Change default branch from 'master' to 'main' (#1589)

The default branch has been changed. This PR cleans up references to `master` and fixes links that would otherwise be broken. For more background see the following references: * https://www.independent.co.uk/life-style/gadgets-and-tech/news/github-master-slave-slavery-whitelist-language-inclusive-a9568576.html * https://tools.ietf.org/id/draft-knodel-terminology-00.html
2026-09-15 12:47:56 +08:00 · 2020-06-25 14:04:30 -07:00
parent 0fd3d4b8f4
commit 152c07a28e
25 changed files with 63 additions and 62 deletions
--- a/.github/workflows/compatibility_tests.yml
+++ b/.github/workflows/compatibility_tests.yml
@@ -5,7 +5,7 @@ on:
    - cron: '0 8 7 * 2'
  push:
    branches:
-      - master
+      - main

 env:
  JEST_ENV: prod
@@ -22,7 +22,7 @@ jobs:
      - name: Build docker image
        run: docker build .

-  cellxgene-master-with-python-and-anndata-versions:
+  cellxgene-main-with-python-and-anndata-versions:
    name: python versions x anndata versions
    runs-on: ubuntu-latest
    strategy:
@@ -86,8 +86,8 @@ jobs:
      - name: Tests
        run: cd cellxgene && make unit-test ${{ matrix.test-suite }}

-  cellxgene-master-with-anndata-master:
-    name: cellxgene master with anndata master
+  cellxgene-main-with-anndata-master:
+    name: cellxgene main with anndata master
    runs-on: ubuntu-latest
    strategy:
      matrix:
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -2,7 +2,7 @@ name: Deploy via single cell infra repo

 on:
  push:
-    branches: master
+    branches: main

 jobs:
  deploy:
--- a/.github/workflows/push_tests.yml
+++ b/.github/workflows/push_tests.yml
@@ -2,7 +2,7 @@ name: Push Tests

 on:
  push:
-    branches: master
+    branches: main
  pull_request:
    branches: "*"

--- a/.gitignore
+++ b/.gitignore
@@ -43,6 +43,7 @@ npm-debug.log
 __pycache__
 *.DS_Store*
 data
+tags

 # Jekyll
 docs/_site/
--- a/2
+++ b/2
@@ -94,7 +94,7 @@ pydist: build

 # RELEASE HELPERS

-# create new version to commit to master
+# create new version to commit to main
 .PHONY: release-stage-1
 release-stage-1: dev-env bump clean-lite gen-package-lock
 	@echo "Version bumped part:$(PART) and client built. Ready to commit and push"
--- a/README.md
+++ b/README.md
@@ -5,13 +5,13 @@ _an interactive explorer for single-cell transcriptomics data_
 [![DOI](https://zenodo.org/badge/105615409.svg)](https://zenodo.org/badge/latestdoi/105615409) [![PyPI](https://img.shields.io/pypi/v/cellxgene)](https://pypi.org/project/cellxgene/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/cellxgene)](https://pypistats.org/packages/cellxgene) [![GitHub last commit](https://img.shields.io/github/last-commit/chanzuckerberg/cellxgene)](https://github.com/chanzuckerberg/cellxgene/pulse)
 [![Push Tests](https://github.com/chanzuckerberg/cellxgene/workflows/Push%20Tests/badge.svg)](https://github.com/chanzuckerberg/cellxgene/actions?query=workflow%3A%22Push+Tests%22)
 [![Compatibility Tests](https://github.com/chanzuckerberg/cellxgene/workflows/Compatibility%20Tests/badge.svg)](https://github.com/chanzuckerberg/cellxgene/actions?query=workflow%3A%22Compatibility+Tests%22)
-![Code Coverage](https://codecov.io/gh/chanzuckerberg/cellxgene/branch/master/graph/badge.svg)
+![Code Coverage](https://codecov.io/gh/chanzuckerberg/cellxgene/branch/main/graph/badge.svg)

 cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the [Human Cell Atlas](https://humancellatlas.org). Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.

