* Improve diffexp for tiledb
- The rows from the A and B sets are gathered and processed at the same time. In this
way the matrix is only accessed once instead of twice for each tile.
- There is now a single thread queue that gets shared between all callers of the diffexp.
This will slow down work if diffexp gets too busy.
- There is a target_workunit amount of work given to each thread. Previously the
workunit was (rows selected * width of tile), which could be small. Now multiple
column tiles can be combined into one workunit. If the target is too small then
thread and other overheads may reduce performance. If target_workunit is too large
then the size of the gathered sub matrix may take up too much memory.
- add configuration parameters (max_workers, cpu_multiplier, and target_workunit)
* Specialize diffexp for tiledb
This patch adds a new diffexp algorithm which is tuned for tiledb.
This algorithm was written by Bruce and is adapted here to plug into the
current framework. The anndata_adaptor still calls the original
algotithm (which was move from diffexp.py to diffexp_generic.py).
The cxg_adaptor now calls the new diffexp_tiledb version. Some
code is shared between the two.
This is part 1 of the diffexp for tiledb. Further tuning and
global throttles are still needed.
A script to run and time diffexp with various options is also
added: test/run_diffexp.py.
* Improvements to the matrix cache
- Add a timelimit for the matrix in the cache.
Once the timelimit is reached, the matrix can be removed.
- If a DatasetAccessError occurs, then remove the dataset
from the matrix cache.
Fixes#1322
* work around anndata bug 344
* fix accidental cut and paste error
* Use modified make_index_unique function
Temporarily copy code from https://github.com/theislab/anndata/pull/345
until the issue is resolved and released.
* Add notes and test for make_index_unique
* Lint fix
* Format python
Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
* black reformat
* tighten up error reporting
* lint
* fine tuning
* additional improvements in exception handling
* lint
* include exception and traceback in log
* fix typo
* Introduce a config file to cellxgene
The config file format is in yaml. The default config is located
in server/common/default_config.py. A user may create a yaml file
that contains a subset of these fields. It can be used during cellxgene
launch, or for hosted cellxgene.
The code has also been refactored. Much of the logic to check arguments
has moved from launch to app config.
It is now possible to set the tiledb context parameters using the config
file. Other feature will soon be handled in a similar way.
* allow DataLocator to accept another locator as init param
* migrate to DataLocator
* migrate to DataLocator
* lint
* migrate to DataLocator
* add check for erroroneous use of remote path and annotations
* lint
* revert default data location - now back go CWD
* remove unused import
* first cut at re-embedding route and back-end support
* update and expand config route tests
* add scanpy_umap
* add reembedding to config route parameters
* front-end support for reembedding fetch and UI
* remove unused imports
* add loading state
* save reembedding in reducer state
* improve withColsFrom
* transmit reembed schema to client; pick unique embedding names
* display embeddings
* format
* lint
* spaces, tab size 2
* lint
* test hack for smoke-test race
* back out hack sleep
* add check for backed mode
* add unit test for reembedding
* lint
* hide re-embedding CLI param from help
* Add user-generated annotations tests to the server
Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969
* Auto-format python code
* @skip_if: passing lambdas > than property strings
* Respond to feedback from @bkmartinjr
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.
