Dev #48
Merged
Dev #48
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
added 30 commits
February 23, 2023 10:48
- build dependencies: pyproject.toml - requirements and more: setup.cfg - editable installs: setup.py
- fix constraint (upper constraints still need to be removed) - ignore build folder
- folder needs to be renamed asap (vaep -> pimms)
- currently fails on M1/M2 amd64 architectures as no build is available for R=3.6.3 (check if R version could be updated)
- works locally with same version of pandas and numpy as in the github runner. - remove test for now as function isn't used anywhere
- id only allowed for nbformat >= 4.5
- make VAE similar to DAE
- os matrix was only used in naming...
- remove UNIX specific step ("ls")
- could also use larger runner for mac-os-xl with 30GB of memory (and 12 CPUs)
- change environment channel list and cuda dependencies - unify environment file again
- rrcovNA dependencies needed
- ubuntu installation takes forever.
- github runners (mac-os and ubuntu-latest) don't seem to install otherwise even using mamba
- also check for unnecessary imports, etc
- see if this helps for windows packages - remove cuda for now as no gpu runner is connected
added 18 commits
August 16, 2023 17:32
- speed up workflow again
- try to get windows-server installation to run
- minor updates in formatting in "sklearn" folder
- see if only rrcovNA source build fails now (-> "-k" for keep-going) - regular execution of workflow
- small changes to previous version
Parse all xml parameter files on erda. MaxQuant paramter file is a mix of 3-4 different types of parameter specifications (probably grown cont.)
- bottom line: they are all identical. - rename and select files of PRIDE submission - dropped filepaths of output folder
- just revisited to check some details
cannot install rrcovNA on windows-server. Works on windows desktop, so testing will be done manually from time to time on a desktop machine.
- add some plots and description - check if in colab
- link colab example - reference pip package - WIP: get M1 and M2 chips installation to run
- try to autoupdate newly tagged releases
- command line execution failed if num_workers>0 on windows. FastAi normally captures that, but for now set a default - This should be furhter investigated
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.