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Releases: FelixBaensch/MORTAR

MORTAR v1.2.0.0

24 May 15:32
@JonasSchaub JonasSchaub
v1.2.0.0
be20359
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MORTAR v1.2.0.0 Latest
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Change notes

  • Settings menus now have proper option strings in drop-down boxes and every option has a specific tooltip
  • Minor GUI rework concerning button and other control sizes
  • Switched licence to MIT
  • Now using GitHub pages: https://felixbaensch.github.io/MORTAR/
  • Updated ErtlFunctionalGroupsFinder (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder) to v1.3 which has some new functionality and less input restrictions (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder/releases/tag/V1.3.0.0)
  • Updated from Java 17 to Java 21
  • SDF and SMILES import routines improved and augmented
  • Changed CSV export separator char from being set directly to an enum constant defining the character
  • New fragmentation option in ScaffoldGeneratorFragmenter to dissect a scaffold into its single rings
  • A few changes and additions in headers of exported files
  • Added MORTAR icon to all alerts and dialogs
  • Revision of exception handling at import
  • Fixed import without adding implicit hydrogen atoms
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV
  • New row added in pipeline settings view is now pre-set to selected fragmenter and other issues fixed there
  • Keep last fragment setting for pipeline was removed since the fragmentation algorithms can be configured in this regard now
  • Fixed bug with file extension on export for Linux
  • Fixed issue #56 that coordinates were not generated for fragments exported to separate SD files
  • Added drag and drop feature for file import (issue #33)
  • Fixed issue #72 that parent structures overview of fragments resulting from a pipeline fragmentation showed only one parent structure
  • Added ".tsv" as accepted import file extension (issue #81)
  • Fixed issue #86 that "data will be lost" dialogue appeared two times
  • Fixed issue #88 regarding pipeline settings dialogue
  • Changed arrangement of fragments tab (issue #84)
  • Fixed unnecessary scroll bars in molecules tab
  • Added note to tutorial about forwarding MORTAR from a remote server using X (#85)
  • Added more tooltips to fragments tab
  • Fixed issue #108, a major problem with the deployment on Windows by restructuring the automatically created start scripts (batch files)
  • Fixed issue #100, the unnecessary scroll bar in the items tab
  • Multiple other small bug fixes
  • Code only:
    • Now using the spotless plugin for automatic code formatting
    • Now using SonarCloud for automatics code analysis
    • Copied source files from ErtlFunctionalGroupsFinder, Scaffold Generator (now CDK-Scaffold), and Sugar Removal Utility were replaced with their artifacts taken from Maven Central
    • Updated Gradle to v8.5, CDK to v2.9, JavaFx to 21.0.1, and spotless to v6.25
    • Updated JavaFx Gradle plugin (0.0.14 -> 0.1.0) (issue #23)
    • Conducted general code base review guided by SonarCloud analysis (https://sonarcloud.io/project/issues?resolved=false&types=CODE_SMELL&id=FelixBaensch_MORTAR)
    • Introduced a configuration properties file to read paths to icons and other resource files from
    • Fixed all the "bugs" that SonarCloud reported (https://sonarcloud.io/summary/overall?id=FelixBaensch_MORTAR): putting readers and writers in try-with-resources blocks, logic error in PreferenceContainer.addWithoutChecks(), retrieval of example parent molecule in FragmentDataModel, preventing possible division by zero in FragmentationService, better handling of InterruptedExceptions at ExecutorService shutdown
    • Most strings like log messages are now formatted correctly instead of using string concatenation
    • Improved casting and typing in most places
    • Throwing defined exception types instead of general ones in some places
    • Manual code linting and additional documentation
    • Overhaul of exporter, mostly exception treatment (more is passed on to export thread now, so that it fails properly)
    • Introduced separate display names for settings (general and for fragmenters)
    • Added SimpleIDisplayEnumConstantProperty as new JavaFX property that wraps an enum constant with associated display name and tooltip to be used in the GUI and replaced all SimpleEnumConstantNameProperty settings with SimpleIDisplayEnumConstantProperty settings
    • Reduced duplication by moving translation of preferences to properties and check of properties for preference restrictions to PreferenceUtil for SettingsContainer, FragmentationService, and ViewToolsManager
    • Added separate display names to fragmenters for usage in GUI
    • Changed integer and double filters of settings view text fields to positive value filter including zero
    • Collection util rework

What's Changed (auto-generated release notes)

