Minor refactoring (renaming) and doc tweaks

bidscoin/__init__.py

@@ -56,23 +56,23 @@
 """
 
 # Define the default paths
-tracking         = {'url': 'https://telemetry.donders.ru.nl/bidscoin', 'sleep': 1}                  # Sleep = Nr of sleeping hours during which usage is not tracked
-tutorialurl      = 'https://surfdrive.surf.nl/files/index.php/s/HTxdUbykBZm2cYM/download'
-bidscoinfolder   = Path(__file__).parent
-schemafolder     = bidscoinfolder/'schema'
-pluginfolder     = bidscoinfolder/'plugins'
+tracking       = {'url': 'https://telemetry.donders.ru.nl/bidscoin', 'sleep': 1}        # Sleep = Nr of sleeping hours during which usage is not tracked
+tutorialurl    = 'https://surfdrive.surf.nl/files/index.php/s/HTxdUbykBZm2cYM/download'
+bidscoinfolder = Path(__file__).parent
+schemafolder   = bidscoinfolder/'schema'
+pluginfolder   = bidscoinfolder/'plugins'
 
 # Create a BIDScoin user configuration directory if needed and load the BIDScoin user settings
-configfile       = Path.home()/'.bidscoin'/__version__/'config.toml'
-heuristicsfolder = configfile.parent/'templates'
-heuristicsfolder.mkdir(parents=True, exist_ok=True)
+configfile     = Path.home()/'.bidscoin'/__version__/'config.toml'
+templatefolder = configfile.parent/'templates'
+templatefolder.mkdir(parents=True, exist_ok=True)
 if not configfile.is_file():
     configfile.write_text(f"[bidscoin]\n"
-                          f"bidsmap_template = '{configfile.parent}/templates/bidsmap_dccn.yaml'    # The default template bidsmap\n"
-                          f"trackusage       = 'yes'\t# Upload anonymous usage data if 'yes' (maximally 1 upload every {tracking['sleep']} hour) (see `bidscoin --tracking show`)\n")
+                          f"bidsmap_template = '{templatefolder}/bidsmap_dccn.yaml'     # The default template bidsmap (change to use a different default)\n"
+                          f"trackusage       = 'yes'     # Upload anonymous usage data if 'yes' (maximally 1 upload every {tracking['sleep']} hour) (see `bidscoin --tracking show`)\n")
 for template in (bidscoinfolder/'heuristics').glob('*.yaml'):
-    if not (heuristicsfolder/template.name).is_file():
-        shutil.copyfile(template, heuristicsfolder/template.name)
+    if not (templatefolder/template.name).is_file():
+        shutil.copyfile(template, templatefolder/template.name)
 with configfile.open('+rb') as fid:
     config = tomllib.load(fid)
 bidsmap_template = Path(config['bidscoin']['bidsmap_template'])
@@ -162,6 +162,6 @@ def trackusage(event: str, dryrun: bool=False) -> dict:
         req = urllib.request.Request(f"{tracking['url']}?{urllib.parse.urlencode(data)}", headers={'User-agent': 'bidscoin-telemetry'})
         with urllib.request.urlopen(req, timeout=5) as f: pass
     except urllib.error.URLError as urlerror:
-        print(urlerror)
+        print(f"{tracking['url']}:\n{urlerror}")
 
     return data

bidscoin/bcoin.py

@@ -23,7 +23,7 @@
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import heuristicsfolder, pluginfolder, bidsmap_template, tutorialurl, trackusage, tracking, configfile, config
+from bidscoin import templatefolder, pluginfolder, bidsmap_template, tutorialurl, trackusage, tracking, configfile, config
 
 yaml = YAML()
 
@@ -204,9 +204,9 @@ def list_plugins(show: bool=False) -> Tuple[List[Path], List[Path]]:
     :return:     List of the installed plugins and template bidsmaps
     """
 
-    if show: LOGGER.info(f"Installed template bidsmaps ({heuristicsfolder}):")
+    if show: LOGGER.info(f"Installed template bidsmaps ({templatefolder}):")
     templates = []
-    for template in heuristicsfolder.glob('*.yaml'):
+    for template in templatefolder.glob('*.yaml'):
         if template.stem != '__init__':
             templates.append(template)
             if show: LOGGER.info(f"- {template.stem}{' (default)' if template.samefile(bidsmap_template) else ''}")
@@ -241,7 +241,7 @@ def install_plugins(filenames: List[str]=()) -> None:
     for file in files:
 
         # Copy the file to their target folder
-        targetfolder = heuristicsfolder if file.suffix == '.yaml' else pluginfolder
+        targetfolder = templatefolder if file.suffix == '.yaml' else pluginfolder
         LOGGER.info(f"Installing: '{file}'")
         try:
             shutil.copyfile(file, targetfolder/file.name)
@@ -301,7 +301,7 @@ def uninstall_plugins(filenames: List[str]=(), wipe: bool=True) -> None:
 
