Move images and downloads directories to root (#82)

* Move images dir to root

* Move downloads dir to root

src/_templates/footer_end.html

@@ -1,34 +1,34 @@
 <div class="things-in-a-row">
     <a href="https://neurogears.org/">
-        <img src="{{ pathto('_static/images/light-logo-neurogears.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-neurogears.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-neurogears.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-neurogears.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://www.datajoint.com/">
-        <img src="{{ pathto('_static/images/light-logo-datajoint.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-datajoint.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-datajoint.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-datajoint.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://wellcome.org/">
-        <img src="{{ pathto('_static/images/light-logo-wellcome.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-wellcome.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-wellcome.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-wellcome.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://www.sainsburywellcome.org/web/">
-        <img src="{{ pathto('_static/images/light-logo-swc.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-swc.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-swc.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-swc.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://www.ucl.ac.uk/">
-        <img src="{{ pathto('_static/images/light-logo-ucl.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-ucl.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-ucl.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-ucl.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit">
-        <img src="{{ pathto('_static/images/light-logo-gatsby.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-gatsby.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-gatsby.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-gatsby.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://www.ukri.org/councils/bbsrc/">
-        <img src="{{ pathto('_static/images/light-logo-bbsrc.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-bbsrc.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-bbsrc.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-bbsrc.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
     <a href="https://www.simonsfoundation.org/">
-        <img src="{{ pathto('_static/images/light-logo-simons.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
-        <img src="{{ pathto('_static/images/dark-logo-simons.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
+        <img src="{{ pathto('images/light-logo-simons.png', 1) }}" alt="Sponsors" class="only-light img-sponsor"/>
+        <img src="{{ pathto('images/dark-logo-simons.png', 1) }}" alt="Sponsors" class="only-dark img-sponsor"/>
     </a>
 </div>

src/conf.py

@@ -117,8 +117,8 @@ def get_current_release_tag():
     ),
     "logo": {
         "text": f"{project} {release}"
-        # "image_light": "_static/images/logo-light.png",
-        # "image_dark": "_static/images/logo-dark.png",
+        # "image_light": "images/logo-light.png",
+        # "image_dark": "images/logo-dark.png",
     },
     "icon_links": [
         {
@@ -139,10 +139,10 @@ def get_current_release_tag():
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_css_files = [
     "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css",
-    "css/custom.css",	
+    "css/custom.css",
 ]
 
 # linkcheck will skip checking these URLs entirely

src/getting_started/index.md

@@ -18,7 +18,7 @@ Further information about the project can be found in the
 :::{grid-item-card} {fas}`location-crosshairs;sd-text-primary` Multi-animal tracking
 :link: target-multianimal-tracking
 :link-type: ref
-:img-bottom: ../_static/images/getting-started-ma.png
+:img-bottom: ../images/getting-started-ma.png
 :img-alt:
 
 Online tracking of multiple animals in the Aeon arena.
@@ -27,7 +27,7 @@ Online tracking of multiple animals in the Aeon arena.
 :::{grid-item-card} {fas}`brain;sd-text-primary` Neuropixels recordings
 :link: target-npx-recording
 :link-type: ref
-:img-bottom: ../_static/images/getting-started-npx.png
+:img-bottom: ../images/getting-started-npx.png
 :img-alt:
 
 Week-long recording and analysis of Neuropixels data.

src/index.md

@@ -1,6 +1,6 @@
 (target-home)=
 
-![Banner](_static/images/landing-banner.png){align=center}
+![Banner](images/landing-banner.png){align=center}
 # Aeon
 
 An open-source platform to study the neural basis of ethological behaviours over naturalistic timescales.
@@ -11,7 +11,7 @@ An open-source platform to study the neural basis of ethological behaviours over
 :::{grid-item}
 :columns: 4
 :child-align: center
-![247Experiment](_static/images/landing-247.png){align=left}
+![247Experiment](images/landing-247.png){align=left}
 :::
 :::{grid-item}
 :columns: 8
@@ -45,13 +45,13 @@ To the Reference Guide
 :::{grid-item}
 :columns: 4
 :child-align: center
-![Feeder](_static/images/landing-feeder.png){align=right} 
+![Feeder](images/landing-feeder.png){align=right} 
 :::
 
