An ML project template with sensible defaults

ThoughtWorksInc, updated 🕥 2022-01-21 20:01:57

ml-app-template

An ML project template with sensible defaults: - Dockerised dev setup - Unit test setup - Automated tests for model metrics - CI pipeline as code

For infrastructure-related stuff (e.g. provisioning of CI server, deployments, etc.), please refer to https://github.com/ThoughtWorksInc/ml-cd-starter-kit.

Getting started

Fork repository: https://github.com/ThoughtWorksInc/ml-app-template
Clone repository: git clone https://github.com/YOUR_USERNAME/ml-app-template
To develop on local environment with installed Python packages, run: pipenv install then activate environment with pipenv shell 3.b. to run anything without activating the virtual environment, for example, nosetests, try pipenv run nosetests
Install Docker (Mac, Linux)
Start Docker on your desktop
Build image and start container:

```shell

build docker image [Mac/Linux users]

docker build . -t ml-app-template

build docker image [Windows users]

MSYS_NO_PATHCONV=1 docker build . -t ml-app-template

start docker container [Mac/Linux users]

docker run -it -v $(pwd):/home/ml-app-template \ -p 8080:8080 \ -p 8888:8888 \ ml-app-template bash

start docker container [Windows users]

winpty docker run -it -v C:\Users\path\to\your\ml-app-template:/home/ml-app-template -p 8080:8080 -p 8888:8888 ml-app-template bash

Note: to find the path, you can run `pwd` in git bash, and manually replace forward slashes (/) with double backslashes (\)

```

You're ready to roll! Here are some common commands that you can run in your dev workflow. Run these in the container.

```shell

add some color to your terminal

source bin/color_my_terminal.sh

activate virtual environment for python

pipenv shell

run unit tests

nosetests

run unit tests in watch mode and color output

nosetests --with-watch --rednose --nologcapture

train model

SHOULD_USE_MLFLOW=false python src/train.py

start flask app in development mode

python src/app.py

make requests to your app

1. In your browser, visit http://localhost:8080

2. Open another terminal in the running container (detailed instructions below) and run:

bin/predict.sh http://localhost:8080

You can also use this script to test your deployed application later:

bin/predict.sh http://my-app.com ```

Here are some other commands that you may find useful ```shell

see list of running containers

docker ps

start a bash shell in a running container

docker exec -it bash

starting jupyter notebook server on http://localhost:8888

jupyter notebook --ip 0.0.0.0 --no-browser --allow-root ```

What's in this repo?

We've created a project template to help you with the boilerplate code that we usually have to write in any typical project.

To reduce incidental complexity, we used a simple dataset (boston housing prices) to train a simple linear regression model. Replace the (i) data, (ii) data preprocessing code and (iii) model specification for your use case.

This is the project structure:

```sh . ├── Dockerfile ├── README.md ├── requirements-dev.txt # specify dev dependencies (e.g. jupyter) here ├── requirements.txt # specify app dependencies here ├── ci.gocd.yaml # specify your CI pipeline here └── src # place your code here ├── app.py ├── app_with_logging.py
├── tests # place your tests here │ ├── test.py │ └── test_model_metrics.py └── settings.py # define environment variables here └── train.py ├── bin # store shell scripts here │ ├── color_my_terminal.sh │ ├── configure_venv_locally.sh │ ├── predict.sh │ ├── start_server.sh │ ├── test.sh │ ├── test_model_metrics.sh │ └── train_model.sh ├── docs │ ├── FAQs.md │ └── mlflow.md ├── models # serialize stuff here │ ├── _keep │ ├── column_order.joblib │ └── model.joblib

```

For logging, app_with_logging.py contains the code for logging (i) inputs to the model, (ii) model outputs and (iii) LIME metrics. You can refer to this file to send logs to elasticsearch using fluentd. To keep the main app simple to accessible to people who may not be familiar with these technologies, we've kept it in a separate file app_with_logging.py for reference.

IDE configuration

Please refer to FAQs for instructions on how to configure VS Code or PyCharm to give you intellisense and auto-complete suggestions as you code.

