+
# Getting started
### The comprehensive guide to cellxgene
diff --git a/dev_docs/developer_guidelines.md b/dev_docs/developer_guidelines.md
index 409d34ed..e7a4dce7 100644
--- 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
diff --git a/dev_docs/release_process.md b/dev_docs/release_process.md
index 2b67adfc..6a02280c 100644
--- 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
diff --git a/docs/_site/index.html b/docs/_site/index.html
index 51bd2b56..53d91c0f 100644
--- a/docs/_site/index.html
+++ b/docs/_site/index.html
@@ -5,7 +5,7 @@
-
+
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:
diff --git a/docs/_site/posts/methods.html b/docs/_site/posts/methods.html
index a69bdeec..120cb803 100644
--- a/docs/_site/posts/methods.html
+++ b/docs/_site/posts/methods.html
@@ -5,7 +5,7 @@
-
+
Methods | cellxgene
@@ -16,10 +16,10 @@
+{"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"}
-
+
@@ -114,7 +114,7 @@
Differential expression
We’re actively working on how to improve differential expression within the app.
-N.B.: the current implementation assumes normally distributed values on a linear scale.
+N.B.: the current implementation assumes normally distributed values on a linear scale.
Currently, we use a Welch’s 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.
diff --git a/docs/_site/posts/methods.md b/docs/_site/posts/methods.md
index 17a72da2..22a5407e 100644
--- 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).
diff --git a/docs/_site/posts/prepare.html b/docs/_site/posts/prepare.html
index 05f88230..b1ea7137 100644
--- a/docs/_site/posts/prepare.html
+++ b/docs/_site/posts/prepare.html
@@ -5,7 +5,7 @@
-
+
prepare | cellxgene
@@ -16,10 +16,10 @@
+{"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"}
-
+
@@ -103,7 +103,7 @@
Expression values (raw or normalized) in anndata.X
At least one embedding (e.g., tSNE, UMAP) in anndata.obsm, specified with the prefix X_ (e.g., by default scanpy stores UMAP coordinates in anndata.obsm['X_umap'])
A unique identifier is required for each cell, which by default will be pulled from the obs DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with --obs-names
- A unique identifier is required for each gene, which by default will be pulled from the var DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with --var-names
+ A unique identifier is required for each gene, which by default will be pulled from the var DataFrame index. If the index is not unique or does not contain the gene ID, an alternative column can be specified with --var-names
What about R objects from seurat / bioconductor!?
diff --git a/docs/_site/posts/roadmap.html b/docs/_site/posts/roadmap.html
index 1d053152..54859937 100644
--- a/docs/_site/posts/roadmap.html
+++ b/docs/_site/posts/roadmap.html
@@ -5,7 +5,7 @@
-
+
roadmap | cellxgene
@@ -16,10 +16,10 @@
+{"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"}
-
+
diff --git a/docs/_site/posts/troubleshooting.html b/docs/_site/posts/troubleshooting.html
index f0586b56..4449c0f3 100644
--- a/docs/_site/posts/troubleshooting.html
+++ b/docs/_site/posts/troubleshooting.html
@@ -5,7 +5,7 @@
-
+
Troubleshooting | cellxgene
@@ -16,10 +16,10 @@
+{"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"}
-
+
diff --git a/docs/posts/launch.md b/docs/posts/launch.md
index 5046eb71..7a486ae2 100644
--- 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:
diff --git a/docs/posts/methods.md b/docs/posts/methods.md
index 17a72da2..22a5407e 100644
--- 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).
diff --git a/server/test/test_anndata_adaptor_data_load.py b/server/test/test_anndata_adaptor_data_load.py
index f7848b9f..c80935f3 100644
--- 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)