Avogadro 1.1.0 rc next week

Hi,

Geoff and I were chatting on IRC - the 1.1.0 release is well overdue.
I was going over patches this morning. I would like to ask anyone who
has pending patches they would like in the 1.1.0_rc1 to get them
submitted to Gerrit ASAP. I will make a tag early next week (depending
on feedback) and we will aim to get some binaries out.

There are some great new features in master, and we should make sure
more people see them. I would also like to put some time into finding
bugs causing segfaults in master, but they can come after the first
rc.

Thanks,

Marcus

On Tue, Apr 17, 2012 at 1:21 PM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

Hi,

Geoff and I were chatting on IRC - the 1.1.0 release is well overdue.
I was going over patches this morning. I would like to ask anyone who
has pending patches they would like in the 1.1.0_rc1 to get them
submitted to Gerrit ASAP. I will make a tag early next week (depending
on feedback) and we will aim to get some binaries out.

Sounds great! It has been a while.

Which version of openbabel will this get linked against? I have a very
old request for a format parser that I’m almost ready to merge, and
I’d like to get this in before the RC is built if it will use trunk
OB.

Dave

I’d like to get this in before the RC is built if it will use trunk
OB.

I think our usual policy has been to link Mac and Windows versions against OB trunk. Linux, I’d obviously advise to use OB-2.3, but one can’t guarantee what distributions will use.

-Geoff

On Tue, Apr 17, 2012 at 1:40 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

I’d like to get this in before the RC is built if it will use trunk
OB.

I think our usual policy has been to link Mac and Windows versions against OB trunk. Linux, I’d obviously advise to use OB-2.3, but one can’t guarantee what distributions will use.

The request came from a Windows user, so that is perfect.

Thanks,
Dave

Heya,

On Tue, Apr 17, 2012 at 01:21:55PM -0400, Marcus D. Hanwell wrote:

Geoff and I were chatting on IRC - the 1.1.0 release is well overdue.
I was going over patches this morning. I would like to ask anyone who
has pending patches they would like in the 1.1.0_rc1 to get them
submitted to Gerrit ASAP. I will make a tag early next week (depending
on feedback) and we will aim to get some binaries out.

Any news on this?

Michael

On Wed, May 2, 2012 at 11:32 AM, Michael Banck mbanck@debian.org wrote:

Heya,

On Tue, Apr 17, 2012 at 01:21:55PM -0400, Marcus D. Hanwell wrote:

Geoff and I were chatting on IRC - the 1.1.0 release is well overdue.
I was going over patches this morning. I would like to ask anyone who
has pending patches they would like in the 1.1.0_rc1 to get them
submitted to Gerrit ASAP. I will make a tag early next week (depending
on feedback) and we will aim to get some binaries out.

Any news on this?

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Thanks,

Marcus

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Thanks,
-Geoff

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

Thanks,

Marcus

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Thanks,

Marcus

Marcus D. Hanwell, Ph.D.
R&D Engineer, Kitware Inc.
(518) 881-4937

On Wed, May 2, 2012 at 12:17 PM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Please find the Avogadro 1.1.0_rc1 tarballs on SourceForge,

https://sourceforge.net/projects/avogadro/files/avogadro-beta/1.1.0_rc1/

This is built from bb1002da (the current tip of master). Please test
this and let us know of any issues. I would like to clear up any
remaining issues and get an rc2 out next week. I will see about making
some binaries early next week, any help with this would certainly be
appreciated!

There are some awesome new features in 1.1, and it is past time we
showed them off to the wider community. There are still some crashers
and other bugs that have crept in, so let’s please spend some time
ironing these issues out.

I will be away for most of the weekend, but back for Monday to push on
the 1.1.0 release. This is a beta series which should culminate in a
1.2.0 release once master has stabilized. Remember we already broke
ABI after 1.0, the distro maintainers will need to be aware of this
when packaging.

Thanks and May the 4th be with you :wink:

Marcus

Hi,

On Wed, May 02, 2012 at 12:17:40PM -0400, Marcus D. Hanwell wrote:

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Just for the record, I built it the other day on Debian stable and
didn’t see any obvious big issues. The german translation is still
sub-optimal and sometimes buggy (resulting in multiple Extension menus
etc.), but the english version looks fine.

Debian is freezing in a couple of weeks, when is the final release to be
expected?