Infrastructure

To provision the infrastructure used in this repo (e.g. GoCD, MLFlow, EFK), please check out the ml-cd-starter-kit repo and follow the instrutions in the README.

When you're done setting up the infrastructure, do the following: - in src/settings.py, update the ip addresses with that of your own infrastructure. - in ci.gocd.yaml, replace davified/ml-app-template with YOUR_USERNAME/YOUR_IMAGE_NAME

Troubleshooting

If you encounter any errors, please refer to FAQs for a list of common errors and how to fix them.

Issues

Bump ipython from 7.5.0 to 7.16.3

opened on 2022-01-21 20:01:56 by dependabot[bot]

Bumps ipython from 7.5.0 to 7.16.3.

Commits

d43c7c7 release 7.16.3
5fa1e40 Merge pull request from GHSA-pq7m-3gw7-gq5x
8df8971 back to dev
9f477b7 release 7.16.2
138f266 bring back release helper from master branch
5aa3634 Merge pull request #13341 from meeseeksmachine/auto-backport-of-pr-13335-on-7...
bcae8e0 Backport PR #13335: What's new 7.16.2
8fcdcd3 Pin Jedi to <0.17.2.
2486838 release 7.16.1
20bdc6f fix conda build
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Bump pillow from 6.0.0 to 8.3.2

opened on 2021-09-08 01:29:21 by dependabot[bot]

Bumps pillow from 6.0.0 to 8.3.2.

Release notes

Sourced from pillow's releases.

8.3.2

https://pillow.readthedocs.io/en/stable/releasenotes/8.3.2.html

Security

CVE-2021-23437 Raise ValueError if color specifier is too long [hugovk, radarhere]

Fix 6-byte OOB read in FliDecode [wiredfool]

Python 3.10 wheels

Add support for Python 3.10 #5569, #5570 [hugovk, radarhere]

Fixed regressions

Ensure TIFF RowsPerStrip is multiple of 8 for JPEG compression #5588 [kmilos, radarhere]

Updates for ImagePalette channel order #5599 [radarhere]

Hide FriBiDi shim symbols to avoid conflict with real FriBiDi library #5651 [nulano]

8.3.1

https://pillow.readthedocs.io/en/stable/releasenotes/8.3.1.html

Changes

Catch OSError when checking if fp is sys.stdout #5585 [@radarhere]

Handle removing orientation from alternate types of EXIF data #5584 [@radarhere]

Make Image.array take optional dtype argument #5572 [@t-vi]

8.3.0

https://pillow.readthedocs.io/en/stable/releasenotes/8.3.0.html

Changes

Use snprintf instead of sprintf #5567 [@radarhere]

Limit TIFF strip size when saving with LibTIFF #5514 [@kmilos]

Allow ICNS save on all operating systems #4526 [@newpanjing]

De-zigzag JPEG's DQT when loading; deprecate convert_dict_qtables #4989 [@gofr]

Do not use background or transparency index for new color #5564 [@radarhere]

Simplified code #5315 [@radarhere]

Replaced xml.etree.ElementTree #5565 [@radarhere]

... (truncated)

Changelog

Sourced from pillow's changelog.

8.3.2 (2021-09-02)

CVE-2021-23437 Raise ValueError if color specifier is too long [hugovk, radarhere]

Fix 6-byte OOB read in FliDecode [wiredfool]

Add support for Python 3.10 #5569, #5570 [hugovk, radarhere]

Ensure TIFF RowsPerStrip is multiple of 8 for JPEG compression #5588 [kmilos, radarhere]

Updates for ImagePalette channel order #5599 [radarhere]

Hide FriBiDi shim symbols to avoid conflict with real FriBiDi library #5651 [nulano]

8.3.1 (2021-07-06)

Catch OSError when checking if fp is sys.stdout #5585 [radarhere]

Handle removing orientation from alternate types of EXIF data #5584 [radarhere]

Make Image.array take optional dtype argument #5572 [t-vi, radarhere]

8.3.0 (2021-07-01)

Use snprintf instead of sprintf. CVE-2021-34552 #5567 [radarhere]

Limit TIFF strip size when saving with LibTIFF #5514 [kmilos]

Allow ICNS save on all operating systems #4526 [baletu, radarhere, newpanjing, hugovk]

De-zigzag JPEG's DQT when loading; deprecate convert_dict_qtables #4989 [gofr, radarhere]

Replaced xml.etree.ElementTree #5565 [radarhere]

... (truncated)

Commits

8013f13 8.3.2 version bump
23c7ca8 Update CHANGES.rst
8450366 Update release notes
a0afe89 Update test case
9e08eb8 Raise ValueError if color specifier is too long
bd5cf7d FLI tests for Oss-fuzz crash.
