Rebranding Docs (#852)

* adaptions for rebranding

* cofnig

* remove extra.css config

* webKnossos -> WEBKNOSSOS

* new favicon

* more renames

Co-authored-by: Norman Rzepka <[email protected]>

Author: jstriebel

CONTRIBUTING.md

@@ -1,12 +1,12 @@
 # Contributing Guide
 
-**Welcome to the webKnossos-libs contributing guide :sparkles: **
+**Welcome to the WEBKNOSSOS-libs contributing guide :sparkles: **
 
-Thank you for taking the time to contribute to this project! The following is a set of guidelines for contributing to the different webKnossos related Python libraries, which are part of the [webKnossos-libs repository on GitHub](https://github.com/scalableminds/webknossos-libs). These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
+Thank you for taking the time to contribute to this project! The following is a set of guidelines for contributing to the different WEBKNOSSOS related Python libraries, which are part of the [WEBKNOSSOS-libs repository on GitHub](https://github.com/scalableminds/webknossos-libs). These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
 
 ## Code of Conduct
 
-webKnossos-libs and everyone contributing and collaborating on this project is expected to follow the [webKnossos-libs Code of Conduct](CODE_OF_CONDUCT.md). Please report unacceptable behavior to [[email protected]](mailto:[email protected]).
+WEBKNOSSOS-libs and everyone contributing and collaborating on this project is expected to follow the [WEBKNOSSOS-libs Code of Conduct](CODE_OF_CONDUCT.md). Please report unacceptable behavior to [[email protected]](mailto:[email protected]).
 
 
 ## How can I help?
@@ -20,20 +20,20 @@ We welcome community feedback and contributions! We are happy to have
 
 ## Feedback, Observations and Questions
 
-We'd love to hear your feedback on the webKnossos Python libraries!
+We'd love to hear your feedback on the WEBKNOSSOS Python libraries!
 We're also interested in hearing if these tools don't work for your usecase,
 or if you have questions regarding their usage.
 
 Please leave a message on the [image.sc forum](https://forum.image.sc/tag/webknossos)
 using the `webknossos` tag to enable public communication on those topics.
-If you prefer to share information only with the webKnossos team, please write an email
+If you prefer to share information only with the WEBKNOSSOS team, please write an email
 to [[email protected]](mailto:[email protected]). For commercial support please
 reach out to [scalable minds](https://scalableminds.com).
 
 
 ## Issues: Feature Suggestions and Bug Reports
 
-We track feature requests and bug reports in the [webKnossos-libs repository issues](https://github.com/scalableminds/webknossos-libs/issues).
+We track feature requests and bug reports in the [WEBKNOSSOS-libs repository issues](https://github.com/scalableminds/webknossos-libs/issues).
 Before opening a new issue, please do a quick search of existing issues to make sure your suggestion hasn’t already been added.
 If your issue doesn’t already exist, and you’re ready to create a new one, make sure to state what you would like to implement, improve or bugfix.
 Please use one of the provided templates to make this process easier for you.
@@ -54,8 +54,8 @@ that you use the API as intended. If that's the case, please
 
 If you are missing a feature to support your use-case, please consider the following points:
 
-1. Please verify if this feature is directly related to webKnossos.
-   Does it belong into the webKnossos Python libraries?
+1. Please verify if this feature is directly related to WEBKNOSSOS.
+   Does it belong into the WEBKNOSSOS Python libraries?
 2. Double-check if an issue for this feature exists already. If there is one with a very similar scope,
    please considering commenting there.
 3. If possible, consider how the implementation might look like (e.g. how would the public API change),
@@ -88,13 +88,13 @@ Please include the following in your pull request:
 * Adapt or add the documentation.
 * Consider enhancing the examples.
 
