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Update Bio-Formats to 6.13.0 #103

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merged 4 commits into from
May 18, 2023
Merged

Update Bio-Formats to 6.13.0 #103

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c371f16
Update Bio-Formats to 6.13.0
melissalinkert May 3, 2023
a187d92
Switch from formats-bsd to formats-gpl, to pull in org.json:json
melissalinkert May 16, 2023
a1290ec
Revert "Switch from formats-bsd to formats-gpl, to pull in org.json:j…
melissalinkert May 16, 2023
3afc1f1
Update org.json:json to match version in Bio-Formats 6.13.0
melissalinkert May 16, 2023
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2 changes: 1 addition & 1 deletion build.gradle
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Expand Up @@ -39,7 +39,7 @@ dependencies {
implementation 'com.bc.zarr:jzarr:0.3.5'
implementation 'info.picocli:picocli:4.2.0'
implementation 'me.tongfei:progressbar:0.9.0'
implementation 'ome:formats-bsd:6.12.0'
implementation 'ome:formats-bsd:6.13.0'
// be careful here, this is a newer version of org.json:json than formats-gpl uses
implementation 'org.json:json:20190722'
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Now that this dependency has been upgraded in the Bio-Formats stack, do we want to look into dropping this dependency and consume the transitive one?

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That required switching to formats-gpl, since formats-bsd does not have a dependency on org.json:json. I'm fine with that, but can also revert a187d92 and just bump the org.json:json version if you prefer.

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Thank Melissa, I had missed this aspect of the dependency tree.
Although, it would be certainly fine to use formats-gpl, I think it's probably better to only depend formats-bsd and indeed increment the version of the json dependency to match the one in formats-gpl 6.13.0 (with the latest release addressing CVEs notably).

implementation group: 'ch.qos.logback', name: 'logback-classic', version: '1.3.4'
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