refactor: migration and tooling

[TomasBalak]

Migrating from GitLab to GitHub (1/6)

Overview

This PR contains the following changes:

• Migration from GitLab to GitHub
• Tooling updates
• Installation guide updates
• Small fixes to docs and linting

Merge Order

master
  └── 1️⃣ refactor/migration-and-tooling
        └── 2️⃣ refactor/staining-api-update
              └── 3️⃣ refactor/deprecated-skimage-api
                    └── 4️⃣ refactor/output-schema-unification
                          └── 5️⃣ fix/folding-improvements
                                └── 6️⃣ chore/docs-and-cleanup

Out of the 6 PRs containing the latest features and changes, this one needs to be merged first.

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[gemini-code-assist]

Code Review

This pull request migrates the project's dependency management and development environment setup from PDM to UV, updates documentation and configuration files accordingly, and adds exclusions for an external PIQE module. While the changes are a great step forward, several issues were identified in the documentation and configuration. Specifically, there is an incorrect module path in .mypy.ini, a Python 3.11 syntax error in the documentation's f-string examples, a variable name mismatch causing a NameError, and outdated parameter descriptions for the folding function. Additionally, the git sources in pyproject.toml should be updated to point to GitHub instead of GitLab.

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[gemini-code-assist]

The module name is incorrectly specified as rationai.qc.focus.piqe instead of rationai.qc.blur.piqe. Since the file is located at rationai/qc/blur/piqe.py, the correct module path is rationai.qc.blur.piqe. Because of this mismatch, mypy will not correctly ignore errors in the intended file.

[mypy-rationai.qc.blur.piqe]

[gemini-code-assist]

In Python 3.11 (which is the target version specified in .ruff.toml), nesting double quotes inside a double-quoted f-string results in a SyntaxError. Please use single quotes for the dictionary keys to ensure compatibility with Python 3.11.

Suggested change

	print(f"Number of flagged pixels: {artifacts["number_of_flagged_pixels"]}")
	print(f"Number of examined pixels: {artifacts["number_of_examined_pixels"]}")
	print(f"Number of flagged pixels: {artifacts['number_of_flagged_pixels']}")
	print(f"Number of examined pixels: {artifacts['number_of_examined_pixels']}")

[gemini-code-assist]

There is a mismatch in the variable name used for the local area image. On line 208, it is defined as local_area_image =img_area = ... (which also lacks a space around the = operator), but on lines 218 and 228, local_area_img is used. This will cause a NameError when running the example. Please update line 208 to define local_area_img directly:

local_area_img = np.asarray(Image.open("fold_area.png").convert("RGB")) # Local area of investigated image

[gemini-code-assist]

The description refers to non-existent parameters level_downsample and nuclues_diameter_at_base_level (which also has a typo) for the folding function. The actual parameters are mpp and cell_nucleus_size. Please update the documentation to describe the correct parameters.

[gemini-code-assist]

Since this PR is migrating the project from GitLab to GitHub, the git sources for rationai-masks and rationai-staining should also be updated to point to their new GitHub repository URLs under the RationAI organization, rather than continuing to reference GitLab.