Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[2023.05.2-base] DL_edition release prep #368

Merged
merged 187 commits into from
Jun 2, 2023
Merged

[2023.05.2-base] DL_edition release prep #368

merged 187 commits into from
Jun 2, 2023

Conversation

mbackenkoehler
Copy link
Collaborator

@mbackenkoehler mbackenkoehler commented May 24, 2023 •
edited by AndreaVolkamer
Loading

Description

Here, we collect the work on the TeachOpenCADD deep learning edition and prepare its release.

Todos

Status

  • Ready to go

AndreaVolkamer and others added 30 commits December 6, 2022 11:36
@AndreaVolkamer
include pytorch
9dd5520
@joschka-gross
fix pytorch channel, include torch geometric
1995e44
@mbackenkoehler
Start branch
0824751
Start branch
9e21758
@Old-Shatterhand
Add deepchem as pip dependency
fc54b1e
@mbackenkoehler
Start talktorial using the T000 template
42aeed4
@joschka-gross
start commit
f3d4c6d
@mbackenkoehler
First work on uncertainty est. talktorial
bb293b7
@mbackenkoehler
add bagging (resampling training data)
841652b
@mbackenkoehler
some more structure
004c1d6
@joschka-gross
theory mostly done, practical part mosly done
24e31e5
@joschka-gross
label plots, minor write-up changes
c89eff0
@Old-Shatterhand
T038 first draft with a proof of concept
3c36352
@Old-Shatterhand
Optimizer included
663b39b
@Old-Shatterhand
Batching problem solved
02a06e1
@Old-Shatterhand
Missing image
50d84f1
@joschka-gross
gcn training, move random split to earlier section to ensure we use t…
f044d61 
…he same for both models
@joschka-gross
sync for review
31347ac
first version
20178cb
@joschka-gross
replace mean aggr with sum
3efdc10
@Old-Shatterhand
Minor bugs in talktorial fixed and improved visualization
1992e7e
@gerritgr
Start branch
09a3483
@AndreaVolkamer
Add DL_branch to CI
e77f426
@Old-Shatterhand
KiBA filtering and downloading
60d1fac
@Old-Shatterhand
trained model for 2 epochs and some minor code adjustments
2772519
@mbackenkoehler
continue writing and structuring
620844f
@mbackenkoehler
ensemble image
76dfeb8
@joschka-gross
version for review
8539713
@gerritgr
inital suggestion
a14908d
@joschka-gross
typos, formatting, comments, other readability improvements
df9e545
mbackenkoehler and others added 27 commits May 26, 2023 12:26
@mbackenkoehler
T038: install pyg manually
be1dada
@mbackenkoehler
T036: install pyg manually
5403962
@mbackenkoehler
Docs CI: ignore some 403 in linkcheck
f0b873b
@mbackenkoehler
Docs CI: run on PR on dev
a6d67e5
@mbackenkoehler
Docs CI: ignore wiley links
8153d72
@mbackenkoehler
CI: ignore flaky T001; ignore T035 under mac
6f74ac7
@mbackenkoehler
CI: fix typo
1d7e168
@mbackenkoehler
CI: ignore T035 in mac
063b3a3
@AndreaVolkamer
Merge pull request #380 from volkamerlab/369-dl_edition-windows-ci-ma…
9eba101 
…mba-setup-fails

369 dl edition windows ci mamba setup fails and environment fixes - exclude pyg for now
@jaketanderson
Added square root to make it RMSD. Currently it's MSD.
6651851
@mbackenkoehler
T033: datamol.io link fix
45349d7
@mbackenkoehler
T037: link typo
ca36830
@mbackenkoehler
Merge pull request #383 from jaketanderson/fix-rmsd
86e9fed 
Fix: Added square root to make talktutorial 20 RMSD. Currently it's MSD.
@mbackenkoehler
Merge pull request #382 from volkamerlab/378-dl-edition-ignore-unresp…
e9fcea9 
…onsive-sites

Docs CI: ignore some 403 in linkcheck
@PaulaKramer
added overview image, small formatting changes, added citation and ex…
c77453e 
…t dep
@mbackenkoehler
T037: regen readme
9474abd
@mbackenkoehler
T004: re-run
1c87b3f
@mbackenkoehler
T004: re-run (reinstall env)
0e8abde
@PaulaKramer
title inconsistency T033
49505c9
@mbackenkoehler
Merge pull request #384 from volkamerlab/website-update
ab919a5 
[DL edition] Website update
@mbackenkoehler
environment: fix jupyter_client (nglview)
2c0db0b
@mbackenkoehler
rerun faling notebooks
f35288d
@mbackenkoehler
T008: re-run
2d79aa3
@mbackenkoehler
CI: ignore T018 temporarily under mac and linux
0fd5da7
@mbackenkoehler
rename home directories
371c6f2
@mbackenkoehler
skip link checks [TEMPORARY; first deploy]
5ba817f
@mbackenkoehler
CI: typo in T018 ignore
54125aa
@AndreaVolkamer AndreaVolkamer self-requested a review June 2, 2023 07:35
@AndreaVolkamer AndreaVolkamer merged commit d875d36 into master Jun 2, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@AndreaVolkamer AndreaVolkamer AndreaVolkamer approved these changes

Assignees
No one assigned
Labels
2023.05.2 (DL edition) [tmp] All PRs for DL edition enhancement New feature or request new talktorial New talktorial
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
10 participants
@mbackenkoehler @AndreaVolkamer @joschka-gross @Old-Shatterhand @gerritgr @azmtag @PaulaKramer @dominiquesydow @f-sod @jaketanderson