Merge pull request #49 from yarikoptic/enh-codespell

Add codespell config and action, and fix typos in already existing talks

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git,*.pdf,*.svg,package-lock.json,*.css,.codespellrc,*.js
+check-hidden = true
+# ignore-regex = 
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# 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: Codespell
+        uses: codespell-project/actions-codespell@v2

README.md

@@ -17,7 +17,7 @@ PDFs of the slides are in ``talks/PDFs``.
 - ``clone`` the repository to your local computer. From the root of the dataset, run ``git submodule update`` on relevant submodules. Those will be ``reveal.js``, and, if you want to access all images, ``pics/artwork`` Afterwards, you should be able to open the HTML's in a web browser and see them nicely rendered
 - to generate a PDF from your slides, open the HTML of your talk in Chrome or Chromium, and append ``?print-pdf`` to the URL. Afterwards, you should be able to print to PDF from your browser. Alternatively, start an npm server and use ``decktape`` to generate it from HTML to PDF using ``docker run --rm -t --net=host -v `pwd`:/slides astefanutti/decktape http://localhost:8000 slides.pdf -s  1024x768``
 - The tool [directpoll](https://directpoll.com/) works fantastic for virtual talks. See [#34](https://github.com/datalad-handbook/course/issues/34) for info on how to use it
-- We have made good experiences with live code demonstrations. The ``tools/cast_live`` script is used for this. It is highly advised to test whether this script works on your set-up beforehand! You can write custom casts if you want to. Everything thats within a ``run '<code here>'`` statement is executed on ``Enter``, everything within a ``say '<note>'`` is written to your private terminal as a note.
+- We have made good experiences with live code demonstrations. The ``tools/cast_live`` script is used for this. It is highly advised to test whether this script works on your set-up beforehand! You can write custom casts if you want to. Everything that's within a ``run '<code here>'`` statement is executed on ``Enter``, everything within a ``say '<note>'`` is written to your private terminal as a note.
 
 ## License
 

casts/02_reproducible_execution

@@ -27,7 +27,7 @@ datalad run -m "create a list of podcast titles" "bash code/list_titles.sh > rec
 say 'Let'"'"'s now check what has been written into the history. (runrecord)'
 run '### Code snippet 45
 git log -p -n 1'
-say 'A run command that does not result in changes (no modifcations, no additional files) will not produce a record in the dataset history. So what happens if we do the same again?'
+say 'A run command that does not result in changes (no modifications, no additional files) will not produce a record in the dataset history. So what happens if we do the same again?'
 run '### Code snippet 46
 datalad run -m "Try again to create a list of podcast titles" "bash code/list_titles.sh > recordings/podcasts.tsv"'
 say 'as the result is byte-identical, there is no new commit'

talks/HCPdata.html

@@ -62,7 +62,7 @@ <h2>Research data management (RDM)</h2>
                 code, software/tools, raw data, processed data, results, manuscripts ...</li>
             <li class="fragment fade-in-then-semi-out" data-fragment-index="1">
                 Data needs to be managed <a href="https://www.go-fair.org/fair-principles/" target="_blank">FAIR</a>ly- from creation to use, publication,
-            sharing, archiving, re-use, or destruction: </li>
+            sharing, archiving, reuse, or destruction: </li>
         </ul>
     <img src="../pics/datalifecycle_jisc_ccbysand.png" class="fragment fade-in" height="550">
     <ul>