94a0cf1 Fix 6-byte OOB read in FliDecode
cece64f Add 8.3.2 (2021-09-02) [CI skip]
e422386 Add release notes for Pillow 8.3.2
08dcbb8 Pillow 8.3.2 supports Python 3.10 [ci skip]
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Bump urllib3 from 1.25.3 to 1.26.5

opened on 2021-06-02 00:04:39 by dependabot[bot]

Bumps urllib3 from 1.25.3 to 1.26.5.

Release notes

Sourced from urllib3's releases.

1.26.5

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

Fixed deprecation warnings emitted in Python 3.10.

Updated vendored six library to 1.16.0.

Improved performance of URL parser when splitting the authority component.

If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

1.26.4

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

Changed behavior of the default SSLContext when connecting to HTTPS proxy during HTTPS requests. The default SSLContext now sets check_hostname=True.

If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

1.26.3

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

Fixed bytes and string comparison issue with headers (Pull #2141)

Changed ProxySchemeUnknown error message to be more actionable if the user supplies a proxy URL without a scheme (Pull #2107)

If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

1.26.2

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

Fixed an issue where wrap_socket and CERT_REQUIRED wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)

1.26.1

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

Fixed an issue where two User-Agent headers would be sent if a User-Agent header key is passed as bytes (Pull #2047)

1.26.0

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)

Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning should opt-in explicitly by setting ssl_version=ssl.PROTOCOL_TLSv1_1 (Pull #2002) Starting in urllib3 v2.0: Connections that receive a DeprecationWarning will fail

Deprecated Retry options Retry.DEFAULT_METHOD_WHITELIST, Retry.DEFAULT_REDIRECT_HEADERS_BLACKLIST and Retry(method_whitelist=...) in favor of Retry.DEFAULT_ALLOWED_METHODS, Retry.DEFAULT_REMOVE_HEADERS_ON_REDIRECT, and Retry(allowed_methods=...) (Pull #2000) Starting in urllib3 v2.0: Deprecated options will be removed

... (truncated)

Changelog

Sourced from urllib3's changelog.

1.26.5 (2021-05-26)

Fixed deprecation warnings emitted in Python 3.10.

Updated vendored six library to 1.16.0.

Improved performance of URL parser when splitting the authority component.

1.26.4 (2021-03-15)

Changed behavior of the default SSLContext when connecting to HTTPS proxy during HTTPS requests. The default SSLContext now sets check_hostname=True.

1.26.3 (2021-01-26)

Fixed bytes and string comparison issue with headers (Pull #2141)

Changed ProxySchemeUnknown error message to be more actionable if the user supplies a proxy URL without a scheme. (Pull #2107)

1.26.2 (2020-11-12)

Fixed an issue where wrap_socket and CERT_REQUIRED wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)

1.26.1 (2020-11-11)

Fixed an issue where two User-Agent headers would be sent if a User-Agent header key is passed as bytes (Pull #2047)

1.26.0 (2020-11-10)

NOTE: urllib3 v2.0 will drop support for Python 2. Read more in the v2.0 Roadmap <https://urllib3.readthedocs.io/en/latest/v2-roadmap.html>_.

Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)

Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning

... (truncated)

Commits

d161647 Release 1.26.5
2d4a3fe Improve performance of sub-authority splitting in URL
2698537 Update vendored six to 1.16.0
07bed79 Fix deprecation warnings for Python 3.10 ssl module
d725a9b Add Python 3.10 to GitHub Actions
339ad34 Use pytest==6.2.4 on Python 3.10+
f271c9c Apply latest Black formatting
1884878 [1.26] Properly proxy EOF on the SSLTransport test suite
a891304 Release 1.26.4
8d65ea1 Merge pull request from GHSA-5phf-pp7p-vc2r
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Bump pygments from 2.4.2 to 2.7.4

opened on 2021-03-29 20:03:42 by dependabot[bot]

Bumps pygments from 2.4.2 to 2.7.4.

Release notes

Sourced from pygments's releases.

2.7.4

Updated lexers:

Apache configurations: Improve handling of malformed tags (#1656)

CSS: Add support for variables (#1633, #1666)

Crystal (#1650, #1670)

Coq (#1648)

Fortran: Add missing keywords (#1635, #1665)

Ini (#1624)

JavaScript and variants (#1647 -- missing regex flags, #1651)

Markdown (#1623, #1617)

Shell

Lex trailing whitespace as part of the prompt (#1645)

Add missing in keyword (#1652)

SQL - Fix keywords (#1668)

Typescript: Fix incorrect punctuation handling (#1510, #1511)

Fix infinite loop in SML lexer (#1625)

Fix backtracking string regexes in JavaScript/TypeScript, Modula2 and many other lexers (#1637)

Limit recursion with nesting Ruby heredocs (#1638)

Fix a few inefficient regexes for guessing lexers

Fix the raw token lexer handling of Unicode (#1616)

Revert a private API change in the HTML formatter (#1655) -- please note that private APIs remain subject to change!

Fix several exponential/cubic-complexity regexes found by Ben Caller/Doyensec (#1675)

Fix incorrect MATLAB example (#1582)

Thanks to Google's OSS-Fuzz project for finding many of these bugs.

2.7.3

Updated lexers:

Ada (#1581)

HTML (#1615, #1614)

Java (#1594, #1586)

JavaScript (#1605, #1589, #1588)

JSON (#1569 -- this is a complete rewrite)

Lean (#1601)

LLVM (#1612)

Mason (#1592)

MySQL (#1555, #1551)

Rust (#1608)

Turtle (#1590, #1553)

Deprecated JsonBareObjectLexer, which is now identical to JsonLexer (#1600)

The ImgFormatter now calculates the exact character width, which fixes some issues with overlapping text (#1213, #1611)

... (truncated)

Changelog

Sourced from pygments's changelog.

Version 2.7.4

(released January 12, 2021)

Updated lexers:

Apache configurations: Improve handling of malformed tags (#1656)

CSS: Add support for variables (#1633, #1666)

Crystal (#1650, #1670)

Coq (#1648)

Fortran: Add missing keywords (#1635, #1665)

Ini (#1624)

JavaScript and variants (#1647 -- missing regex flags, #1651)

Markdown (#1623, #1617)

Shell

Lex trailing whitespace as part of the prompt (#1645)

Add missing in keyword (#1652)

SQL - Fix keywords (#1668)

Typescript: Fix incorrect punctuation handling (#1510, #1511)

Fix infinite loop in SML lexer (#1625)

Fix backtracking string regexes in JavaScript/TypeScript, Modula2 and many other lexers (#1637)

Limit recursion with nesting Ruby heredocs (#1638)

Fix a few inefficient regexes for guessing lexers

Fix the raw token lexer handling of Unicode (#1616)

Revert a private API change in the HTML formatter (#1655) -- please note that private APIs remain subject to change!

Fix several exponential/cubic-complexity regexes found by Ben Caller/Doyensec (#1675)

Fix incorrect MATLAB example (#1582)

Thanks to Google's OSS-Fuzz project for finding many of these bugs.

