11 cli #14

jrm5100 · 2019-07-11T18:05:08Z

Closes #11

…bcommands

…ce it caused difficulty with the SurveyDesignSpec object

…nt_na

…t done with the categorize CLI, but need to decide on 'describe' commands listing results for non-category types

…module since they aren't one-in, one-out

…ariables

…and move functions

…n convenience

… load data function.

…gging

…th missing weights

codecov-io · 2019-07-11T18:16:12Z

Codecov Report

Merging #14 into master will increase coverage by 10.93%.
The diff coverage is 79.01%.

@@             Coverage Diff             @@
##           master      #14       +/-   ##
===========================================
+ Coverage   33.53%   44.47%   +10.93%     
===========================================
  Files          25       21        -4     
  Lines        1297     1313       +16     
===========================================
+ Hits          435      584      +149     
+ Misses        862      729      -133

Impacted Files	Coverage Δ
clarite/modules/survey/__init__.py	`100% <ø> (ø)`	⬆️
clarite/modules/survey/survey_model.py	`10.86% <ø> (ø)`	⬆️
clarite/modules/survey/survey_design.py	`9.84% <ø> (ø)`	⬆️
clarite/modules/plot.py	`10.96% <0%> (ø)`	⬆️
clarite/tests/clarite/test_df_accessor.py	`100% <100%> (ø)`	⬆️
clarite/tests/modify/test_modify.py	`100% <100%> (ø)`	⬆️
clarite/tests/conftest.py	`100% <100%> (ø)`	⬆️
clarite/__init__.py	`100% <100%> (ø)`	⬆️
clarite/tests/io/test_io.py	`100% <100%> (ø)`
clarite/tests/analyze/test_analyze.py	`100% <100%> (ø)`	⬆️
... and 11 more

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jrm5100 added 30 commits June 28, 2019 11:18

Bump statsmodels to 0.10

0f890c7

Set up basic structure for cli which is run as 'clarite-cli'

edda6d3

Revised cli structure to have several commands each with their own su…

e2b9e4b

…bcommands

Merge remote-tracking branch 'upstream/master'

c7c98ee

Merge branch 'master' into 11-cli

d2dbae7

Finish adding all commands

6a426ed

WIP: Support saving dtypes and write tests for IO

4e2a569

WIP: Added support for saving dtypes. All current tests passing.

7b12969

Fix default arguments for the rowfilter

1b0d001

Enforce a single input index rather than converting a multiindex, sin…

002f80a

…ce it caused difficulty with the SurveyDesignSpec object

Fix doc

85266e2

Fixed ewas test, but most tests are currently broken due to DNS failure

db0e4a1

Add describe.correlations CLI

85a29c9

Add describe.freq_table cli

96dfe59

Add describe.percent_na cli

96ba962

Updated colfilter_percent_zero to use 0-100 percent, similar to perce…

7711507

…nt_na

WIP: Realized there is a need for a function to move variables. Almos…

afc1ff2

…t done with the categorize CLI, but need to decide on 'describe' commands listing results for non-category types

Move the merge_variables and move_variables functions to the process …

e4e821b

…module since they aren't one-in, one-out

Allow string inputs to 'skip' and 'only' in order to specify single v…

d4d9faa

…ariables

Merge CLI

633ea32

Move variables CLI, and rename data/other to left/right in the merge …

f6a9df6

…and move functions

Add log for move variables and started adding modify CLI

f800eba

Add percent zero cli

af99360

Remove DataFrame accessors- I think they would add more confusion tha…

71f677d

…n convenience

Fix leftover references to df accessors

2d2ff27

Fix tests, mostly due to changed log message

89d5d0d

Fix bug in reporting results of recode-values

5898d14

Finished more cli for modify

5fb5edc

Finished with CLI for 'modify'

e54867c

load-data CLI done. Gave more control to the dtypes file usage in the…

0c8f01f

… load data function.

jrm5100 added 19 commits July 8, 2019 10:43

Add plot histogram CLI and filter out NAs in the histogram function

99e1779

Fix default index column and add cli for distributions plot

289c27b

WIP: manhattan plot CLI not working with categories yet

48f2e82

Plot CLI is done

da72b12

Add some verification to loading of ewas results

577bcd7

WIP: Need some testing with weights for EWAS function

309feda

Handle (not) saving empty dataframes when categorizing

92e1c5c

Remove print statement

8cffbf5

Fix saving data with dtypes. Add skip and only to load_data

091cd52

Add colfilter method to modify cli for dropping columns

9bd0677

Added merge-rows, colfilter, and rowfilter functions

b7f5a4b

Make output an argument in the categorize cli and slightly improve lo…

a25650a

…gging

Change argument order in plot histogram CLI for consistency

cd03352

Add transform variable CLI function

6ebd174

Add analyze get-significant CLI

a96a40f

Fix indentation

aa1e547

Validate weight file input to the ewas CLI and check for variables wi…

5ff441d

…th missing weights

Update dtypes print statement to skip logging anything by default

c1653ef

Update docs to include a separate section for the CLI

06c4ba3

jrm5100 added the enhancement New feature or request label Jul 11, 2019

jrm5100 self-assigned this Jul 11, 2019

Fix tests

765825a

jrm5100 merged commit f10e991 into HallLab:master Jul 11, 2019

jrm5100 deleted the 11-cli branch July 11, 2019 18:23

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11 cli #14

11 cli #14

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11 cli #14

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