Michael

On Tue, May 15, 2012 at 12:08 PM, Michael Banck mbanck@gmx.net wrote:

Hi,

On Wed, May 02, 2012 at 12:17:40PM -0400, Marcus D. Hanwell wrote:

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Just for the record, I built it the other day on Debian stable and
didn’t see any obvious big issues. The german translation is still
sub-optimal and sometimes buggy (resulting in multiple Extension menus
etc.), but the english version looks fine.

Debian is freezing in a couple of weeks, when is the final release to be
expected?

Hoping to get it out this week unless someone points out any blockers.
I am hoping to get a Windows build verified, Mac and Linux look good
here.

Thanks for the feedback.

Marcus

Avogadro on Ubuntu 10.10 looks solid. I will try a CentOS 6.2 build
during the week.

Casper

On Tue, May 15, 2012 at 6:12 PM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Tue, May 15, 2012 at 12:08 PM, Michael Banck mbanck@gmx.net wrote:

Hi,

On Wed, May 02, 2012 at 12:17:40PM -0400, Marcus D. Hanwell wrote:

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Just for the record, I built it the other day on Debian stable and
didn’t see any obvious big issues. The german translation is still
sub-optimal and sometimes buggy (resulting in multiple Extension menus
etc.), but the english version looks fine.

Debian is freezing in a couple of weeks, when is the final release to be
expected?

Hoping to get it out this week unless someone points out any blockers.
I am hoping to get a Windows build verified, Mac and Linux look good
here.

Thanks for the feedback.

Marcus


Live Security Virtual Conference
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Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.
As always, we can make a subsequent release (1.1.1) if more issues are
revealed after the release. One of the major changes I am aware of
from a packaging perspective is that we require Open Babel built with
Eigen now.

Thanks,

Marcus

On Tue, May 15, 2012 at 12:14 PM, Casper Steinmann
casper.steinmann@gmail.com wrote:

Avogadro on Ubuntu 10.10 looks solid. I will try a CentOS 6.2 build
during the week.

Casper

On Tue, May 15, 2012 at 6:12 PM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Tue, May 15, 2012 at 12:08 PM, Michael Banck mbanck@gmx.net wrote:

Hi,

On Wed, May 02, 2012 at 12:17:40PM -0400, Marcus D. Hanwell wrote:

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

We were just talking about this. I will make a tag/tarball now and
let’s start testing this out.

Any chance I can put in the minor changes David requested for the slab builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Just for the record, I built it the other day on Debian stable and
didn’t see any obvious big issues. The german translation is still
sub-optimal and sometimes buggy (resulting in multiple Extension menus
etc.), but the english version looks fine.

Debian is freezing in a couple of weeks, when is the final release to be
expected?

Hoping to get it out this week unless someone points out any blockers.
I am hoping to get a Windows build verified, Mac and Linux look good
here.

Thanks for the feedback.

Marcus


Live Security Virtual Conference
Exclusive live event will cover all the ways today’s security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

On Fri, May 25, 2012 at 02:48:03PM -0400, Marcus D. Hanwell wrote:

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.

I tried again yesterday and noticed a couple of visibility bugs when
vieweing e.g. methane. If I set the VDW engine and rotated around the
molecule, one of the atoms remains “on top” even rotated to the back.
Similar probelm with sticks - sometimes I got one of the
backwards-facing sticks overlaying the one pointing front.

However, I tried to reproduce it today and it works fine now, not sure
what lead to that issue :-/

Michael

On Wed, May 30, 2012 at 8:26 AM, Michael Banck mbanck@gmx.net wrote:

On Fri, May 25, 2012 at 02:48:03PM -0400, Marcus D. Hanwell wrote:

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.

I tried again yesterday and noticed a couple of visibility bugs when
vieweing e.g. methane. If I set the VDW engine and rotated around the
molecule, one of the atoms remains “on top” even rotated to the back.
Similar probelm with sticks - sometimes I got one of the
backwards-facing sticks overlaying the one pointing front.

However, I tried to reproduce it today and it works fine now, not sure
what lead to that issue :-/

We’ve noticed something similar happening once the “Overlay” display type
is enabled – try turning it on and let us know if that’s what you saw. The
effect persists after the engine is turned off, too.

