"),
+        'ICA accepted mir denoised',
         ref_img,
     )
 
     # Make denoised version of T1-corrected time series
     medn_ts = optcom_mean + ((mehk_noT1gs + resid) * optcom_std)
     io.filewrite(
         utils.unmask(medn_ts, mask),
-        op.join(out_dir, "desc-optcomMIRDenoised_bold.nii.gz"),
+        'mir denoised',
         ref_img,
     )
 
@@ -258,7 +260,7 @@ def minimum_image_regression(optcom_ts, mmix, mask, comptable, ref_img, out_dir=
     comp_pes_norm = np.linalg.lstsq(mmix_noT1gs_z.T, optcom_z.T, rcond=None)[0].T
     io.filewrite(
         utils.unmask(comp_pes_norm[:, 2:], mask),
-        op.join(out_dir, "desc-ICAAcceptedMIRDenoised_components.nii.gz"),
+        'ICA accepted mir component weights',
         ref_img,
     )
     mixing_df = pd.DataFrame(data=mmix_noT1gs.T, columns=comptable["Component"].values)

tedana/info.py

@@ -11,8 +11,6 @@
 
 __author__ = 'tedana developers'
 __copyright__ = 'Copyright 2018, tedana developers'
-__credits__ = ['Elizabeth DuPre', 'Prantik Kundu', 'Ross Markello',
-               'Taylor Salo', 'Kirstie Whitaker', 'Dan Handwerker']
 __license__ = 'LGPL 2.1'
 __maintainer__ = 'Elizabeth DuPre'
 __email__ = 'emd222@cornell.edu'