update ToxTree to CDK 2.9 (or better)

[egonw]

• https://toxtree.sourceforge.net/

cc @vedina

[vedina]

depends on #12

[RvdPloeg]

Made a repository on GitHub using the https://toxtree.sourceforge.net/ see link: https://github.com/RvdPloeg/Toxtree.
Made changes in the code to update the software to use cdk-2.9, the build is successful.

[RvdPloeg]

Additional changes were made to get toxtree to successfully install it, see RvdPloeg/Toxtree#1.

[egonw]

@RvdPloeg, is that repository private?

@vedina, is this interesting to you?

[RvdPloeg]

The repository is now public. 🙂 Cheers, René

…

________________________________ From: Egon Willighagen ***@***.***> Sent: Friday, November 8, 2024 12:26 To: cdk/nwo-openscience-2024 ***@***.***> Cc: René van der Ploeg ***@***.***>; Mention ***@***.***> Subject: Re: [cdk/nwo-openscience-2024] update ToxTree to CDK 2.9 (or better) (Issue #13) LET OP: Deze e-mail komt van een afzender buiten de HU. Klik niet op links en bijlagen als de afzender niet bekend of vertrouwd is. Caution: This email is from a sender outside HU. Do not click on links and attachments if the sender is not known or trusted. @RvdPloeg<https://github.com/RvdPloeg>, is that repository private? @vedina<https://github.com/vedina>, is this interesting to you? — Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AFRINBEHW622V7UBGVYPA7LZ7SNWNAVCNFSM6AAAAABRK3BZAGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINRUGQ3TAMRWHE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[vedina]

can we also get this in a branch in Toxreee repository ? It will be hard to update with a separate repository.
Also , please have in mind, that just updating Toxrtee repository may not be sufficient, because it uses ambit package as dependency and majority of rules use functionality (SMARTS) from AMBIT package and we are aware there are incompatibilities with newer cdk version (and working on upgrade)

[egonw]

can we also get this in a branch in Toxreee repository ? It will be hard to update with a separate repository.

This one, right? https://sourceforge.net/p/toxtree/git/ci/master/tree/

Should be trivial. When you confirmed, I will figure out how to make a PR on SourceForge (never done that before).

Also , please have in mind, that just updating Toxrtee repository may not be sufficient, because it uses ambit
package as dependency and majority of rules use functionality (SMARTS) from AMBIT package and we
are aware there are incompatibilities with newer cdk version (and working on upgrade)

Recording all these things is part of this grant. I see the following things to work out:

1. what tests to run to make such upgrade regressions visible
2. to identify updates needed in dependencies
3. figure out upgrade suggestions