diff --git a/dev_docs/developer_guidelines.md b/dev_docs/developer_guidelines.md index e7a4dce7..f72929b6 100644 --- a/dev_docs/developer_guidelines.md +++ b/dev_docs/developer_guidelines.md @@ -151,3 +151,18 @@ If you would like to run the smoke tests against a hot-reloaded version of the c - You can also install/launch the server side code from npm scrips (requires python3.6 with virtualenv) with the `scripts/backend_dev` script. - Check out [e2e Tests](e2e_tests.md) for more details + +## Doc changes + +To evaluate changes to documentation in `cellxgene/docs`, you must install [jekyll](https://jekyllrb.com/docs/installation/), then run: + +```bash +cd docs +bundle install +bundle exec jekyll serve +``` + +If changes look good, run the following, then commit and push: +```bash +bundle exec jekyll build +``` diff --git a/docs/_site/index.html b/docs/_site/index.html index 51b1d42b..18d2548e 100644 --- a/docs/_site/index.html +++ b/docs/_site/index.html @@ -5,9 +5,9 @@ - + Index | cellxgene - + @@ -16,10 +16,10 @@ +{"@type":"WebSite","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Index","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/","name":"cellxgene","@context":"https://schema.org"} - + @@ -99,7 +99,7 @@

Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data.

-

To install cellxgene you need Python 3.6+. We recommend installing cellxgene into a conda or virtual environment.

+

To install cellxgene you need Python 3.6+. We recommend installing cellxgene into a conda or virtual environment.

Install the package.

pip install cellxgene
@@ -110,8 +110,8 @@
 
cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
 

 
-
To explore more datasets already formatted for cellxgene, check out the Demo data or
-see Preparing your data to learn more about formatting your own
+
To explore more datasets already formatted for cellxgene, check out the Demo data or
+see Preparing your data to learn more about formatting your own
 data for cellxgene.

 
 
Getting help

diff --git a/docs/_site/posts/annotations.html b/docs/_site/posts/annotations.html
index 57a31083..dee480ce 100644
--- a/docs/_site/posts/annotations.html
+++ b/docs/_site/posts/annotations.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 annotations | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"annotations","description":"Creating annotations","url":"https://chanzuckerberg.github.io/cellxgene/posts/annotations.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/contact.html b/docs/_site/posts/contact.html
index 59412b03..626caf57 100644
--- a/docs/_site/posts/contact.html
+++ b/docs/_site/posts/contact.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Contact | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Contact","description":"Contact","url":"https://chanzuckerberg.github.io/cellxgene/posts/contact.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/contribute.html b/docs/_site/posts/contribute.html
index 8e793a58..fc72f0e0 100644
--- a/docs/_site/posts/contribute.html
+++ b/docs/_site/posts/contribute.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Code of conduct | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Code of conduct","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/posts/contribute.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/demo-data.html b/docs/_site/posts/demo-data.html
index 3879a512..24a69dff 100644
--- a/docs/_site/posts/demo-data.html
+++ b/docs/_site/posts/demo-data.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 demo-data | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"demo-data","description":"Demo datasets","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/gallery.html b/docs/_site/posts/gallery.html
index 976c88f6..e78b4d61 100644
--- a/docs/_site/posts/gallery.html
+++ b/docs/_site/posts/gallery.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Gallery | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Gallery","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/posts/gallery.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/hosted.html b/docs/_site/posts/hosted.html
index ec586a6f..3f3a3d79 100644
--- a/docs/_site/posts/hosted.html
+++ b/docs/_site/posts/hosted.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Hosting cellxgene on the web | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Hosting cellxgene on the web","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/posts/hosted.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/install.html b/docs/_site/posts/install.html
index c7614f4b..d4c43acd 100644
--- a/docs/_site/posts/install.html
+++ b/docs/_site/posts/install.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Install | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Install","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/posts/install.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/launch.html b/docs/_site/posts/launch.html
index ac4bea95..5abb7fb0 100644
--- a/docs/_site/posts/launch.html
+++ b/docs/_site/posts/launch.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 demo-data | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"demo-data","description":"Demo datasets","url":"https://chanzuckerberg.github.io/cellxgene/posts/launch.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/methods.html b/docs/_site/posts/methods.html
index 2840a3d6..4fa847df 100644
--- a/docs/_site/posts/methods.html
+++ b/docs/_site/posts/methods.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Methods | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Methods","description":"An interactive explorer for single-cell transcriptomics data","url":"https://chanzuckerberg.github.io/cellxgene/posts/methods.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/prepare.html b/docs/_site/posts/prepare.html
index adf0c529..801e9efd 100644
--- a/docs/_site/posts/prepare.html
+++ b/docs/_site/posts/prepare.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 prepare | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"prepare","description":"Preparing your data","url":"https://chanzuckerberg.github.io/cellxgene/posts/prepare.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/roadmap.html b/docs/_site/posts/roadmap.html
index 5a795d78..9a5eb8aa 100644
--- a/docs/_site/posts/roadmap.html
+++ b/docs/_site/posts/roadmap.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 roadmap | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"roadmap","description":"Roadmap","url":"https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/_site/posts/troubleshooting.html b/docs/_site/posts/troubleshooting.html
index 8132fce3..18b7defa 100644
--- a/docs/_site/posts/troubleshooting.html
+++ b/docs/_site/posts/troubleshooting.html
@@ -5,9 +5,9 @@
     
     
 
-
+
 Troubleshooting | cellxgene
-
+
 
 
 
@@ -16,10 +16,10 @@
 
 
 
+{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"Troubleshooting","description":"Troubleshooting","url":"https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html","@context":"https://schema.org"}
 
 
-    
+    
     
diff --git a/docs/index.md b/docs/index.md
index 9afd0e61..b147a754 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -7,7 +7,7 @@ layout: default
 
 Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data.
 
-To install cellxgene you need Python 3.6+. We recommend [installing cellxgene into a conda or virtual environment.](install)
+To install cellxgene you need Python 3.6+. We recommend [installing cellxgene into a conda or virtual environment.](posts/install)
 
 Install the package.
 ``` bash
@@ -20,8 +20,8 @@ Launch cellxgene with an example [anndata](https://anndata.readthedocs.io/en/lat
 cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
 ```
 
-To explore more datasets already formatted for cellxgene, check out the [Demo data](demo-data) or
-see [Preparing your data](prepare) to learn more about formatting your own
+To explore more datasets already formatted for cellxgene, check out the [Demo data](posts/demo-data) or
+see [Preparing your data](posts/prepare) to learn more about formatting your own
 data for cellxgene.
 
 # Getting help