gruber-sciencelab / mapp Goto Github PK

New CI should probably reflect the old one as in .gitlab-ci.yml.
Maybe add static code analysis too? Maybe codefactor?

Is your feature request related to a problem? Please describe.
I have stumbled upon better frameworks to easily build simple dynamic websites (Bootstrap, Vue, Dash); I can use them to create the final MAPP report. But I need to investigate these frameworks first.

Describe the solution you'd like
Refactor MAPP script related to HTML-report generation.

Additional context
Just for aesthetics and so that the results are presented in a more readable manner.

Expected behavior

Configfile is still generated based on config template fields.
Precomputed paths shared as resources only.

Suggestions by Maciek + Dominik have been implemented.

Is your feature request related to a problem? Please describe.
Too much time/disk space used for:

• conda envs
• singularity containers

Describe the solution you'd like
Implement a flag for the exeuction script to use pre-built resources

Is your feature request related to a problem? Please describe.
Impact Maps are not always visible; scaling is a little off for very high number of samples/windows.

Describe the solution you'd like
Refactor the plotting script.

Additional context
We would like MAPP to create beautiful publication-ready Impact Maps for RBPs.

We might still have a chance to solve the issue of "Code Owner" rank;
I will investigate further here:

• https://github.blog/2017-07-06-introducing-code-owners/
• https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners

Per advised, transfer from zavolanlab/PAQR2#13 to here.

Include some new cool GitHub repo mechanisms I have learned recently:

• refactor ci: installation test as 1 job? dev env?
• .gitattributes w/ langauges, .gitignore refactor
• flake8 / lintr check
• codefactor check + shield
• dev env: YAML or requirements.TXT? conda is needed anyway...
• Makefile: dry integration tests, lint, build envs,
• Dockerfile run/dev
• DevPod configuration
• Changelog + update workflow
• linting CI
• new issue/PR templates
• codespaces configuration
• black, stylr, isort tests?
• PR workflows: size labels, title check, auto assign
• Contributing: better instructions, specific rules, more tests
• version file + autotag ci
• twitter shield
• stale pr ci
• contributor covenant shield?

Is your feature request related to a problem? Please describe.
Support for MAPP execution in conda envs on Mac machines - nice to have but not essential.

Additional context
In the recent PR I have adjusted the conda envs so that they can be build on my personal Mac as well as the main testscript so that it triggers the pipeline testrun on my machine too.
We need someone else with a Mac to confirm the testrun finished succesfully.
@IanKouzel - I heard that you are running the pipeline on a Mac<?>

CC @ajgruber

Is your feature request related to a problem? Please describe.
Similarly to others; needs to be tested once we have Singularity on a GE cluster.