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

-<img src="https://github.com/chanzuckerberg/cellxgene/raw/master/docs/images/crossfilter.gif" width="350" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/raw/master/docs/images/category-breakdown.gif" width="350" height="200" hspace="30">
+<img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif" width="350" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif" width="350" height="200" hspace="30">

 # Getting started
 ### The comprehensive guide to cellxgene
--- a/dev_docs/developer_guidelines.md
+++ b/dev_docs/developer_guidelines.md
@@ -18,7 +18,7 @@ You can set these environment variables manually with the `export` shell command

 ## Running test suite

-Client and server tests run on Travis CI for every push, PR, and commit to master on github. End to end tests run nightly on master only.
+Client and server tests run on Travis CI for every push, PR, and commit to `main` on github. End to end tests run nightly on `main` only.

 ### Unit tests

--- a/dev_docs/release_process.md
+++ b/dev_docs/release_process.md
@@ -33,7 +33,7 @@ Follow these steps to create a release.
 4.  Commit and push the new branch
 5.  Create a PR for the release.
    -   [optional] As needed, conduct PR review.
-6.  Merge to master
+6.  Merge to the `main` branch
 7.  Publish to pypi by performing the following steps (assumes you that you have registered for pypi,
    and that you have write access to the cellxgene pypi package):
    -   Build the distribution and upload to test pypi `make release-stage-2`
@@ -44,7 +44,7 @@ Follow these steps to create a release.
    ([instructions](https://help.github.com/articles/creating-releases/)).
    -   Draft new release
    -   Type version name matching release version number from (1)
-    -   Select `master` as release branch (ensure you merged the release PR)
+    -   Select `main` as release branch (ensure you merged the release PR)
    -   Type title `Release {version num}`
    -   [optional] Check pre-release if this release is not ready for production
    -   Publish Release
@@ -55,7 +55,7 @@ change the packaging (e.g. new bundled files, new dependencies, etc.)

 ### Point release (special case)

-To make a bugfix release (a point release) when there are already other changes in master we need to do a modified version of our release process. The difference is that instead of using master we are going make our release branch off of the tag for the release we want to patch. We cherrypick the commits that we want to include in the patch. Then instead of merging to master, we create the release directly off of the branch.
+To make a bugfix release (a point release) when there are already other changes in `main` we need to do a modified version of our release process. The difference is that instead of using `main` we are going make our release branch off of the tag for the release we want to patch. We cherrypick the commits that we want to include in the patch. Then instead of merging to `main`, we create the release directly off of the branch.

 1.  (same as above) Preparation:
    -   python3.6 environment, and a cellxgene clone
@@ -68,10 +68,10 @@ To make a bugfix release (a point release) when there are already other changes
    -   Create a branch from that tag. `git branch release-0.9.1`
 3.  Cherrypick the commits that you want included in this patch.
    -   Test that the cherrypicked commits landed and fixed the issue
-    -   We WILL NOT merge this branch back into master, these commits should already exist in master.
+    -   We WILL NOT merge this branch back into `main`, these commits should already exist in `main`.
 4.  In the release branch:
    -   Run `make release-stage-1 PART=patch`.
-5.  Commit and push the new branch. DO NOT MAKE A PR OR MERGE TO MASTER.
+5.  Commit and push the new branch. DO NOT MAKE A PR OR MERGE TO `main`.
    -   wait for release to pass the tests
 6.  Publish to pypi by performing the following steps (assumes you that you have registered for pypi,
    and that you have write access to the cellxgene pypi package): - Build the distribution and upload to test pypi `make release-stage-2` - Test the test installation in a fresh virtual environment using `make install-release-test` - Upload the package to real pypi using `make release-stage-final` - Test the installation in a fresh virtual environment using
--- a/docs/_site/index.html
+++ b/docs/_site/index.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Index | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Index" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebSite","headline":"Index","url":"https://chanzuckerberg.github.io/cellxgene/","name":"cellxgene","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebSite","url":"https://chanzuckerberg.github.io/cellxgene/","headline":"Index","name":"cellxgene","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/annotations.html
+++ b/docs/_site/posts/annotations.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>annotations | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="annotations" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/annotations.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Creating annotations","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"annotations","url":"https://chanzuckerberg.github.io/cellxgene/posts/annotations.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Creating annotations","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/annotations.html","headline":"annotations","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/contact.html
+++ b/docs/_site/posts/contact.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Contact | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Contact" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/contact.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Contact","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Contact","url":"https://chanzuckerberg.github.io/cellxgene/posts/contact.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Contact","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/contact.html","headline":"Contact","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/contribute.html
+++ b/docs/_site/posts/contribute.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Code of conduct | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Code of conduct" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/contribute.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Code of conduct","url":"https://chanzuckerberg.github.io/cellxgene/posts/contribute.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/contribute.html","headline":"Code of conduct","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/demo-data.html
+++ b/docs/_site/posts/demo-data.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>demo-data | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="demo-data" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Demo datasets","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Demo datasets","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","headline":"demo-data","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/gallery.html
+++ b/docs/_site/posts/gallery.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Gallery | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Gallery" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/gallery.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Gallery","url":"https://chanzuckerberg.github.io/cellxgene/posts/gallery.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/gallery.html","headline":"Gallery","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/hosted.html
+++ b/docs/_site/posts/hosted.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Hosting cellxgene on the web | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Hosting cellxgene on the web" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/hosted.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Hosting cellxgene on the web","url":"https://chanzuckerberg.github.io/cellxgene/posts/hosted.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/hosted.html","headline":"Hosting cellxgene on the web","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/install.html
+++ b/docs/_site/posts/install.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Install | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Install" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/install.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Install","url":"https://chanzuckerberg.github.io/cellxgene/posts/install.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/install.html","headline":"Install","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/launch.html
+++ b/docs/_site/posts/launch.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>demo-data | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="demo-data" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/launch.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Demo datasets","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"https://chanzuckerberg.github.io/cellxgene/posts/launch.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Demo datasets","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/launch.html","headline":"demo-data","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
@@ -114,7 +114,7 @@