-The specific coding styles, test frameworks and documentation setup of webKnossos-libs are described
+The specific coding styles, test frameworks and documentation setup of WEBKNOSSOS-libs are described
 in the following sections:
 
 
 ### Development
 
-The [webknossos-libs repository](https://github.com/scalableminds/webknossos-libs) is structured as a mono-repo, containing multiple packages:
+The [WEBKNOSSOS-libs repository](https://github.com/scalableminds/webknossos-libs) is structured as a mono-repo, containing multiple packages:
 
 * `cluster_tools`
 * `webknossos`
@@ -136,10 +136,10 @@ Internal workflows for scalable minds:
 
 The `webknossos` folder contains examples, which are not part of the package, but are tested via `tests/test_examples.py` and added to the documentation (see `docs/src/webknossos-py/examples`).
 
-The tests also contain functionality for the webKnossos client. There a two modes to run the tests:
+The tests also contain functionality for the WEBKNOSSOS client. There a two modes to run the tests:
 
-1. `./test.sh --refresh-snapshots`, sending network requests to a webKnossos instance:
-  This expects a local webKnossos setup with specific test data, which is shipped with webKnossos. If you're starting and running webKnossos manually, please use port 9000 (the default) and run the `tools/postgres/prepareTestDb.sh` script in the webKnossos repository (⚠️ this overwrites your local webKnossos database). Alternatively, a docker-compose setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
+1. `./test.sh --refresh-snapshots`, sending network requests to a WEBKNOSSOS instance:
+  This expects a local WEBKNOSSOS setup with specific test data, which is shipped with WEBKNOSSOS. If you're starting and running WEBKNOSSOS manually, please use port 9000 (the default) and run the `tools/postgres/prepareTestDb.sh` script in the WEBKNOSSOS repository (⚠️ this overwrites your local WEBKNOSSOS database). Alternatively, a docker-compose setup is started automatically for the tests, see `./test.sh` and `tests/docker-compose.yml` for details. The network requests & response are recorded as "cassettes" by [vcr.py](https://vcrpy.readthedocs.io), see next point:
 2. `./test.sh` replays responses from previous network snapshots using [vcr.py](https://vcrpy.readthedocs.io) via [pytest-recording](https://github.com/kiwicom/pytest-recording). No additional network requests are allowed in this mode.
 
 `./test.sh --store-durations` updates the durations for
@@ -171,15 +171,15 @@ For testing the `kubernetes` setup, we recommend a [Kubernetes-in-Docker setup](
 
 ### Documentation
 
-We render a common documentation for webKnossos itself and webknossos-libs from this repository using [mkdocs](https://www.mkdocs.org/). Source-files for the documentation are stored at `docs/src`:
+We render a common documentation for WEBKNOSSOS itself and WEBKNOSSOS-libs from this repository using [mkdocs](https://www.mkdocs.org/). Source-files for the documentation are stored at `docs/src`:
 
 * `docs/src/webknossos`: Server & Website documentation, linked from the [webknossos repository](https://github.com/scalableminds/webknossos) (must be available under `docs/wk-repo`, see below).
 * `docs/src/api`: Generated using [pdoc](https://pdoc.dev) from Python docstrings.
 * `docs/src/webknossos-py` & `docs/src/wkcuber`: Documentation for the respective Python Packages
 
 The structure of the documentation page is given by `docs/mkdocs.yml`.
 
