Merge pull request #216 from yarikoptic/enh-codespell

Add codespell: configuration, workflow + make it fix some typos

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

bidscoin/bcoin.py

@@ -557,7 +557,7 @@ def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins
                     LOGGER.warning(f"Failed test: {plugin.stem}")
 
     if not success:
-        LOGGER.warning('Not all tests finishd successfully (this may be ok, but check the output above)')
+        LOGGER.warning('Not all tests finished successfully (this may be ok, but check the output above)')
         trackusage('bidscoin_error')
     else:
         LOGGER.success('All tests finished successfully :-)')

bidscoin/bids.py

@@ -853,7 +853,7 @@ def load_bidsmap(yamlfile: Path, folder: Path=Path(), plugins:Union[tuple,list]=
     """
     Read the mapping heuristics from the bidsmap yaml-file. If yamlfile is not fullpath, then 'folder' is first searched before
     the default 'heuristics'. If yamfile is empty, then first 'bidsmap.yaml' is searched for, then 'bidsmap_template'. So fullpath
-    has precendence over folder and bidsmap.yaml has precedence over the bidsmap_template.
+    has precedence over folder and bidsmap.yaml has precedence over the bidsmap_template.
 
     NB: A run['datasource'] = DataSource object is added to every run-item
 

bidscoin/bidseditor.py

@@ -349,7 +349,7 @@ def set_tab_bidsmap(self, dataformat):
     def set_tab_options(self):
         """Set the options tab"""
 
-        # Create the bidscoin tabel
+        # Create the bidscoin table
         bidscoin_options = self.output_bidsmap['Options']['bidscoin']
         self.options_label['bidscoin'] = bidscoin_label = QLabel('BIDScoin')
         bidscoin_label.setToolTip(TOOLTIP_BIDSCOIN)
@@ -376,7 +376,7 @@ def set_tab_options(self):
         layout.addWidget(bidscoin_label)
         layout.addWidget(bidscoin_table)
 
-        # Add the plugin tabels
+        # Add the plugin tables
         for plugin, options in self.output_bidsmap['Options']['plugins'].items():
             plugin_label, plugin_table = self.plugin_table(plugin, options)
             layout.addWidget(plugin_label)
@@ -1182,7 +1182,7 @@ def fill_table(self, table: QTableWidget, data: list):
                 suffix_dropdown.addItems(suffixes)
                 suffix_dropdown.setCurrentIndex(suffix_dropdown.findText(suffix))
                 suffix_dropdown.currentIndexChanged.connect(self.suffix_dropdown_change)
-                suffix_dropdown.setToolTip('The suffix that sets the different run types apart. First make sure the "Data type" dropdown-menu is set correctly before chosing the right suffix here')
+                suffix_dropdown.setToolTip('The suffix that sets the different run types apart. First make sure the "Data type" dropdown-menu is set correctly before choosing the right suffix here')
                 for n, suffix in enumerate(suffixes):
                     suffix_dropdown.setItemData(n, bids.get_suffixhelp(suffix, self.target_datatype), QtCore.Qt.ItemDataRole.ToolTipRole)
                 table.setCellWidget(i, 1, self.spacedwidget(suffix_dropdown))
@@ -1490,7 +1490,7 @@ def accept_run(self):
             self.done(2)
 
     def export_run(self):
-        """Export the editted run to a (e.g. template) bidsmap on disk"""
+        """Export the edited run to a (e.g. template) bidsmap on disk"""
 
         yamlfile, _ = QFileDialog.getOpenFileName(self, 'Export run item to (template) bidsmap',
                                                   str(bidsmap_template), 'YAML Files (*.yaml *.yml);;All Files (*)')

bidscoin/cli/_bidsmapper.py

@@ -39,7 +39,7 @@ def get_parser() -> argparse.ArgumentParser:
     parser.add_argument('-n','--subprefix',   help="The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'sub-'")
     parser.add_argument('-m','--sesprefix',   help="The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'ses-'")
     parser.add_argument('-u','--unzip',       help='Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap')
-    parser.add_argument('-s','--store',       help='Store provenance data samples in the bidsfolder/code/provenance folder (useful for inspecting e.g. zipped or transfered datasets)', action='store_true')
+    parser.add_argument('-s','--store',       help='Store provenance data samples in the bidsfolder/code/provenance folder (useful for inspecting e.g. zipped or transferred datasets)', action='store_true')
     parser.add_argument('-a','--automated',   help='Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor', action='store_true')
     parser.add_argument('-f','--force',       help='Discard the previously saved bidsmap and logfile', action='store_true')
     parser.add_argument('--no-update',        help="Do not update any sub/sesprefixes in or prepend the sourcefolder name to the <<filepath:regex>> expression that extracts the subject/session labels. This is normally done to make the extraction more robust, but could cause problems for certain use cases", action='store_true')

bidscoin/plugins/dcm2niix2bids.py

@@ -272,7 +272,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
         bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
         isbids   = BIDSValidator().is_bids(bidstest)
         if not isbids and not bidsignore:
-            LOGGER.warning(f"The '{bidstest}' ouput name did not pass the bids-validator test")
+            LOGGER.warning(f"The '{bidstest}' output name did not pass the bids-validator test")
 
