From 252ede33155272c8f09acac8c384a055752c1faf Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 20 Sep 2023 11:42:06 -0400 Subject: [PATCH 1/6] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..3ebbf55 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,22 @@ +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +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 From 74319354b76cac957c1d6ff48b61040511d2677b Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 20 Sep 2023 11:42:06 -0400 Subject: [PATCH 2/6] Add rudimentary codespell config --- .codespellrc | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 0000000..7bc54b3 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,4 @@ +[codespell] +skip = .git,*.pdf,*.svg,versioneer.py +# +# ignore-words-list = From 3e4a8353ebf61add3890c0cb23ac6de287befdb2 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 20 Sep 2023 11:43:09 -0400 Subject: [PATCH 3/6] fix ambigous typo --- docs/source/HedPythonTools.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md index e57b101..75b5629 100644 --- a/docs/source/HedPythonTools.md +++ b/docs/source/HedPythonTools.md @@ -436,7 +436,7 @@ 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)= From e3d62533b0dd5f851065f89f1e41dce9bf7576ff Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 20 Sep 2023 11:43:22 -0400 Subject: [PATCH 4/6] ignore bids per sub json files and word covert --- .codespellrc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.codespellrc b/.codespellrc index 7bc54b3..5e2191d 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,4 +1,4 @@ [codespell] -skip = .git,*.pdf,*.svg,versioneer.py +skip = .git,*.pdf,*.svg,versioneer.py,sub-*.json # -# ignore-words-list = +ignore-words-list = covert From ce6a2842d14396f6a056790b090d8f6a34dbabaa Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 20 Sep 2023 11:45:05 -0400 Subject: [PATCH 5/6] Remove incomplete thought (I think it is not needed there) --- docs/source/HedPythonTools.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/source/HedPythonTools.md b/docs/source/HedPythonTools.md index 75b5629..9a8a683 100644 --- a/docs/source/HedPythonTools.md +++ b/docs/source/HedPythonTools.md @@ -290,10 +290,6 @@ 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 - #### BIDS-specific dictionaries of files Files in BIDS have unique names that indicate not only what the file represents, From 16cd5201c9534b5e251ed48833498d9d2400e0b4 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 20 Sep 2023 11:45:10 -0400 Subject: [PATCH 6/6] [DATALAD RUNCMD] run codespell throughout fixing typo automagically === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- datasets/eeg_ds002893s_hed_attention_shift/README | 2 +- .../fmri_ds002790s_hed_aomic/participants.json | 2 +- docs/source/HedConditionsAndDesignMatrices.md | 2 +- docs/source/HedMatlabTools.md | 4 ++-- docs/source/HedOnlineTools.md | 2 +- docs/source/HedSchemaDevelopersGuide.md | 2 +- docs/source/HedSearchGuide.md | 2 +- hedcode/data/schema_data/HED7.2.0.xml | 4 ++-- hedcode/data/schema_data/HED8.0.0.mediawiki | 14 +++++++------- hedcode/data/schema_data/HED8.0.0.xml | 14 +++++++------- hedcode/data/schema_data/HED8.0.1.xml | 12 ++++++------ 11 files changed, 30 insertions(+), 30 deletions(-) diff --git a/datasets/eeg_ds002893s_hed_attention_shift/README b/datasets/eeg_ds002893s_hed_attention_shift/README index afdbd5d..9b2113a 100644 --- a/datasets/eeg_ds002893s_hed_attention_shift/README +++ b/datasets/eeg_ds002893s_hed_attention_shift/README @@ -58,7 +58,7 @@ between 200 and 800 ms. **Note 1**: ERP measure results for the FA and FV conditions only were presented in Ceponiene, R., Westerfield, M., Torki, M. and Townsend, J., 2008. Modality-specificity of sensory aging in vision and audition: evidence from event-related potentials.?Brain research,?1215, pp.53-68. Some unpublished results by Christian Kothe and Scott Makeig on the SH condition may be available from the authors . -**Note 2**: The code subdirectory has several auxilliary files that were produced during +**Note 2**: The code subdirectory has several auxiliary files that were produced during the curation process. The curation was done using a series of Jupyter notebooks that are available as run in the code/curation_notebooks subdirectory. diff --git a/datasets/fmri_ds002790s_hed_aomic/participants.json b/datasets/fmri_ds002790s_hed_aomic/participants.json index 00aac70..51a94cf 100644 --- a/datasets/fmri_ds002790s_hed_aomic/participants.json +++ b/datasets/fmri_ds002790s_hed_aomic/participants.json @@ -34,7 +34,7 @@ "Description": "Self-reported religious affiliation", "Levels": { "no": "No religious affiliation", - "yes": "Considers him/herself to be religous" + "yes": "Considers him/herself to be religious" } }, "raven_score": { 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/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 d6d17e1..88ad1c0 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/hedcode/data/schema_data/HED7.2.0.xml b/hedcode/data/schema_data/HED7.2.0.xml index d62c07a..a6fbeb8 100644 --- a/hedcode/data/schema_data/HED7.2.0.xml +++ b/hedcode/data/schema_data/HED7.2.0.xml @@ -280,7 +280,7 @@ From version 2.2, HED adheres to http://semver.org/ versioning. Object - Visually