1.95.0 Black screen instead of a molecule

[yurivict]

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: 1.95.0
• Qt: 5.15.2

Desktop version: (please complete the following information):

• OS: FreeBSD 13
• Version: 1.95.0
• Compiler clang-11

Describe the bug
avogadro2 starts with an entirely black molecule widget.
When *.pdb file is opened it only shows a box in white lines and nothing else.

This is a regression against 1.94.0 which showed *.pdb files fine.

$ avogadro2 
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-yuri'
Locale:  "C"
Extension plugins dynamically found... 35
Checking for  "commands"  scripts in "/home/yuri/.local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/local/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/share/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/usr/local/bin/../lib/avogadro2/scripts/commands"
OBProcess::executeObabel: Running "obabel" "-L formats read"
OBProcess::executeObabel: Running "obabel" "-L formats write"
OBProcess::executeObabel: Running "obabel" "-L forcefields"
OBProcess::executeObabel: Running "obabel" "-L charges"
OBProcess::executeObabel: Running "obabel" "-V"
"obabel"  found:  ""
Checking for  "inputGenerators"  scripts in "/home/yuri/.local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/local/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/share/OpenChemistry/Avogadro/inputGenerators"
Checking for  "inputGenerators"  scripts in "/usr/local/bin/../lib/avogadro2/scripts/inputGenerators"
Checking for  "formatScripts"  scripts in "/home/yuri/.local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/local/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/share/OpenChemistry/Avogadro/formatScripts"
Checking for  "formatScripts"  scripts in "/usr/local/bin/../lib/avogadro2/scripts/formatScripts"
"Navigator" added
"Editor" added
"Selection" added
"Manipulator" added
"BondCentric" added
"MeasureTool" added
"PlayerTool" added
Process encountered an error, and did not execute correctly.
	Exit code: 0
	Exit status: QProcess::NormalExit
	Exit output: ""
Open Babel formats ready:  0
Process encountered an error, and did not execute correctly.
	Exit code: 0
	Exit status: QProcess::NormalExit
	Exit output: ""
Process encountered an error, and did not execute correctly.
	Exit code: 255
	Exit status: QProcess::NormalExit
	Exit output: ""
Process encountered an error, and did not execute correctly.
	Exit code: 0
	Exit status: QProcess::NormalExit
	Exit output: ""

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4. See error

Expected behavior
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Screenshots
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Additional context
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[welcome]

Thanks for opening your first issue here! Please try to include example files and screenshots if possible. If you're looking for support, please post on our forum: https://discuss.avogadro.cc/

[ghutchis]

Can you give us a screenshot or two? It would be very helpful, thanks.

[yurivict]

avogadro2-2021-08-17_12.06.22.mp4

[ghutchis]

I'm not sure of the bug at the moment - but the workaround is to click the "Ball and Stick" or "Cartoon" or "Wireframe" display types.

[ghutchis]

(The bug would be that "Ball and Stick" should be the default on a new install.)

[yurivict]

Can you release a fix in a new release?

[ghutchis]

Sure, although did you have previous settings on that account? I'll test a bit later with cleared settings.

[yurivict]

Sure, although did you have previous settings on that account?

Probably not.

Now this version creates settings files but doesn't initialize this value, so the problem is reproducible on reruns.

[ghutchis]

I can confirm that the default value is somehow getting ignored.

Now this version creates settings files but doesn't initialize this value

Well, if you enable "Ball and Stick" or any other display type, it will be saved to the settings on re-run.

[ghutchis]

I'll take a closer look into the code later this afternoon.

[avo-bot]

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

https://discuss.avogadro.cc/t/avogadro2-is-on-flathub/3481/9

[yurivict]

@ghutchis

Somehow the #744 patch didn't solve it for me.

I applied it on top of avogadrolibs-1.95.0 and deleted ~/.config/OpenChemistry - still same problem.

