Bruce Martin
b284e6f820
Improve CLI help ( #1025 )
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* launch option changes
* more CLI help improvements
* change plot help
* additional changes requested
* change metavars for options and subcommand
2019-11-14 13:02:40 -08:00
Bruce Martin
e581dec8f5
release 0.12.0 ( #981 )
2019-10-08 12:34:21 -07:00
Bruce Martin
711f3b7048
Add support for anndata backed mode ( #943 )
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* initial cut at backed mode
* make flask multithreading conditional on debug flag
* update X access to support backed mode
* lint
* improve help message for backed mode
* fix tests
* add MatrixProxy to normalize supported matrix types
* add FAQ entry for --backed
* remove use of matrix.T
* clean up
* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user
* fix tests
* do not print diffexp speed warning if diffexp is disabled
* tweak wording of diffexp speed messages
* add FAQ entry on --disable-diffexp
* revise heuristic for warning about slow diffexp
* use quick tooltip delay on diffexp button
2019-10-08 11:16:07 -07:00
Severiano Badajoz
44cb276cdf
Add configurable about this dataset links ( #907 )
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* add about arg
* add simple url validator
* attach about link to config api
* add links to configDefaults
* add conditional link in top left and menu item
* whitespace
* change to lower case
* move --about arg before click.command()
if this fixes it I have no idea why
* change link>URL
* be more descriptive about URL
* Make error more explicit
* refactor attach_data to accept about
* format
* change icon
* add trailing parenthesis
* whitespace
2019-09-25 19:23:49 -07:00
Bruce Martin
3660a6cc27
Experimental - manual annotations ( #837 )
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* icons, partway
* redux for values
* onChange
* cancel
* annotations lifecycle for category names
* copy categorical
* edit category
* add Dataframe.withColsFrom
* render user annotations; default add/delete annotation category
* add label name to actions
* category name edit
* error checking improvements
* change schema field isUserAnnotation to writable
* always have an unassigned label; implement delete label
* implement add new label and edit label name
* label current cell selection
* fix select exact bug in crossfilter
* clean up categorical reducer
* fix tests
* remove debugging printf
* implement subset/reset for user annotations
* undo redo support for user annotations
* remove duplicate button from categories
* add modal
* remove obsolete duplicate annotation reducers
* remove old debugging printf
* connect modal to annotation create and dup
* initial full-stack wiring
* finish up end-to-end wiring
* fix existing unit tests
* fix pytests to match new schema API
* remove debugging printfs
* add label file rotation
* remove obsolete comment
* add fbs encode/decode tests
* add tests for writable annotations
* simplify code
* fix hashing bug with FBS encoding
* lint
* fix smoke tests
* improve error checking in Dataframe.withColsFrom
* add unit test for Dataframe.withColsFrom
* add unit test for Dataframe.columns and Dataframe.renameCol
* fix bug in FBS encode, add better error checks, refactor
* add FBS encode/decode test
* add clarifying comment
* clean up action type names; fix state inconsistency in crossfilter update
* change autosave timer to 2.5sec
* sort categorical metadata render order so it remains consistent
* add temporary autogenerated label for add-new-label operation
* fix hover-over label menu interference with cell highlighting
* remove debugging code
* add missing reducer cases & fix typo
* make dataframe memoize more general purpose
* add dev mode for annos
* fix error on select duplicate
* handle zero occupancy categories
* correctly maintain unclipped AND clipped world
* correctly handle zero length FBS matrix and label files
* ensure all writable categorical schema contains an unassigned category
* handle case where building occupancy stack for category with no members
* dialog for creating label, disable button if duplicate or empty
* visually separate writeable
* edit category
* fix edit category name
* remove debugging code
* fix edit annotation label
* visually define unassigned, change options
* Pull in requirements.txt from `master`
* label currently selected cells
* duplicate label
* lint
* fix pytest merge issues
* rename --label-file to --experimental-label-file
* remove debugging console log
* spelling error fix; fix bug found in PR review.
