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annotations cli updates (#1190)

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* Switch logic from `--annotations` to `--disable-annotations

* Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental`

* update docs

* update makefile

* update tests

* Disable annotations on standard client smoke test

* Update docs/posts/annotations.md

Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com>

* Update docs/posts/annotations.md

* Renaming

* Docs

* Update tests

* Pesky typo -_-

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
This commit is contained in:
Sidney Bell
2020-03-11 11:57:52 -07:00
committed by GitHub
co-authored by Matt Weiden
parent 8beeb57c96
commit 9089fc98f2
7 changed files with 50 additions and 55 deletions
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docs/posts/annotations.md
+6 -12
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@@ -13,7 +13,7 @@ We are _piloting_ a new feature in cellxgene that enables users to create and ed
To get started, run:
```
cellxgene launch mydata.h5ad --experimental-annotations
cellxgene launch mydata.h5ad
```
To preserve data provenance, **`cellxgene` does not alter the input h5ad file**. Rather, newly-created annotations are saved in a specified CSV file:
@@ -21,8 +21,7 @@ To preserve data provenance, **`cellxgene` does not alter the input h5ad file**.
annotations-directory/name-########.csv
```
- The default `annotations-directory` is your current working directory (i.e., the directory you were in when you started cellxgene).
- The default `annotations-directory` is your current working directory (i.e., the directory you were in when you started cellxgene).
- You will be prompted to enter a name for your annotations the first time you create a new category.
- We also assign a unique identifier in the form of an 8-character suffix, `########`; this helps cellxgene identify your file to avoid overwriting your work.
@@ -36,10 +35,7 @@ There are two options for updating draft annotations.
### Autodetect annotations csv
Cellxgene can automatically find and reload your draft annotations in editable mode like so:
```
annotations-directory$ cellxgene launch mydata.h5ad --experimental-annotations
```
Cellxgene will automatically find and reload your draft annotations in editable mode.
This assumes that:
1 - The h5ad filename is the same
@@ -52,7 +48,7 @@ This assumes that:
If you'd like to specify the complete file path for your annotations, you can do so by running:
```
cellxgene launch mydata.h5ad --experimental-annotations --experimental-annotations-file path/to/myfile.csv
cellxgene launch mydata.h5ad --annotations-file path/to/myfile.csv
```
Any changes you make will be reflected in the original CSV. If the file does not exist, it will be created.
@@ -83,7 +79,7 @@ Specifying a single file name for multiple contributors will result in data over
To specify an output directory, run:
```
cellxgene launch mydata.h5ad --experimental-annotations --experimental-annotations-output-dir path/to/annotations-directory/
cellxgene launch mydata.h5ad --annotations-dir path/to/annotations-directory/
```
For each user, annotations will be saved as follows:
@@ -93,8 +89,6 @@ For each user, annotations will be saved as follows:
## FAQ
### How do I know my annotations are saved?
@@ -113,4 +107,4 @@ This is most likely because the h5ad file you are working with is not the origin
We place a small cookie (file) in your browser that identifies where your draft annotations are saved. This file never leaves your machine, and is never sent to the cellxgene team or anyone else.
### I have feedback and ideas for you!
Wonderful! This is a very new and complex feature; we would _love_ to [hear your feedback](contact) :)
Wonderful! This is a relatively new feature; we would _love_ to [hear your feedback](contact) :)