jalview

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Commits this week: 5
Total Committers: 70
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Commits this week: 5

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Friday 04 Dec 2020
5:35 pm

Ben Soares

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

5:31 pm

Ben Soares

Agree this is just touching on a much bigger task. However... The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview...

Agree this is just touching on a much bigger task.
However...
The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview.bin.Launcher, jalview.bin.HiDPISetting, jalview.bin.MemorySetting) run very early on (especially jalview.bin.Launcher!). This means Cache.log has perhaps not yet been initialised, so a Cache.log.debug doesn't log (unless you count reams of NullPointerExceptions as logging!).

In the case of HiDPISetting and MemorySetting that also get used in Getdown, where there is no jalview.bin.Cache, they currently have to use System.out and System.err [or maybe I could stub jalview.bin.Cache too]. I'd prefer them to use Cache.log when they can so this is an attempt at starting to decouple jalview.bin.Cache from other jalview things so it can be used standalone within Getdown. The main reason for wanting to do that is to have shared code to read the preferences between Jalview and Getdown.

Wednesday 02 Dec 2020
5:56 pm

Jim Procter

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly u...

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly useful in spirit), but now is most definitely not the time to optimise and beautify code.

5:53 pm

Jim Procter

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS,...

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS, so probably not a dealbreaker. Do you agree ?

5:20 pm

Jim Procter

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
Monday 28 Sep 2020
4:57 pm

Ben Soares

JAL-3753 ensure correct dependencies for shadowJar task

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    • +24
    /build.gradle
12:12 pm

Ben Soares

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

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    • +1
    /build.gradle
    • -1
    • +2
    /gradle.properties
Friday 25 Sep 2020
9:39 am

Ben Soares

JAL-3577 Removed default JALVIEW_VERSION from gradle.properties. Now being set by build.gradle

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    /gradle.properties
Thursday 24 Sep 2020
6:16 pm

Ben Soares

JAL-3577 Quick fix adding quotation marks for findProperty("JALVIEW_VERSION")==null...

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    • +1
    /build.gradle
2:49 pm

Jim Procter

2:49 pm

Jim Procter

2:48 pm

Jim Procter

2:39 pm

Jim Procter

JAL-3751 only merge strictly contiguous ranges of mappings
JAL-3751 only merge strictly contiguous ranges of mappings
Wednesday 23 Sep 2020
5:19 pm

Ben Soares

Merge branch 'develop' into bug/JAL-3753_resources_duplicated_in_jalview_jar

Options
4:49 pm

Ben Soares

JAL-3477 Added 10k leeway to amount of memory reserved for OS test for float rounding errors (needed to fix failing test)

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    • +19
    /test/jalview/bin/MemorySettingTest.java
4:48 pm

Ben Soares

JAL-3753 Resources seen in tests and appropriate filters now being used as file opt-in rather than opt-out.

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    • -19
    • +28
    /build.gradle
Monday 21 Sep 2020
12:01 pm

Jim Procter

Merge branch 'merge_review/JAL-3490_2_11_2_develop' into develop

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    /src/jalview/gui/AlignFrame.java
Sunday 20 Sep 2020
8:33 pm

Ben Soares

JAL-3753 put resources in gradle run and test path

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    /.gitignore
    • -64
    • +75
    /build.gradle
Friday 18 Sep 2020
6:18 pm

Ben Soares

JAL-3753 JAL-3754 first rejig

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    /build.gradle
    • -1
    • +0
    /gradle.properties
Wednesday 16 Sep 2020
6:47 am

Jim Procter

JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
JAL-3700: Complement sequence correspondence is broken for CDS with shared dataset sequence
Tuesday 15 Sep 2020
12:58 pm

Jim Procter

Monday 14 Sep 2020
11:24 pm

Ben Soares

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Options
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown jar and version files

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    /getdown/lib/FJVL_VERSION
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    /getdown/lib/JVL_VERSION
    • binary
    /getdown/lib/getdown-core.jar
    • binary
    /getdown/lib/getdown-launcher-local.jar
    • binary
    /getdown/lib/getdown-launcher.jar
    • binary
    /j11lib/getdown-core.jar
    • binary
    /j8lib/getdown-core.jar
11:23 pm

Ben Soares

JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown src files

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    /getdown/src/getdown/ant/pom.xml
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    /getdown/src/getdown/core/pom.xml
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    /getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
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    /getdown/src/getdown/launcher/pom.xml
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    /getdown/src/getdown/mvn_cmd
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    /getdown/src/getdown/pom.xml
6:11 pm

Ben Soares

Merge branch 'feature/JAL-3615gzipXfam' into develop

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Thursday 10 Sep 2020
5:41 pm

Jim Procter

JAL-3746 bump release version for 2.11.2 series (currently on develop)

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    /RELEASE
Friday 04 Sep 2020
6:29 pm

Ben Soares

JAL-3679 Added externally specified plugins dir to J2sPlugin check

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    /build.gradle
6:29 pm

Ben Soares

JAL-3679 Added externally specified plugins dir to J2sPlugin check

Options
    • -5
    • +20
    /build.gradle
Thursday 03 Sep 2020
4:27 pm

Ben Soares

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

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Tuesday 01 Sep 2020
4:37 pm

Ben Soares

Decision made in the issue to just check release build_properties.

Decision made in the issue to just check release build_properties.