Feature/precommit codespell

.codespellignore

@@ -0,0 +1,5 @@
+createR
+afterAll
+xdescribe
+optinist
+Optinist

.pre-commit-config.yaml

@@ -26,3 +26,9 @@ repos:
     rev: 6.1.0
     hooks:
     -   id: flake8
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    -   id: codespell
+        additional_dependencies:
+        -   tomli

.readthedocs.yaml

@@ -11,4 +11,4 @@ sphinx:
   configuration: docs/conf.py
 python:
   install:
-  - requirements: docs/requirements.txt
+  - requirements: docs/requirements.txt

README.md

@@ -41,7 +41,7 @@ OptiNiSt also supports reproducibility of scientific research, standardization o
 
 ### Postprocessing
 - [x] Basic Neural Analysis(Event Trigger Average...)
-- [x] Dimenstion Reduction(PCA...)
+- [x] Dimension Reduction(PCA...)
 - [x] Neural Decoding(LDA...)
 - [x] Neural Population Analysis(Correlation...)
 
@@ -85,7 +85,7 @@ https://optinist.readthedocs.io/en/latest/
 
 ## Using GUI
 ### Workflow
-- OptiNiSt allows you to make your analysis pipelines by graph style using nodes and edges on GUI. Parameters for each analysis are easily changeable. 
+- OptiNiSt allows you to make your analysis pipelines by graph style using nodes and edges on GUI. Parameters for each analysis are easily changeable.
 <p align="center">
   <img width="400px" src="docs/_static/workflow/whole.png" alt="workflow" />
 </p>
@@ -99,7 +99,7 @@ https://optinist.readthedocs.io/en/latest/
 </p>
 
 ### Record
-- OptiNiSt supports you in recording and reproducing workflow pipelines in an organized manner. 
+- OptiNiSt supports you in recording and reproducing workflow pipelines in an organized manner.
 <p align="center">
   <img width="400px" src="docs/_static/record/whole.png" alt="record" />
 </p>
@@ -118,8 +118,8 @@ Kenji Doya, Yukako Yamane [OIST Neural Computation Unit](https://groups.oist.jp/
 
 
 ## References
-[[Suite2p]](https://github.com/MouseLand/suite2p) Marius Pachitariu, Carsen Stringer, Mario Dipoppa, Sylvia Schröder, L. Federico Rossi, Henry Dalgleish, Matteo Carandini, Kenneth D. Harris. "Suite2p: beyond 10,000 neurons with standard two-photon microscopy". 2017  
-[[CaImAn]](https://github.com/flatironinstitute/CaImAn) Andrea Giovannucci Is a corresponding author, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon L Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L Gauthier, Pengcheng Zhou, Baljit S Khakh, David W Tank, Dmitri B Chklovskii, Eftychios A Pnevmatikakis. "CaImAn: An open source tool for scalable Calcium Imaging data Analysis". 2019  
+[[Suite2p]](https://github.com/MouseLand/suite2p) Marius Pachitariu, Carsen Stringer, Mario Dipoppa, Sylvia Schröder, L. Federico Rossi, Henry Dalgleish, Matteo Carandini, Kenneth D. Harris. "Suite2p: beyond 10,000 neurons with standard two-photon microscopy". 2017
+[[CaImAn]](https://github.com/flatironinstitute/CaImAn) Andrea Giovannucci Is a corresponding author, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon L Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L Gauthier, Pengcheng Zhou, Baljit S Khakh, David W Tank, Dmitri B Chklovskii, Eftychios A Pnevmatikakis. "CaImAn: An open source tool for scalable Calcium Imaging data Analysis". 2019
 [[LCCD]](https://github.com/magnetizedCell/lccd-python) Tsubasa Ito, Keisuke Ota, Kanako Ueno, Yasuhiro Oisi, Chie Matsubara, Kenta Kobayashi, Masamichi Ohkura, Junichi Nakai, Masanori Murayama, Toru Aonishi, "Low computational-cost cell detection method for calcium imaging data", 2022
 [[PyNWB]](https://github.com/NeurodataWithoutBorders/pynwb) Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard, "The Neurodata Without Borders ecosystem for neurophysiological data science", bioRxiv 2021.03.13.435173, March 15, 2021
 

docs/gui/index.rst

@@ -8,4 +8,4 @@ GUI GUIDE
 
   workflow
   visualize
-  record
+  record

docs/gui/visualize.md

@@ -188,7 +188,7 @@ The plotting box (ID:0) shows the background image and detected cells.
 </p>
 
