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Update OpenCSV version: 3.9 -> 5.2#135

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ctrueden merged 2 commits into
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update-opencsv
Sep 1, 2020
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Update OpenCSV version: 3.9 -> 5.2#135
ctrueden merged 2 commits into
masterfrom
update-opencsv

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@imagejan

@imagejan imagejan commented Jul 9, 2020

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I'm not sure which components other than saalfeldlab/bigwarp make use of OpenCSV. The basic usage of CSVReader and CSVWriter doesn't seem to be affected.

API changes can be browsed at https://abi-laboratory.pro/?view=timeline&lang=java&l=opencsv.

/cc @bogovicj

@bogovicj

bogovicj commented Jul 9, 2020

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Can do, thanks @imagejan

@bogovicj bogovicj mentioned this pull request Jul 9, 2020
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@bogovicj

bogovicj commented Jul 16, 2020

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bigwarp now uses opencsv v 5.2

@ctrueden

ctrueden commented Jul 17, 2020 •
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Thanks @bogovicj !

@imagejan Here are all the ones I found:

$ for f in $(grep -l opencsv */*/pom.xml)
do (
cd "$(dirname "$f")"
git remote -v
) done | grep fetch
origin	git://github.com/saalfeldlab/bigwarp (fetch)
origin	git://github.com/saalfeldlab/trakem2-tps (fetch)
origin	git://github.com/scijava/pom-scijava (fetch)
origin	git://github.com/hadim/FilamentDetector (fetch)
origin	git://github.com/brouhardlab/Kappa (fetch)

CC @axtimwalde @hadim

@ctrueden

ctrueden commented Aug 13, 2020

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trakem2-tps and Kappa still compile with opencsv 5.2.

FilamentDetector does not:

[ERROR] .../FilamentDetector/src/main/java/sc/fiji/filamentdetector/analyzer/LengthOverTimeAnalyzer.java:[116,60] no suitable constructor found for CSVWriter(java.io.FileWriter,char)
    constructor com.opencsv.CSVWriter.CSVWriter(java.io.Writer) is not applicable
      (actual and formal argument lists differ in length)
    constructor com.opencsv.CSVWriter.CSVWriter(java.io.Writer,char,char,char,java.lang.String) is not applicable
      (actual and formal argument lists differ in length)
[ERROR] .../FilamentDetector/src/main/java/sc/fiji/filamentdetector/exporter/CSVTrackedFilamentExporter.java:[100,44] no suitable constructor found for CSVWriter(java.io.FileWriter,char)
    constructor com.opencsv.CSVWriter.CSVWriter(java.io.Writer) is not applicable
      (actual and formal argument lists differ in length)
    constructor com.opencsv.CSVWriter.CSVWriter(java.io.Writer,char,char,char,java.lang.String) is not applicable
      (actual and formal argument lists differ in length)
[ERROR] .../FilamentDetector/src/main/java/sc/fiji/filamentdetector/exporter/CSVFilamentExporter.java:[99,44] no suitable constructor found for CSVWriter(java.io.FileWriter,char)
    constructor com.opencsv.CSVWriter.CSVWriter(java.io.Writer) is not applicable
      (actual and formal argument lists differ in length)
    constructor com.opencsv.CSVWriter.CSVWriter(java.io.Writer,char,char,char,java.lang.String) is not applicable
      (actual and formal argument lists differ in length)
[INFO] 3 errors

@hadim If you have time to upgrade to OpenCSV 5.2, that would be very helpful. Otherwise, I'll try to submit a PR eventually, so we can move forward with the upgrade.

@bogovicj

bogovicj commented Aug 13, 2020

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trakem2-tps is on me. I can deal with it quickly.

@ctrueden

ctrueden commented Aug 13, 2020 •
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@bogovicj Like I said, it builds with passing tests when pinned to opencsv 5.2. You probably don't need to do anything or release a new version. If you could just try doing something that uses the CSV-related features of trakem2-tps at runtime, and make sure it still behaves, that would be great!

@hadim

hadim commented Aug 13, 2020

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Sorry, @ctrueden. Will do that soon.

#mylife: @ctrueden I moved away from academia a few months ago and so I don't do any imaging things anymore :-( . I work for a company that does drug discovery. In consequence, I probably won't be very active in the community anymore (I wasn't extremly active anyway...). I wish you plenty of luck with the future of the community @ctrueden and it was a pleasure to work with you!

@ctrueden

ctrueden commented Aug 13, 2020 •
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@hadim Thanks for the update! Likewise: it was a pleasure working with you. 😄

Since it sounds like you won't have time to maintain your Fiji components anymore: would you be willing to transfer them to the Fiji organization? Then I can do it for the moment, and we can potentially look for new maintainers.

@hadim

hadim commented Aug 13, 2020

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@ctrueden I am totally fine for FilamentDetector (not sure this plugin is used anyway).

For Kappa, I think that would be the best since this plugin is used by a small community but I need to talk to my supervisor about it.

Give me a few days for the OpenCSV bump.

@hadim

hadim commented Aug 14, 2020

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Kappa has been updated to the latest pom-scijava and opencsv 5.2.

For FilamentDetector I have some issues. See fiji/FilamentDetector#21

@imagejan

imagejan commented Sep 1, 2020

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Both Kappa (see fiji/Kappa@b1b3f42) and FilamentDetector (see fiji/FilamentDetector#21) use OpenCSV 5.2 now, so this pull request should be good to go.

imagejan and others added 2 commits September 1, 2020 17:02
@ctrueden ctrueden merged commit 363039c into master Sep 1, 2020
@ctrueden ctrueden deleted the update-opencsv branch September 1, 2020 22:11
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4 participants

@imagejan @bogovicj @ctrueden @hadim