Merge pull request #75 from dandi/enh-codespell

Add codespell + pre-commit support and make them fix typos etc

.codespellrc

@@ -0,0 +1,7 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,*.svg,*.lock,*.min.*,.codespellrc
+check-hidden = true
+# ignore variable definitions in the headers
+ignore-regex = ^ *var +\S+\s*=
+ignore-words-list = rouge

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within .codespellrc
+---
+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@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.gitignore

@@ -3,4 +3,4 @@ _site
 .jekyll-metadata
 .DS_Store
 .idea
-.ruby-version
+.ruby-version

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+exclude_types: [ binary ]
+exclude: >
+  (?x)(
+      \.svg$|
+      \.js$
+  )
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    -   id: codespell

CNAME

@@ -1 +1 @@
-www.dandiarchive.org
+www.dandiarchive.org

Gemfile

@@ -1,4 +1,3 @@
 source 'https://rubygems.org'
 
 gem "jekyll", ">= 3.6.3"
-

README.md

@@ -1,9 +1,9 @@
 # DANDI project website
 
-This website is powered by Jekyll and some Bootstrap, Bootwatch. Go to 
-*aboutwebsite.md*  to learn how to copy and modify this page for your purpose. 
+This website is powered by Jekyll and some Bootstrap, Bootwatch. Go to
+*aboutwebsite.md*  to learn how to copy and modify this page for your purpose.
 
 ## Acknowledgements
 
-A big thank you to https://github.com/mpa139/allanlab for setting up this 
+A big thank you to https://github.com/mpa139/allanlab for setting up this
 framework.

_config.yml

@@ -42,4 +42,3 @@ kramdown:
   smart_quotes: lsquo,rsquo,ldquo,rdquo
   enable_coderay: false
   parse_block_html: true # default for kramdown is false. This will enable using Markdown links
-

_data/alumni_members.yml

@@ -7,4 +7,3 @@
   education1: BS Biology and Biotechnology, Worcester Polytechnic Institute
   education2: MS Candidate Bioinformatics, Johns Hopkins University
   education3: <a href="https://www.linkedin.com/in/bhavya-kandimalla-a02248100">Full CV</a>
-

_data/news.yml

@@ -54,8 +54,8 @@
     <a href="https://neurodatawithoutborders.github.io/nwb_hackathons/HCK17_2023_OpenNeuroDataShowcase/">Open Neurodata Showcase 2023</a>
 
 - date: 2022 10 04
-  headline: > 
-    Paper outline the Neurodata Without Borders ecosystem including DANDI published in ELife 
+  headline: >
+    Paper outline the Neurodata Without Borders ecosystem including DANDI published in ELife
     (<a href="https://elifesciences.org/articles/78362">Link</a>).
 
 - date: 2022 03 08

_data/team_members.yml

@@ -1,7 +1,7 @@
 - name: Satrajit S Ghosh
   photo: ../assets/team/Satrajit_S_Ghosh.png
   info: >
-    Director of Open Data in Neuroscience Initiative and Principal Research Scientist at MIT; Assistant 
+    Director of Open Data in Neuroscience Initiative and Principal Research Scientist at MIT; Assistant
     Professor of Otolaryngology at Harvard Medical School
   email: satra@mit.edu
   number_educ: 3
@@ -105,7 +105,7 @@
   info: Research Scientist, MIT
   email: kabi@mit.edu
   number_educ: 2
-  education1: PhD Biomedical Engineering, Case Western Reserve University  
+  education1: PhD Biomedical Engineering, Case Western Reserve University
   education2: MD, Case Western Reserve University
 
 - name: Aaron Kanzer

_includes/footer.html

@@ -3,7 +3,7 @@
 	<div class="container-fluid">
 	  <div class="row">
 		<div class="col-sm-4">
-			
+
 		  <p>&copy 2019-2024 DANDI contributors</p>
 		  <p>Site adapted from
 			  <a href="https://github.com/mpa139/allanlab">Allan Lab</a>.