Version 2.7.3

(released December 6, 2020)

Updated lexers:

Ada (#1581)

HTML (#1615, #1614)

Java (#1594, #1586)

JavaScript (#1605, #1589, #1588)

JSON (#1569 -- this is a complete rewrite)

Lean (#1601)

LLVM (#1612)

Mason (#1592)

... (truncated)

Commits

4d555d0 Bump version to 2.7.4.
fc3b05d Update CHANGES.
ad21935 Revert "Added dracula theme style (#1636)"
e411506 Prepare for 2.7.4 release.
275e34d doc: remove Perl 6 ref
2e7e8c4 Fix several exponential/cubic complexity regexes found by Ben Caller/Doyensec
eb39c43 xquery: fix pop from empty stack
2738778 fix coding style in test_analyzer_lexer
02e0f09 Added 'ERROR STOP' to fortran.py keywords. (#1665)
c83fe48 support added for css variables (#1633)
Additional commits viewable in compare view

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Bump pyyaml from 5.1 to 5.4

opened on 2021-03-25 23:01:51 by dependabot[bot]

Bumps pyyaml from 5.1 to 5.4.

Changelog

Sourced from pyyaml's changelog.

5.4 (2021-01-19)

yaml/pyyaml#407 -- Build modernization, remove distutils, fix metadata, build wheels, CI to GHA

yaml/pyyaml#472 -- Fix for CVE-2020-14343, moves arbitrary python tags to UnsafeLoader

yaml/pyyaml#441 -- Fix memory leak in implicit resolver setup

yaml/pyyaml#392 -- Fix py2 copy support for timezone objects

yaml/pyyaml#378 -- Fix compatibility with Jython

5.3.1 (2020-03-18)

yaml/pyyaml#386 -- Prevents arbitrary code execution during python/object/new constructor

5.3 (2020-01-06)

yaml/pyyaml#290 -- Use is instead of equality for comparing with None

yaml/pyyaml#270 -- Fix typos and stylistic nit

yaml/pyyaml#309 -- Fix up small typo

yaml/pyyaml#161 -- Fix handling of slots

yaml/pyyaml#358 -- Allow calling add_multi_constructor with None

yaml/pyyaml#285 -- Add use of safe_load() function in README

yaml/pyyaml#351 -- Fix reader for Unicode code points over 0xFFFF

yaml/pyyaml#360 -- Enable certain unicode tests when maxunicode not > 0xffff

yaml/pyyaml#359 -- Use full_load in yaml-highlight example

yaml/pyyaml#244 -- Document that PyYAML is implemented with Cython

yaml/pyyaml#329 -- Fix for Python 3.10

yaml/pyyaml#310 -- Increase size of index, line, and column fields

yaml/pyyaml#260 -- Remove some unused imports

yaml/pyyaml#163 -- Create timezone-aware datetimes when parsed as such

yaml/pyyaml#363 -- Add tests for timezone

5.2 (2019-12-02)

Repair incompatibilities introduced with 5.1. The default Loader was changed, but several methods like add_constructor still used the old default yaml/pyyaml#279 -- A more flexible fix for custom tag constructors yaml/pyyaml#287 -- Change default loader for yaml.add_constructor yaml/pyyaml#305 -- Change default loader for add_implicit_resolver, add_path_resolver

Make FullLoader safer by removing python/object/apply from the default FullLoader yaml/pyyaml#347 -- Move constructor for object/apply to UnsafeConstructor

Fix bug introduced in 5.1 where quoting went wrong on systems with sys.maxunicode <= 0xffff yaml/pyyaml#276 -- Fix logic for quoting special characters

Other PRs: yaml/pyyaml#280 -- Update CHANGES for 5.1

5.1.2 (2019-07-30)

Re-release of 5.1 with regenerated Cython sources to build properly for Python 3.8b2+

... (truncated)

Commits

58d0cb7 5.4 release
a60f7a1 Fix compatibility with Jython
ee98abd Run CI on PR base branch changes
ddf2033 constructor.timezone: _copy & deepcopy
fc914d5 Avoid repeatedly appending to yaml_implicit_resolvers
a001f27 Fix for CVE-2020-14343
fe15062 Add 3.9 to appveyor file for completeness sake
1e1c7fb Add a newline character to end of pyproject.toml
0b6b7d6 Start sentences and phrases for capital letters
c976915 Shell code improvements
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Bump bleach from 3.1.0 to 3.3.0

opened on 2021-02-02 22:19:22 by dependabot[bot]

Bumps bleach from 3.1.0 to 3.3.0.