 <p>You can also launch from a URL directly like this:</p>

-<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/master/example-dataset/pbmc3k.h5ad
+<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/main/example-dataset/pbmc3k.h5ad
 </code></pre></div></div>

 <p>Support for S3 and GCS is not enabled by default. If you wish to directly access S3 or GFS, install one or both of the following packages:</p>
--- a/docs/_site/posts/methods.html
+++ b/docs/_site/posts/methods.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Methods | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Methods" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/methods.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Methods","url":"https://chanzuckerberg.github.io/cellxgene/posts/methods.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/methods.html","headline":"Methods","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
@@ -114,7 +114,7 @@
 <h2 id="differential-expression">Differential expression</h2>

 <p>We’re actively working on how to improve differential expression within the app.
-<strong>N.B.: the <a href="https://github.com/chanzuckerberg/cellxgene/blob/master/server/app/scanpy_engine/diffexp.py#L40">current implementation</a> assumes normally distributed values on a linear scale.</strong></p>
+<strong>N.B.: the <a href="https://github.com/chanzuckerberg/cellxgene/blob/main/server/app/scanpy_engine/diffexp.py#L40">current implementation</a> assumes normally distributed values on a linear scale.</strong></p>

 <p>Currently, we use a <a href="https://en.wikipedia.org/wiki/Welch%27s_t-test">Welch’s <em>t</em>-test</a>, which assumes that the two populations are each normally distributed, but may have unequal variance. We use a two-sided t-test against the null hypothesis that the two populations have <strong>equal</strong> means. P-values are adjusted with the <a href="https://en.wikipedia.org/wiki/Bonferroni_correction">Bonferroni corrrection</a>.</p>

--- a/docs/_site/posts/methods.md
+++ b/docs/_site/posts/methods.md
@@ -17,7 +17,7 @@ cellxgene looks for embeddings (e.g., tSNE, UMAP, PCA, spatial coordinates) in `
 ## Differential expression

 We're actively working on how to improve differential expression within the app.
-**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/master/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**
+**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/main/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**

 Currently, we use a [Welch's _t_-test](https://en.wikipedia.org/wiki/Welch%27s_t-test), which assumes that the two populations are each normally distributed, but may have unequal variance. We use a two-sided t-test against the null hypothesis that the two populations have **equal** means. P-values are adjusted with the [Bonferroni corrrection](https://en.wikipedia.org/wiki/Bonferroni_correction).