         # Remove the file from the target folder
         LOGGER.info(f"Uninstalling: '{file}'")
-        sourcefolder = heuristicsfolder if file.suffix == '.yaml' else pluginfolder
+        sourcefolder = templatefolder if file.suffix == '.yaml' else pluginfolder
         try:
             (sourcefolder/file.name).unlink()
         except IOError as uninstall_error:

bidscoin/bids.py

@@ -28,7 +28,7 @@
 if find_spec('bidscoin') is None:
     import sys
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import bcoin, schemafolder, heuristicsfolder, bidsmap_template, lsdirs, __version__
+from bidscoin import bcoin, schemafolder, templatefolder, bidsmap_template, lsdirs, __version__
 from bidscoin.utilities import dicomsort
 from ruamel.yaml import YAML
 yaml = YAML()
@@ -866,7 +866,7 @@ def load_bidsmap(yamlfile: Path, folder: Path=Path(), plugins:Union[tuple,list]=
 
     # Input checking
     if not folder.name or not folder.is_dir():
-        folder = heuristicsfolder
+        folder = templatefolder
     if not yamlfile.name:
         yamlfile = folder/'bidsmap.yaml'
         if not yamlfile.is_file():
@@ -881,7 +881,7 @@ def load_bidsmap(yamlfile: Path, folder: Path=Path(), plugins:Union[tuple,list]=
         if (folder/yamlfile).is_file():
             yamlfile = folder/yamlfile
         else:
-            yamlfile = heuristicsfolder/yamlfile
+            yamlfile = templatefolder/yamlfile
 
     if not yamlfile.is_file():
         LOGGER.verbose(f"No existing bidsmap file found: {yamlfile}")
@@ -916,7 +916,7 @@ def load_bidsmap(yamlfile: Path, folder: Path=Path(), plugins:Union[tuple,list]=
         if not bidsmap['Options']['plugins'].get(plugin):
             LOGGER.info(f"Adding default bidsmap options from the {plugin} plugin")
             bidsmap['Options']['plugins'][plugin] = module.OPTIONS if 'OPTIONS' in dir(module) else {}
-        if 'BIDSMAP' in dir(module) and yamlfile.parent == heuristicsfolder:
+        if 'BIDSMAP' in dir(module) and yamlfile.parent == templatefolder:
             for dataformat, bidsmappings in module.BIDSMAP.items():
                 if dataformat not in bidsmap:
                     LOGGER.info(f"Adding default bidsmappings from the {plugin} plugin")

bidscoin/cli/_bcoin.py

@@ -7,7 +7,8 @@
   $ bidsmapper sourcefolder bidsfolder        # This produces a study bidsmap and launches a GUI
   $ bidscoiner sourcefolder bidsfolder        # This converts your data to BIDS according to the study bidsmap
 
-Set the environment variable BIDSCOIN_DEBUG=TRUE in your console to run BIDScoin in its more verbose DEBUG logging mode
+Set the environment variable BIDSCOIN_DEBUG=TRUE in your console to run BIDScoin in its more verbose DEBUG logging mode.
+Default setting are stored in the ".bidscoin" folder in your home directory
 
 For more documentation see: https://bidscoin.readthedocs.io
 """
@@ -46,7 +47,7 @@ def get_parser() -> argparse.ArgumentParser:
     parser.add_argument('-d', '--download',    help='Download tutorial MRI data to the DOWNLOAD folder')
     parser.add_argument('-t', '--test',        help='Test the bidscoin installation and template bidsmap', nargs='?', const=bidsmap_template)
     parser.add_argument('-b', '--bidsmaptest', help='Test the run-items and their bidsnames of all normal runs in the study bidsmap. Provide the bids-folder or the bidsmap filepath')
-    parser.add_argument(      '--tracking',    help='Show the usage tracking info [show], or set usage tracking to [yes] or [no]', choices=['yes','no','show'])
+    parser.add_argument(      '--tracking',    help='Show the usage tracking info {show}, or set usage tracking to {yes} or {no}', choices=['yes','no','show'])
     parser.add_argument('-v', '--version',     help='Show the installed version and check for updates', action='version', version=f"BIDS-version:\t\t{bidsversion()}\nBIDScoin-version:\t{__version__}, {versionmessage}")
 
     return parser

docs/CHANGELOG.md

@@ -10,7 +10,7 @@ All notable changes to this project will be documented in this file. The format
 - Optional usage tracking (github issue #200)
 
 ### Changed
-- The template bidsmaps are now stored in `[home]/.bidscoin/templates`
+- The template bidsmaps are now stored in `[home]/.bidscoin/[version]/templates`
 
 ## [4.1.1] - 2023-09-14
 

docs/bidsmap.rst

@@ -81,7 +81,7 @@ The run-items in the default 'bidsmap_dccn' template bidsmap have values that ar
 - Finally, it is a good practice for the first run-item in each BIDS datatype section of your template bidsmap to have all empty `properties` and `attributes` values. The benefit of this is that you can dereference ('copy') it in other run-items (see the editing section below), and in this way improve your consistency and reduce the maintenance burden of keeping your template bidsmap up-to-date. The first run-item is also the item that is selected when a user manually sets the run-item to this BIDS datatype in the bidseditor GUI.
 
