[REF] Merge CLI into workflows

docs/api.rst

@@ -12,8 +12,8 @@ API
    :template: function.rst
    :toctree: generated/
 
-   tedana.workflows.tedana
-   tedana.workflows.t2smap
+   tedana.workflows.tedana_workflow
+   tedana.workflows.t2smap_workflow
 
 .. currentmodule:: tedana
 

docs/usage.rst

@@ -14,21 +14,21 @@ Run tedana
 This is the full tedana workflow, which runs multi-echo ICA and outputs
 multi-echo denoised data along with many other derivatives.
 To see which files are generated by this workflow, check out the workflow
-documentation: :py:func:`tedana.workflows.tedana`.
+documentation: :py:func:`tedana.workflows.tedana_workflow`.
 
 .. argparse::
-   :ref: tedana.cli.run_tedana.get_parser
+   :ref: tedana.workflows.tedana._get_parser
    :prog: tedana
-   :func: get_parser
+   :func: _get_parser
 
 Run t2smap
 ----------
 This workflow uses multi-echo data to optimally combine data across echoes and\
 to estimate T2* and S0 maps or time series.
 To see which files are generated by this workflow, check out the workflow
-documentation: :py:func:`tedana.workflows.t2smap`.
+documentation: :py:func:`tedana.workflows.t2smap_workflow`.
 
 .. argparse::
-   :ref: tedana.cli.run_t2smap.get_parser
+   :ref: tedana.workflows.t2smap._get_parser
    :prog: t2smap
-   :func: get_parser
+   :func: _get_parser

setup.py

@@ -41,8 +41,8 @@ def main():
         tests_require=ldict['TESTS_REQUIRES'],
         extras_require=ldict['EXTRA_REQUIRES'],
         entry_points={'console_scripts': [
-            't2smap=tedana.cli.run_t2smap:main',
-            'tedana=tedana.cli.run_tedana:main'
+            't2smap=tedana.workflows.t2smap:_main',
+            'tedana=tedana.workflows.tedana:_main'
         ]},
         packages=find_packages(exclude=("tests",)),
         package_data=ldict['PACKAGE_DATA'],

tedana/tests/test_model_combine.py

@@ -1,6 +1,7 @@
 """
 Tests for tedana.model.combine
 """
+
 import numpy as np
 
 from tedana.model import combine

tedana/tests/test_model_fit.py

@@ -1,6 +1,7 @@
 """
 Tests for tedana.model.fit
 """
+
 import numpy as np
 
 from tedana.model import fit

tedana/tests/test_model_monoexponential.py

@@ -1,6 +1,7 @@
 """
 Tests for tedana.model.monoexponential
 """
+
 import os.path as op
 
 import pytest