_includes/home-banner.html

@@ -4,12 +4,12 @@
       <h1>DANDI: Distributed Archives for Neurophysiology Data Integration</h1>
       <p>The DANDI platform is supported by the <a href="https://braininitiative.nih.gov/" target="_blank">
         BRAIN Initiative</a> for publishing, sharing, and processing neurophysiology data.
-        The archive accepts cellular neurophysiology data including electrophysiology, 
-        optophysiology, and behavioral time-series, and images from immunostaining experiments. The 
+        The archive accepts cellular neurophysiology data including electrophysiology,
+        optophysiology, and behavioral time-series, and images from immunostaining experiments. The
         platform is now available for data upload and distribution. The storage of data in the archive
-        is also supported by the <a href="https://registry.opendata.aws/" target=""_blank">Amazon Opendata 
-        program</a>. </p> 
-      <p>The data in the archive can be browsed using the <a href="https://dandiarchive.org">Data Portal</a>. 
+        is also supported by the <a href="https://registry.opendata.aws/" target=""_blank">Amazon Opendata
+        program</a>. </p>
+      <p>The data in the archive can be browsed using the <a href="https://dandiarchive.org">Data Portal</a>.
         For detailed instructions on how to interact (view, upload, download, process) with DANDI
         <a href="https://www.dandiarchive.org/handbook/">click here</a>.</p>
     </div>

_includes/news.html

@@ -8,5 +8,5 @@ <h4>News</h4>
 {% endfor %}
 
 <h4><a href="{{ site.url }}{{ site.baseurl }}/allnews.html">... see all News</a></h4>
-    
-    </div>
+
+    </div>

_layouts/blog.html

@@ -3,4 +3,4 @@
 ---
 <div id="blog" class="col-sm-12">
   {{ content }}
-</div>
+</div>

_layouts/collab.html

@@ -4,4 +4,3 @@
 <div id="collab" class="col-sm-12">
   {{ content }}
 </div>
-

_layouts/team.html

@@ -4,4 +4,3 @@
 <div id="team" class="col-sm-12">
   {{ content }}
 </div>
-

_pages/404.md

@@ -7,4 +7,3 @@ permalink: /404.html
 ---
 
 Sorry, but the page you were trying to view does not exist.
-

_pages/aboutwebsite.md

@@ -8,19 +8,19 @@ permalink: /aboutwebsite.html
 
 # Use this website as a template for your academic research group
 
-This website is powered by [Jekyll](https://jekyllrb.com) and uses some [Bootstrap](http://www.getbootstrap.com) and  [Bootswatch](http://www.bootswatch.com). We tried to make it simple yet adaptable, so that it is easy for you to re-use it for your purpose. 
+This website is powered by [Jekyll](https://jekyllrb.com) and uses some [Bootstrap](http://www.getbootstrap.com) and  [Bootswatch](http://www.bootswatch.com). We tried to make it simple yet adaptable, so that it is easy for you to reuse it for your purpose.
 
 ### Getting started
 All pages are written in [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) for easy editing, and [Jekyll](https://jekyllrb.com) uses Liquid for the data-driven pages. The publicaion list, news items, and group members are stored as `.yml` data sheets (plain text) in the `_data folder`, so that one can update the website easily. The pages are in the `_pages` folder. Updating and maintaining is easy using [Github](http://www.github.com) (not worldpress-easy, but there are other advantages (see e.g. [this](https://www.taniarascia.com/make-a-static-website-with-jekyll/), or [this](http://www.webdesignerdepot.com/2015/11/jekyll-against-the-rest-of-the-world/)). [Jekyll](https://jekyllrb.com) takes all the markdown and data files, and creates beautiful `html` files in the `_site` folder.
 
-If you never used [Jekyll](https://jekyllrb.com), read the [wikipedia article](https://en.wikipedia.org/wiki/Jekyll_(software)) article and check out [their website](https://jekyllrb.com). Same for [Github](http://www.github.com), which will host your first website draft. 
+If you never used [Jekyll](https://jekyllrb.com), read the [wikipedia article](https://en.wikipedia.org/wiki/Jekyll_(software)) article and check out [their website](https://jekyllrb.com). Same for [Github](http://www.github.com), which will host your first website draft.
 
-Create and open a github account, go to [our repository](https://github.com/allanlab/allanlab), and click 'fork'. This is now your copy of the website, and you can change and adapt it as you want. You don't have to link to us or mention us (but of course we appreciate it). Then change the name of the repository to "your_username" and the name of the branch to "gh-pages".  Your website is now automatically published under *your_username.github.io/your_username/*. Except that it probably still looks like our website. 
+Create and open a github account, go to [our repository](https://github.com/allanlab/allanlab), and click 'fork'. This is now your copy of the website, and you can change and adapt it as you want. You don't have to link to us or mention us (but of course we appreciate it). Then change the name of the repository to "your_username" and the name of the branch to "gh-pages".  Your website is now automatically published under *your_username.github.io/your_username/*. Except that it probably still looks like our website.
 