Dave

On Wed, May 30, 2012 at 02:26:55PM +0200, Michael Banck wrote:

On Fri, May 25, 2012 at 02:48:03PM -0400, Marcus D. Hanwell wrote:

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.

I tried again yesterday and noticed a couple of visibility bugs when
vieweing e.g. methane. If I set the VDW engine and rotated around the
molecule, one of the atoms remains “on top” even rotated to the back.
Similar probelm with sticks - sometimes I got one of the
backwards-facing sticks overlaying the one pointing front.

Ahhh - it only happens when the “overlay” engine is activated - is this
intentional then? Anyway, I get the same behaviour with 1.0.3, so
nevermind WRT 1.1.

Michael

On Wed, May 30, 2012 at 9:00 AM, Michael Banck mbanck@gmx.net wrote:

On Wed, May 30, 2012 at 02:26:55PM +0200, Michael Banck wrote:

On Fri, May 25, 2012 at 02:48:03PM -0400, Marcus D. Hanwell wrote:

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.

I tried again yesterday and noticed a couple of visibility bugs when
vieweing e.g. methane. If I set the VDW engine and rotated around the
molecule, one of the atoms remains “on top” even rotated to the back.
Similar probelm with sticks - sometimes I got one of the
backwards-facing sticks overlaying the one pointing front.

Ahhh - it only happens when the “overlay” engine is activated - is this
intentional then? Anyway, I get the same behaviour with 1.0.3, so
nevermind WRT 1.1.

The Overlay engine “Renders color scale for gradients”. It’s surprising
that it messes up the z-ordering so badly – it’s certainly not
intentional! :slight_smile:

Certainly “surprise” bugs should be fixed or disabled, IMHO.

Geoff

On May 30, 2012, at 9:05 AM, David Lonie david.lonie@kitware.com wrote:

On Wed, May 30, 2012 at 9:00 AM, Michael Banck mbanck@gmx.net wrote:
On Wed, May 30, 2012 at 02:26:55PM +0200, Michael Banck wrote:

On Fri, May 25, 2012 at 02:48:03PM -0400, Marcus D. Hanwell wrote:

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.

I tried again yesterday and noticed a couple of visibility bugs when
vieweing e.g. methane. If I set the VDW engine and rotated around the
molecule, one of the atoms remains “on top” even rotated to the back.
Similar probelm with sticks - sometimes I got one of the
backwards-facing sticks overlaying the one pointing front.

Ahhh - it only happens when the “overlay” engine is activated - is this
intentional then? Anyway, I get the same behaviour with 1.0.3, so
nevermind WRT 1.1.

The Overlay engine “Renders color scale for gradients”. It’s surprising that it messes up the z-ordering so badly – it’s certainly not intentional! :slight_smile:

Live Security Virtual Conference
Exclusive live event will cover all the ways today’s security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

On Wed, May 30, 2012 at 09:05:59AM -0400, David Lonie wrote:

On Wed, May 30, 2012 at 9:00 AM, Michael Banck mbanck@gmx.net wrote:

On Wed, May 30, 2012 at 02:26:55PM +0200, Michael Banck wrote:

On Fri, May 25, 2012 at 02:48:03PM -0400, Marcus D. Hanwell wrote:

I haven’t received a lot of feedback, but feel quite comfortable
tagging master as 1.1.0. It is largely unchanged from 1.1.0_rc1, and I
think we should be able to get binaries etc ready for early next week.
I will work on updating the release announcement etc.

Please let me know if you hit any compilation issues or serious bugs.

I tried again yesterday and noticed a couple of visibility bugs when
vieweing e.g. methane. If I set the VDW engine and rotated around the
molecule, one of the atoms remains “on top” even rotated to the back.
Similar probelm with sticks - sometimes I got one of the
backwards-facing sticks overlaying the one pointing front.

Ahhh - it only happens when the “overlay” engine is activated - is this
intentional then? Anyway, I get the same behaviour with 1.0.3, so
nevermind WRT 1.1.

The Overlay engine “Renders color scale for gradients”. It’s surprising
that it messes up the z-ordering so badly – it’s certainly not
intentional! :slight_smile:

Heh ok :slight_smile:

Given that it seems to mess up rendering even after deactivation, maybe
it might be better to remove it, so users don’t get a pretty useless
Avogadro in case they accidently (like me) activate it and have no idea
what happened?

What is the use-case for “Renders color scale for gradients”?

Michael