Merge pull request #35 from lochhh/landing-page

Update landing page
SainsburyWellcomeCentre · Oct 2, 2024 · 63b28fd · 63b28fd
2 parents 47329ed + a2ee86b
commit 63b28fd
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diff --git a/make.bat b/make.bat
@@ -12,11 +12,13 @@ set BUILDDIR=docs
 
 if "%1" == "" goto help
 
-echo "Building API docs..."
-python make_api_doctree.py
+if not "%1" == "clean" (
+	@echo Building API docs...
+	python make_api_doctree.py
 
-echo "Copying example notebooks into src..."
-python copy_examples_to_src.py
+	@echo Copying example notebooks into 'src'...
+	python copy_examples_to_src.py
+) 
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (

diff --git a/make_api_doctree.py b/make_api_doctree.py
@@ -12,8 +12,8 @@ def make_api_doctree():
     Create a doctree of all modules in aeon_mecha/aeon.
     """
     doctree = ""
-
-    for root, dirs, files in os.walk("./aeon_mecha/aeon"):
+    api_path = os.path.join(".", "aeon_mecha", "aeon")
+    for root, dirs, files in os.walk(api_path):
         # remove leading "./"
         root = root[2:]
         for file in sorted(files):

diff --git a/readme.md b/readme.md
@@ -32,7 +32,7 @@ You can view the local build by opening `docs/html/index.html` in a browser.
 
 To apply new changes to the documentation, remove all automatically generated files and folders, and rebuild:
 ```bash
-make clean html
+make clean && make html
 ```
 
 To check that external URLs are correctly resolved, run:

diff --git a/src/_static/css/custom.css b/src/_static/css/custom.css
@@ -0,0 +1,41 @@
+html[data-theme=dark] {
+  --pst-color-primary: #f0b810;
+  --pst-color-secondary: #2B8D6B;
+  --pst-color-link: var(--pst-color-primary);
+  /*--pst-color-secondary-bg: #574FA9;*/
+}
+
+html[data-theme=light] {
+  --pst-color-primary: #3f5d86;
+  --pst-color-secondary: #453F86;
+  --pst-color-link: var(--pst-color-primary);
+  /*--pst-color-secondary-bg: #37B489;*/
+}
+
+.sponsor {
+  height: 100px;
+  padding-top: 5px;
+  padding-right: 5px;
+  padding-bottom: 5px;
+  padding-left: 5px;
+}
+
+.img-sponsor {
+  height: 50px;
+  padding-top: 5px;
+  padding-right: 5px;
+  padding-bottom: 5px;
+  padding-left: 5px;
+}
+
+.things-in-a-row {
+  display: flex;
+  flex-wrap: wrap;
+  justify-content: space-between;
+}
+
+.sd-card-img-bottom {
+  width: 100%;
+  height: 15vw;
+  object-fit: contain;
+}
diff --git a/src/_static/images/dark-logo-bbsrc.png b/src/_static/images/dark-logo-bbsrc.png
diff --git a/src/_static/images/dark-logo-datajoint.png b/src/_static/images/dark-logo-datajoint.png
diff --git a/src/_static/images/dark-logo-gatsby.png b/src/_static/images/dark-logo-gatsby.png
diff --git a/src/_static/images/dark-logo-neurogears.png b/src/_static/images/dark-logo-neurogears.png
diff --git a/src/_static/images/dark-logo-simons.png b/src/_static/images/dark-logo-simons.png
diff --git a/src/_static/images/dark-logo-swc.png b/src/_static/images/dark-logo-swc.png
diff --git a/src/_static/images/dark-logo-ucl.png b/src/_static/images/dark-logo-ucl.png
diff --git a/src/_static/images/dark-logo-wellcome.png b/src/_static/images/dark-logo-wellcome.png
diff --git a/src/_static/images/getting-started-ma.png b/src/_static/images/getting-started-ma.png
diff --git a/src/_static/images/getting-started-npx.png b/src/_static/images/getting-started-npx.png
diff --git a/src/_static/images/hardware-overview-arena.png b/src/_static/images/hardware-overview-arena.png
diff --git a/src/_static/images/hardware-overview-feeder.png b/src/_static/images/hardware-overview-feeder.png
diff --git a/src/_static/images/hardware-overview-nest.png b/src/_static/images/hardware-overview-nest.png
diff --git a/src/_static/images/landing-247.png b/src/_static/images/landing-247.png
diff --git a/src/_static/images/landing-banner.png b/src/_static/images/landing-banner.png
diff --git a/src/_static/images/landing-digging.png b/src/_static/images/landing-digging.png
diff --git a/src/_static/images/landing-feeder.png b/src/_static/images/landing-feeder.png
diff --git a/src/_static/images/landing-hexslot.png b/src/_static/images/landing-hexslot.png
diff --git a/src/_static/images/landing-sleeping.png b/src/_static/images/landing-sleeping.png
diff --git a/src/_static/images/light-logo-bbsrc.png b/src/_static/images/light-logo-bbsrc.png
diff --git a/src/_static/images/light-logo-datajoint.png b/src/_static/images/light-logo-datajoint.png
diff --git a/src/_static/images/light-logo-gatsby.png b/src/_static/images/light-logo-gatsby.png
diff --git a/src/_static/images/light-logo-neurogears.png b/src/_static/images/light-logo-neurogears.png
diff --git a/src/_static/images/light-logo-simons.png b/src/_static/images/light-logo-simons.png
diff --git a/src/_static/images/light-logo-swc.png b/src/_static/images/light-logo-swc.png
diff --git a/src/_static/images/light-logo-ucl.png b/src/_static/images/light-logo-ucl.png
diff --git a/src/_static/images/light-logo-wellcome.png b/src/_static/images/light-logo-wellcome.png
diff --git a/src/_static/images/ma-identifying-animals.png b/src/_static/images/ma-identifying-animals.png
diff --git a/src/_static/images/ma-live-position-tracking.png b/src/_static/images/ma-live-position-tracking.png
diff --git a/src/_static/images/ma-pose-estimation.png b/src/_static/images/ma-pose-estimation.png
diff --git a/src/_static/images/npx-commutator-location.png b/src/_static/images/npx-commutator-location.png
diff --git a/src/_static/images/npx-commutator-rotation.png b/src/_static/images/npx-commutator-rotation.png
diff --git a/src/_static/images/npx-recording-sites.png b/src/_static/images/npx-recording-sites.png
diff --git a/src/_templates/footer_end.html b/src/_templates/footer_end.html
@@ -0,0 +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"/>
+    </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"/>
+    </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"/>
+    </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"/>
+    </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"/>
+    </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"/>
+    </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"/>
+    </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"/>
+    </a>
+</div>
diff --git a/src/_templates/footer_start.html b/src/_templates/footer_start.html
@@ -0,0 +1,9 @@
+<p class="sphinx-version"></p>
+    {% trans sphinx_version=sphinx_version|e %}Created using <a href="https://sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
+    <br/>
+    </p>
+    <p class="theme-version">
+    {{ _("Built with the") }}
+    <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a>
+    {{ theme_version }}.
+    </p>
diff --git a/src/about/index.md b/src/about/index.md
@@ -1,13 +1,23 @@
 (target-about)=
 # About
 