--- a/docs/_site/posts/prepare.html
+++ b/docs/_site/posts/prepare.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>prepare | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="prepare" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/prepare.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Preparing your data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"prepare","url":"https://chanzuckerberg.github.io/cellxgene/posts/prepare.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Preparing your data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/prepare.html","headline":"prepare","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
@@ -103,7 +103,7 @@
  <li>Expression values (raw or normalized) in <code class="language-plaintext highlighter-rouge">anndata.X</code></li>
  <li>At least one embedding (e.g., tSNE, UMAP) in <code class="language-plaintext highlighter-rouge">anndata.obsm</code>, specified with the prefix <code class="language-plaintext highlighter-rouge">X_</code> (e.g., by default scanpy stores UMAP coordinates in <code class="language-plaintext highlighter-rouge">anndata.obsm['X_umap']</code>)</li>
  <li>A unique identifier is required for each cell, which by default will be pulled from the <code class="language-plaintext highlighter-rouge">obs</code> DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with <code class="language-plaintext highlighter-rouge">--obs-names</code></li>
-  <li>A unique identifier is required for each gene, which by default will be pulled from the <code class="language-plaintext highlighter-rouge">var</code> DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with <code class="language-plaintext highlighter-rouge">--var-names</code></li>
+  <li>A unique identifier is required for each gene, which by default will be pulled from the <code class="language-plaintext highlighter-rouge">var</code> DataFrame index. If the index is not unique or does not contain the gene ID, an alternative column can be specified with <code class="language-plaintext highlighter-rouge">--var-names</code></li>
 </ul>

 <h4 id="what-about-r-objects-from-seurat--bioconductor">What about R objects from seurat / bioconductor!?</h4>
--- a/docs/_site/posts/roadmap.html
+++ b/docs/_site/posts/roadmap.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>roadmap | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="roadmap" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Roadmap","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"roadmap","url":"https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Roadmap","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html","headline":"roadmap","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/_site/posts/troubleshooting.html
+++ b/docs/_site/posts/troubleshooting.html
@@ -5,7 +5,7 @@
    <meta http-equiv="X-UA-Compatible" content="IE=edge">
    <meta name="viewport" content="width=device-width, initial-scale=1">

-<!-- Begin Jekyll SEO tag v2.5.0 -->
+<!-- Begin Jekyll SEO tag v2.6.1 -->
 <title>Troubleshooting | cellxgene</title>
 <meta name="generator" content="Jekyll v3.8.5" />
 <meta property="og:title" content="Troubleshooting" />
@@ -16,10 +16,10 @@
 <meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html" />
 <meta property="og:site_name" content="cellxgene" />
 <script type="application/ld+json">
-{"description":"Troubleshooting","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Troubleshooting","url":"https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html","@context":"http://schema.org"}</script>
+{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Troubleshooting","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html","headline":"Troubleshooting","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->

-    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
+    <link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
    <!--[if lt IE 9]>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
    <![endif]-->
--- a/docs/posts/launch.md
+++ b/docs/posts/launch.md
@@ -25,7 +25,7 @@ You should see your web browser open with the following
 You can also launch from a URL directly like this:

 ```
-cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/master/example-dataset/pbmc3k.h5ad
+cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/main/example-dataset/pbmc3k.h5ad
 ```

 Support for S3 and GCS is not enabled by default. If you wish to directly access S3 or GFS, install one or both of the following packages:
--- a/docs/posts/methods.md
+++ b/docs/posts/methods.md
@@ -17,7 +17,7 @@ cellxgene looks for embeddings (e.g., tSNE, UMAP, PCA, spatial coordinates) in `
 ## Differential expression

 We're actively working on how to improve differential expression within the app.
-**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/master/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**
+**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/main/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**

 Currently, we use a [Welch's _t_-test](https://en.wikipedia.org/wiki/Welch%27s_t-test), which assumes that the two populations are each normally distributed, but may have unequal variance. We use a two-sided t-test against the null hypothesis that the two populations have **equal** means. P-values are adjusted with the [Bonferroni corrrection](https://en.wikipedia.org/wiki/Bonferroni_correction).

--- a/server/test/test_anndata_adaptor_data_load.py
+++ b/server/test/test_anndata_adaptor_data_load.py
@@ -65,7 +65,7 @@ class DataLocatorAdaptorTest(unittest.TestCase):
        self.stdAsserts(data)

    def test_url_https(self):
-        url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
+        url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
        locator = DataLocator(url)
        config = AppConfig()
        config.update(**self.args)
@@ -73,7 +73,7 @@ class DataLocatorAdaptorTest(unittest.TestCase):
        self.stdAsserts(data)

    def test_url_http(self):
-        url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
+        url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
        locator = DataLocator(url)
        config = AppConfig()
        config.update(**self.args)