talks/IRTG_workshop.html

@@ -74,7 +74,7 @@ <h2>What is (research) data management?</h2>
         <li class="fragment fade-in">(Research) Data = every digital object involved in your project:
             code, software/tools, raw data, processed data, results, manuscripts ...</li>
         <li class="fragment fade-in">... needs to be properly managed - from its creation to its use, publication,
-        sharing, archiving, re-use, or destruction... (keyword:
+        sharing, archiving, reuse, or destruction... (keyword:
         <a href="https://www.go-fair.org/fair-principles/" target="_blank">FAIR</a> data) </li>
     </ul>
     <img src="../pics/datalifecycle_jisc_ccbysand.png" class="fragment fade-in">
@@ -108,7 +108,7 @@ <h2>How do you spend your time?</h2>
                 <td><img class="fragment fade-in" height="400" src="../pics/sciencetime.jpg"></td>
         </table>
         <blockquote class="fragment fade-in" cite="Thomas Wachtler">
-    Collaborative work and re-use of data are hampered by the effort it takes to access and
+    Collaborative work and reuse of data are hampered by the effort it takes to access and
     understand the data. <br>
     <small>Thomas Wachtler</small></blockquote></td>
         <li class="fragment fade-in">Good data management can make your and others work & life much easier!</li>

talks/MPI_Berlin_01.html

@@ -316,7 +316,7 @@ <h3>Real world examples for Research Data Management gone wrong ...</h3>
 </section>
 
 <section>
-    <h3>Real world examples for Research Data Managament gone wrong ...</h3>
+    <h3>Real world examples for Research Data Management gone wrong ...</h3>
     <img src="../pics/newconversation_economics_excel_screen1.png" style="box-shadow: 10px 10px 8px #888888;height=200px" height="170"><br>
     <img src="../pics/newconversation_economics_excel_screen2.png" style="box-shadow: 10px 10px 8px #888888;height=300px" height="150">
     <img src="../pics/newconversation_economics_excel_screen3.png" style="box-shadow: 10px 10px 8px #888888;height=200px" height="120"><br>
@@ -325,7 +325,7 @@ <h3>Real world examples for Research Data Managament gone wrong ...</h3>
 </section>
 
 <section>
-    <h3>Real world examples for Research Data Managament gone wrong ...</h3>
+    <h3>Real world examples for Research Data Management gone wrong ...</h3>
     <img src="../pics/theverge_excel_genetics_screen1.png" style="box-shadow: 10px 10px 8px #888888;height=200px" height="200"><br>
     <img src="../pics/theverge_excel_genetics_screen2.gif" style="box-shadow: 10px 10px 8px #888888;height=300px" height="300"><br>
     <img src="../pics/theverge_excel_genetics_screen3.png" style="box-shadow: 10px 10px 8px #888888;height=200px" height="200"><br>
@@ -343,7 +343,7 @@ <h2>Data change!</h2>
     <img src="../pics/phd052810s.gif" style="box-shadow: 10px 10px 8px #888888;height=600px" height="600"><br>
     <ul>
         <li class="fragment fade-in">New data are added and old data removed</li>
-        <li class="fragment fade-in">Erros are detected, fixed and introduced again 👻</li>
+        <li class="fragment fade-in">Errors are detected, fixed and introduced again 👻</li>
         <li class="fragment fade-in">Separate data versions are created or merged</li>
     </ul>
 </section>

talks/MPI_Berlin_02.html

@@ -373,7 +373,7 @@ <h2>Git versus Git-annex</h2>
 
          <li>Annexed contents are not available right after cloning,
              only content identity and availability information (as they are stored in Git).
-             Everything that is annexed needs to be retrieved with <code>datalad get</code> from whereever it is stored.
+             Everything that is annexed needs to be retrieved with <code>datalad get</code> from wherever it is stored.
          </li>
       </ul>
   </section>

talks/MPI_Berlin_03.html

@@ -496,7 +496,7 @@ <h2>Preserved modularity</h2>
 ![](../pics/data_origin.png)
 
 - Link individual datasets to declare data-dependencies (e.g. as subdatasets).
-- Record data's orgin with appropriate commands, for example
+- Record data's origin with appropriate commands, for example
   to record access URLs for individual files obtained from (unstructured) sources "in the cloud".
 - Keep a dataset self-contained with relative paths in scripts to subdatasets or files.
 - Share and publish datasets to collaborate.

talks/MPI_Berlin_04.html

@@ -380,7 +380,7 @@ <h2>Creating a remote repository</h2>
 2fa> # just press enter if you don't use 2FA
 </code></pre> <!-- .element: class="fragment" data-fragment-index="1" -->
 