* lint
2019-09-18 07:33:41 -04:00
Bruce Martin
922c375333
Rename "layout" to "embedding" in the UI ( #921 )
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* rename "layout" to "embedding" in the UI
* docs changes for layout
* fix typo in data docs
* new help text, per PR review
2019-09-16 15:34:14 -07:00
Bruce Martin
20317fd08f
Add URL data locators to launch sub-command ( #920 )
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* initial commit of URL support for launch
* lint
* modify tests to use new data locator
* add locator unit tests
* fix typo in faq
* more lint
* update faq per PR review
2019-09-15 09:01:53 -07:00
Charlotte Weaver
77de22d1ed
merge louvain and prepare extra requires ( #897 )
2019-08-29 12:49:19 -07:00
Charlotte Weaver
28c4d28308
extract prepare from main install ( #887 )
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* extract prepare from main install
* add requirements-prepare to manifest
2019-08-21 14:26:01 -07:00
Colin Megill
d16a69e158
bump version to 0.11.0 ( #850 )
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* bump version to 0.11.0
* manually fix version number
2019-07-16 14:27:41 -04:00
Charlotte Weaver
8afb22a017
GUI UI Elements ( #816 )
2019-06-27 17:30:57 -07:00
Charlotte Weaver
5effe4bbbb
removed --diffexp cli param ( #826 )
2019-06-26 14:46:58 -07:00
Charlotte Weaver
d5deb1579f
[EASY] fix max-category-items ( #813 )
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* fix max-category-items
* match default for max category items
fe had 1000, be had 100
2019-06-13 15:45:43 -07:00
Bruce Martin
ca9a6796d8
release 0.10.1 ( #797 )
2019-05-30 13:44:42 -07:00
Bruce Martin
c6252825f3
release 0.10.0 ( #794 )
2019-05-29 16:55:43 -07:00
Bruce Martin
4b96b3a635
fix incompatibility of flask reload and port searching ( #793 )
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* WIP
* add --developer; fix incompatibility of --port and --debug
* put REST tests on separate ports
* PR review
2019-05-29 16:38:57 -07:00
Charlotte Weaver
ab4c74a321
remove psutil ( #773 )
2019-05-18 10:53:45 -07:00
Bruce Martin
efa1709158
add multi-layout support to back-end ( #766 )
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* add multi-layout support to back-end
* remove obsolete code
* temporary code to apply heuristic choice of default layout
* fix tests
* update python tests
* more py lint
* PR review changes
* more PR lint
* PR lint
2019-05-16 14:49:22 -07:00
Charlotte Weaver
d6040f687a
port retry ( #761 )
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* WIP
* import find_available_port method
* move method to utils
so I can add to eventually add to gui
* add fixed-port flag to tests
* Update server/utils/utils.py
Co-Authored-By: Tony Tung <tonytung@merly.org >
* pr review suggestions
* pr review suggestions
* fix outdated package.json
* update error message
* simplify find_available_port function
* Auto scan for ports unless port is specified.
* fix tests
* fix comment for find_available_port
* lint error
* differentiate port error from generic os error
* add errno to OSerror
* pr review fixes
* raise e -> raise
* oserror -> socket error
2019-05-14 14:04:13 -07:00
Bruce Martin
b9a1e30652
large file size guardrails ( #763 )
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* large file guardrails
* fix lint
* PR review
* remove unused import
* use standard slice for CSR
* revert change
2019-05-13 18:13:16 -07:00
Charlotte Weaver
c12cb2424a
release bugfix ( #749 )
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* add __init__.py
* bump version
2019-05-06 10:16:36 -07:00
Bruce Martin
1471d6b214
release 0.9.0 ( #746 )
2019-05-04 08:41:56 -07:00
Charlotte Weaver
9f10d8095a
GUI app (experimental) ( #730 )
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* add default config
* first pass
* flake8
* cleanup
* first pass at using qthreads
* cleanup
* WIP
* better error handling
* improved UI
* bugfix
* fix merge bugs
* import order
* cleanup
* make gui requirements optional
* pr review requested changes
* Update server/gui/main.py
Co-Authored-By: csweaver <charlottesweaver@gmail.com >
* pr review request
* qt child class methods -> camelCase
* whitespace
2019-04-30 12:52:15 -07:00
Charlotte Weaver
ea187f48e0
add scripts from cli ( #680 )
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* add scripts from cli
* add warning when including scripts
* flake8 fixes
* confirm scripts injection
2019-04-22 12:30:57 -07:00
Charlotte Weaver
9c6273eb94
core library ( #711 )
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* move app creation to function
* create engine without load
* flake 8 fixes
* cleanup original scanpy test
* add default config
* handle missing data
* test data changes
* unify update