-Development of Project Aeon is supported by... 
-
-The goals of Project Aeon are to
-* ...
-* ...
-
-For an in-depth look at the unique challenges and opportunities presented by the datasets collected in Project Aeon, please refer to our [Design Considerations](target-design-considerations).
+The development of Aeon is funded by the [Gatsby Charitable Foundation](http://www.gatsby.org.uk/) and [Wellcome](https://wellcome.ac.uk/). This joint initiative involves people from the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/) and the [Gatsby Computational Neuroscience Unit](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit) at UCL, [NeuroGEARS Ltd](https://neurogears.org/), and [DataJoint Inc](https://www.datajoint.com/). For a full list of people involved, please refer to this [page](target-people).
+
+The brain's computations are shaped by evolutionary pressures related to survival and the resulting behavioural responses. 
+Understanding the neural basis of natural behaviours is crucial for advancing our knowledge of the brain, as it sheds light on the functions of neural circuits in processing real-world stimuli. 
+However, replicating natural conditions in a laboratory setting presents a challenge, as it requires simulating complex and dynamic environments which include the presence of conspecifics. 
+It also requires monitoring over extended periods of time, all while allowing parametric control over key experimental variables and rigorous measurement of behaviour and neural activity.
+
+Aeon is an open-source platform designed to study the neural basis of ethological behaviours over naturalistic timescales, ranging from weeks to months.
+At its core, the setup is a modular, scalable, and programmable arena in which animals live. 
+The arena can be equipped with various combinations of [interactive and non-interactive modules](target-hardware),
+including, but not limited to, feeders, nesting areas, microphones, RFID readers, magnetic encoders, weighing scales, and high-speed cameras. 
+This allows mimicking of complex and dynamic environments, thereby enabling animals to exhibit different natural behaviours, 
+such as foraging, nesting, escape and social interaction. 
+The large array of sensors in the arena additionally allows for continuous tracking of animal position, pose and identity, which in turn enables
+multidimensional quantification of behavioural dynamics and internal states at millisecond resolution.
+
+For an in-depth look at the unique challenges and opportunities presented by the datasets collected in Aeon, please refer to our [Design Considerations](target-design-considerations).
 If you have any questions or need further information, feel free to reach out to the [project maintainers](target-project-maintainers).
 
 (target-project-maintainers)=
@@ -18,19 +28,15 @@ If you have any questions or need further information, feel free to reach out to
 * Dario Campagner ([email protected])
 * Chang Huan Lo ([email protected])
 
-(target-project-contributors)=
-## Contributors
-
-List researchers and support staff at UCL's SWC, Neurogears, and Datajoint...
-
 ## Code of Conduct
 
-Project Aeon is dedicated to providing a welcoming and positive experience for all its participants. We encourage respectful and considerate behavior, and we expect our community members to adhere to these principles. Please read our [Code of Conduct](target-code-of-conduct) for more details on our community guidelines and expectations.
+Aeon is dedicated to providing a welcoming and positive experience for all its participants. We encourage respectful and considerate behavior, and we expect our community members to adhere to these principles. Please read our [Code of Conduct](target-code-of-conduct) for more details on our community guidelines and expectations.
 
 :::{toctree}
 :maxdepth: 1
 :hidden:
 