Full Changelog: v1.1.1.0...v1.2.0.0

Contributors

JonasSchaub, FelixBaensch, and SamuelBehr
Assets 7
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MORTAR v1.2.0.0-beta.2

08 May 15:42
@JonasSchaub JonasSchaub
v1.2.0.0-beta.2
0e30057
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
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MORTAR v1.2.0.0-beta.2 Pre-release
Pre-release

Change notes

  • Added more tooltips to fragments tab
  • Fixed issue #108, a major problem with the deployment on Windows by restructuring the automatically created start scripts (batch files)
  • Fixed issue #100, the unnecessary scroll bar in the items tab

What's Changed (according to GitHub pull requests)

Full Changelog: v1.1.1.0...v1.2.0.0-beta.2

Contributors

JonasSchaub, FelixBaensch, and SamuelBehr
Assets 5
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MORTAR v1.2.0.0-beta.1

30 Apr 15:33
@JonasSchaub JonasSchaub
v1.2.0.0-beta.1
789429d
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MORTAR v1.2.0.0-beta.1 Pre-release
Pre-release

Change notes

  • Added drag and drop feature for file import (issue #33)
  • Fixed issue #72 that parent structures overview of fragments resulting from a pipeline fragmentation showed only one parent structure
  • Added ".tsv" as accepted import file extension (issue #81)
  • Fixed issue #86 that "data will be lost" dialogue appeared two times
  • Updated JavaFx Gradle plugin (0.0.14 -> 0.1.0) (issue #23)
  • Fixed issue #88 regarding pipeline settings dialogue
  • Changed arrangement of fragments tab (issue #84)
  • Fixed unnecessary scroll bars in molecules tab
  • Added note about forwarding MORTAR from a remote server using X (#85)

What's Changed (according to GitHub pull requests)

Full Changelog: v1.1.1.0...v1.2.0.0-beta.1

Contributors

JonasSchaub, FelixBaensch, and SamuelBehr
Assets 5
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MORTAR v1.2.0.0-beta

15 Apr 11:49
@JonasSchaub JonasSchaub
v1.2.0.0-beta
11e9174
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MORTAR v1.2.0.0-beta Pre-release
Pre-release

Change notes

  • Settings menus now have proper option strings in drop-down boxes and every option has a specific tooltip
  • Minor GUI rework concerning button and other control sizes
  • Switched licence to MIT
  • Now using GitHub pages: https://felixbaensch.github.io/MORTAR/ (not updated for this beta release)
  • Updated ErtlFunctionalGroupsFinder (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder) to v1.3 which has some new functionality and less input restrictions (https://github.com/JonasSchaub/ErtlFunctionalGroupsFinder/releases/tag/V1.3.0.0)
  • Updated from Java 17 to Java 21
  • SDF and SMILES import routines improved and augmented
  • Changed CSV export separator char from being set directly to an enum constant defining the character
  • New fragmentation option in ScaffoldGeneratorFragmenter to dissect a scaffold into its single rings
  • A few changes and additions in headers of exported files
  • Added MORTAR icon to all alerts and dialogs
  • Revision of exception handling at import
  • Fixed import without adding implicit hydrogen atoms
  • Separator character is now replaced with _ in molecule names when items tab is exported to CSV
  • New row added in pipeline settings view is now pre-set to selected fragmenter and other issues fixed there
  • Keep last fragment setting for pipeline was removed since the fragmentation algorithms can be configured in this regard now
  • Fixed bug with file extension on export for Linux
  • Fixed issue #56 that coordinates were not generated for fragments exported to separate SD files
  • Multiple other small bug fixes
  • Code only:
    • Now using the spotless plugin for automatic code formatting
    • Now using SonarCloud for automatics code analysis
    • Copied source files from ErtlFunctionalGroupsFinder, Scaffold Generator (now CDK-Scaffold), and Sugar Removal Utility were replaced with their artifacts taken from Maven Central
    • Updated Gradle to v8.5, CDK to v2.9, JavaFx to 21.0.1, and spotless to v6.25
    • Conducted general code base review guided by SonarCloud analysis (https://sonarcloud.io/project/issues?resolved=false&types=CODE_SMELL&id=FelixBaensch_MORTAR)
    • Introduced a configuration properties file to read paths to icons and other resource files from
    • Fixed all the "bugs" that SonarCloud reported (https://sonarcloud.io/summary/overall?id=FelixBaensch_MORTAR): putting readers and writers in try-with-resources blocks, logic error in PreferenceContainer.addWithoutChecks(), retrieval of example parent molecule in FragmentDataModel, preventing possible division by zero in FragmentationService, better handling of InterruptedExceptions at ExecutorService shutdown
    • Most strings like log messages are now formatted correctly instead of using string concatenation
    • Improved casting and typing in most places
    • Throwing defined exception types instead of general ones in some places
    • Manual code linting and additional documentation
    • Overhaul of exporter, mostly exception treatment (more is passed on to export thread now, so that it fails properly)
    • Introduced separate display names for settings (general and for fragmenters)
    • Added SimpleIDisplayEnumConstantProperty as new JavaFX property that wraps an enum constant with associated display name and tooltip to be used in the GUI and replaced all SimpleEnumConstantNameProperty settings with SimpleIDisplayEnumConstantProperty settings
    • Reduced duplication by moving translation of preferences to properties and check of properties for preference restrictions to PreferenceUtil for SettingsContainer, FragmentationService, and ViewToolsManager
    • Added separate display names to fragmenters for usage in GUI
    • Changed integer and double filters of settings view text fields to positive value filter including zero
    • Collection util rework

