Update testing workflow and dependencies #81

Fontanapink · 2024-10-04T15:43:41Z

This pull request updates the testing workflow by adding a test and coverage GitHub action. It also includes an environment.yml file for Conda installation during testing. The version of the Miniconda action in the testing GitHub action has been updated. The dependencies in the requirements.in file have been specified and updated. The environment.yml file has been modified to fix issues with auto-generated tests action. The versions of gpflow, tensorflow, and tensorflow-probability have been modified to ensure compatibility. pytest-mock has been added to the environment.yml file for testing. Both the environment.yml file and the requirements.in file have been modified and updated. The README file has been updated with the new installation process. Redundant steps in the test examples have been deleted. The documentation has been updated.

Summary by Sourcery

Update the testing workflow by adding a GitHub action for test and coverage, and modify the environment.yml and setup.py to manage dependencies more effectively. Enhance the CI process with a new workflow for automated testing and coverage reporting. Update documentation to align with the new installation process.

New Features:

Introduce a new GitHub action for test and coverage to automate testing and coverage reporting on push and pull request events.

Enhancements:

Update the setup.py to dynamically read and include requirements from requirements.txt, ensuring dependencies are correctly installed.
Modify the environment.yml file to specify and update dependencies, ensuring compatibility with updated versions of gpflow, tensorflow, and tensorflow-probability.

CI:

Add a new GitHub workflow file, test-and-coverage.yml, to automate testing and coverage reporting using Miniconda and pytest.

Documentation:

Update the README file to reflect the new installation process using the environment.yml file.

…auto-generated tests action

…rsions to be compatible

…ts.in file to be up to date

sourcery-ai · 2024-10-04T15:43:49Z

Reviewer's Guide by Sourcery

This pull request updates the testing workflow, adds a new GitHub action for test and coverage, introduces a Conda environment file, and updates dependencies. The changes aim to improve the testing process, ensure compatibility between packages, and streamline the installation process.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Added a new GitHub Action for test and coverage	Created a new workflow file for running tests and generating coverage reports Set up Miniconda and create the environment from environment.yml Installed the package in editable mode Run tests with coverage reporting Upload the coverage report as an artifact	`.github/workflows/test-and-coverage.yml`
Introduced a Conda environment file	Created an environment.yml file for Conda installation Specified Python version and necessary dependencies Added pytest, pytest-cov, and pytest-mock for testing	`environment.yml`
Updated setup.py to use requirements from requirements.txt	Added code to read requirements from requirements.txt Updated the setup function to use the read requirements Simplified the packages parameter in the setup function	`setup.py`

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sourcery-ai

Hey @Fontanapink - I've reviewed your changes - here's some feedback:

Overall Comments:

Consider using more flexible version specifications in environment.yml to make it easier to incorporate security updates while maintaining compatibility.
The description mentions updating the README with the new installation process, but this change is not visible in the provided diff. Please ensure this update is included in the PR.

Here's what I looked at during the review

🟡 General issues: 1 issue found
🟢 Security: all looks good
🟢 Testing: all looks good
🟢 Complexity: all looks good
🟢 Documentation: all looks good

Sourcery is free for open source - if you like our reviews please consider sharing them ✨

_{Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.}

environment.yml

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

… dependencies problems and checks

… into Fontanapink/issue78

…l file because those need to be installed seperatelly for Windows systems

… into Fontanapink/issue78

…Windows

…ly for windows systems

…of requirements.txt (since it can let pip solve the dependencies)

… so that it matches what it is expected on the GitHub Actions

Update testing workflow and dependencies

Fontanapink added 13 commits October 1, 2024 11:57

Adding a test and coverage github action

6bd11cc

adding a environment.yml file for conda install for testing

6c57635

updated version of miniconda action in testing github action

790266a

updated and specified dependencies in requirements.in

caeaca4

updated requirements.in for propper testing

4f3a3a0

maybe if I update the environment.yml it works better. Trying to fix …

bd63950

…auto-generated tests action

modified versions of gpflow, tensorflow, and tensorflow-probabiliy ve…

f1f0048

…rsions to be compatible

fS

501fcc0

added pytest-mock to the environment.yml file required for testing

578c049

Modyfied and updated both the environment.yml file and the requiremen…

cfc8bf2

…ts.in file to be up to date

Updated the README file with the new install process

7eb6388

deleted redundand steps in the test examples

bda273f

updated documentation

3bfa6cb

Update requirements.txt and format code

6c395fb

sourcery-ai bot reviewed Oct 4, 2024

View reviewed changes

environment.yml Show resolved Hide resolved

Fontanapink and others added 14 commits October 7, 2024 05:07

Update environment.yml

0c72c20

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

Fixxed Tensorflow version to work in a windows OS system

67dcbf5

relaxed versioning

5899c1b

This commit changes all CI checks to run using Conda to help with the…

bc26ad0

… dependencies problems and checks

Fixed conda environment activation bug

ef40349

Update requirements.txt and format code

1669a2f

removed more version constraints to allow Conda resolve it by itself

c5e2582

Merge branch 'Fontanapink/issue78' of https://github.com/ucl-cssb/MIMIC…

a73b11a

… into Fontanapink/issue78

Update requirements.txt and format code

58dda4c

removed tensorflow and tensorflow-probability from the environment.ym…

d776c1e

…l file because those need to be installed seperatelly for Windows systems

updated the README file with new installation steps

52e2ca3

Merge branch 'Fontanapink/issue78' of https://github.com/ucl-cssb/MIMIC…

81ed320

… into Fontanapink/issue78

Update requirements.txt and format code

b296d93

relaxed tensorflow version for Windows and Conda

04ed9d9

Fontanapink and others added 13 commits October 8, 2024 16:04

Merge branch 'Fontanapink/issue78' of https://github.com/ucl-cssb/MIMIC…

16c871f

… into Fontanapink/issue78

Update requirements.txt and format code

1cf883d

testing environment.yml production

630675a

Update requirements.txt and format code

46ddc8f

deleted requirements.txt since it doesn't work for all OS systems

b6b157b

updated the GitHub action to run Conda differently for Mac, Linux or …

ed6951b

…Windows

added a environment_windows.yml file so that conda can work different…

8db906d

…ly for windows systems

added a new channel for envirnomnent.yml

31ffe93

modified setup.py so that it works only with requirements.in instead …

292576c

…of requirements.txt (since it can let pip solve the dependencies)

update README with Windows install instructions

ad3bab3

Update requirements.txt and format code

16e6813

renamed windows conda environment to mimic_env from mimic_env_windows…

eee2c26

… so that it matches what it is expected on the GitHub Actions

Update requirements.txt and format code

db77a61

Fontanapink merged commit ab2d58f into master Oct 10, 2024

Fontanapink deleted the Fontanapink/issue78 branch October 10, 2024 13:58

Fontanapink added a commit that referenced this pull request Oct 23, 2024

Merge pull request #81 from ucl-cssb/Fontanapink/issue78

83fba1f

Update testing workflow and dependencies

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