Changelog

Sourced from bleach's changelog.

Version 3.3.0 (February 1st, 2021)

Backwards incompatible changes

clean escapes HTML comments even when strip_comments=False

Security fixes

Fix bug 1621692 / GHSA-m6xf-fq7q-8743. See the advisory for details.

Features

None

Bug fixes

None

Version 3.2.3 (January 26th, 2021)

Security fixes

None

Features

None

Bug fixes

fix clean and linkify raising ValueErrors for certain inputs. Thank you @Google-Autofuzz.

Version 3.2.2 (January 20th, 2021)

Security fixes

None

Features

Migrate CI to Github Actions. Thank you @hugovk.

Bug fixes

fix linkify raising an IndexError on certain inputs. Thank you @Google-Autofuzz.

Version 3.2.1 (September 18th, 2020)

... (truncated)

Commits

79b7a3c Merge pull request from GHSA-vv2x-vrpj-qqpq
842fcb4 Update for v3.3.0 release
1334134 sanitizer: escape HTML comments
c045a8b Merge pull request #581 from mozilla/nit-fixes
491abb0 fix typo s/vnedoring/vendoring/
10b1c5d vendor: add html5lib-1.1.dist-info/REQUESTED
cd838c3 Merge pull request #579 from mozilla/validate-convert-entity-code-points
612b808 Update for v3.2.3 release
6879f6a html5lib_shim: validate unicode points for convert_entity
90cb80b Update for v3.2.2 release
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Thoughtworks incubator

This is our sandbox GitHub organization for short-term experiments. For our main Github organisation, please visit @thoughtworks.

GitHub Repository

An ML project template with sensible defaults

ml-app-template

Getting started

build docker image [Mac/Linux users]

build docker image [Windows users]

start docker container [Mac/Linux users]

start docker container [Windows users]

Note: to find the path, you can run pwd in git bash, and manually replace forward slashes (/) with double backslashes (\)

add some color to your terminal

activate virtual environment for python

run unit tests

run unit tests in watch mode and color output

train model

start flask app in development mode

make requests to your app

1. In your browser, visit http://localhost:8080

2. Open another terminal in the running container (detailed instructions below) and run:

You can also use this script to test your deployed application later:

see list of running containers

start a bash shell in a running container

starting jupyter notebook server on http://localhost:8888

What's in this repo?

IDE configuration

Infrastructure

Troubleshooting

Issues

Bump ipython from 7.5.0 to 7.16.3

Bump pillow from 6.0.0 to 8.3.2

8.3.2

Security

Python 3.10 wheels

Fixed regressions

8.3.1

Changes

8.3.0

Changes

8.3.2 (2021-09-02)

8.3.1 (2021-07-06)

8.3.0 (2021-07-01)

Bump urllib3 from 1.25.3 to 1.26.5

1.26.5

1.26.4

1.26.3

1.26.2

1.26.1

1.26.0

1.26.5 (2021-05-26)

1.26.4 (2021-03-15)

1.26.3 (2021-01-26)

1.26.2 (2020-11-12)

1.26.1 (2020-11-11)

1.26.0 (2020-11-10)

Bump pygments from 2.4.2 to 2.7.4

2.7.4

2.7.3

Version 2.7.4

Version 2.7.3

Bump pyyaml from 5.1 to 5.4

5.2 (2019-12-02)

5.1.2 (2019-07-30)

Bump bleach from 3.1.0 to 3.3.0

Version 3.3.0 (February 1st, 2021)

Version 3.2.3 (January 26th, 2021)

Version 3.2.2 (January 20th, 2021)

Thoughtworks incubator

Note: to find the path, you can run `pwd` in git bash, and manually replace forward slashes (/) with double backslashes (\)