* load data isn't static anymore
* make app a class
2019-04-22 12:24:07 -07:00
Sidney Bell
34e5a91dc6
Add calculate_qc_metrics to `prepare ( #697 )
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* Calculate QC metrics
* Add QC metrics to prepare section of readme
* Add pointer to scanpy qc metrics function
* Don't explicitly pass qc flag as arg
* Add explicit toggle for run-qc/skip-qc
* Move qc metrics calculation to separate step/function
2019-04-09 08:56:07 -07:00
Sidney Bell
c9a56fa73a
Update scanpy version ( #688 )
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Update to version 1.3.7
2019-04-04 12:16:30 -07:00
Charlotte Weaver
ce8326ddea
bump version ( #684 )
2019-04-01 14:42:22 -07:00
Sidney Bell
16f93397ae
Support diffmap and phate layouts. Explicitly handle embeddings with >2 components. ( #662 )
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* Add diffmap and phate to supported embeddings
* Explicitly pull the first two components of any given layout
2019-03-21 19:06:05 -07:00
Alex Wolf
82493d1019
Add forced directed graph drawing to allowed layout options ( #626 )
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* added forced directed graph drawing layout options
* added line breaks for 120 character limit
2019-03-05 13:10:07 -08:00
Bruce Martin
d8e3721846
bumpversion to 0.7.0 ( #623 )
2019-03-01 12:25:30 -08:00
Charlotte Weaver
4e67c645f8
bumped version ( #602 )
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0.6.0 was burned on pypi
2019-02-14 10:00:16 -08:00
Charlotte Weaver
8b28d51dfa
bump version ( #601 )
2019-02-13 16:29:14 -08:00
Charlotte Weaver
1103272b95
De-dupe -d CLI option alias ( #575 )
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removed from debug, diffexp gets to keep it
2019-01-30 16:11:21 -08:00
Charlotte Weaver
ecaa32cfb2
bump version ( #563 )
2019-01-17 17:14:44 -08:00
Charlotte Weaver
b02361a6bf
bump version ( #560 )
2019-01-17 16:54:25 -08:00
Bruce Martin
5d60505407
remove --nan-to-num CLI parameter ( #548 )
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* remove --nan-to-num CLI parameter
* factor tests better
* lint - remove unused variables
2019-01-10 15:03:03 -08:00
James Taylor
f2eb2cad82
Use url_root from Flask rather than hardcoding hostname. ( #520 )
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Allows running in a container on a remote host, should also allow running
behind a proxy with a url prefix.
2018-12-19 16:20:26 -08:00
Colin Megill
a297ea30e2
bump version ( #518 )
2018-12-17 14:30:34 -05:00
Charlotte Weaver
83154577e4
Black -- formatter for python ( #508 )
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* Add black
* use black to format code
* Black version
2018-12-12 09:44:47 -08:00
Bruce Martin
95fd20b405
bump version to 0.3 ( #498 )
2018-12-05 14:35:17 -08:00
Charlotte Weaver
5c6cc597c8
Default warning in debug mode ( #497 )
2018-12-05 13:38:34 -08:00
Bruce Martin
3bfeadc2b9
improve handling of non-finite floating point values ( #490 )
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* improve HTTP error reporting
* generate standards-compatible JSON
* add --nan-to-num work-around for non-finite floating point values
* lint
* update tests
* correctly set Infinities to min/max
* REAMDE update for --nan-to-num
* define constant for repetitive warning message
* clarify where NaN errors will occure
2018-12-04 14:56:16 -08:00
Charlotte Weaver
4a50f0ed46
External host option ( #481 )
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* allow specifying host ip instead of listen all
* flask serving
* Limit to ip addresses only
2018-11-29 17:01:49 -08:00
Charlotte Weaver
28f5263c88
bump version ( #475 )
2018-11-27 15:43:19 -08:00
Charlotte Weaver
0c26f227fe
bump version ( #470 )
2018-11-26 15:38:47 -08:00
Charlotte Weaver
f2612707bb
bumped version ( #466 )
2018-11-26 11:42:56 -08:00
Charlotte Weaver
2b5094665f
version 0.2.0 ( #456 )
2018-11-16 15:12:54 -08:00
Jeremy Freeman
a81258bc0d
remove printing ( #455 )
2018-11-16 14:45:06 -08:00
Bruce Martin
141f802824
differential expression improvements ( #452 )
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* add cutoff for low expression genes in topN selection
* remove debugging printfs
* change cli param name for diffexp cutoff
* change CLI param name
* second try at diffexp - using lfc sort with pval cutoff
* use lfc cutoff
* update comments to match code; cap p-value adjustment to max of 1
* lint
* explain diffexp in readme
* add link
* add diffexp-lfc-cutoff to test config
* update test to match revised diffexp spec
* fix latent bug in GET arg handling that was breaking tests
* lint
* comment cleanup
* fix variance overestimation so it is symmetric
* lint
2018-11-16 14:44:56 -08:00