 :::{grid-item}
 :columns: 4
 :child-align: center
-![Sleeping](_static/images/landing-sleeping.png){align=left}
+![Sleeping](images/landing-sleeping.png){align=left}
 :::
 :::{grid-item}
 :columns: 8
@@ -83,7 +83,7 @@ To the Contributor Guide
 :::{grid-item}
 :columns: 4
 :child-align: center
-![Hexslot](_static/images/landing-hexslot.png){align=right}
+![Hexslot](images/landing-hexslot.png){align=right}
 :::
 ::::
 

src/reference/api.md

@@ -7,7 +7,7 @@
 :::{grid-item-card} Data API Reference
 :link: target-mecha-reference
 :link-type: ref
-:img-bottom: ../_static/images/api-python-logo.png
+:img-bottom: ../images/api-python-logo.png
 :class-img-bottom: sd-px-2
 :class-card: sd-height-25
 
@@ -17,7 +17,7 @@ This reference guide contains a detailed description of the `aeon_mecha` low-lev
 :::{grid-item-card} Acquisition API Reference
 :link: target-acquisition-reference
 :link-type: ref
-:img-bottom: ../_static/images/api-bonsai-logo.png
+:img-bottom: ../images/api-bonsai-logo.png
 :class-img-bottom: sd-px-2
 :class-card: sd-height-25
 

src/reference/hardware.md

@@ -7,10 +7,10 @@ This section is still under construction. Some information may be incomplete or
 ## Main modules
 | Module | Files |
 | --- | --- |
-| **Arena** <br>![arena](../_static/images/hardware-overview-arena.png){height=15em align=center} | <ul><li>[Assembly guide](../_static/resources/Arena%20guideline%20Final%201.pdf)</li><li>[Bill of materials](../_static/resources/Arena%20BOM.xlsx)</li></ul> |
-| **Feeder** <br>![feeder](../_static/images/hardware-overview-feeder.png){height=12em align=center} | <ul><li>[Assembly guide](../_static/resources/Feeder%20Guideline%20Final%201.pdf)</li><li>[Bill of materials](../_static/resources/Feeder%20BOM.xlsx)</li></ul> |
-| **Nest** <br>![nest](../_static/images/hardware-overview-nest.png){height=15em align=center} | <ul><li>[Assembly guide](../_static/resources/Nest%20Guideline%20Final%201.pdf)</li></ul> |
-| **Closed-loop translation-commutation system** <br>![linear-rail](../_static/images/hardware-overview-linear-rail.png){height=15em align=center} | <ul><li>[Assembly guide](../_static/resources/Linear%20commutator%20Guideline%20Final%201.pdf)</li></ul> |
+| **Arena** <br>![arena](../images/hardware-overview-arena.png){height=15em align=center} | <ul><li>[Assembly guide](../downloads/Arena%20guideline%20Final%201.pdf)</li><li>[Bill of materials](../downloads/Arena%20BOM.xlsx)</li></ul> |
+| **Feeder** <br>![feeder](../images/hardware-overview-feeder.png){height=12em align=center} | <ul><li>[Assembly guide](../downloads/Feeder%20Guideline%20Final%201.pdf)</li><li>[Bill of materials](../downloads/Feeder%20BOM.xlsx)</li></ul> |
+| **Nest** <br>![nest](../images/hardware-overview-nest.png){height=15em align=center} | <ul><li>[Assembly guide](../downloads/Nest%20Guideline%20Final%201.pdf)</li></ul> |
+| **Closed-loop translation-commutation system** <br>![linear-rail](../images/hardware-overview-linear-rail.png){height=15em align=center} | <ul><li>[Assembly guide](../downloads/Linear%20commutator%20Guideline%20Final%201.pdf)</li></ul> |
 
 ## Harp devices
 | Harp Device                       | Associated Component            | Description                                                   | Quantity | 
@@ -22,7 +22,7 @@ This section is still under construction. Some information may be incomplete or
 | [**Harp SoundCard**](harp-tech:api/Harp.SoundCard.html)                  | SP speaker                      | Control and monitoring of audio speaker                     | 1        | 
 