 
-You can click the <strong>Add ROI</strong> button then drag drop, resize the white cirle to change the new ROI position and size.
+You can click the <strong>Add ROI</strong> button then drag drop, resize the white circle to change the new ROI position and size.
 Press <strong>OK</strong> or <strong>Cancel</strong> button to Add or No
 
 <p align="center">
@@ -198,7 +198,7 @@ Press <strong>OK</strong> or <strong>Cancel</strong> button to Add or No
 Or click on each cell ROI to delete ROI or merge ROIs (when you select 2 or more ROI cells)
 Press <strong>Merge ROI</strong> or <strong>Delete ROI</strong> or <strong>Cancel</strong> button to Merge or Delete or No.
 
-NWB file is overwirtten with the ROI edit information.
+NWB file is overwritten with the ROI edit information.
 
 ```{eval-rst}
 .. note::

docs/gui/workflow.md

@@ -211,11 +211,11 @@ SNAKEMAKE and NWB SETTING buttons are for parameters for snakemake and output NW
     - By configuring this, the output NWB file includes the information set here.
     - The parameter you set here is only for your record and is not used for calculations within OptiNiSt.
     - You can leave this setting as the default.
-    - The details of NWB setting in OptiNiSt are folling.
+    - The details of NWB setting in OptiNiSt are following.
       - session_description: a description of the session where this data was generated
       - identifier: a unique text identifier for the file
       - experiment_description: general description of the experiment
-      - device: device used to aquire the data (information such as manufacturer, firmware version, model etc.)
+      - device: device used to acquire the data (information such as manufacturer, firmware version, model etc.)
       - optical_channel: information about the optical channel used to acquire the data
       - imaging_plane: information about imaging such as sampling rate, excitation wave length, calcium indicator.
       - image_serises: information about imaing time

docs/index.rst

@@ -20,7 +20,7 @@ Main Features
 
 .. _issue: https://github.com/oist/optinist/issues
 .. _here: https://www.biorxiv.org/content/early/2017/07/20/061507
-.. _this paper: Comming Soon
+.. _this paper: Coming Soon
 .. _pypi: https://pypi.org/project/optinist/
 
 .. * :ref:`modindex`

docs/requirements.txt

@@ -7,3 +7,4 @@ sphinx-copybutton==0.5.2
 sphinx-autobuild==2021.3.14
 myst-parser
 sphinx-pyproject
+pre-commit

docs/utils/add_algorithm.md

@@ -225,7 +225,7 @@ img { width: 50%; }
 
 #### Customize plot metadata
 
-You can set plot title and axis labels to some outpus.
+You can set plot title and axis labels to some output.
 
 ![](../_static/add_algorithm/heatmap_with_metadata.png)
 

docs/utils/contributing.md

@@ -9,7 +9,7 @@ See the following guidelines before submitting Pull Requests.
   ```
   pre-commit install
   ```
-  - Once installed, it automatically checkes your code style on every commits.
+  - Once installed, it automatically checks your code style on every commits.
 
 ### Python
 - Format all files using [black](https://black.readthedocs.io/en/stable/#).

docs/utils/cui_execution.md

@@ -30,7 +30,7 @@ It can be executed in CUI by running `run_cluster.py`.
 
 The parameter arguments are as follows.
 - config(string): path of config.yaml file set in step 1
-- cores(int): Specifies the number of CPU cores. (defalt: 2, cores >= 2)
+- cores(int): Specifies the number of CPU cores. (default: 2, cores >= 2)
 - forceall(bool): Whether to overwrite existing results or not. (default: false)
 - use_conda(bool): Whether to use the conda virtual environment or not. If not, it is necessary to have caiman, suite2p, etc. INSTALL the current environment into the execution environment.
 

docs/utils/implemented_analysis.md

@@ -21,4 +21,4 @@
 #### neural decoding
 - [Generalized Linear Models](https://www.statsmodels.org/stable/glm.html)
 - [Linear Discriminant Analysis](https://scikit-learn.org/stable/modules/generated/sklearn.discriminant_analysis.LinearDiscriminantAnalysis.html)
-- [Support Vector Machines](https://scikit-learn.org/stable/modules/svm.html#svm)
+- [Support Vector Machines](https://scikit-learn.org/stable/modules/svm.html#svm)

docs/utils/index.rst

@@ -9,4 +9,4 @@ OTHER
   add_algorithm
   cui_execution
   implemented_analysis
-  contributing
+  contributing

frontend/.dockerignore

@@ -1 +1 @@
-node_modules
+node_modules