wip docs

.gitignore

@@ -7,3 +7,5 @@ src/plugin_examples/*/
 .idea
 deploy/datasets/data/
 .DS_Store
+venv/
+site

docs/Dockerfile

+FROM python:3.7 as builder
+
+COPY . /iav
+WORKDIR /iav
+
+RUN pip install mkdocs mkdocs-material mdx_truly_sane_lists
+RUN mkdocs build
+
+FROM nginx:alpine
+COPY --from=builder /iav/site /usr/share/nginx/html
+COPY --from=builder /iav/docs/nginx.conf /etc/nginx/nginx.conf
+
+ENTRYPOINT ["nginx", "-g", "daemon off;"]

docs/extra.css

+div.autodoc-docstring {
+  padding-left: 20px;
+  margin-bottom: 30px;
+  border-left: 5px solid rgba(230, 230, 230);
+}
+
+div.autodoc-members {
+  padding-left: 20px;
+  margin-bottom: 15px;
+}
+
+/* img {
+  width: 50%;
+  display: block;
+} */
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docs/index.md

+# Interactive Atlas Viewer
+
+Interactive Atlas Viewer is a browser based viewer of brain atlases. Strong integration with the Human Brain Project Knowledge Graph project allow data/datasets that are semantically and spatially anchored to be easily accessible with minimal setup required.
+
+![](images/desktop_bigbrain_cortical.png)
+
+## Important links
+
+- production: <https://interactive-viewer.apps.hbp.eu>
+- production: <https://atlases.ebrains.eu/viewer>
+- contact us: [inm1-bda@fz-juelich.de](mailto:inm1-bda@fz-juelich.de?subject=[IAV]%20Queries)

docs/nginx.conf

+user  nginx;
+worker_processes  auto;
+
+error_log  /var/log/nginx/error.log warn;
+pid        /tmp/nginx.pid;
+
+
+events {
+    worker_connections  1024;
+}
+
+
+http {
+    client_body_temp_path /tmp/client_temp;
+    proxy_temp_path       /tmp/proxy_temp_path;
+    fastcgi_temp_path     /tmp/fastcgi_temp;
+    uwsgi_temp_path       /tmp/uwsgi_temp;
+    scgi_temp_path        /tmp/scgi_temp;
+
+    include       /etc/nginx/mime.types;
+    default_type  application/octet-stream;
+
+    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
+                      '$status $body_bytes_sent "$http_referer" '
+                      '"$http_user_agent" "$http_x_forwarded_for"';
+
+    access_log  /var/log/nginx/access.log  main;
+
+    sendfile        on;
+    #tcp_nopush     on;
+
+    keepalive_timeout  65;
+
+    #gzip  on;
+    
+    server {
+        listen       8080;
+        server_name  localhost;
+
+        #charset koi8-r;
+        #access_log  /var/log/nginx/host.access.log  main;
+
+        location / {
+            root   /usr/share/nginx/html;
+            index  index.html index.htm;
+        }
+
+        #error_page  404              /404.html;
+
+        # redirect server error pages to the static page /50x.html
+        #
+        error_page   500 502 503 504  /50x.html;
+        location = /50x.html {
+            root   /usr/share/nginx/html;
+        }
+
+        # proxy the PHP scripts to Apache listening on 127.0.0.1:80
+        #
+        #location ~ \.php$ {
+        #    proxy_pass   http://127.0.0.1;
+        #}
+
+        # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
+        #
+        #location ~ \.php$ {
+        #    root           html;
+        #    fastcgi_pass   127.0.0.1:9000;
+        #    fastcgi_index  index.php;
+        #    fastcgi_param  SCRIPT_FILENAME  /scripts$fastcgi_script_name;
+        #    include        fastcgi_params;
+        #}
+
+        # deny access to .htaccess files, if Apache's document root
+        # concurs with nginx's one
+        #
+        #location ~ /\.ht {
+        #    deny  all;
+        #}
+    }
+
+}

docs/releases/legacy.md

+# legacy
+
+Apr 2018
+
+First prototype of interactive atlas viewer wrapping nehuba

docs/releases/v0.1.0.md

+# v0.1.0
+
+3 Apr 2018
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v0.1.0)
+
+Implemented plugin APIs.

docs/releases/v0.2.0.md

+# v0.2.0
+
+6 Apr 2018
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v0.2.0)
+
+Updated plugin APIs.