-To modify the webpage, you can either do everything on on github.com (go to a file, click "edit", then "commit", "push"), or install  [Jekyll](https://jekyllrb.com) on your computer and play with your local copy that you sync with the branch on github.com.  The former is much easier in the beginning, but a bit less convenient once you start rewriting everythint. To get it to work on your computer (and to learn a bit more about [Jekyll](https://jekyllrb.com)), [here](https://www.taniarascia.com/make-a-static-website-with-jekyll/) and [here](https://scotch.io/tutorials/getting-started-with-jekyll-plus-a-free-bootstrap-3-starter-theme) are tutorials on how to use it and how set it up locally. Also, consider using the [Github desktop app](http://www.desktop.github.com), I found it helpful.  
+To modify the webpage, you can either do everything on on github.com (go to a file, click "edit", then "commit", "push"), or install  [Jekyll](https://jekyllrb.com) on your computer and play with your local copy that you sync with the branch on github.com.  The former is much easier in the beginning, but a bit less convenient once you start rewriting everythint. To get it to work on your computer (and to learn a bit more about [Jekyll](https://jekyllrb.com)), [here](https://www.taniarascia.com/make-a-static-website-with-jekyll/) and [here](https://scotch.io/tutorials/getting-started-with-jekyll-plus-a-free-bootstrap-3-starter-theme) are tutorials on how to use it and how set it up locally. Also, consider using the [Github desktop app](http://www.desktop.github.com), I found it helpful.
 
 ### Customization
-Now let's make this *your* website. 
+Now let's make this *your* website.
 
 First, go to the `news.ylm`, `publist.ylm`, and `team.ylm` files in the `_data` folder and insert your own data into the data fields. Watch out:  [Jekyll](https://jekyllrb.com) is quite strict about extra or missing spaces etc. Adhere to the format. In the beginning, test each change: commit, push, and check the published website.
 
@@ -34,15 +34,12 @@ Next, change the content of all files in the `_pages` folder.  To change the tit
 
 Lastly, change the footer and perhaps header appropriately (in `_include`).
 
-You might also want to change the style or theme. I imported style files (in sass) from Bootstrap/Bootwatch, you can replace them with your own (in the `_sass directory`). For small changes, just work on the override stuff in the `main.sass` file in the `CSS` folder. Or change some variables in the `_variables.sass` file, like the background color etc. 
+You might also want to change the style or theme. I imported style files (in sass) from Bootstrap/Bootwatch, you can replace them with your own (in the `_sass directory`). For small changes, just work on the override stuff in the `main.sass` file in the `CSS` folder. Or change some variables in the `_variables.sass` file, like the background color etc.
 
 As said, [Jekyll](https://jekyllrb.com) takes all the markdown and data files, and creates beautiful `html` files in the `_site` folder.In the end, either upload these files  to your server, or buy yourself a domain and check the instructions on github on how to host it there.
 
 ### Copyright / credit
 
 We adapted this site from the [Allan Lab](https://github.com/mpa139/allanlab).
 
-Their code was released under the MIT License. 
-
-
-
+Their code was released under the MIT License.

_pages/collab.md

@@ -8,21 +8,21 @@ permalink: /collab/
 
 ## Our collaboration policies are:
 
-- Authorship is a function of intellectual contribution and we try to minimize 
-author bloat in our group. For multi-institution student collaborations, we will 
-identify ahead of time who the primary advisers and collaborators are on a 
+- Authorship is a function of intellectual contribution and we try to minimize
+author bloat in our group. For multi-institution student collaborations, we will
+identify ahead of time who the primary advisers and collaborators are on a
 project.
-- Our work is open. However, there have been prior situations where we have 
+- Our work is open. However, there have been prior situations where we have
 applied for patents during collaborations.
-- We tend to share any data we collect and any code we produce under open 
+- We tend to share any data we collect and any code we produce under open
 licenses (data: PDDL, code: Apache 2.0, doc: CC-BY)
-- Any digital research work we produce together should be re-executable and hopefully 
+- Any digital research work we produce together should be re-executable and hopefully
 reproducible/generalizable.
 
