Bidscoin

Just in time for X-mas, a new and significantly improved BIDScoin release! It's more user-friendly and the codebase has been refactored for a more flexible and powerful usage with plugins and, for advanced use cases, regular expressions. This release is described in more detail in this [Frontiers in Neuroinformatics](https://www.frontiersin.org/articles/10.3389/fninf.2021.770608) paper :-)

Added
- A BIDScoin installation test (`bidscoin -t`)
- Option to install extra packages, such as phys2bids
- A bidseditor button to save the Options to a (default) template bidsmap
- Sub-/ses-prefix settings and BIDS / extra_data / excluded datatypes in bidsmap['Options']['bidscoin']
- Regular expressions for extracting property and attribute substrings from dynamic values via a <<key:regular_expression>> syntax
- A plugin for spec2nii to convert MR spectroscopy data
- An experimental plugin for phys2bids to convert physiological data
- An experimental plugin for pet2bids to convert MR spectroscopy data
- Added a multi-echo deface function `medeface` that uses the same defacemask for all echo-images
- The possibility to extract DICOM values using pydicom-style tag numbers (in addition to the attribute name)
- The possibility for plugins to set default bidsmappings and Options when installed
- A Singularity container configuration file
- Improved (more fine-grained) plugin installation procedures
- The option to remove decimals from age and discard acquisition dates from the meta data

Changed
- Plugins should now have a `is_sourcefile` and a `get_attribute` function and have a simpler/changed API (-> DataSource class)
- The intricate filtering of the `nrfiles` property by the other filesystem properties has been removed and is now a pure/unfiltered file-system property
- The default `<<SourceFilePath>>` keyword has been replaced by the more flexible <<filepath:/sub-(.*?)/>> property to extract the subject / session label
- The dcm2bidsmap and the dcm2niix2bids plugins have been merged
- The dicomsort utility has new naming-scheme functionality
- Removed the obsolete bidsmap_template.yaml file

Fixed
- Avoid storing Python literal structures as strings
- Various small bugs

Fixed
Remove regular expression metacharacters from the source attribute if needed (could cause a regexp compile error)
Fixed for list of dynamic <<Intendended><For>> fields

Fixed
Removed the redundant importlib dependency from the requirements (could cause an installation error)

Thanks marcpabst for reporting!

Fixed
Just a small bugfix release that prevents a possible `bidscoiner` crash for certain data acquisitions (e.g. for multi-echo data). It should be a safe upgrade for everyone using 3.6.0 (you can edit the `3.6.0` version string in the `Options` to `3.6.1` to get rid of the version conflict warning)

Added
- Support for BIDS v1.6.0 (-> PET)
- Separate tabs for DICOM and PAR to edit all the mappings of mixed datasets in a single bidseditor session
- Run-item matching on filesystem properties, i.e. on the pathname, filename and filesize and nr of files in the folder. This can be used in conjunction with the (DICOM/PAR) attributes
- A meta-data dictionary that can be edited with the bidseditor and that will be added to the json sidecar files by the bidscoiner
- More user feedback in the GUI for new BIDS-compliancy checks on missing or invalid bids data
- A right-click menu option to remove a run-item from the bidsmap (advanced usage)
- The option to load a new bidsmap in the bidseditor
- Enable the user to edit json, yaml, tsv and other non-DICOM / non-PAR files with double-clicks in the data browser
- A central 'bidscoin' package function with various utilities, such as listing and installing BIDScoin plugins or executables
- Plugins can have their own 'test' routine that can be called from the bidseditor

Changed
- Using regular expressions instead of fnmatch to match (template bidsmap) attribute values. This makes the templates more powerful and flexible
- Moved the bidsmapping and bidscoining functionality to stand-alone plugins (changed API), making plugins a first-class BIDScoin citizen
- The plugins have moved to the bidsmap['Options'], where they have their own key-value options dictionary (changed API)
- Move IntendedFor field over to the new meta-data dictionary
- Renamed the `leave_out` datatype to `exclude`
- Re-introduced skipping hidden folders (hidden files are also skipped)
- Moved the 'pulltutorial' function over to the new 'bidscoin' function

Removed
- P7 and nifti support (it was never implemented anyhow)
- The option to edit new mappings on-the-fly in the bidsmapper (`-i 2`)

Fixed
- Save non-standard fieldmaps in the derivative folder