 .. tip::
-   - Make a copy of the DCCN template (``[home]/.bidscoin/templates/bidsmap_dccn.yaml``) as a starting point for your own template bidsmap, and adapt it to your needs. You can set your copy as the new default by editing the ``[home]/.bidscoin/config.toml`` file.
+   - Make a copy of the DCCN template (``[home]/.bidscoin/[version]/templates/bidsmap_dccn.yaml``) as a starting point for your own template bidsmap, and adapt it to your needs. You can set your copy as the new default template by editing the ``[home]/.bidscoin/config.toml`` file. Default templates and config file are automatically recreated from source when deleted
    - The power of regular expressions is nearly unlimited, you can e.g. use `negative look aheads <https://docs.python.org/3/howto/regex.html#lookahead-assertions>`__ to **not** match (exclude) certain strings
    - When creating new run-items, make sure to adhere to the YAML format and to the definitions in the BIDS schema files (``[path_to_bidscoin]/bidscoin/schema/datatypes``). You can test your YAML syntax using an online `YAML-validator <https://www.yamllint.com>`__ and your compliance with the BIDS standard with ``bidscoin -t your_template_bidsmap``. If all seems well you can install it using ``bidscoin -i your_template_bidsmap``.
 
@@ -148,6 +148,3 @@ Editing the template bidsmap
        suffix: T2w
 
 *Snippet derived from the bidsmap_dccn template, showing a "DICOM" section with a void "anat" run-item and two normal run-items that dereference the first run-item* (e.g. the ``&anatattributes_dicom`` anchor is dereferenced with the ``<<: *anatattributes_dicom`` alias)
-
-.. tip::
-   The path of the default template bidsmap is set in the ``.bidscoin'/version/'config.toml`` file in your home directory

docs/installation.rst

@@ -63,7 +63,7 @@ Dcm2niix installation
 
 The default 'dcm2niix2bids' plugin relies on an external application named `dcm2niix <https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage>`__ for converting DICOM and PAR/REC source data to NIfTI. To use the plugin you must pip-install dcm2niix when installing BIDScoin or install it yourself (e.g. when pip-installing dcm2niix does not work for your platform) as explained in the `dcm2niix installation instructions <https://github.com/rordenlab/dcm2niix#install>`__. When done, make sure that the dcm2niix executable is on your user or system path (Windows users can add the path permanently, e.g. by running: ``setx path "%path%;C:\Program Files\dcm2niix"``). Otherwise (for instance when you want to use the linux module system or fixate the software version), make sure that the command to run the dcm2niix executable (exactly as if you would run it yourself in your command terminal) is set correctly in the `Options`_ section in your bidsmap. This can be done in two ways:
 
-1. Open your template bidsmap with a text editor and adjust the settings as needed. The default template bidsmap is located in your ``[home]/.bidscoin/templates`` folder (see the output of ``bidscoin -p`` for the fullpath location on your system).
+1. Open your template bidsmap with a text editor and adjust the settings as needed. The default template bidsmap is located in your ``[home]/.bidscoin/[version]/templates`` folder (see the output of ``bidscoin -p`` for the fullpath location on your system).
 2. Go to the `Options`_ tab the first time the BIDScoin GUI is launched and adjust the settings as needed. Then click the [Set as default] button to save the settings to your default template bidsmap.
 
 .. tip::

docs/options.rst

@@ -9,7 +9,7 @@ BIDScoin has different options and settings (see below) that can be adjusted per
    The bidseditor options window with the different settings for BIDScoin and its plugins. The user can manage the plugins that will be used with the [Add] (as shown here) and [Remove] buttons, and save the current options to the template bidsmap by using the [Set as default] button.
 
 .. note::
-   A few more adjustable global settings can be found in the ``.bidscoin'/version/'config.toml`` file in your home directory
+   A few more adjustable global settings can be found in your ``[home]/.bidscoin'/[version]/'config.toml`` file (the original file will be automatically recreated from source when deleted)
 
 BIDScoin
 --------

tests/test_bcoin.py

@@ -6,7 +6,7 @@
 bcoin.setup_logging()
 
 assert bidscoin.schemafolder.is_dir()
-assert bidscoin.heuristicsfolder.is_dir()
+assert bidscoin.templatefolder.is_dir()
 assert bidscoin.pluginfolder.is_dir()
 assert bidscoin.bidsmap_template.is_file()