-To generate the documentation locally, clone or link the webKnossos repository to `docs/wk-repo` first and then start the documentation server
+To generate the documentation locally, clone or link the WEBKNOSSOS repository to `docs/wk-repo` first and then start the documentation server
 ```shell
 git clone --depth 1 [email protected]:scalableminds/webknossos.git docs/wk-repo
 docs/generate.sh

docs/md_extensions/mdlightbox.py

@@ -45,7 +45,7 @@ def __init__(self, md, group = True):
     def run(self, root):
         parent_map = {c:p for p in root.iter() for c in p}
         i = 0
-        images = root.getiterator("img")
+        images = root.iter("img")
         for image in images:
             desc = image.attrib["alt"]
             h = self.hidden_re.match(desc)

docs/mkdocs.yml

@@ -1,4 +1,4 @@
-site_name: webKnossos Documentation
+site_name: WEBKNOSSOS Documentation
 docs_dir: src
 site_dir: out
 site_url: https://docs.webknossos.org/
@@ -10,8 +10,8 @@ edit_uri: ""
 theme:
   name: material
   custom_dir: overrides
-  favicon: https://static.webknossos.org/assets/favicon-docs.png
-  logo: https://static.webknossos.org/assets/icon-white.png
+  favicon: https://static.webknossos.org/assets/favicon-docs2.png
+  logo: https://static.webknossos.org/assets/icon-only-white.svg
   icon:
     repo: fontawesome/brands/github
   font: false
@@ -35,7 +35,7 @@ theme:
     - navigation.top
 
 nav:
-- webKnossos:
+- WEBKNOSSOS:
   - webknossos/index.md
   - webknossos/getting_started.md
   - Guides:
@@ -126,7 +126,7 @@ nav:
       - Commercial Support: https://scalableminds.com" target="_blank
     - GitHub: https://github.com/scalableminds/webknossos-libs/tree/master/webknossos" target="_blank
     - Blog: https://medium.com/scalableminds" target="_blank
-- webKnossos Cuber:
+- WEBKNOSSOS Cuber:
   - wkcuber CLI: wkcuber/index.md
   - wkcuber/changelog.md
   - Getting Help:

docs/overrides/main.html

@@ -10,41 +10,28 @@
 	<link rel="stylesheet" href="{{ base_url }}/css/lists.css">
 	<style type="text/css">
 		@font-face {
-			font-family: "Titillium Web";
-			src: local("Titillium Web"), url("https://static.webknossos.org/assets/fonts/titilliumweb-300.woff2") format("woff2"),
-			url("https://static.webknossos.org/assets/fonts/titilliumweb-300.woff") format("woff");
-			font-weight: 300;
-			font-style: normal;
-		}@font-face {
-			font-family: "Titillium Web";
-			src: local("Titillium Web"), url("https://static.webknossos.org/assets/fonts/titilliumweb-400.woff2") format("woff2"),
-			url("https://static.webknossos.org/assets/fonts/titilliumweb-400.woff") format("woff");
-			font-weight: 400;
+			font-family: "Nunito";
+			src: local("Nunito"), url("https://static.webknossos.org/assets/fonts/Nunito-VariableFont_wght.ttf") format("truetype") tech(variations);
 			font-style: normal;
 		}
 		@font-face {
-			font-family: "Titillium Web";
-			src: local("Titillium Web"), url("https://static.webknossos.org/assets/fonts/titilliumweb-400i.woff2") format("woff2"),
-			url("https://static.webknossos.org/assets/fonts/titilliumweb-400i.woff") format("woff");
-			font-weight: 400;
+			font-family: "Nunito";
+			src: local("Nunito"), url("https://static.webknossos.org/assets/fonts/Nunito-Italic-VariableFont_wght.ttf") format("truetype") tech(variations);
 			font-style: italic;
 		}
 		@font-face {
-			font-family: "Titillium Web";
-			src: local("Titillium Web"), url("https://static.webknossos.org/assets/fonts/titilliumweb-700.woff2") format("woff2"),
-			url("https://static.webknossos.org/assets/fonts/titilliumweb-700.woff") format("woff");
-			font-weight: 700;
-			font-style: normal;
-		}		@font-face {
 			font-family: "Roboto Mono";
 			src: local("Roboto Mono"), url("https://static.webknossos.org/assets/fonts/robotomono-400.woff2") format("woff2"),
 			url("https://static.webknossos.org/assets/fonts/robotomono-400.woff") format("woff");
 			font-weight: 400;
 			font-style: normal;
 		}
 		:root {
-			--md-text-font: "Titillium Web";
+			--md-text-font: "Nunito";
 			--md-code-font: "Roboto Mono";
+			--md-primary-fg-color:        #5660ff;
+			--md-primary-fg-color--light: #AABAFF;
+			--md-primary-fg-color--dark:  #59F8E8;
 		}
 		.pdoc .attr {
 			font-family: var(--md-code-font);

docs/overrides/partials/nav.html

@@ -65,15 +65,15 @@
 
     {% if not rendered_toc %}
     <li class="{{ class }}">
-      <nav class="md-nav md-nav--secondary" aria-label="webKnossos Documentation">
+      <nav class="md-nav md-nav--secondary" aria-label="WEBKNOSSOS Documentation">
         <label class="md-nav__title" for="__toc">
           <span class="md-nav__icon md-icon"></span>
-          webKnossos Documentation
+          WEBKNOSSOS Documentation
         </label>
         <ul class="md-nav__list" data-md-component="toc">
           <li class="md-nav__item">
             <a href="{{ base_url }}/webknossos/" class="md-nav__link">
-              webKnossos
+              WEBKNOSSOS
             </a>
           </li>
           <li class="md-nav__item">

docs/poetry.lock

@@ -4,7 +4,7 @@ This example applies a merger mode annotation to a segmentation.
 
 It downloads a [sample dataset](https://webknossos.org/datasets/scalable_minds/l4_sample_dev/view) with a [sample annotation](https://webknossos.org/annotations/Explorational/6204d2cd010000db0003db91).
 The annotation has been created with "merger mode", where skeleton trees are used to merge segments.
-Read more about the [merger mode in the webKnossos documentation](/webknossos/volume_annotation.html#proof-reading-and-merging-segments).
+Read more about the [merger mode in the WEBKNOSSOS documentation](/webknossos/volume_annotation.html#proof-reading-and-merging-segments).
 The example then uses the [Dataset API](dataset_usage.md) and [fastremap module](https://github.com/seung-lab/fastremap) for reading, remapping and rewriting the `segmentation` layer.
 
 _This example additionally needs the fastremap package._

docs/src/webknossos-py/examples/apply_merger_mode.md

@@ -1,6 +1,6 @@
 # Download segment masks
 
-This example [accesses a volume annotation on webKnososs](../../api/webknossos/annotation/annotation.md#Annotation.open_as_remote_dataset) and creates segment masks from selected segments. The segment masks are stored as tiff sequences. The segments have been selected from the "Segments" tab in webKnossos. The [BufferedSliceReader](../../api/webknossos/dataset/view.md#View.get_buffered_slice_reader) is used to efficiently request sections from the remote segmentation data.
+This example [accesses a volume annotation on webKnososs](../../api/webknossos/annotation/annotation.md#Annotation.open_as_remote_dataset) and creates segment masks from selected segments. The segment masks are stored as tiff sequences. The segments have been selected from the "Segments" tab in WEBKNOSSOS. The [BufferedSliceReader](../../api/webknossos/dataset/view.md#View.get_buffered_slice_reader) is used to efficiently request sections from the remote segmentation data.
 
