diff --git a/.github/workflows/codespell.yaml b/.github/workflows/codespell.yaml new file mode 100644 index 0000000..3deac45 --- /dev/null +++ b/.github/workflows/codespell.yaml @@ -0,0 +1,22 @@ +--- +name: Codespell + +on: + push: + branches: [develop] + pull_request: + branches: [develop] + +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 \ No newline at end of file diff --git a/docs/source/FileRemodelingTools.md b/docs/source/FileRemodelingTools.md index cf1b5fd..5f45133 100644 --- a/docs/source/FileRemodelingTools.md +++ b/docs/source/FileRemodelingTools.md @@ -849,8 +849,8 @@ The resulting columns are called *stopped* and *stop_failed*, respectively. ```json [{ - "operation": "factor_column" - "description": "Create factors for the succesful_stop and unsuccesful_stop values." + "operation": "factor_column", + "description": "Create factors for the succesful_stop and unsuccesful_stop values.", "parameters": { "column_name": "trial_type", "factor_values": ["succesful_stop", "unsuccesful_stop"], @@ -923,12 +923,12 @@ The resulting factor columns are named *correct* and *incorrect*, respectively. ```json [{ - "operation": "factor_hed_tags" - "description": "Create factors based on whether the event represented a correct or incorrect action.", + "operation": "factor_hed_tags", + "description": "Create factors based on whether the event represented a correct or incorrect action.",, "parameters": { "queries": ["correct-action", "incorrect-action"], - "query-names": ["correct", "incorrect"], - "remove-types": [], + "query_names": ["correct", "incorrect"], + "remove_types": [], "expand_context": false } }] @@ -995,8 +995,8 @@ applies and 0's otherwise. ```json [{ - "operation": "factor_hed_type" - "description": "Factor based on the sex of the images being presented." + "operation": "factor_hed_type", + "description": "Factor based on the sex of the images being presented.", "parameters": { "type_tag": "Condition-variable", "type_values": [] @@ -1075,8 +1075,8 @@ have the same values to be merged into a single event. ```json [{ - "operation": "merge_consecutive" - "description": "Merge consecutive *succesful_stop* events that match the *match_columns." + "operation": "merge_consecutive", + "description": "Merge consecutive *succesful_stop* events that match the *match_columns.", "parameters": { "column_name": "trial_type", "event_code": "succesful_stop", diff --git a/docs/source/HedConditionsAndDesignMatrices.md b/docs/source/HedConditionsAndDesignMatrices.md index 72e4b4c..d6223be 100644 --- a/docs/source/HedConditionsAndDesignMatrices.md +++ b/docs/source/HedConditionsAndDesignMatrices.md @@ -346,7 +346,7 @@ Example 9 shows the portion of the [**task-facePerception_events.json**](./_static/data/task-FacePerception_events.json) that encodes information about the *setup_right_sym* event found as the first event in the event file excerpt of Example 8. -This excerpt only contains the relevent definition and the relevant annotation. +This excerpt only contains the relevant definition and the relevant annotation. ````{admonition} Example 9: Excerpt of the JSON sidecar relevant to the *setup_right_sym* event. diff --git a/docs/source/HedMatlabTools.md b/docs/source/HedMatlabTools.md index a70cf7c..da717a2 100644 --- a/docs/source/HedMatlabTools.md +++ b/docs/source/HedMatlabTools.md @@ -329,7 +329,7 @@ in the *EEG.event* data structure in sufficient detail that anyone using the dat in the future will not need to find and read a separate, detailed description of the dataset or study to understand the recorded experimental events. As demonstrated below, such annotation will allow us to extract epochs using meaningful -HED tags instead of the alpha-numeric codes often associated with shared EEG data. +HED tags instead of the alphanumeric codes often associated with shared EEG data. #### Launching EEGLAB HEDTools To add and view HED tags for the dataset, from EEGLAB menu, select: @@ -608,7 +608,7 @@ to indicate the command line version. Use the MATLAB `pyenv` function again without arguments to check that your installation is as expected. -````{Admonition} Example response for pyenv all with no argments after setting environment. +````{Admonition} Example response for pyenv all with no arguments after setting environment. ```matlab PythonEnvironment with properties: diff --git a/docs/source/HedOnlineTools.md b/docs/source/HedOnlineTools.md index f8c880c..b226c2f 100644 --- a/docs/source/HedOnlineTools.md +++ b/docs/source/HedOnlineTools.md @@ -406,7 +406,7 @@ The non-HED portions of the spreadsheet and the prefix-columns are the same as i **Returns:** If there are any errors, the tool returns a downloadable `.txt` file of error messages, -otherise the tool returns a downloadable spreadsheet with the HED tags converted to short. +otherwise the tool returns a downloadable spreadsheet with the HED tags converted to short. `````` (strings-online-tools-anchor)= diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md index e57b101..2bec120 100644 --- a/docs/source/HedPythonTools.md +++ b/docs/source/HedPythonTools.md @@ -290,9 +290,7 @@ file_list = get_file_list(bids_root_path, extensions=[ ".json", ".tsv"], name_su The HED tools provide both generic and BIDS-specific classes for dictionaries of filenames. - -The -Many of the HED data processing tools make extensive use of dictionaries specif +Many of the HED data processing tools make extensive use of dictionaries specifying both data and format. #### BIDS-specific dictionaries of files @@ -436,7 +434,7 @@ and then to log each processing step using the file's key. This allows a processing step to be applied to all the relevant files in the dataset. After all the processing is complete, the `print_log` method outputs the logged messages by key, thus showing all the -processing steps that hav been applied to each file +processing steps that have been applied to each file as shown in the [**previous example**](example-output-hed-logger-anchor). (using-hed-logger-example-anchor)= diff --git a/docs/source/HedSchemaDevelopersGuide.md b/docs/source/HedSchemaDevelopersGuide.md index 74c494e..04c5448 100644 --- a/docs/source/HedSchemaDevelopersGuide.md +++ b/docs/source/HedSchemaDevelopersGuide.md @@ -310,7 +310,7 @@ Drive has tags of interest to driving experiments. ``` ```` -Notice that this schema does not include any auxilliary sections --- these are inherited +Notice that this schema does not include any auxiliary sections --- these are inherited from the standard schema. This schema would be saved in a MediaWiki file called `HED_drive_0.0.1.mediawiki`. diff --git a/docs/source/HedSearchGuide.md b/docs/source/HedSearchGuide.md index ec80019..9bff91a 100644 --- a/docs/source/HedSearchGuide.md +++ b/docs/source/HedSearchGuide.md @@ -127,7 +127,7 @@ The tag short forms are used for the matching to assure consistency. Matching using a tag prefix with the `*` wildcard, matches the starting portion of the tag. Thus, Age/3* matches *Age/3* as well as *Age/34*. -Notice that the query Age* matches a myraid of tags including *Agent*, *Agent-state*, +Notice that the query Age* matches a myriad of tags including *Agent*, *Agent-state*, and *Agent-property*. ### Logical queries diff --git a/setup.cfg b/setup.cfg index cb5476a..5c83106 100644 --- a/setup.cfg +++ b/setup.cfg @@ -57,4 +57,8 @@ style = pep440 versionfile_source = hedcode/_version.py versionfile_build = hedcode/_version.py tag_prefix = -parentdir_prefix = hedcode- \ No newline at end of file +parentdir_prefix = hedcode- + +[codespell] +skip = '*.git,*.pdf,*.xml,*.mediawiki,*.svg,versioneer.py,venv*,*.tsv,*.yaml,*.yml,*.json,*.rdf,*.jsonld,datasets*,' +ignore-words-list = 'te,parms'