Remove unused submodules (#88)

* Remove unused submodules

* Automatically check out all submodules

* Remove submodule dirs

* Remove mentions of `aeon_analysis`

.github/workflows/docs_build_and_deploy.yml

@@ -21,16 +21,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: false # Disable automatic checkout of all submodules
-      - name: Fetch tags
-        run: |
-          git fetch --prune --prune-tags --force --depth=1 --no-recurse-submodules
-      - name: Checkout public submodules # Skip aeon_experiments
-        run: |
-          git submodule sync
-          git submodule update --init aeon_acquisition
-          git submodule update --init aeon_analysis
-          git submodule update --init aeon_mecha
+          submodules: true # Enable automatic checkout of all submodules
 
       - name: Setup .NET
         uses: actions/setup-dotnet@v4

.gitmodules

@@ -2,14 +2,6 @@
 	path = aeon_mecha
 	url = https://github.com/SainsburyWellcomeCentre/aeon_mecha
 	branch = data-preview
-[submodule "aeon_analysis"]
-	path = aeon_analysis
-	url = https://github.com/SainsburyWellcomeCentre/aeon_analysis
-	branch = api-notebooks
-[submodule "aeon_blog"]
-	path = aeon_blog
-	url = https://github.com/SainsburyWellcomeCentre/aeon_blog
-	branch = main
 [submodule "aeon_experiments"]
 	path = aeon_experiments
 	url = https://github.com/SainsburyWellcomeCentre/aeon_experiments

readme.md

@@ -144,10 +144,6 @@ Contains experiment workflows written in the Bonsai visual programming language.
 
 Contains the source code for the 'aeon_acquisition' Bonsai package, which is heavily used in workflows in 'aeon_experiments'.
 
-### [aeon_analysis](https://github.com/SainsburyWellcomeCentre/aeon_analysis)
-
-Contains Python modules for analysis of Aeon experiment data.
-
 ### [aeon_lineardrive](https://github.com/SainsburyWellcomeCentre/aeon_lineardrive)
 
 Contains source code for actuating a linear drive motor used in Aeon experiments (designed primarily for moving electrophysiology cabling during freely-moving experiments).

src/conf.py

@@ -18,7 +18,6 @@
 sys.path.extend(
     [
         os.path.abspath("../aeon_mecha/"),
-        os.path.abspath("../aeon_analysis/aeon_analysis"),
         os.path.abspath("../aeon_acquisition"),
         os.path.abspath("../aeon_experiments"),
     ]
@@ -165,7 +164,6 @@ def get_current_release_tag():
     "ftp": None,
     "mailto": None,
     "aeon-mecha-github": "https://github.com/SainsburyWellcomeCentre/aeon_mecha/{{path}}",
-    "aeon-analysis-github": "https://github.com/SainsburyWellcomeCentre/aeon_analysis/{{path}}",
     "aeon-acquisition-github": "https://github.com/SainsburyWellcomeCentre/aeon_acquisition/{{path}}",
     "aeon-experiments-github": "https://github.com/SainsburyWellcomeCentre/aeon_experiments/{{path}}",
     "aeon-lineardrive-github": "https://github.com/SainsburyWellcomeCentre/aeon_lineardrive/{{path}}",

src/getting_started/index.md

@@ -60,12 +60,6 @@ Source code for the `aeon_acquisition` Bonsai package used in
 Aeon experiment workflows
 :::
 
-:::{grid-item-card} {fas}`chart-line;sd-text-primary` aeon_analysis
-:link: https://github.com/SainsburyWellcomeCentre/aeon_analysis
-:link-type: url
-Python modules for analysis of Aeon experiment data
-:::
-
 :::{grid-item-card} {fas}`gear;sd-text-primary` aeon_lineardrive
 :link: https://github.com/SainsburyWellcomeCentre/aeon_lineardrive
 :link-type: url