 ## Wiring diagrams
-- [Wiring diagram](../_static/resources/Example%20wiring%20diagram.pdf)
+- [Wiring diagram](../downloads/Example%20wiring%20diagram.pdf)
 
 <!--
 :::{toctree}
@@ -32,18 +32,18 @@ hardware/feeder
 
 ::::{grid} 1 3 3 3 
 :::{grid-item-card} Feeder
-:img-top: ../_static/images/hardware-overview-feeder.png
+:img-top: ../images/hardware-overview-feeder.png
 :link: target-feeder
 :link-type: ref
-:img-bottom: ../_static/images/hardware-overview-feeder.png
+:img-bottom: ../images/hardware-overview-feeder.png
 :::
 
 :::{grid-item-card} Arena
-:img-bottom: ../_static/images/hardware-overview-arena.png
+:img-bottom: ../images/hardware-overview-arena.png
 :::
 
 :::{grid-item-card} Nest
-:img-bottom: ../_static/images/hardware-overview-nest.png
+:img-bottom: ../images/hardware-overview-nest.png
 :::
 ::::
 -->

src/reference/hardware/feeder.md

@@ -1,48 +1,48 @@
 (target-feeder)=
 # Feeder
-![Feeder](../../_static/images/feeder.png){align=center}
+![Feeder](../../images/feeder.png){align=center}
 Insert description of the feeder.
 
 ## Parts List
-![Parts1](../../_static/images/feeder-main.png)
-![Parts2](../../_static/images/feeder-parts.png)
+![Parts1](../../images/feeder-main.png)
+![Parts2](../../images/feeder-parts.png)
 
 ## Assembly Guide
 ### Pellet Hopper
 ::::{dropdown} Steps 1-5
-:::{figure} ../../_static/images/feeder-pellet-hopper1.png
+:::{figure} ../../images/feeder-pellet-hopper1.png
 :alt: step1
 1\. Trim slightly the motor metal pin using a grinding wheel or a handheld Dremel. Trim until you create a flat surface on the pin. 
 :::
-:::{figure} ../../_static/images/feeder-pellet-hopper2.png
+:::{figure} ../../images/feeder-pellet-hopper2.png
 :alt: step2
 2\. Rotate the feeder base and insert the motor. Screw the motor in place from the front using three screws (ID 2).
 :::
-:::{figure} ../../_static/images/feeder-pellet-hopper1.png
+:::{figure} ../../images/feeder-pellet-hopper1.png
 :alt: step3
 3\. Carefully handle the track and gently insert it in the feeder making sure of aligning the holes. Rotate the feeder base and hold the track in place by using six screws (ID 5).
 :::
-:::{figure} ../../_static/images/feeder-pellet-hopper1.png
+:::{figure} ../../images/feeder-pellet-hopper1.png
 :alt: step4
 4\. Lower the disk into the feeder base making sure to orient the grub screw tapped hole toward the flat surface previously created on the motor metal pin (see step 1). Push down the disk until the top of the pin is flushed to the disk itself and use a grub screw (ID 10) to hold the disk in place. Make sure the grub screw touches the flat surface of the trimmed motor pin.
 :::
-:::{figure} ../../_static/images/feeder-pellet-hopper1.png
+:::{figure} ../../images/feeder-pellet-hopper1.png
 :alt: step5
 5\. Insert two short silicon tubes in each pellet stopper pin and screw it in place with two screws (ID 4). 
 :::
 ::::
 
 ### IR Sensor
 ::::{dropdown} Steps 6-8 
-:::{figure} ../../_static/images/feeder-ir-sensor1.png
+:::{figure} ../../images/feeder-ir-sensor1.png
 :alt: step6
 6\. Place the wheel frame on the feeder base with 4 screws (ID 4).
 :::
-:::{figure} ../../_static/images/feeder-ir-sensor2.png
+:::{figure} ../../images/feeder-ir-sensor2.png
 :alt: step7
 7\. Carefully insert the beam break PCB board into the beam break holder (ID 12).
 :::
-:::{figure} ../../_static/images/feeder-ir-sensor1.png
+:::{figure} ../../images/feeder-ir-sensor1.png
 :alt: step8
 8\. Slot the beam break holder in the back of the feeder base and screw it in place from the front (ID 1).
 :::

src/reference/index.md

@@ -9,28 +9,28 @@ This reference manual details all software and hardware components, and a glossa
 :::{grid-item-card} Hardware Overview
 :link: target-hardware
 :link-type: ref
-:img-bottom: ../_static/images/noun-hardware-setup-6046729.svg
+:img-bottom: ../images/noun-hardware-setup-6046729.svg
 :class-img-bottom: .sd-img-bottom-small
 :::
 
