Minor tweaks

Author: marcelzwiers

docs/options.rst

@@ -24,6 +24,7 @@ These setting can be used by all the BIDScoin tools:
 - ``unknowntypes``: Datatypes that are not part of BIDS but that are converted to a BIDS-like entries in the BIDS folder
 - ``ignoretypes``: Datatypes that are excluded/not converted"""
 - ``anon``: Set this anonymization flag to 'y' to round off age and to discard acquisition date from the metadata
+- ``stripsuffix``: Strips off the suffix from bids-values (to reduce redundancy within filenames)
 - ``unzip``: Wildcard pattern to select tarball/zip-files in the source folders that need to be unzipped (in a tempdir) to expose the data. Use for instance '\*.tar.gz' if your source data looks like ``sub-01\01_MPRAGE\dcmfiles.tar.gz``, etc
 
 The core working of BIDScoin and its plugins can be tested by clicking the corresponding [Test] button and inspection of the terminal output.

docs/workflow.rst

@@ -89,12 +89,12 @@ Here is how to run the bidsmapper command:
 
     ::
 
-    examples:
-      bidsmapper myproject/raw myproject/bids
-      bidsmapper myproject/raw myproject/bids -t bidsmap_custom  # Uses a template bidsmap of choice
-      bidsmapper myproject/raw myproject/bids -p nibabel2bids    # Uses a plugin of choice
-      bidsmapper myproject/raw myproject/bids -n patient- -m '*' # Handles DICOMDIR datasets
-      bidsmapper myproject/raw myproject/bids -u '*.tar.gz'      # Unzip tarball source files
+        examples:
+          bidsmapper myproject/raw myproject/bids
+          bidsmapper myproject/raw myproject/bids -t bidsmap_custom  # Uses a template bidsmap of choice
+          bidsmapper myproject/raw myproject/bids -p nibabel2bids    # Uses a plugin of choice
+          bidsmapper myproject/raw myproject/bids -n patient- -m '*' # Handles DICOMDIR datasets
+          bidsmapper myproject/raw myproject/bids -u '*.tar.gz'      # Unzip tarball source files
 
 After the source data has been scanned, the bidsmapper will automatically launch `step 1b <#step-1b-running-the-bidseditor>`__ to let the user check and edit the automatically generated study bidsmap. For a fully automated workflow users can skip this interactive step using the ``-i`` option (see above).
 

release_procedure.rst

@@ -14,7 +14,6 @@ This document describes how to prepare a new BIDScoin release from within the DC
     tox
     conda deactivate
     module load bidscoin/dev
-    source activate /opt/bidscoin
     bidscoin -t
     # Perform integration tests from the command line and PyCharm
 
@@ -41,7 +40,7 @@ DCCN deployment
 
 1. Copy the dev folder, update the bidsmaps and module::
 
-    VERSION="4.6.1"
+    VERSION="4.6.2"
     cp -r /opt/bidscoin/dev /opt/bidscoin/$VERSION
     cd /opt/_modules/bidscoin
     ln -s .common $VERSION
@@ -50,10 +49,8 @@ DCCN deployment
 3. Run a test::
 
     module load bidscoin
-    source activate /opt/bidscoin
     bidscoin -v
     bidscoin -t
-    conda deactivate
 
 4. Post a release message on the MM data management channel
 
@@ -68,7 +65,7 @@ Neurodesk
 1. Pull and edit the bidscoin neurocontainer in a separate release branch
 2. In the VM, build and test a neurodocker image::
 
-    VERSION="4.6.1"
+    VERSION="4.6.2"
     cd ~/PycharmProjects/neurocontainers/recipes/bidscoin
     conda activate neurodocker
     ./build.sh -ds