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Extra practical - Manage conflicts

Conflicts at push

It may happen that you tried to push new commits to GitLab, but it somehow fails.

To solve it, in most cases, you simply need to first pull commits from GitLab, and then redo the push. But let's simulate that.

  1. On GitLab, open the README.md file in edition mode.
  2. Update it by adding the following short description of the macro It first denoises the image with a median filter, threshold it to make it binary, apply somr morphological operations to clean binary objects and finally invoke the Analyze particles plugin to create measurements and ROIs.
  1. Commit the changes
  2. On your local code, add, at the end of the README.md file, the following text
The macro outputs : 
- A binary image, showing the detected blobs in white
- ROIs objects, as a list in the ROI Manager and as overlay on the image 
- a ResultsTable object, containing multiple measurements for each blob
  1. Commit the changes.
  2. Now, try to make a push. It should fail with grace because you have a commit on GitLab that wasn't yet added to your local history.
  1. Try to do a pull.
  1. Redo the push. It should now work.

Conflicts at pull

In the first part, we've seen how to solve an easy conflict. But conflicts are not always so easy to solve. Especially if conflicts occurred when you try to pull. In that case, it means that the same file is modified at the same place, but in different commits (at least one locally and one remotely). This scenario generally occurs when multiple persons collaborate on the same project.

In this part, we'll simulate a collaboration on the blob-detection macro file, to create a conflict, and we'll see how to solve it.

  1. Open the macro file locally and edit it as following
    • Change the median radius to 3
    • Change the thresholding method to Otsu dark
    • Commit changes
  1. On GitLab, open and edit the macro file as following
    • Change the median radius to 2
    • Change the thresholding method to Li dark
    • Commit changes
  1. From the first part, you've learnt to first pull commits from GitLab before pushing the ones locally. So, try to do a git pull origin main. Git terminal should display a conflict message like the one below.
  1. In order to solve it, you have to open each file in conflict and manually choose what code you would like to keep and what code you would like to discard.
  • Open the blob-detection macro file. You should see added lines showing you which part is in conflict. The code in between HEAD and === corresponds to the local code and the one in between === and 8872fc... corresponds to the remote code.
  • Delete first the code you would like to discard (i.e. the remote code on lines 11-13) and then delete the highlighted lines
  • Commit changes (we generally put as commit message solving conflicts or similar)

Note : The way to solve conflicts we presented there is a very manual way. The goal was to make you aware of what happens when such conflict occurs. In most projects, you'll use an IDE to create your code and conflict solving will be a little bit easier (you'll still have to manually choose between the remote and local code but everything is nicely handled in a dedicated window). We'll cover the resolution of conflicts using the IDE in the next workshop on IntelliJ.