 :::{grid-item-card} API Reference
 :link: target-api-reference
 :link-type: ref
-:img-bottom: ../_static/images/noun-code-6878936.svg
+:img-bottom: ../images/noun-code-6878936.svg
 :class-img-bottom: .sd-img-bottom-small 
 :::
 
 :::{grid-item-card} Data Contract
 :link: target-data-schema
 :link-type: ref
-:img-bottom: ../_static/images/noun-data-modeling-6688047.svg
+:img-bottom: ../images/noun-data-modeling-6688047.svg
 :class-img-bottom: .sd-img-bottom-small 
 :::
 
 :::{grid-item-card} Glossary
 :link: target-glossary
 :link-type: ref
-:img-bottom: ../_static/images/noun-lexicon-7107720.svg
+:img-bottom: ../images/noun-lexicon-7107720.svg
 :class-img-bottom: .sd-img-bottom-small 
 :::
 ::::

src/user/tutorials/multianimal_tracking.md

@@ -1,7 +1,7 @@
 (target-multianimal-tracking)=
 # Multi-animal tracking
 
-:::{figure} ../../_static/images/ma-main.png
+:::{figure} ../../images/ma-main.png
 :height: 300px
 :alt: multi-animal-tracking
 
@@ -17,7 +17,7 @@ This is possible through the multipronged approach using multiple cameras as wel
 :::{grid-item}
 :columns: 4
 :child-align: center
-![live-position-tracking](../../_static/images/ma-live-position-tracking.png)
+![live-position-tracking](../../images/ma-live-position-tracking.png)
 :::
 :::{grid-item}
 :columns: 8
@@ -37,7 +37,7 @@ continuously estimates the animals' x, y positions, body length, and orientation
 :::{grid-item}
 :columns: 4
 :child-align: center
-![identifying-animals](../../_static/images/ma-identifying-animals.png)
+![identifying-animals](../../images/ma-identifying-animals.png)
 :::
 :::{grid-item}
 :columns: 8
@@ -59,7 +59,7 @@ allow us to quantify their visits to important sites (nest, foraging patches, ga
 :::{grid-item}
 :columns: 4
 :child-align: center
-![pose-estimation](../../_static/images/ma-pose-estimation.png)
+![pose-estimation](../../images/ma-pose-estimation.png)
 :::
 :::{grid-item}
 :columns: 8

src/user/tutorials/npx_recording.md

@@ -1,7 +1,7 @@
 (target-npx-recording)=
 # Neuropixels recordings
 
-:::{figure} ../../_static/images/npx-main.png
+:::{figure} ../../images/npx-main.png
 :height: 300px
 :alt: neuropixels-recording
 
@@ -23,7 +23,7 @@ To address these challenges, we developed a closed-loop control system capable o
 :::{grid-item}
 :columns: 4
 :child-align: center
-![commutator-location-control](../../_static/images/npx-commutator-location.png)
+![commutator-location-control](../../images/npx-commutator-location.png)
 :::
 :::{grid-item}
 :columns: 8
@@ -42,7 +42,7 @@ Using the live position estimate from the overhead camera, we can control the ho
 :::{grid-item}
 :columns: 4
 :child-align: center
-![commutator-rotation-control](../../_static/images/npx-commutator-rotation.png)
+![commutator-rotation-control](../../images/npx-commutator-rotation.png)
 :::
 :::{grid-item}
 :columns: 8
@@ -61,7 +61,7 @@ Using the heading direction computed by the IMU sensor on the [Onix neuropixels
 :::{grid-item}
 :columns: 4
 :child-align: center
-![npx-20-recordings](../../_static/images/npx-recording-sites.png)
+![npx-20-recordings](../../images/npx-recording-sites.png)
 :::
 :::{grid-item}
 :columns: 8