 ```python
 --8<--

docs/src/webknossos-py/examples/download_segments.md

@@ -8,4 +8,4 @@ webknossos/examples/upload_image_data.py
 --8<--
 ```
 
-![Cell Dataset uploaded to webKnossos](./upload_image_data_dataset.jpg)
+![Cell Dataset uploaded to WEBKNOSSOS](./upload_image_data_dataset.jpg)

docs/src/webknossos-py/examples/upload_image_data.md

@@ -1,6 +1,6 @@
 # Upload tiff stack
 
-This example shows how to [create a new dataset from a tiff sequence](../../api/webknossos/dataset/dataset.md#Dataset.from_images), [compress](../../api/webknossos/dataset/dataset.md#Dataset.compress) it, [downsample](../../api/webknossos/dataset/dataset.md#Dataset.downsample) it and [upload](../../api/webknossos/dataset/dataset.md#Dataset.upload) it to webKnossos.
+This example shows how to [create a new dataset from a tiff sequence](../../api/webknossos/dataset/dataset.md#Dataset.from_images), [compress](../../api/webknossos/dataset/dataset.md#Dataset.compress) it, [downsample](../../api/webknossos/dataset/dataset.md#Dataset.downsample) it and [upload](../../api/webknossos/dataset/dataset.md#Dataset.upload) it to WEBKNOSSOS.
 
 ```python
 --8<--