MORTAR v1.2 release to do

[JonasSchaub]

No description provided.

[JonasSchaub]

Update required Java version in readme and tutorial - done

[JonasSchaub]

Release v1.1.2 soon with all the patches and fixes of the last months. Last release is more than a year ago already!

[JonasSchaub]

Since I have reviewed the entire code base now, mostly guided by the issues SonarCloud detected but also documenting code in more detail in some places and fixing problems I encountered along the way (#49), also improving the GUI considerably in the settings view, I would now make the new release a minor one instead of a patch release. So MORTAR v1.2 instead of v1.1.2.

Bugs that should still be fixed before that:

• KeepLastFragment setting throws an unexpected error #11
• Molecule with "query bonds" not imported without adding implicit hydrogens #36
• CSV export, escape used separator in molecules names etc. that are supposed to be exported #46
• Overview button too small? #54
• Fix preservation of recent directory path, it seems to fail quite often #55
• Export to seperated SD files without coordinates #56
• No 3D coordinates dialog not very intuitive #57

All other issues that are marked as "to do" or "enhancement" can then be dealt with after the release of v1.2. Also the integrations of the clustering functionality and the alkyl and aromatic systems fragmenters should then be finalised.

@FelixBaensch I plan to do all this myself but most likely I will ask your opinion on some of it. E.g. the "keepLastFragmentInPipeline" setting we should discuss together once.

[JonasSchaub]

To do: test all MORTAR functionalities, primarily following the tutorial, and update the tutorial for the release. - done

[JonasSchaub]

Add Pipeline settings view: incorrect behaviour when empty row is removed to the list. And potentially also Handling of illegal values in settings views is not very intuitive if a quick fix can be found.

[JonasSchaub]

Issues set aside for now that were listed here earlier:

• Handling of illegal values in settings views is not very intuitive but I don't know whether sth could really be done there... #58
• Fix preservation of recent directory path, it seems to fail quite often #55

Apart from that, all issues designated to be resolved for this release are resolved now.
Current to dos: update tutorial and maybe send around a beta version for testing.

[JonasSchaub]

Adjust CITATION.cff when the 1.2 release is actually marked

[JonasSchaub]

Fix #72 and then send around beta version for testing.

[JonasSchaub]

Issues to fix from the beta version:

• Fragmenter settings in the pipeline view reflect back to the general fragmentation settings for the respective fragmenter. #88
• Data will be lost dialog appears two times, once before and once after the file chooser #86
• Add section to tutorial about the possibility to run MORTAR remotely on a server and tunnel the GUI to desktop using X #85
• Swap parent structure column and parent ID/name column in fragments tab (more consistent with the other tabs where IDs/names always come first) #84
• Menu bar not working when fragmentation is running #83
• In Readme, use markdown instead of HTML formatting for the console input; GitHub will then make them immediately copyable #82
• add .tsv extension (tab-separated values) to list of valid input files #81
• Parent structures overview in fragments tab of pipeline results shows only one parent #72 (almost done)

[JonasSchaub]

Still to fix:

• Unnecessary vertical scroll bar in items tab #100
• Fix deployment of version 1.2-beta.1 #108