Add notes for first session

documentation/docs/pages/decoding_mom6.md

@@ -1,31 +1,75 @@
 # Season 1
+
+## General info on decoding MOM6 sessions
+- The early sessions of these “Decoding MOM6” segments will talk through the tools that might be useful to navigate the MOM6 code
+- The later sessions will dive deeper into the code itself
+
 ## How to use github's search functionality to find code: MOM6 as an example.
-Presenter: @dougiesquire (4/12).
+Presenter: @dougiesquire
+
+Searching [the MOM6 code repository in the ACCESS-NRI GitHub org](https://github.com/access-nri/mom6).
+Contains all of the MOM6 Fortran code used in ACCESS-OM3
 
-Working example, [the MOM6 code repository](https://github.com/access-nri/mom6).
-Contains all of the MOM6 Fortran code
+### Quick summary of GitHub search functionality
 
-Pro:
+Pros:
 
  - Easy and convenient
  - Allows you to see how parts of the model work
 
 Cons:
 
- - Can only search on the default branch of the repo'.
+ - Can only search on the default branch of the repo.
  - GitHub doesn't actually index everything.
- - Can't search branches
 
-Workflow suggestions: 
 
- - Initiate a seach by clicking in the search bar top-right or click `/`
- - Search for the word `"global"` for example, [using this](https://github.com/search?q=repo%3AACCESS-NRI%2FMOM6%20global&type=code).
- - Clicking on a line, will take you to specifically to that line, in that script.
- - Containing things in quotes will look for exact matches `"example phrase"`. Further [details here](https://docs.github.com/en/search-github/github-code-search/understanding-github-code-search-syntax#query-for-an-exact-match).
- - Regex searches are also possible.
- - You can also specify paths within the repo for example `path:src/core`.
+### More detailed notes
+
+- Why use the GitHub search bar?
+    - See how a specific piece of code is written - how is it implemented in MOM6? Need to search through the code
+- Dougie’s screen: Looking at [MOM6 fork on ACCESS-NRI GitHub org](https://github.com/ACCESS-NRI/MOM6)
+    - Can click on search at top or click “/“ to start a search
+    - Eg [search `global`](https://github.com/search?q=repo%3AACCESS-NRI%2FMOM6%20global&type=code)
+        - Will return all files in this repo with “Global” (not case sensitive by default)
+        - Get the summary of the files, and can click to expand more lines of code
+        - Can click on the line itself and it will take you to that line in the file
+    - Can search on multiple terms
+        - Eg `Global Mean` - searches all files with global or mean
+        - Eg `“Global Mean”` - search for specific phrase
+        - Eg `“Global mean ocean salinity”` - can search directly for this diagnostic
+            - Finds where it’s registered, and can backtrack to find the code
+    - Can search on patterns (regex) rather than words
+        - Eg search `Global` but only at specific path: `Global path:src/core`
+    - Fast, powerful, easy to use
+    - Can share searches with people (can’t do this if you are, eg, using “grep” on Gadi terminal)
+- Gotchas
+    - Can only search on default branch
+    - GitHub doesn’t index everything, and opaque which code is indexed
+        - Eg doesn’t index vendor code, but not clear what that means
+        - If you search something and it seems weird that nothing is found, then this might be the main issue
+
+#### Questions from the audience
+- _Q: Can it organize the search in order of the subroutines called?_
+    - MOM6 docs does include schematics on subroutines that are called from specific file
+        - But may not be generated anymore, so may be out of date
+- _Q: Can searches be case sensitive?_
+    - Yes, you can use regex: `/(?-i)Global/`
+    - By default they aren’t case sensitive
+- _Q: What is regex?_
+    - Language for pattern matching
+    - Stands for regular expression
+    - Lots of resources online
+        - Just be sure to use the correct version of regex, as there are different types
+    - Can click “Search syntax tips” - link at bottom of search popup in GitHub - provides quick help for lots of common regex uses
+- _Q: OM3 configurations are all on a branch - does that mean we’ve eliminated the ability to search through OM3 configurations?_
+    - Yes, we can’t search OM3 configurations at the moment using this tool, because there is almost nothing on the default branch. This is definitely a limitation.
+    - Some parameter documentation has been moved to main branch specifically to be able to search on them
+    - There are other ways to search through other branches, but no examples were given
+    - Lots of people would like GitHub to add functionality to search on a branch other than the default, but not the case currently
+
+### More resources
+[Understanding GitHub Code Search syntax](https://docs.github.com/en/search-github/github-code-search/understanding-github-code-search-syntax#query-for-an-exact-match)
 
-Further details on search strategies are [here](https://docs.github.com/en/search-github/github-code-search/understanding-github-code-search-syntax).