* first cut at hosted gs routes
* lint
* update tests to match csv parser changes
* update tests to new API
* update gene set name validation rules to match requirements
* add path mapping from dataset to geneset
* add test cases for geneset GET route
* fix test assertion
* remove debugging code
* update gene set uri mapping function
* fix error message
* allow extra user-specified headers in gene set csv file
* clarify comment
* colorby histo
* color graph by mean expression
* move var index after returns
* add genesets as an argument
* varindex
* undo redo for mean expression
* destructure
* ternary
* Revert "destructure"
This reverts commit 2d9432c1c7.
* color by mean for diffexp
* geneset description add
* edit geneset description
* default state for desc
* remove log
* naming, todo
* check for both dup name and desc
* fixes
* do not store gene set modal state in history stack
* Update createGenesetDialogue.js
* Update editGenesetNameDialogue.js
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
* first cut at GET /genesets route
* update existing tests to match code changes
* more GET /genesets and initial tests
* add missing test fixture
* geneset validation accepts OTA format
* genesets route: better error handling, more tests
* lint
* genesets reducer and initial load
* fix lint
* add autosave support for genesets
* remove debug logging
* fix typo
* fix another typo
* update smoke test config for genesets
* smoke test fixes
* more fiddling with smoke tests
* first cut at GET /genesets route
* update existing tests to match code changes
* more GET /genesets and initial tests
* add missing test fixture
* geneset validation accepts OTA format
* genesets route: better error handling, more tests
* lint
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
This PR adds some more text and direct links to the cellxgene Galaxy section.
Thanks!
#### Reviewers
**Functional:**
**Readability:**
---
## Changes
- add
- remove
- modify
Until numpy version 1.20.0, numpy.unicode was an alias for str in python3. In 1.20.0, it's fully deprecated and is an int. This is bad and breaks things. This commit drops the np.unicode alias and just uses str, as is advised here:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
In this solution, all the server requirements are installed.
This is a slightly overkill, but it avoid having to restructure
any of the server or test code to avoid unnecessary imports.
#2019
The HistogramFooter needs to distinguish between an undefined
value and a value of 0. If the pvalAdj was 0, then the logFolChange
was previously not showing up.
#1888
Bumps [ini](https://github.com/isaacs/ini) from 1.3.5 to 1.3.7.
<details>
<summary>Commits</summary>
<ul>
<li><a href="c74c8af35f"><code>c74c8af</code></a> 1.3.7</li>
<li><a href="024b8b55ac"><code>024b8b5</code></a> update deps, add linting</li>
<li><a href="032fbaf5f0"><code>032fbaf</code></a> Use Object.create(null) to avoid default object property hazards</li>
<li><a href="2da90391ef"><code>2da9039</code></a> 1.3.6</li>
<li><a href="cfea636f53"><code>cfea636</code></a> better git push script, before publish instead of after</li>
<li><a href="56d2805e07"><code>56d2805</code></a> do not allow invalid hazardous string as section name</li>
<li>See full diff in <a href="https://github.com/isaacs/ini/compare/v1.3.5...v1.3.7">compare view</a></li>
</ul>
</details>
<details>
<summary>Maintainer changes</summary>
<p>This version was pushed to npm by <a href="https://www.npmjs.com/~isaacs">isaacs</a>, a new releaser for ini since your current version.</p>
</details>
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