[ghutchis]

Can you try this patch to avogadroapp, which absolutely positively removes all settings?

diff --git a/avogadro/mainwindow.cpp b/avogadro/mainwindow.cpp
index d2676c6..9479b16 100644
--- a/avogadro/mainwindow.cpp
+++ b/avogadro/mainwindow.cpp
@@ -248,11 +248,11 @@ MainWindow::MainWindow(const QStringList& fileNames, bool disableSettings)
   m_ui->setupUi(this);
 
   // If disable settings, ensure we create a cleared QSettings object.
-  if (disableSettings) {
+  //if (disableSettings) {
     QSettings settings;
     settings.clear();
     settings.sync();
-  }
+  //}
   // The default settings will be used if everything was cleared.
   readSettings();

The #744 patch definitely works on Mac and Windows:

For reasons I don't understand, some settings seem to be cached on my Mac - either by Qt or the OS even when I rm the settings files. So i've been testing with this avogadroapp branch.

[yurivict]

Still same problem with the patch in avogadro/mainwindow.cpp

[avo-bot]

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

https://discuss.avogadro.cc/t/avogadro2-is-on-flathub/3481/14

[ghutchis]

Everyone else has tested and it works for them. I'd like to close this and get it working for you. Can you send me your patched source? That would seem to be the best way to get to the bottom of it. Thanks.

[yurivict]

I tarballed source directories as used by ports:

• https://people.freebsd.org/~yuri/avogadrolibs-1.95.0.tgz
• https://people.freebsd.org/~yuri/avogadroapp-1.95.0.tgz

[ghutchis]

I built from that source on my Mac and on an Ubunutu VM I had around. (Sorry I don't yet have a FreeBSD image running.)

It seems to work fine. 🤷‍♂️

I'm going to release 1.95.1 - but I'd definitely like to figure out what's happening for you, so I'll reopen this.

[serk12]

I think I solved the problem with the black screen.
Yuri is not only starting a fresh install, but also opening a file. So ballandstick/enable patch the 1º run but MainWindow/plugin has not changed, so when the file is opened it gets back to false.
This should solve it, but we need the plugin name which is set up in the CMakeList.txt, any clean solution?

@@ -89,9 +89,11 @@ void PluginLayerManager::setEnabled(bool enable)
     if (m_name == BallAndStick::getName()) {
       enable = settings.value("ballandstick/enable", true).toBool();
       settings.setValue("ballandstick/enable", false);
+      settings.setValue("MainWindow/" + pluginName, false);
     } else if (m_name == Cartoons::getName()) {
       enable = settings.value("cartoon/enable", true).toBool();
       settings.setValue("cartoon/enable", false);
+      settings.setValue("MainWindow/" + pluginName, false);
     }

[ghutchis]

I still don't understand why the code is calling setValue() with false - shouldn't we be using enable so that on 2nd run, etc. it's correct?

As far as loading from a file, I think that needs to be solved in avogadroapp - perhaps a check if a file doesn't have any plugins enabled, to turn one on for the user .. but it's a small population that has files like this.

[serk12]

Yes, if we add a isDefault to ScenePlugin then all of this can be solved trivialy in avogadroapp.

[PeterKraus]

Has this been resolved? I'm seeing the same issue (ball & stick unchecked every time I open an xyz file, even if previously checked) on Linux with 1.95.1.

[yurivict]

I didn't see it resolved. I stopped updating the FreeBSD until this is resolved.

[serk12]

The PR #807 and avogadrolibs#235 should fix this. But they are posterior to 1.95.1.

[ghutchis]

We need a 1.96 release, but I'm marking this closed.

[ghutchis]

If problems re-occur with HEAD, please open a new bug report.

[yurivict]

We need a 1.96 release, but I'm marking this closed.

Does this mean that the problem will be fixed in 1.96 ?

[ghutchis]

Yes. As far as I can tell, it's fixed in HEAD with #807 and avogadroapp#235