docs/releases/v0.2.9.md

+# v0.2.9
+
+19 Nov 2018
+
+!!! info
+    v0.2.9 is the last version that supports Bootstrap v3
+
+!!! info
+    v0.2.9 is the last version that is purely frontend. From [v0.3.0-beta](v0.3.0-beta.md) onwards, interactive atlas viewer requires a backend to function properly.
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v0.2.9)
+
+- Refactor to allow for faster transpiling, faster loading (via Angular AOT compilation)
+- Improving performance on rendering nested hierarchy
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docs/releases/v0.3.0-beta.md

+# v0.3.0-beta
+
+26 Apr 2019
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v0.3.0-beta)
+
+- Using Bootstrap 4
+- Using webgl 2
+- Supporting Andorid mobile devices
+- Allow querying of Knowledge Graph on semantically linked data
+- Landmark sizes now scale with brain sizes (Because mouse brains are a lot smaller than human brains)
+- Allow setting of GPU limit. On lower end devices, this can reduce the likelihood of a crash.
+- Allow user login via HBP OIDC
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docs/releases/v2.0.0.md

+# v2.0.0
+
+18 Oct 2019
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v2.0.0)
+
+- Added support for new atlases:
+  - cytoarchitechtonic maps (mapped and interpolated) in Big Brain template space
+
+  - JuBrain v18 in Colin 27 and MNI 152 2009c Nonlinear Asymmetric
+
+  - Waxholm v1.01
+  
+  - Waxholm v3
+  
+  - Allen CCF 2017
+
+- Most assets are gz or br compressed. Should drastically improve load speed
+
+- Shiny new splash screen
+
+- Use base64 to hash selected regions and viewer state. This should drastically reduce URL length (see [PR](https://github.com/HumanBrainProject/interactive-viewer/pull/241))
+
+- Allow files to be bundled into a zip file with README.txt and LICENCE.md bundled
+
+- Allow animation to be turned off. For lower end devices, this could improve performance
+
+- Allow nifti file to be drag and dropped and visualised directly (beta)
+
+- Dark mode via SASS, toggled on automatically via template (system pref incoming. Watch this space)
+
+- You can now favouriting dataset
+
+- Lower res preview images are also served to reduce load time
+
+- New API for plugins: `getUserInput` and `getUserConfirm`
+
+- Allow toggle between single panel and four panel view
+
+- Chores
+
+  - Added terms of use and cookie disclaimer
+  
+  - Move spatial search to backend
+  
+  - Upgraded to Angular 7 and using material design
+  
+  - Use cdkDrag instead of js implementation
+  
+  - Use virtual scrolling on long lists (I am looking at you, region hierarchy of Allen Mouse Brain Atlas)
+  
+  - UI bug in FF
+  
+  - Centrally logging via fluentD
+
+  - added `.well-known/security.txt`
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docs/releases/v2.0.1.md

+# v2.0.1
+
+21 Oct 2019
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v2.0.1)
+
+- Bugfix:
+  - fixed commonsense filter
+  - fixed fetching allen, waxholm datasets
+
+- Chore:
+  - Changed `Mouse` to `Cursor`
+  - Fixed terms of use
\ No newline at end of file

docs/releases/v2.0.2.md

+# v2.0.2
+
+30 Oct 2019
+
+[release](https://github.com/HumanBrainProject/interactive-viewer/releases/tag/v2.0.2)
+
+- Included ebrain logo
+
+- Improve modal appearance on mobile 
+
+- Bugfix:
+  - Incorrectly scoped access token
+  - Fixes dataset information window too small
+  - `humanbrainproject.org` deprecated
+  - Fixes splashscreen not scrollable bug
+  - Fixes scroll bar flickering bug
+  - Fixes region browser yields different region indicators [issue](https://github.com/HumanBrainProject/interactive-viewer/issues/388)
+
+- Chore:
+  - More strict species filter
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docs/usage/gettingStarted.md

+# Getting Started
+
+## Requirements
+
+Interactive Atlas Viewer uses webgl 2.0 under the hood. While modern operating system and browser supports webgl 2.0, specific hardware combinations may yield limited support for webgl 2.0. 
+
+!!! info
+    To check if your device support webgl 2.0, you can visit <https://get.webgl.org/webgl2/>.
+
+### Desktop
+- PC (Windows/Linux/MacOS)
+- Chrome/Firefox
+- Dedicated GPU (not required, but will greatly enhance the experience)
+
+### Mobile
+- Android Smartphone
+- Chrome/Firefox
+
+## URL
+
+- <https://interactive-viewer.apps.hbp.eu>
+- <https://atlases.ebrains.eu/viewer>
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