-Don't enter a Keeper library name! Here, we will configure one Seafile rclone remote that you can re-use across your projects 😎<!-- .element: class="fragment" data-fragment-index="2" -->
+Don't enter a Keeper library name! Here, we will configure one Seafile rclone remote that you can reuse across your projects 😎<!-- .element: class="fragment" data-fragment-index="2" -->
 
 <pre><code class="bash" style="max-height:none" data-line-numbers="1,3">Name of the library. Leave blank to access all non-encrypted libraries.
 Enter a string value. Press Enter for the default ("").
@@ -409,7 +409,7 @@ <h2>Creating a remote repository</h2>
   y/n> y # type 'y' and press enter
   </code></pre> <!-- .element: class="fragment" data-fragment-index="1" -->
 
-Allow rclone to create non-existing libaries on Keeper <!-- .element: class="fragment" data-fragment-index="2" -->
+Allow rclone to create non-existing libraries on Keeper <!-- .element: class="fragment" data-fragment-index="2" -->
 
 <pre><code class="bash" style="max-height:none" data-line-numbers="1,3">Should rclone create a library if it doesn't existing
 Enter a boolean value (true or false). Press Enter for the default ("false").
@@ -527,7 +527,7 @@ <h2>Creating a remote repository</h2>
 publish(ok): . (dataset) [refs/heads/git-annex->origin:refs/heads/git-annex [new branch]]
 </code></pre> <!-- .element: class="fragment" data-fragment-index="1" -->
 
-  - DataLad succesfully published our dataset to GitLab and pushed the annexed contents to Seafile / Keeper 🍾🤩🥳 <!-- .element: class="fragment" data-fragment-index="2" -->
+  - DataLad successfully published our dataset to GitLab and pushed the annexed contents to Seafile / Keeper 🍾🤩🥳 <!-- .element: class="fragment" data-fragment-index="2" -->
 
 <img src="../pics/in_case_of_fire.png" style="border:20px; margin:0px; float:center; width:500px;"/> <!-- .element: class="fragment" data-fragment-index="3" -->
 <img src="../pics/stolenlaptop.jpg" style="border:0px; margin:0px; float:center; height:200px;"></div> <!-- .element: class="fragment" data-fragment-index="4" -->

talks/MPI_Leipzig.html

@@ -60,7 +60,7 @@ <h2>Research data management (RDM)</h2>
                 code, software/tools, raw data, processed data, results, manuscripts ...</li>
             <li class="fragment fade-in-then-semi-out" data-fragment-index="1">
                 Data needs to be managed <a href="https://www.go-fair.org/fair-principles/" target="_blank">FAIR</a>ly- from creation to use, publication,
-            sharing, archiving, re-use, or destruction: </li>
+            sharing, archiving, reuse, or destruction: </li>
         </ul>
     <img src="../pics/datalifecycle_jisc_ccbysand.png" class="fragment fade-in" height="550">
     <ul>

talks/datalad-for-ml.html

@@ -711,7 +711,7 @@ <h2>Dataset nesting</h2>
             puzzled together into new research objects, while being uniquely identified and versioned</li>
         </ul>
 
-        At this point: Fixed data management, layed a foundation for updating data
+        At this point: Fixed data management, laid a foundation for updating data
     </aside>
 </section>
 

talks/datamanagement01.html

@@ -228,7 +228,7 @@ <h2>DataLad Datasets for data analysis</h2>
 ![](../pics/data_origin.png)
 
 - Link individual datasets to declare data-dependencies (e.g. as subdatasets).
-- Record data's orgin with appropriate commands, for example
+- Record data's origin with appropriate commands, for example
   to record access URLs for individual files obtained from (unstructured) sources "in the cloud".
 - Keep a dataset self-contained with relative paths in scripts to subdatasets or files.
 - Share and publish datasets to collaborate.

