jalview

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Commits this week: 3
Total Committers: 72
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Commits this week: 3

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Friday 05 Mar
5:18 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'task/JAL-3796_notarization' into develop

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5:18 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'develop' into task/JAL-3796_notarization

Options
    • -15
    • +1
    /utils/install4j/install4j8_template.install4j
5:07 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

JAL-3796 minimal steps for notarization and the entitlements.txt file needed for the codesign tool

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    • -0
    • +4
    /utils/install4j/install4j8_template.install4j
    • -0
    • +32
    /utils/osx_signing/README
    • -0
    • +24
    /utils/osx_signing/entitlements.txt
11:24 am

Ben Soares

JAL-3618 Enable appBundleIsTraversable in JFileChooser on macOS

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    • -0
    • +8
    /src/jalview/jbgui/GPreferences.java
Thursday 04 Mar
7:19 pm

Ben Soares

JAL-3594 Allow a channel to use a different preferences file than .jalview_properties, with initial read from .jalview_properties

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    • -3
    • +20
    /src/jalview/bin/Cache.java
    • -6
    • +6
    /src/jalview/util/ChannelProperties.java
    • -0
    • +1
    /utils/channels/default/resources/channel.props
    • -0
    • +1
    /utils/channels/develop/resources/channel.props
    • -0
    • +1
    /utils/channels/jalviewjs/resources/channel.props
    • -0
    • +1
    /utils/channels/release/resources/channel.props
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    • +1
    /utils/channels/test-release/resources/channel.props
Thursday 25 Feb
3:57 pm

Mungo Carstairs

3:56 pm

Mungo Carstairs

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

2:21 pm

Mungo Carstairs

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

2:17 pm

Mungo Carstairs

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

2:14 pm

Mungo Carstairs

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

Wednesday 24 Feb
4:45 pm

Jim Procter

4:43 pm

Jim Procter

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
Thursday 18 Feb
6:42 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3822 pass panel height and width to wrapped geometry calculations

Options
    • -1
    • +1
    /src/jalview/gui/SeqCanvas.java
    • -0
    • +6
    /src/jalview/gui/SeqPanel.java
    • -11
    • +167
    /test/jalview/gui/SeqPanelTest.java
11:43 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2422 remove temporary patch (requires ChimeraX Daily or 1.2 build)

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    • -2
    • +2
    /src/jalview/gui/JalviewChimeraXBindingModel.java
Thursday 11 Feb
5:06 pm

Mungo Carstairs

Or can it be compiled to Java 8 bytecode?

Or can it be compiled to Java 8 bytecode?

3:00 pm

Mungo Carstairs

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly). Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatibl...

'var' is since Java 10. We are still supporting Java 8 runtime which will not run this code (sadly).
Compile with JDK 8 to find other occurrences (also Preferences, line 596 is not Java 8 compatible syntax).

2:27 pm

Mungo Carstairs

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

Above statement is a duplicate - should only be inside the check for service != null. It fails with NPE if service is null.

2:26 pm

Mungo Carstairs

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

startjob and canceljob are only referenced in jbinit() so should be local variables in that method.

2:17 pm

Mungo Carstairs

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

Field startJob used to be the return value of showRunDialog(). As it no longer is, it can be removed.

12:29 pm

Mungo Carstairs

JAL-3809: Edit web service parameters dialog does not work in jalviewjs
JAL-3809: Edit web service parameters dialog does not work in jalviewjs
Wednesday 10 Feb
5:19 pm

Ben Soares

JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName to set the grouped application name in the taskbar

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    • -10
    • +49
    /src/jalview/gui/Desktop.java
12:12 am

Ben Soares

JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

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    • +1
    /build.gradle
Monday 08 Feb
7:00 pm

Ben Soares

JAL-3521 Adding a build_properties into sourceDist tarball, with INSTALLATION=SourceDist git-commit...

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    • -1
    • +11
    /build.gradle
Friday 05 Feb
9:20 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2422 updated unit test for ChimeraX command change

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    • -1
    • +1
    /test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
Thursday 04 Feb
5:50 pm

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-2422 a fix and a fudge for two failing ChimeraX commands

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    • +1
    /src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
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    • +3
    /src/jalview/gui/JalviewChimeraXBindingModel.java
Thursday 28 Jan
2:02 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'task/JAL-3796_notarization_no_uninstaller' into develop

Options
1:50 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'task/JAL-3805_Remove_Uninstall_Old_Jalview_application_for_develop_branch' into task/JAL-3796_notarization_no_uninstaller

Options
    • -6
    • +0
    /build.gradle
    • -15
    • +1
    /utils/install4j/install4j8_template.install4j
12:46 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'develop' into task/JAL-3796_notarization_no_uninstaller

Options
    • -4
    • +37
    /build.gradle
    • -1
    • +13
    /gradle.properties
12:42 pm

Jalview Development Admin <jalview-dev-owner@jalview.org>

Merge branch 'develop' into task/JAL-3796_notarization

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    • -4
    • +37
    /build.gradle
    • -1
    • +13
    /gradle.properties
Tuesday 26 Jan
3:27 pm

Ben Soares

JAL-3521 Updating file opening marker to %u

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    • -1
    • +1
    /utils/debian/debian/jalview.desktop
    • -1
    • +1
    /utils/debian/mime_types_for_debian.pl