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.
* make testing plan
* create annotaions sets for different num categories/dataset size
* annotation creation testing
* create scale and perf tests for annotations
* create make commands for tests
* get cell count if not set in test_datasets dict
* split out config
* add tests for base and app config, refactor client config out of app config
* refactor default config retrieval
* create config test class and helper functions
* move default_config into server to fix import issue
* add lint-client and lint-diff-client targets
* add lint-diff and lint targets
* prettier
* add lint-diff call to lint task
* temp
* tweak lint-diff
* add lint for PRs and lint for master
* remove temp
* remove incorrect branches syntax, use github_ref
* pull all branches
* format
* proper target and comment
* create separate steps with conditionals
* fix indentation
* refactor lint->lint-server, introduce lint to lint all
* trade diff-index for diff, do check against base instead of master
* remove fetching all branches
* Revert "remove fetching all branches"
This reverts commit 26ce7a0f05.
* tweak comparison
* use local eslint
* add eslint dep install
* temp
* grab only base
* simplify fetch
* add pull_request type trigger
* specify pushes only to master
* change conditionals to be based on event name
* Revert "temp"
This reverts commit 3d59134cc0.
* "branch" => "branches"
* create separate installation step
* change command based on os
Currently, if there is no build directory, the `make install` target
will attempt to cd into the build directory, fail, and run pip install
-e . in the root directory anyway. This causes cellxgene to be installed
from the source tree instead of what the user would expect.
This commit changes the behavior such that the `make install` will fail
if there is no build directory.
* early, non-working eb config
* hosted cellxgene
In this PR, contains scripts and instructions for deploying cellxgene
for AWS elastic beanstalk. It supports the multi-dataset option.
The Makefile in the server/eb directory creates an artifact.zip
file, which can be deploy at AWS EB.
The server/eb directory contains:
app.py - flask app to run the server
Makefile - which creates an artifact.zip file which can be deployed.
README.md - instructions for setting up and deploying the eb app.
* hosted cellxgene (#38)
In this PR, contains scripts and instructions for deploying cellxgene
for AWS elastic beanstalk. It supports the multi-dataset option.
The Makefile in the server/eb directory creates an artifact.zip
file, which can be deploy at AWS EB.
The server/eb directory contains:
app.py - flask app to run the server
Makefile - which creates an artifact.zip file which can be deployed.
README.md - instructions for setting up and deploying the eb app.
* Update how artifact.zip is created
prune the server/test and server/eb directories
* Remove debugging print statements
* fixes from review comments
* fix lint
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
This PR contains a refactoring to make adding new features easier.
The new features include supporting the tiledb format, and the multi dataset application.
The refactoring includes
Simplifying the directory structure and files.
a class structure to handle annotations (currently one type: AnnotationsLocalFile).
a class to handle application configuration
a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb.
Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface.
The multi dataset option is not fully supported yet, and so the option to use it is hidden.
Use "cli launch --dataroot ..."
To access this feature.
All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
* Collect all env vars in one, easy-to-find place
Past state:
* Default environement variables were stored in both client/package.json
and client/__tests__/e2e/config.js
* Constants that should have been linked--like the cellxgene server port
during testing--were repeated.
With this commit:
* All environment variables are parameterized
* All environment variables are packaged in default env files
* Move npm scripts to client Makefile
* Respond to feedback from @seve and @bkmartinjr
Currently the client build is not reproducible since, each time you run
`make build-client` the package lockfile is updated. This should be
handled separately by `make gen-package-lock` when developers actually
want to update the dependencies.
`npm ci` installs dependencies directly from the lockfile without
updating them, making builds reproducible.
* Fix Makefile whitespace and .PHONY use
* Fix Makefile filename
* Modularize Makefile into client and server Makefiles
Part of the reason that the Makefile in the root directory is a bit
complicated is that it tries to handle tasks that can be handled
separately in the client and server modules.
This commit pushes some of the make logic specific to each module into
their own makefiles and calls out to those makefiles from that in the
project root.
* Add auto-formatting to client and server modules
One thing that can make linting faster is auto-formatting. This commit
adds the yapf auto-formatting tool to the server module and uses
eslint's "fix" functionality to speed up the linting/formatting process.
* Add yapf for automatic code formatting
* Add a root test target that calls sub-tests
* Apply yapf to python files
* Do not duplicate npm commands, simply pass through
* Update documentation
* Do not shadow reserved word len
* Add general test target
* Fix make call in dev-env
* Use black instead of yapf
* Run flake8 from the root directory
* Revert "Apply yapf to python files"
This reverts commit cdca128a01.
* Apply black to python code
* Resolve lint errors resulting from black format
* Add explanation of server unit tests in dev guidelines