talks/datamanagement02.html

@@ -222,7 +222,7 @@ <h2>Now what I can do with that?</h2>
       <dt>Local version control</dt>
       <li>Version control changing small files (code, manuscripts (text!), ...)</li>
       <li>Add large files to a dataset history</li>
-      <li>Meaninful and well-described commits will make future interactions with the dataset history easier</li>
+      <li>Meaningful and well-described commits will make future interactions with the dataset history easier</li>
       <br>
       <dt>Dataset installation and nesting</dt>
       <li>Consume existing datasets</li>
@@ -312,7 +312,7 @@ <h2>How does a here-document work?</h2>
 <br>
   <p align="left" class="fragment fade-in"> Why is it used?</p>
   <ul align="left" class="fragment fade-in">
-    <li>Allows pretty formating (e.g., line breaks)</li>
+    <li>Allows pretty formatting (e.g., line breaks)</li>
     <li>Allows writing documents from the terminal </li>
   </ul>
   </p>

talks/datamanagement03.html

@@ -461,7 +461,7 @@ <h2>How does a here-document work?</h2>
 <br>
   <p align="left" class="fragment fade-in"> Why is it used?</p>
   <ul align="left" class="fragment fade-in">
-    <li>Allows pretty formating (e.g., line breaks)</li>
+    <li>Allows pretty formatting (e.g., line breaks)</li>
     <li>Allows writing documents from the terminal </li>
   </ul>
   </p>

talks/debconf_datalad.html

@@ -215,7 +215,7 @@ <h3>The good news, the bad news</h3>
         <tr style="vertical-align:middle"></tr>
         <tr>
             <td class="fragment fade-in-then-semi-out" data-fragment-index="1">Data sharing</td>
-            <td class="fragment fade-in" data-fragment-index="2">Heterogenous distribution and updating, scientists lack data management skills</td>
+            <td class="fragment fade-in" data-fragment-index="2">Heterogeneous distribution and updating, scientists lack data management skills</td>
         </tr>
         <tr>
             <td class="fragment fade-in-then-semi-out" data-fragment-index="3">Patient data</td>
@@ -250,7 +250,7 @@ <h3>The good news, the bad news</h3>
     also exist for software and are solved, for example software
     packing, distribution, and updates
   - package managers can easily and - importantly - generically distribute and update software
-  - version control for data management in software development is indispensible
+  - version control for data management in software development is indispensable
   - WHAT ELSE??
 </aside>
 </script>
@@ -384,7 +384,7 @@ <h2>Version Control: Nesting</h2>
             puzzled together into new research objects, while being uniquely identified and versioned</li>
         </ul>
 
-        At this point: Fixed data management, layed a foundation for updating data
+        At this point: Fixed data management, laid a foundation for updating data
     </aside>
 </section>
 

talks/dgpa_2022.html

@@ -472,7 +472,7 @@ <h2>Git versus Git-annex</h2>
 
          <li>Annexed contents are not available right after cloning,
              only content identity and availability information (as they are stored in Git).
-             Everything that is annexed needs to be retrieved with <code>datalad get</code> from whereever it is stored.
+             Everything that is annexed needs to be retrieved with <code>datalad get</code> from wherever it is stored.
          </li>
       </ul><br><br>
       <small>Read
@@ -505,7 +505,7 @@ <h2>Git versus Git-annex</h2>
       <h2>Dataset nesting</h2>
 
       <ul>
-          <li>Typically, Git repositories are cumbersome to link to eachother.
+          <li>Typically, Git repositories are cumbersome to link to each other.
               DataLad provides seamless nesting mechanisms:
               <img data-fragment-index="3" height="330" src="../pics/artwork/src/linkage_subds.svg">
           <li class="fragment fade-in" data-fragment-index="1">
@@ -519,7 +519,7 @@ <h2>Dataset nesting</h2>
       <h2>Dataset nesting</h2>
 
       <ul>
-          <li>Typically, Git repositories are cumbersome to link to eachother.
+          <li>Typically, Git repositories are cumbersome to link to each other.
               DataLad provides seamless nesting mechanisms:
               <img src="../pics/Provenance_alpha.png" height="500px">
           <li >

talks/hhu.html

@@ -171,7 +171,7 @@ <h2>Version Control: Nesting</h2>
             puzzled together into new research objects, while being uniquely identified and versioned</li>
         </ul>
 