+people
 design_considerations
 code_of_conduct
 license
diff --git a/src/about/people.md b/src/about/people.md
@@ -0,0 +1,52 @@
+(target-people)=
+# People
+Aeon is made possible thanks to the dedication and hard work of numerous individuals. In alphabetical order:
+
+```{csv-table}
+Athena Akrami,Sainsbury Wellcome Centre - UCL
+André Almeida,NeuroGEARS Ltd
+Jaerong Ahn,DataJoint Inc
+Joseph Burling,DataJoint Inc
+Robb Barret,Sainsbury Wellcome Centre - UCL
+Tim Behrens,Sainsbury Wellcome Centre - UCL
+Jai Bhagat,Sainsbury Wellcome Centre - UCL
+Jacek Budziszewski,Sainsbury Wellcome Centre - UCL
+Tiago Branco,Sainsbury Wellcome Centre - UCL
+Neil Burgess,Sainsbury Wellcome Centre - UCL
+Lorenza Calcaterra,Sainsbury Wellcome Centre - UCL
+Dario Campagner,"Sainsbury Wellcome Centre - UCL, Gatsby Computational Neuroscience Unit - UCL"
+Filipe Carvalho,NeuroGEARS Ltd
+Roger Chen,Sainsbury Wellcome Centre - UCL
+Bruno Cruz,NeuroGEARS Ltd
+Chunyu Ann Duan,Sainsbury Wellcome Centre - UCL
+Jeffrey Erlich,Sainsbury Wellcome Centre - UCL
+Andrew Erskine,NeuroGEARS Ltd
+Orsolya Folsz,Sainsbury Wellcome Centre - UCL
+Sean Hammet,Sainsbury Wellcome Centre - UCL
+Julia Harris,Sainsbury Wellcome Centre - UCL
+Del Halpin,Sainsbury Wellcome Centre - UCL
+Sonja Hofer,Sainsbury Wellcome Centre - UCL
+Yoh Isogai ,Sainsbury Wellcome Centre - UCL
+Peter Latham,Gatsby Computational Neuroscience Unit - UCL
+Zimo Li,Gatsby Computational Neuroscience Unit - UCL
+Chang Huan Lo,Sainsbury Wellcome Centre - UCL
+Gonçalo Lopes,NeuroGEARS Ltd
+Troy Margrie,Sainsbury Wellcome Centre - UCL
+Milagros Marín,DataJoint Inc
+Thomas Mrsic-Flogel,Sainsbury Wellcome Centre - UCL
+Sian Murphy,Sainsbury Wellcome Centre - UCL
+Graeme McPhillips,Sainsbury Wellcome Centre - UCL
+Gordon Mills,Sainsbury Wellcome Centre - UCL
+Thinh Nguyen,DataJoint Inc
+Svenja Nierwetberg,Sainsbury Wellcome Centre - UCL
+John O’Keefe,Sainsbury Wellcome Centre - UCL
+Tom Otis,Sainsbury Wellcome Centre - UCL
+Anaya Pouget,Sainsbury Wellcome Centre - UCL
+Joaquin Rapela,Gatsby Computational Neuroscience Unit - UCL
+Thomas Ryan,NeuroGEARS Ltd
+Maneesh Sahani,Gatsby Computational Neuroscience Unit - UCL
+Andrew Saxe,"Sainsbury Wellcome Centre - UCL, Gatsby Computational Neuroscience Unit - UCL"
+Simon Townsend,Sainsbury Wellcome Centre - UCL
+Max Townsend,Sainsbury Wellcome Centre - UCL
+William Walker,Gatsby Computational Neuroscience Unit - UCL
+``` 
diff --git a/src/conf.py b/src/conf.py
@@ -27,7 +27,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "aeon_docs"
+project = "Aeon"
 author = "Jai Bhagat, Goncalo Lopes, Chang Huan Lo"
 copyright = f"2022–{date.today().year}, {author}"
 organisation = "Sainsbury Wellcome Centre"
@@ -50,7 +50,7 @@ def get_current_release_tag():
 release = get_current_release_tag()
 
 # GitHub repo URL
-github_url = f"https://github.com/{organisation.replace(' ', '')}/{project}"
+github_url = f"https://github.com/{organisation.replace(' ', '')}/aeon_docs"
 
 # -- General configuration ---------------------------------------------------
 
@@ -111,11 +111,14 @@ def get_current_release_tag():
 #
 html_theme = "pydata_sphinx_theme"
 html_theme_options = {
-    "announcement": f"{project} is a WIP. Please report any issues on <a href='{github_url}/issues'>GitHub</a>.",
+    "announcement": (
+        f"This website is currently under active development. "
+        f"Please report any issues on <a href='{github_url}/issues'>GitHub</a>."
+    ),
     "logo": {
         "text": f"{project} {release}"
-        # "image_light": "_static/logo-light.png",
-        # "image_dark": "_static/logo-dark.png",
+        # "image_light": "_static/images/logo-light.png",
+        # "image_dark": "_static/images/logo-dark.png",
     },
     "icon_links": [
         {
@@ -130,13 +133,16 @@ def get_current_release_tag():
         }
     ],
     "show_toc_level": 3,  # Show the first 3 levels of the local TOC
+    "footer_start": ["footer_start"],
+    "footer_end": ["footer_end"],
 }
 # 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"
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css",
+    "css/custom.css",	
 ]
 
 # linkcheck will skip checking these URLs entirely
@@ -157,6 +163,11 @@ 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}}",
+    "aeon-feeder-github": "https://github.com/SainsburyWellcomeCentre/aeon_feeder/{{path}}",
     "semver": "https://semver.org/",
     "harp-tech": "https://harp-tech.org/{{path}}#{{fragment}}",
     "python-pep": "https://peps.python.org/pep-{{path}}",