discernable objects. This item excludes sounds that are Items but not objects + Visually discernible objects. This item excludes sounds that are Items but not objects Vehicle @@ -3645,7 +3645,7 @@ From version 2.2, HED adheres to http://semver.org/ versioning. Pyramids and palm trees task - Rapid automatized naming test + Rapid automated naming test Rapid serial object transformation diff --git a/hedcode/data/schema_data/HED8.0.0.mediawiki b/hedcode/data/schema_data/HED8.0.0.mediawiki index 3a68cfe..bc4cbf3 100644 --- a/hedcode/data/schema_data/HED8.0.0.mediawiki +++ b/hedcode/data/schema_data/HED8.0.0.mediawiki @@ -170,7 +170,7 @@ This schema is the first official release that includes an xsd and requires unit ** Learn [Adaptively change behavior as the result of experience.] ** Memorize [Adaptively change behavior as the result of experience.] ** Plan [Think about the activities required to achieve a desired goal. ] -** Predict [Say or estimate that something will happen or will be a consequence of something without having exact informaton.] +** Predict [Say or estimate that something will happen or will be a consequence of something without having exact information.] ** Recognize [Identify someone or something from having encountered them before.] ** Respond [React to something such as a treatment or a stimulus.] ** Recall [Remember information by mental effort.] @@ -324,7 +324,7 @@ This schema is the first official release that includes an xsd and requires unit ***** Clock [A device designed to indicate the time of day or to measure the time duration of an event or action.] ****** Clock-face [A location identifier based on clockface numbering or anatomic subregion.] **** Robot [A mechanical device that sometimes resembles a living animal and is capable of performing a variety of often complex human tasks on command or by being programmed in advance.] -**** Tool [A component that is not part of a device but is designed to support its assemby or operation.] +**** Tool [A component that is not part of a device but is designed to support its assembly or operation.] *** Document [A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.] **** Letter [A written message addressed to a person or organization.] **** Note [A brief written record.] @@ -370,7 +370,7 @@ This schema is the first official release that includes an xsd and requires unit **** Cart [A cart is a vehicle which has two wheels and is designed to transport human passengers or cargo.] **** Tractor [A mobile machine specifically designed to deliver a high tractive effort at slow speeds, and mainly used for the purposes of hauling a trailer or machinery used in agriculture or construction.] **** Train [A connected line of railroad cars with or without a locomotive.] -**** Truck [A motor vehicle which, as its primary funcion, transports cargo rather than human passangers.] +**** Truck [A motor vehicle which, as its primary function, transports cargo rather than human passangers.] ** Natural-object [Something that exists in or is produced by nature, and is not artificial or man-made.] *** Mineral [A solid, homogeneous, inorganic substance occurring in nature and having a definite chemical composition.] *** Natural-feature [A feature that occurs in nature. A prominent or identifiable aspect, region, or site of interest.] @@ -380,7 +380,7 @@ This schema is the first official release that includes an xsd and requires unit **** River [A natural freshwater surface stream of considerable volume and a permanent or seasonal flow, moving in a definite channel toward a sea, lake, or another river.] **** Waterfall [A sudden descent of water over a step or ledge in the bed of a river.] * Sound [Mechanical vibrations transmitted by an elastic medium. Something that can be heard.] -** Environmental-sound[Sounds occuring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities.] +** Environmental-sound[Sounds occurring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities.] *** Crowd-sound [Noise produced by a mixture of sounds from a large group of people.] *** Signal-noise [Any part of a signal that is not the true or original signal but is introduced by the communication mechanism.] ** Musical-sound [Sound produced by continuous and regular vibrations, as opposed to noise.] @@ -581,7 +581,7 @@ This schema is the first official release that includes an xsd and requires unit **** Weight [The relative mass or the quantity of matter contained by something.] ***** # {takesValue, valueClass=numericClass, unitClass=weightUnits} *** Quantitative-value [Something capable of being estimated or expressed with numeric values.] -**** Fraction [A numerical value betwee 0 and 1.] +**** Fraction [A numerical value between 0 and 1.] ***** # {takesValue, valueClass=numericClass} **** Item-count [The integer count of something which is usually grouped with the entity it is counting. (Item-count/3, A) indicates that 3 of A have occurred up to this point.] ***** # {takesValue, valueClass=numericClass} @@ -608,7 +608,7 @@ This schema is the first official release that includes an xsd and requires unit ***** # {takesValue, valueClass=numericClass} **** Statistical-precision [A quantitative representation of the degree of accuracy necessary for