Merge branch 'master' of https://github.com/physiopy/phys2bids into a…

…dd/logger

phys2bids/cli/run.py

@@ -1,4 +1,7 @@
 # -*- coding: utf-8 -*-
+"""
+Parser for phys2bids
+"""
 
 import argparse
 
@@ -13,10 +16,12 @@ def _get_parser():
     -------
     parser.parse_args() : argparse dict
 
-    """
-    parser = argparse.ArgumentParser()
+    Notes
+    -----
     # Argument parser follow template provided by RalphyZ.
     # https://stackoverflow.com/a/43456577
+    """
+    parser = argparse.ArgumentParser()
     optional = parser._action_groups.pop()
     required = parser.add_argument_group('Required Argument:')
     required.add_argument('-in', '--input-file',

phys2bids/interfaces/acq.py

@@ -11,7 +11,22 @@
 
 def populate_phys_input(filename, chtrig):
     """
-    Populate object phys_input
+    Populate object phys_input from acq files.
+
+    Parameters
+    ----------
+    filename: str
+        path to the txt labchart file
+    chtrig : int
+        index of trigger channel
+
+    Returns
+    -------
+    BlueprintInput
+
+    See Also
+    --------
+    physio_obj.BlueprintInput
     """
 
     data = read_file(filename).channels

phys2bids/interfaces/txt.py

@@ -18,16 +18,21 @@ def populate_phys_input(filename, chtrig):
     """
     Populate object phys_input
     for now this works only with labchart files
-        Input (Properties)
-    ------------------
+
+    Parameters
+    ----------
     filename: str
         path to the txt labchart file
     chtrig : int
         index of trigger channel
 
-    Output
-    ------------------
-    BlueprintInput object for more see BlueprintInput docs
+    Returns
+    -------
+    BlueprintInput
+
+    See Also
+    --------
+    physio_obj.BlueprintInput
     """
     header = []
     channel_list = []

phys2bids/phys2bids.py

@@ -47,8 +47,8 @@ def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, out
     """
     Prints a summary onscreen and in file with informations on the files.
 
-    Input
-    -----
+    Parameters
+    ----------
     filename: str
         Name of the input of phys2bids.
     ntp_expected: int
@@ -62,8 +62,9 @@ def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, out
     outfile: str or path
         Fullpath to output file.
 
-    Outcome
-    -------
+    Notes
+    -----
+    Outcome:
     summary: str
         Prints the summary on screen
     outfile: .log file
@@ -87,8 +88,8 @@ def print_json(outfile, samp_freq, time_offset, ch_name):
     """
     Prints the json required by BIDS format.
 
-    Input
-    -----
+    Parameters
+    ----------
     outfile: str or path
         Fullpath to output file.
     samp_freq: float
@@ -98,9 +99,9 @@ def print_json(outfile, samp_freq, time_offset, ch_name):
     ch_name: list of str
         List of channel names, as specified by BIDS format.
 
-    Outcome
-    -------
-
+    Notes
+    -----
+    Outcome:
     outfile: .json file
         File containing information for BIDS.
     """
@@ -117,8 +118,8 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     Import the heuristic file specified by the user and uses its output
     to rename the file.
 
-    Input
-    -----
+    Parameters
+    ----------
     heur_file: path
         Fullpath to heuristic file.
     sub: str or int
@@ -133,28 +134,27 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     record_label: str
         Optional label for the "record" entry of BIDS.
 
-    Output
+    Returns
     -------
     heurpath: str or path
         Returned fullpath to tsv.gz new file (post BIDS formatting).
     """
 
     if sub[:4] != 'sub-':
-        name = 'sub-' + sub
+        name = f'sub-{sub}'
     else:
         name = sub
 
-    fldr = outdir + '/' + name
+    fldr = os.path.join(outdir, name)
 
     if ses:
         if ses[:4] != 'ses-':
-            fldr = fldr + '/ses-' + ses
-            name = name + '_ses-' + ses
-        else:
-            fldr = fldr + '/' + ses
-            name = name + ses
+            ses = f'ses-{ses}'
 
-    fldr = fldr + '/func'
+        fldr = os.path.join(fldr, ses)
+        name = f'{name}_{ses}'
+
+    fldr = os.path.join(fldr, 'func')
     utils.path_exists_or_make_it(fldr)
 
     cwd = os.getcwd()
@@ -167,7 +167,7 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
     if record_label:
         recording = f'_recording-{record_label}'
 
-    heurpath = fldr + '/' + name + recording + '_physio'
+    heurpath = os.path.join(fldr, f'{name}{recording}_physio')
     # for ext in ['.tsv.gz', '.json', '.log']:
     #     move_file(outfile, heurpath, ext)
     os.chdir(cwd)
@@ -184,6 +184,11 @@ def _main(argv=None):
     Otherwise, it operates on the input to return a .tsv.gz file, possibily
     in BIDS format.
 
+    Raises
+    ------
+    NotImplementedError
+        If the file extension is not supported yet.
+
     """
     options = _get_parser().parse_args(argv)
     # Check options to make them internally coherent