Merge branch 'main' into sjspielman/122-conda-setup

docs/contributing-to-analyses/doing-analyses/index.md

@@ -0,0 +1,5 @@
+# Doing an analysis
+
+_This content is a stub._
+
+This section includes information about doing an analyses, including creating a new module and working with Git.

docs/contributing-to-analyses/doing-analyses/working-with-git/index.md

@@ -0,0 +1,5 @@
+# Working with Git
+
+_This content is a stub._
+
+This section includes information about working with Git while contributing to OpenScPCA.

docs/contributing.md

@@ -31,9 +31,9 @@ Documentation is written as a series of markdown files nested by topic in direct
   - Each top-level directory should contain an `index.md` file with an overview of what that section contains.
   - The `index.md` should have an L1 header with the same title as the `navbar` section.
   - Markdown files in each directory represent sections shown along the left sidebar.
-- Nested directories within each `navbar` section should be used to add an additional bold header on the left sidebar and _may_ also have an `index.md` file.
-  - Markdown files within each nested directory will fall under this additional bold header.
-  - These nested directories will also have `index.md` files with an overview of what that section contains.
+- Nested directories within each `navbar` section should be used to add an sections along the left sidebar.
+  - We can have multiple levels of nested directories.
+  - Nested directories may also have an `index.md` file with an L1 header and an overall description of what that section contains.
 - Any visual aids used in the docs should be placed in `docs/img` (see the [adding images section](#adding-images)).
 
 ## Adding new documentation

mkdocs.yml

@@ -14,8 +14,8 @@ theme:
     - search.suggest         # displays in light gray how you might complete the word
     - navigation.tabs        # persistent navbar on the top
     - navigation.tabs.sticky # sticky navbar
-    - navigation.sections    # enables sections along the left side bar via nested directories in docs/
     - navigation.indexes     # allow index pages to serve as overview pages for sections
+    - navigation.expand      # collapsible sections are expanded by default
 
 plugins:
   - search  # search bar
@@ -24,6 +24,8 @@ markdown_extensions:
   - admonition  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition
   - attr_list   # https://github.com/squidfunk/mkdocs-material/blob/master/docs/setup/extensions/python-markdown.md#attribute-lists
   - md_in_html  # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#markdown-in-html
+
+
 # Here is the basic structure of our navigation setup.
 #nav:
 #  - Navbar section: <!-- Contents for this navbar section are stored in the directory called `section-path` -->
@@ -50,6 +52,10 @@ nav:
     - communications-tools/index.md
   - Contributing to analyses:  # Setting up an analysis, all the git stuff
     - contributing-to-analyses/index.md
+    - Doing an analysis:
+      - contributing-to-analyses/doing-analyses/index.md
+      - Working with Git: # Creating branches, adding commits, all git interactions
+        - contributing-to-analyses/doing-analyses/working-with-git/index.md
   - Software platforms:            # LSfR, AWS, Docker, etc
     - software-platforms/index.md
   - Getting Help and FAQ:      # troubleshooting and FAQ