         # Check if the output file already exists (-> e.g. when a static runindex is used)
         if (outfolder/bidsname).with_suffix('.json').is_file():

bidscoin/plugins/nibabel2bids.py

@@ -220,7 +220,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> None:
         bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
         isbids   = BIDSValidator().is_bids(bidstest)
         if not isbids and not bidsignore:
-            LOGGER.warning(f"The '{bidstest}' ouput name did not pass the bids-validator test")
+            LOGGER.warning(f"The '{bidstest}' output name did not pass the bids-validator test")
 
         # Check if file already exists (-> e.g. when a static runindex is used)
         if bidsfile.is_file():

bidscoin/plugins/spec2nii2bids.py

@@ -230,7 +230,7 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None
         bidstest = (Path('/')/subid/sesid/datasource.datatype/bidsname).with_suffix('.json').as_posix()
         isbids   = BIDSValidator().is_bids(bidstest)
         if not isbids and not bidsignore:
-            LOGGER.warning(f"The '{bidstest}' ouput name did not pass the bids-validator test")
+            LOGGER.warning(f"The '{bidstest}' output name did not pass the bids-validator test")
 
         # Check if file already exists (-> e.g. when a static runindex is used)
         if sidecar.is_file():

docs/bidsmap.rst

@@ -110,7 +110,7 @@ Editing the template bidsmap
        filename:                    # File name, e.g. ".*fmap.*" or ".*(fmap|field.?map|B0.?map).*"
        filesize:                    # File size, e.g. "2[4-6]\d MB" for matching files between 240-269 MB
        nrfiles:                     # Number of files in the folder that match the above criteria, e.g. "5/d/d" for matching a number between 500-599
-     attributes: &anat_dicomattr    # An empty / non-matching "reference" dictionary that can be derefenced in other run-items of this data type
+     attributes: &anat_dicomattr    # An empty / non-matching "reference" dictionary that can be dereferenced in other run-items of this data type
        Modality:
        ProtocolName:
        SeriesDescription:

docs/plugins.rst

@@ -189,7 +189,7 @@ As can be seen in the API code snippet below (but also see the default plugins f
    def bidsmapper_plugin(session: Path, bidsmap_new: dict, bidsmap_old: dict, template: dict, store: dict) -> None:
        """
        All the logic to map the Philips PAR/REC fields onto bids labels go into this plugin function. The function is
-       expecte to update / append new runs to the bidsmap_new data structure. The bidsmap options for this plugin can
+       expected to update / append new runs to the bidsmap_new data structure. The bidsmap options for this plugin can
        be found in:
 
        bidsmap_new/old['Options']['plugins']['README']

docs/workflow.rst

@@ -71,7 +71,7 @@ Step 1a: Running the bidsmapper
                             need to be unzipped (in a tempdir) to make the data readable. Default: the
                             value of the study/template bidsmap
       -s, --store           Store provenance data samples in the bidsfolder/code/provenance folder
-                            (useful for inspecting e.g. zipped or transfered datasets)
+                            (useful for inspecting e.g. zipped or transferred datasets)
       -a, --automated       Save the automatically generated bidsmap to disk and without interactively
                             tweaking it with the bidseditor
       -f, --force           Discard the previously saved bidsmap and logfile
@@ -151,7 +151,7 @@ If the preview of the BIDS filename and meta-data both look good, you can store
 
    The edit window for customizing a bidsmap run item, featuring the DICOM attributes mapped onto BIDS values and (dynamic) metadata values (e.g. ``Comments``). BIDS values that are restricted to a limited set are presented with a drop-down menu.
 
-Finally, if all BIDS output names in the main window are fine, you can click on the [Save] button and proceed with running the bidscoiner tool (step 2). Note that re-running the bidsmapper or bidseditor is always a safe thing to do since these tools will re-use the existing bidsmap yaml-file and will not delete or write anything to disk except to the bidsmap yaml-file.
+Finally, if all BIDS output names in the main window are fine, you can click on the [Save] button and proceed with running the bidscoiner tool (step 2). Note that re-running the bidsmapper or bidseditor is always a safe thing to do since these tools will reuse the existing bidsmap yaml-file and will not delete or write anything to disk except to the bidsmap yaml-file.
 
 Field maps
 ``````````

pyproject.toml

@@ -118,3 +118,10 @@ commands         = make -C docs html
                    linkchecker docs/_build/html/index.html
                    pyspelling -c docs/.pyspelling.yml
 """
+
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,go.sum'
+check-hidden = true
+ignore-regex = '\b(PULS|TE|ALS)\b'
+ignore-words-list = 'compliancy,uptodate,mis'