ENH: Additional Secondary Structures

[TactfulDeity]

Enhancements

• added 3-10 and pi helices

Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or

(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or

(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
it.

(d) I understand and agree that this project and the contribution
are public and that a record of the contribution (including all
personal information I submit with it, including my sign-off) is
maintained indefinitely and may be redistributed consistent with
this project or the open source license(s) involved.

[welcome]

Thanks for opening this pull request! Please check out our contributing guidelines and check for the automated tests.

[ghutchis]

No idea why the self-hosted runner is failing. Likely a transient since the error message is about creating the disk image, not the compile.

[TactfulDeity]

I would just download the log and force an actions re-reun on that one specifically to see if it is consistently reproducible

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Win64.exe
Artifacts will only be retained for 90 days.

[TactfulDeity]

So this is a niche bug but I came across this forum where the exact issue is mentioned back in 2012:
https://cmake.org/pipermail/cmake-developers/2012-February/003319.html

I also found this which mentions the same thing, that might be causing the issue.

This is the issue I dredged up:
https://gitlab.kitware.com/cmake/cmake/-/issues/7523

Which was derived from this forum issue:
https://cmake.org/Bug/view.php?id=7523

In which the cmake autogenerated mount point can exceed the 90 character limit on MacOS X. Obviously its running on a newer OS, but it does help narrow down where the issue could be, in that it is likely something wrong with how it is attempting to mount

[TactfulDeity]

I noticed the error code it is reporting is -1401, which is the system error code that is reported via CPack*. So I dug around and found out this corresponds to a specific error code on Mac, thread here
errFSBadFSRef = -1401, /* FSRef parameter is bad */

The FSRefParam unfortunately has no public documentation I could find aside from this. Each of the listed instance properties seem to function as "member variables" in the Apple/cocoa/Objective-C ecosystem as demonstrated in this stack overflow post. One of them is nameLength that likely coincides with the issue mentioned in the previous post of a volume name being to long. This means one of the other 21 variables could be the issue causing it, or the length issue made a comeback I am not sure. Without a ARM Mac on hand and not much of an error message to go off of I am stuck.

* see lines 478-494 here in the Cmake source.

[ghutchis]

I'm good to merge. I can check the runner in person on Monday, but the build before was fine -- and it clearly has nothing related to the change.

(The MacOS runners seem to have periodic transient issues with generating the DMG.)

[welcome]

Congrats on merging your first pull request! 🎉 Thanks for making Avogadro better for everyone!

[avo-bot]

This pull request has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/october-2024-live-updates/6373/1

[github-actions]

Here are the build results
Avogadro2.AppImage
Win64.exe
Artifacts will only be retained for 90 days.