What's Changed (according to GitHub pull requests)

Full Changelog: v1.1.1.0...v1.2.0.0-beta

Contributors

JonasSchaub, FelixBaensch, and SamuelBehr
Assets 5
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MORTAR v1.1.1.0

27 Jun 14:28
@FelixBaensch FelixBaensch
v1.1.1.0
dd5c110
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MORTAR v1.1.1.0

Change notes

  • GUI:
    • Settings of histogram view and overview view are now persisted during a session and between sessions
  • Code:
    • Histogram view and overview view functionalities are now more unified and more encapsulated via IViewToolController interface and ViewToolsManager class
    • Extensive restructuring of HistogramViewController and OverviewViewController
    • ListUtil class was renamed to CollectionUtil and extended
    • Junit updated v4.13 to 5.9.3 with some minor adaptions of the test classes
    • Bug fix in pipeline fragmenter depersistence
    • Central SMILES code parsing method added to ChemUtil class

What's Changed

  • Rework of HashMap initialisations by @JonasSchaub in #5
  • Histogram unification by @B-s123 in #8
  • Unifying view tools, histogram and overview, to some extend and persisting their settings within and between sessions by @JonasSchaub in #6

Full Changelog: v1.1.0.0...v1.1.1.0

Contributors

JonasSchaub and B-s123
Assets 5
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MORTAR v1.1.0.0

21 Feb 17:27
@FelixBaensch FelixBaensch
v1.1.0.0
e2edab2
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MORTAR v1.1.0.0
  • Added overview feature as an alternative, grid-based visualization of molecular structures
  • Bug in the mapping of the "parent molecules" for the fragments has been fixed
  • Minor bug fixes
Assets 5
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MORTAR v1.0.6.0

09 Nov 12:49
@FelixBaensch FelixBaensch
v1.0.6.0
597915c
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MORTAR v1.0.6.0
  • Invalid Java version alert is now a warning that can be dismissed and is suppressed when MORTAR is started from the automatically generated batch files on Windows (in response to a bug that was reported)
  • Updated Scaffold Generator to v1.0.3
  • Changed default fragmentation of Scaffold Generator to Schuffenhauer fragmentation
  • Adjustments of (re-)sizing behavior of some dialogues
Assets 5
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MORTAR v1.0.5.0

13 Oct 11:42
@FelixBaensch FelixBaensch
v1.0.5.0
074ce59
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MORTAR v1.0.5.0

Fixed a NullPointerException;

Assets 5
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MORTAR v1.0.4.0

05 Oct 10:04
@FelixBaensch FelixBaensch
v1.0.4.0
af73738
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MORTAR v1.0.4.0

Updated CDK to version 2.8;
Updated integrated fragmentation algorithms to CDK v2.8;
Changed DefaultChemObjectBuilder objects to SilentChemObjectBuilder objects;
If installed on Windows via installer batch files now have a MORTAR icon in start menu;

Assets 5
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MORTAR v1.0.3.0

30 Aug 14:33
@FelixBaensch FelixBaensch
v1.0.3.0
31f138b
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MORTAR v1.0.3.0

MORTAR now supports x64 on Windows, Linux and MacOS and offers a specific "fat jar" for AArch64 on Linux and MacOS;

Assets 5
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