 # Collaborators
 
-<em>** This list may not always be accurate. We apologize if we missed your name, 
-listed incorrect information or did not ask you before listing you. Please let us 
+<em>** This list may not always be accurate. We apologize if we missed your name,
+listed incorrect information or did not ask you before listing you. Please let us
 know so we can rectify the situation.</em>
 
 {% for site in site.data.collaborators %}

_pages/home.md

@@ -14,19 +14,19 @@ necessary data and metadata that you need, is at least what we should be storing
 
 DANDI provides:
 
-1. A cloud-based platform to store, process, and disseminate data. You can use 
+1. A cloud-based platform to store, process, and disseminate data. You can use
    DANDI to collaborate and publish datasets.
-2. Open access to data to enable secondary uses of data outside the intent 
+2. Open access to data to enable secondary uses of data outside the intent
    of the study.
-3. Optimize data storage and access through partnerships, compression and 
+3. Optimize data storage and access through partnerships, compression and
    accessibility technologies.
-4. Enables reproducible practices and publications through data standards such 
+4. Enables reproducible practices and publications through data standards such
    as NWB and BIDS, which provide extensive metadata.
 5. The platform is not just an endpoint to dump data, it is intended as a living
    repository that enables collaboration within and across labs, and for others,
    the entry point for research.
 
-For a better view of how DANDI might help you, please see these 
+For a better view of how DANDI might help you, please see these
 <a href="https://docs.google.com/presentation/d/1hqw0vgNmelNnkPLuCSA1L5Rlu2rXeZEF6bsgc0y6Ve4/edit#slide=id.g113edc9c042_0_67" target="_blank"> onboarding slides</a>.
 
 <!--

_pages/maintenance.md

@@ -7,4 +7,3 @@ permalink: /maintenance
 ---
 
 DANDI is undergoing maintenance and is currently offline. We expect it to be back online by April 22nd, Noon Eastern Time.
-

_pages/research.md

@@ -8,33 +8,33 @@ permalink: /research/
 
 # Research
 
-A fundamental problem in psychiatry is that there are no biological markers for 
-diagnosing mental illness or for indicating how best to treat it. Treatment 
-decisions are based entirely on symptoms, and doctors and their patients will 
-typically try one treatment, then if it does not work, try another, and perhaps 
-another. Our group hopes to change this picture, and our research suggests 
-that individual brain scans and speaking patterns can hold valuable information 
-for guiding psychiatrists and patients. Current areas include depression, 
+A fundamental problem in psychiatry is that there are no biological markers for
+diagnosing mental illness or for indicating how best to treat it. Treatment
+decisions are based entirely on symptoms, and doctors and their patients will
+typically try one treatment, then if it does not work, try another, and perhaps
+another. Our group hopes to change this picture, and our research suggests
+that individual brain scans and speaking patterns can hold valuable information
+for guiding psychiatrists and patients. Current areas include depression,
 suicide, anxiety disorders, autism, Parkinson disease, and brain tumors.
 
-To support this broader goal, our group develops novel analytic platforms that 
-use such information to create robust, predictive models around human health. 
+To support this broader goal, our group develops novel analytic platforms that
+use such information to create robust, predictive models around human health.
 
-Our research interests span computer science and neuroscience, specifically in 
-the areas of applied machine learning, signal processing, and translational 
-medicine. Our current research portfolio comprises projects on spoken 
-communication, brain imaging, and informatics to address gaps in scientific 
-knowledge in three areas: the neural basis and translational applications of 
-speaking, precision psychiatry and medicine, and preserving information for 
+Our research interests span computer science and neuroscience, specifically in
+the areas of applied machine learning, signal processing, and translational
+medicine. Our current research portfolio comprises projects on spoken
+communication, brain imaging, and informatics to address gaps in scientific
+knowledge in three areas: the neural basis and translational applications of
+speaking, precision psychiatry and medicine, and preserving information for
 reproducible research.
 
-Many of the tools we develop can be used across domains. If you have a 
+Many of the tools we develop can be used across domains. If you have a
 need we can address, we would like to hear from you.
 
-If you have solved problems associated with any of the projects below, we would 
-love to hear from you. For us, a solution typically implies available data, 
+If you have solved problems associated with any of the projects below, we would
+love to hear from you. For us, a solution typically implies available data,
 code, and/or replicated results.
- 
+
 ## Highlights
 
 For a full list see [below](#full-list)
@@ -88,4 +88,3 @@ For a full list see [below](#full-list)
   <a href="{{ proj.link.url }}">{{ proj.link.display }}</a>
 
 {% endfor %}
-

_pages/team.md

@@ -68,4 +68,3 @@ permalink: /team
 {% if even_odd == 1 %}
 </div>
 {% endif %}
-