squash commits

dcm2bids/acquisition.py

@@ -6,7 +6,7 @@
 from os.path import join as opj
 
 from dcm2bids.utils.utils import DEFAULT
-from dcm2bids.utils.tools import __version__
+from dcm2bids.version import __version__
 
 
 class Acquisition(object):

dcm2bids/cli/dcm2bids.py

@@ -10,7 +10,7 @@
 from dcm2bids.dcm2bids_gen import Dcm2BidsGen
 from dcm2bids.utils.tools import check_latest
 from dcm2bids.utils.utils import DEFAULT
-
+from dcm2bids.version import __version__
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__, epilog=DEFAULT.doc,
@@ -53,6 +53,11 @@ def _build_arg_parser():
                    choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
                    help="Set logging level. [%(default)s]")
 
+    p.add_argument("-v", "--version",
+                   action="version",
+                   version=f"dcm2bids version:\t{__version__}\nBased on BIDS version:\t{DEFAULT.bids_version}",
+                   help="Report dcm2bids version and the BIDS version.")
+
     return p
 
 

dcm2bids/cli/dcm2bids_scaffold.py

@@ -47,7 +47,7 @@ def main():
                  "https://github.com/bids-standard/bids-starter-kit")
     # CHANGES
     write_txt(opj(args.output_dir, "CHANGES"),
-              bids_starter_kit.CHANGES.replace('DATA',
+              bids_starter_kit.CHANGES.replace('DATE',
                                                datetime.date.today().strftime("%Y-%m-%d")))
 
     # dataset_description

dcm2bids/dcm2bids_gen.py

@@ -19,8 +19,8 @@
 from dcm2bids.participant import Participant
 from dcm2bids.utils.utils import DEFAULT, run_shell_command
 from dcm2bids.utils.io import load_json, save_json, valid_path
-from dcm2bids.utils.tools import __version__, check_latest, dcm2niix_version
-
+from dcm2bids.utils.tools import check_latest, dcm2niix_version
+from dcm2bids.version import __version__
 
 class Dcm2BidsGen(object):
     """ Object to handle dcm2bids execution steps

dcm2bids/participant.py

@@ -5,7 +5,7 @@
 from os.path import join as opj
 
 from dcm2bids.utils.utils import DEFAULT
-from dcm2bids.utils.tools import __version__
+from dcm2bids.version import __version__
 
 
 class Participant(object):

dcm2bids/utils/args.py

@@ -47,5 +47,5 @@ def check(path):
 
 def add_overwrite_arg(parser):
     parser.add_argument(
-        '-f', dest='overwrite', action='store_true',
+        '--force', dest='overwrite', action='store_true',
         help='Force overwriting of the output files.')

dcm2bids/utils/io.py

@@ -30,9 +30,8 @@ def save_json(filename, data):
 
 
 def write_txt(filename, lines):
-    with open(filename, "a") as f:
-        for row in lines:
-            f.write("%s\n" % row)
+    with open(filename, "a+") as f:
+        f.write(f"{lines}\n")
 
 
 def get_scaffold_dir():

dcm2bids/utils/scaffold.py

@@ -2,15 +2,13 @@
 
 class bids_starter_kit(object):
 
-    CHANGES = """
-Revision history for your dataset
+    CHANGES = """Revision history for your dataset
 
 1.0.0 DATE
  - Initialized study directory
  """
 
-    dataset_description = """
-{
+    dataset_description = """{
     "Name": "",
     "BIDSVersion": "BIDS_VERSION",
     "License": "",
@@ -29,8 +27,7 @@ class bids_starter_kit(object):
 }
 """
 
-    participants_json = """
-{
+    participants_json = """{
     "age": {
         "LongName": "",
         "Description": "age of the participant",
@@ -63,15 +60,13 @@ class bids_starter_kit(object):
 }
 """
 
-    participants_tsv = """
-participant_id	age	sex	group
+    participants_tsv = """participant_id	age	sex	group
 sub-01	34	M	control
 sub-02	12	F	control
 sub-03	33	F	patient
 """
 
-    README = """
-# README
+    README = """# README
 
 The README is usually the starting point for researchers using your data
 and serves as a guidepost for users of your data. A clear and informative

dcm2bids/utils/tools.py

@@ -2,17 +2,14 @@
 
 """This module take care of the versioning"""
 
-# dcm2bids version
-__version__ = "2.1.9"
-
 
 import logging
 import shlex
 from packaging import version
-from distutils.version import LooseVersion
 from subprocess import check_output, CalledProcessError, TimeoutExpired
 from shutil import which
 
+from dcm2bids.version import __version__
 
 logger = logging.getLogger(__name__)
 
@@ -38,7 +35,7 @@ def check_github_latest(githubRepo, timeout=3):
     Returns:
         A string of the version
     """
-    url = "https://github.com/{}/releases/latest".format(githubRepo)
+    url = f"https://github.com/{githubRepo}/releases/latest"
     try:
         output = check_output(shlex.split("curl -L --silent " + url), timeout=timeout)
     except CalledProcessError:
@@ -52,7 +49,7 @@ def check_github_latest(githubRepo, timeout=3):
     # The output should have this format
     # <html><body>You are being <a href="https://github.com/{gitRepo}/releases/tag/{version}">redirected</a>.</body></html>
     try:
-        version = output.decode().split("{}/releases/tag/".format(githubRepo))[1].split('"')[0]
+        version = output.decode().split(f"{githubRepo}/releases/tag/")[1].split('"')[0]
 
         # Versions are X.X.X
         if len(version) > 5:

dcm2bids/utils/utils.py

@@ -28,7 +28,6 @@ class DEFAULT(object):
 
     # dcm2niix.py
     dcm2niixOptions = "-b y -ba y -z y -f '%3s_%f_%p_%t'"
-    dcm2niixVersion = "v1.0.20181125"
 
     # sidecar.py
     compKeys = ["SeriesNumber", "AcquisitionTime", "SidecarFilename"]

tests/test_scaffold.py

@@ -8,5 +8,5 @@ def test_help_option(script_runner):
     assert ret.success
 
 def test_run_scaffold(script_runner):
-    ret = script_runner.run(['dcm2bids_scaffold', '-o', 'o_scaffold', '-f'])
+    ret = script_runner.run(['dcm2bids_scaffold', '-o', 'o_scaffold', '--force'])
     assert ret.success