or associated with a particular action.] ***** # {takesValue, valueClass=numericClass} -**** Statistical-recall [Sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1.] +**** Statistical-recall [Sensitivity is a measurement datum qualifying a binary classification test and is computed by subtracting the false negative rate to the integral numeral 1.] ***** # {takesValue, valueClass=numericClass} **** Statistical-uncertainty [A measure of the inherent variability of repeated observation measurements of a quantity including quantities evaluated by statistical methods and by other means.] ***** # {takesValue, valueClass=numericClass} @@ -689,7 +689,7 @@ This schema is the first official release that includes an xsd and requires unit ** Urban [Relating to, located in, or characteristic of a city or densely populated area.] ** Rural [Of or pertaining to the country as opposed to the city.] ** Terrain [Characterization of the physical features of a tract of land.] -*** Composite-terrain [Tracts of land characterized by a mixure of physical features.] +*** Composite-terrain [Tracts of land characterized by a mixture of physical features.] *** Dirt-terrain [Tracts of land characterized by a soil surface and lack of vegetation.] *** Grassy-terrain [Tracts of land covered by grass.] *** Gravel-terrain [Tracts of land covered by a surface consisting a loose aggregation of small water-worn or pounded stones.] diff --git a/hedcode/data/schema_data/HED8.0.0.xml b/hedcode/data/schema_data/HED8.0.0.xml index 24a5241..d781e5a 100644 --- a/hedcode/data/schema_data/HED8.0.0.xml +++ b/hedcode/data/schema_data/HED8.0.0.xml @@ -770,7 +770,7 @@ Predict - Say or estimate that something will happen or will be a consequence of something without having exact informaton. + Say or estimate that something will happen or will be a consequence of something without having exact information. Recognize @@ -1397,7 +1397,7 @@ Tool - A component that is not part of a device but is designed to support its assemby or operation. + A component that is not part of a device but is designed to support its assembly or operation. @@ -1581,7 +1581,7 @@ Truck - A motor vehicle which, as its primary funcion, transports cargo rather than human passangers. + A motor vehicle which, as its primary function, transports cargo rather than human passangers. @@ -1623,7 +1623,7 @@ Mechanical vibrations transmitted by an elastic medium. Something that can be heard. Environmental-sound - Sounds occuring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities. + Sounds occurring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities. Crowd-sound Noise produced by a mixture of sounds from a large group of people. @@ -2751,7 +2751,7 @@ Something capable of being estimated or expressed with numeric values. Fraction - A numerical value betwee 0 and 1. + A numerical value between 0 and 1. # @@ -2940,7 +2940,7 @@ Statistical-recall - Sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1. + Sensitivity is a measurement datum qualifying a binary classification test and is computed by subtracting the false negative rate to the integral numeral 1. # @@ -3526,7 +3526,7 @@ Characterization of the physical features of a tract of land. Composite-terrain - Tracts of land characterized by a mixure of physical features. + Tracts of land characterized by a mixture of physical features. Dirt-terrain diff --git a/hedcode/data/schema_data/HED8.0.1.xml b/hedcode/data/schema_data/HED8.0.1.xml index 402a32f..bc13075 100644 --- a/hedcode/data/schema_data/HED8.0.1.xml +++ b/hedcode/data/schema_data/HED8.0.1.xml @@ -770,7 +770,7 @@ Predict - Say or estimate that something will happen or will be a consequence of something without having exact informaton. + Say or estimate that something will happen or will be a consequence of something without having exact information. Recognize @@ -1397,7 +1397,7 @@ Tool - A component that is not part of a device but is designed to support its assemby or operation. + A component that is not part of a device but is designed to support its assembly or operation. @@ -1581,7 +1581,7 @@ Truck - A motor vehicle which, as its primary funcion, transports cargo rather than human passangers. + A motor vehicle which, as its primary function, transports cargo rather than human passangers. @@ -1623,7 +1623,7 @@ Mechanical vibrations transmitted by an elastic medium. Something that can be heard. Environmental-sound - Sounds occuring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities. + Sounds occurring in the environment. An accumulation of noise pollution that occurs outside. This noise can be caused by transport, industrial, and recreational activities. Crowd-sound Noise produced by a mixture of sounds from a large group of people. @@ -2948,7 +2948,7 @@ Statistical-recall - Sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1. + Sensitivity is a measurement datum qualifying a binary classification test and is computed by subtracting the false negative rate to the integral numeral 1. # @@ -3534,7 +3534,7 @@ Characterization of the physical features of a tract of land. Composite-terrain - Tracts of land characterized by a mixure of physical features. + Tracts of land characterized by a mixture of physical features. Dirt-terrain