Hey @bblhd!

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I have attempted to unmodify submodules without success, both in the past and currently, though I was unaware how much of a problem it was.

I've tried all suggested fixes unsuccessfully, either commit ids are not found or the commands have no effect at all. It seems to be something wrong with my version of git or my repository. For context, I'm using git version 2.51.2_1, on linux, with a basic command line and no IDE.

In theory, this could be fixed by creating a new branch and pull request, but the contributors guide specifically requests not to.

Does anyone know how to solve this?

Commit: bb58664
Diffs: csl-locales, csl-styles

I have attempted to unmodify submodules without success, both in the past and currently, though I was unaware how much of a problem it was.

I've tried all suggested fixes unsuccessfully, either commit ids are not found or the commands have no effect at all. It seems to be something wrong with my version of git or my repository. For context, I'm using git version 2.51.2_1, on linux, with a basic command line and no IDE.

In theory, this could be fixed by creating a new branch and pull request, but the contributors guide specifically requests not to.

Does anyone know how to solve this?

Commit: bb58664 Diffs: csl-locales, csl-styles

Fixed this by doing submodule checkout in IntelliJ IDEA, unsure what exactly the issue was, but submodules are now unmodified from main.

I apologise for force pushing, the only difference was a single incorrect author email in the previous commit I pushed.

Hi, bblhd! Thank you for looking into this feature. This is a very good issue for the first contribution!

The External File Prefs were touched here #14619
I will create a follow up issue @calixtus

While the PR was in progress, a new version of JabRef has been released.

You have to merge upstream/main and move your entry in CHANGELOG.md up to the section ## [Unreleased].

There is a failing check on merge: https://github.com/JabRef/jabref/actions/runs/20642230526/job/59275496096
@bblhd could you investigate if related/actionable?

Yep, they do seem relevant:

              LinkedFileTransferHelperTest

                check(FileTestConfigurationBuilder, BibTestConfigurationBuilder, BibTestConfigurationBuilder)

                  Test "path/to/file.pdf" with "pdf" should be "file.pdf" with empty citation key FAILED

                  org.opentest4j.AssertionFailedError: expected: <file.pdf> but was: <path/to/file.pdf>
                      at app/org.jabref.jablib/org.jabref.logic.externalfiles.LinkedFileHandlerTest.getSuggestedFileNameWithMissingKey(LinkedFileHandlerTest.java:116)


                  getSuggestedFileName(String, String, String)

                    Test "path/to/other.pdf" with "pdf" should be "other.pdf" with empty citation key FAILED

                    org.opentest4j.AssertionFailedError: expected: <other.pdf> but was: <path/to/other.pdf>
                        at app/org.jabref.jablib/org.jabref.logic.externalfiles.LinkedFileHandlerTest.getSuggestedFileNameWithMissingKey(LinkedFileHandlerTest.java:116)


    BibtexParserTest

      CitaviXmlImporterFilesTest

        FileUtilTest

          checkFileExtensionAreTheSameForStringsAndPaths(String)

            Test [2] "te.st.PdF  " FAILED

            java.nio.file.InvalidPathException: Trailing char < > at index 10: te.st.PdF
                at org.jabref.jablib/org.jabref.logic.util.io.FileUtilTest.checkFileExtensionAreTheSameForStringsAndPaths(FileUtilTest.java:255)

They are failing on Windows

I reverted the PR for now due to the failng window tests, you can re-create it or re.open this one

Very strange the failing test did not show up in CI on this PR

Very strange the failing test did not show up in CI on this PR

Yeah that is on us.
After splitting JabRef into CLI, GUI. library and server, the windows tests were taking excruciatingly long (30+min, if I remember correctly) to finish. @koppor and I finally decided that we will skip the jablib windows test on PR commits, as ~95% PRs don't deal with paths, and even less deal with paths in a way that requires differentiated handling for windows.

This PR was one of them 😄

Very strange the failing test did not show up in CI on this PR

Yeah that is on us. After splitting JabRef into CLI, GUI. library and server, the windows tests were taking excruciatingly long (30+min, if I remember correctly) to finish. @koppor and I finally decided that we will skip the jablib windows test on PR commits, as ~95% PRs don't deal with paths, and even less deal with paths in a way that requires differentiated handling for windows.

This PR was one of them 😄

@koppor lets make a new workflow based on an old idea - File system related classes touched in a commit => jablib windows test runs

Yep, they do seem relevant:

              LinkedFileTransferHelperTest

                check(FileTestConfigurationBuilder, BibTestConfigurationBuilder, BibTestConfigurationBuilder)

                  Test "path/to/file.pdf" with "pdf" should be "file.pdf" with empty citation key FAILED

                  org.opentest4j.AssertionFailedError: expected: <file.pdf> but was: <path/to/file.pdf>
                      at app/org.jabref.jablib/org.jabref.logic.externalfiles.LinkedFileHandlerTest.getSuggestedFileNameWithMissingKey(LinkedFileHandlerTest.java:116)


                  getSuggestedFileName(String, String, String)

                    Test "path/to/other.pdf" with "pdf" should be "other.pdf" with empty citation key FAILED

                    org.opentest4j.AssertionFailedError: expected: <other.pdf> but was: <path/to/other.pdf>
                        at app/org.jabref.jablib/org.jabref.logic.externalfiles.LinkedFileHandlerTest.getSuggestedFileNameWithMissingKey(LinkedFileHandlerTest.java:116)


    BibtexParserTest

      CitaviXmlImporterFilesTest

        FileUtilTest

          checkFileExtensionAreTheSameForStringsAndPaths(String)

            Test [2] "te.st.PdF  " FAILED

            java.nio.file.InvalidPathException: Trailing char < > at index 10: te.st.PdF
                at org.jabref.jablib/org.jabref.logic.util.io.FileUtilTest.checkFileExtensionAreTheSameForStringsAndPaths(FileUtilTest.java:255)

I think these are actually test errors, as in the test assumes not windows so it fails, but the functionality is correct. These were both tests I changed, so I will make sure they're correct and open a new PR