-        At this point: Fixed data management, layed a foundation for updating data
+        At this point: Fixed data management, laid a foundation for updating data
     </aside>
 </section>
 

talks/introduction_2h.html

@@ -71,7 +71,7 @@ <h2>What is (research) data management?</h2>
         <li class="fragment fade-in">(Research) Data = every digital object involved in your project:
             code, software/tools, raw data, processed data, results, manuscripts ...</li>
         <li class="fragment fade-in">... needs to be properly managed - from creation to use, publication,
-        sharing, archiving, re-use, destruction... (keyword:
+        sharing, archiving, reuse, destruction... (keyword:
         <a href="https://www.go-fair.org/fair-principles/" target="_blank">FAIR</a> data) </li>
     </ul>
     <img src="../pics/datalifecycle_jisc_ccbysand.png" class="fragment fade-in" width="500">

talks/uke-fileoperations.html

@@ -144,7 +144,7 @@ <h2>Removing wrongly</h2>
 $ echo "This file content will only exist locally" > local-file.txt
 $ datalad save -m "Added a file without remote content availability"</code></pre>
       </li>
-      <li class="fragment fade-in" >Removing it the wrong way causes chaos and leaves an usuable dataset corpse behind:
+      <li class="fragment fade-in" >Removing it the wrong way causes chaos and leaves an usable dataset corpse behind:
       <pre><code>$ rm -rf local-dataset
 rm: cannot remove 'local-dataset/.git/annex/objects/Kj/44/MD5E-s42--8f008874ab52d0ff02a5bbd0174ac95e.txt/
 MD5E-s42--8f008874ab52d0ff02a5bbd0174ac95e.txt': Permission denied

talks/uke_basics.html

@@ -268,7 +268,7 @@ <h2>Questions!</h2>
 <section>
     <section>
         <h2>Teaser: Time-travelling</h2>
-        <small>Comprehensive walk-through<a href="http://handbook.datalad.org/en/lastest/basics/101-137-history.html" target="_blank">
+        <small>Comprehensive walk-through<a href="http://handbook.datalad.org/en/latest/basics/101-137-history.html" target="_blank">
             handbook.datalad.org/basics/101-137-history.html
         </a></small>
         <ul style="font-size:30px">
@@ -473,7 +473,7 @@ <h2>Git versus Git-annex</h2>
 
          <li>Annexed contents are not available right after cloning,
              only content identity and availability information (as they are stored in Git).
-             Everything that is annexed needs to be retrieved with <code>datalad get</code> from whereever it is stored.
+             Everything that is annexed needs to be retrieved with <code>datalad get</code> from wherever it is stored.
          </li>
       </ul>
   </section>
@@ -731,7 +731,7 @@ <h3>Summary - Underneath the hood</h3>
           <br>
         <dt class="fragment fade-in">Annexed files behave differently from files kept in Git:</dt>
           <dd class="fragment fade-in">They can be retrieved and dropped from local or remote locations, they are write-protected,
-              their content is unkown to Git (and thus easy to keep private).</dd>
+              their content is unknown to Git (and thus easy to keep private).</dd>
         <br>
           <dt class="fragment fade-in"><em>datalad clone</em> installs datasets from URLs or local or remote paths</dt>
           <dd class="fragment fade-in">Annexed files contents can be retrieved or dropped on demand, file contents of

talks/yale.html

@@ -425,7 +425,7 @@ <h2>Git versus Git-annex</h2>
 
          <li>Annexed contents are not available right after cloning,
              only content identity and availability information (as they are stored in Git).
-             Everything that is annexed needs to be retrieved with <code>datalad get</code> from whereever it is stored.
+             Everything that is annexed needs to be retrieved with <code>datalad get</code> from wherever it is stored.
          </li>
       </ul><br><br>
       <small>Read