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Merge lates main to analyze/scrub_emr #11

Merged

KrishPatel13 merged 23 commits into KrishPatel13:analyze/scrub_emr from OpenAdaptAI:main

Jul 18, 2023

Owner

KrishPatel13 commented Jul 4, 2023

What kind of change does this PR introduce?

Summary

Checklist

My code follows the style guidelines of OpenAdapt
I have performed a self-review of my code
If applicable, I have added tests to prove my fix is functional/effective
I have linted my code locally prior to submission
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation (e.g. README.md, requirements.txt)
New and existing unit tests pass locally with my changes

How can your code be run and tested?

Other information

dianzrong and others added 23 commits

July 3, 2023 15:55


          feat(install): download and install MacOS dependencies

25b70c0

* add messages

* add download python line

* created cleanup func

* helper functions created

* partially down python downloading

* python installation script complete

* added git (and brew)

* added git (and brew)

* add tesseract and refactor

* works on current macbook

* install python with brew

* install python with brew

* check if pyenv is needed

* merge2

* merge2

* simplify brew call

* finished testing

* Less output

* split line

* Revert adding svg file
This reverts commit 5601407.

* remove unnecessary things

* remove ps1 edit

* remove ps1 edits

* make the ps1 the same

* Remove space

* add poetry and aesthetic changes

* small changes

* add brew to path if needed

* switch to pip3

* switch to pip3.10


          chore(release): v0.4.0

d15f683

Automatically generated by python-semantic-release


          feat: add progress bar in record.py and visualize.py

3e12fd4

* run `poetry lock --no-update`

* add alive-progress via poetry and in code

* add progress bar in visualization

* add a check for MAX_EVENT = None

* update the title for the Progress bAr
 (better for USer pov)

* update the requirement.txt

* ran ` black --line-length 80 <file>`
on record.py and visualize.py

* remove all progress bar from record

* add tqdm progress bar in recrod.py

* add tqdm for visualiztion

* remove alive-progress

* consistent tqdm api

--add dynamic_cols: to enable adjustments when window is resized

Order:
--total
-description
--unit
--Optional[bar_format]
--colour
--dynamic_ncols

* Update requirements.txt

Co-authored-by: Aaron <57018940+0dm@users.noreply.github.com>

* Address comemnt:
#318 (comment)

* remove incorrect indent

* remove rows

* try to fix distorted table in html

* add custom queue class

* lint --line-length 80

* fix `NotImplementedError` for MacOs
-- using custom MyQueue class

* rename custom -> thirdparty_customization

* rename to something useful

* address comments

* rename dir to customized_imports

* rename to extensions
#318 (comment)

---------

Co-authored-by: Aaron <57018940+0dm@users.noreply.github.com>


          chore(release): v0.5.0

7d0433a

Automatically generated by python-semantic-release


          fix: add pympler and psutil

f853839


          chore(release): v0.5.1

e2015f3

Automatically generated by python-semantic-release


          docs: update install section of README.md (#344)

755dd55

* run `poetry lock --no-update`

* fix: update CONTRIBUTING.md

fix typo in 3 words and make pytest code word

* fix: add required dependencies

* add seup.md

* add setup.md

* remove typo

* rename temporarily

* rename to SETUP.md

* update README to include more documentation on

-- when someone should use the install script vs. follow the steps here?

* remove requirements.txt

* add link to installation

* rename typo: prerequisite

* link to start: https://openadapt.ai/#start

* reomve .venv as requirements.txt is no longer used

* update installation instructions

* update the Windows Installtion command (in favour of):

1. https://github.com/OpenAdaptAI/OpenAdaptWeb/pull/30/files#r1252126510
2. https://github.com/OpenAdaptAI/OpenAdaptWeb/pull/30/files#r1252128457

* addressing comment:
#344 (comment)

* address the comment:

#344 (comment)

* address the comment:

https://github.com/OpenAdaptAI/OpenAdapt/pull/344/files#r1252175602

* add .venv to address the comment:

https://github.com/OpenAdaptAI/OpenAdapt/pull/344/files#r1252172932

and

https://github.com/OpenAdaptAI/OpenAdapt/pull/289/files#r1252150636


          docs: Create Use Case issue template (#324)

20fb5a3

* initial draft

* new line issue

* update link

* address comment

* add numbers


          chore: add isort as pre-commit hook (#319)

72da341

* Add precommit hooks for isort, check-yaml, end-of-file-fixer, trailing-whitespaces

* Updated README on setting up precommit hooks

* Add updated poetry.lock

* Fix step numbering of pre-commit section in README.md


          update config.SCRUB_ENABLED to False (#373)

3f32883


          fix: windows.get_active_window() (#333)

d3f07c9

* return top_window of the active app

* remove runtime exception

* handle runtime error

* handle COMerror

* add logger.warning

* add logger.warning

* add get_properties

* remove unnecessary imports

* remove -> Desktop

* monkey patching

* fix get_properties

* monkey patch __class__

* fix monkey patching

* format with black


          0.5.2

0d6a155

Automatically generated by python-semantic-release


          fix: support more objective-c objects (#323)

be0774f

* Update _macos.py

* Update _macos.py

* Update _macos.py

* add bug report option

* Update _macos.py

* undo formatting

* refactor

* split

* remove debug line

* Update _macos.py

* Update _macos.py

* Update _macos.py

* Update _macos.py

* reorganize

* Update _macos.py

* Update _macos.py

* nonetype

* Update _macos.py


          0.5.3

c82ca8b

Automatically generated by python-semantic-release


          fix: add test fixtures (#356)

0ee5397

* fix: add test fixtures

* revert test_summary.py


          fix(utils): prevent duplicate log messages (#339) (#366)

cf1a782

* fix(utils): prevent duplicate log messages (#339)

Acquire a lock in utils.configure_logging. Otherwise this function has
a race where two threads can both call logger.remove(), and then both
call logger.add(), creating two identical sinks.

* refactor(record): remove redundant configure_logging calls

configure_logging is already called at the module level so there's no
need to call it with identical arguments in various functions.

* fixup! fix(utils): prevent duplicate log messages (#339)


          0.5.4

74e4af4

Automatically generated by python-semantic-release


          fix: loguru exception handling for invalid recordings (#361)

7aba45b

* raise ValueError

* improve exception handling

* Update crud.py

* use assert

* reorganize catch

* Update openadapt/replay.py

* Update openadapt/visualize.py

* Update openadapt/events.py

* Update openadapt/crud.py

---------

Co-authored-by: Richard Abrich <richard.abrich@gmail.com>


          0.5.5

5a6f67c

Automatically generated by python-semantic-release


          chore: configure isort with black profile and add black precommit hook (

2e7496b

#384)

* chore: configure isort with black profile and add black precommit hook

* update black version

* add advanced isort settings to match CONTRIBUTING.md


          docs: Update README.md (#390)


          docs: update readme (take transpose of installation table) (#397)

fe39c73


          docs: update README (installation table) (#398)

KrishPatel13 merged commit 42b0d19 into KrishPatel13:analyze/scrub_emr

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