From 80ba54f173bd693d3665ff76f301277aa4cf0ea6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 19:53:50 +0200
Subject: [PATCH 1/9] feat: add workflows

---
 .github/workflows/mkdocs-build.yml | 11 +++++++++++
 .github/workflows/pytest.yml       | 11 +++++++++++
 .github/workflows/python-lint.yml  | 11 +++++++++++
 .gitlab-ci.yml                     |  6 ------
 4 files changed, 33 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/mkdocs-build.yml
 create mode 100644 .github/workflows/pytest.yml
 create mode 100644 .github/workflows/python-lint.yml
 delete mode 100644 .gitlab-ci.yml

diff --git a/.github/workflows/mkdocs-build.yml b/.github/workflows/mkdocs-build.yml
new file mode 100644
index 0000000..7cc105b
--- /dev/null
+++ b/.github/workflows/mkdocs-build.yml
@@ -0,0 +1,11 @@
+name: MkDocs Build (RationAI Standard)
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+jobs:
+  run:
+    uses: RationAI/.github/.github/workflows/mkdocs-build.yml@main
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
new file mode 100644
index 0000000..3cef152
--- /dev/null
+++ b/.github/workflows/pytest.yml
@@ -0,0 +1,11 @@
+name: Pytest (RationAI Standard)
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+jobs:
+  run:
+    uses: RationAI/.github/.github/workflows/pytest.yml@main
diff --git a/.github/workflows/python-lint.yml b/.github/workflows/python-lint.yml
new file mode 100644
index 0000000..6bf101f
--- /dev/null
+++ b/.github/workflows/python-lint.yml
@@ -0,0 +1,11 @@
+name: Python Lint (RationAI Standard)
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+jobs:
+  run:
+    uses: RationAI/.github/.github/workflows/python-lint.yml@main
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
deleted file mode 100644
index b132c47..0000000
--- a/.gitlab-ci.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-include:
-  project: rationai/digital-pathology/templates/ci-templates
-  file: Python-Lint.gitlab-ci.yml
-
-stages:
-  - lint

From fd19a47803f04c04741a86565b19c5c86b33f056 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:06:40 +0200
Subject: [PATCH 2/9] chore: point to the github repo

---
 scripts/submit_annotation_masks.py       | 2 +-
 scripts/submit_fix_mask_icc_profile.py   | 2 +-
 scripts/submit_qc.py                     | 2 +-
 scripts/submit_remap_annotation_masks.py | 2 +-
 scripts/submit_tiling.py                 | 2 +-
 scripts/submit_tissue_masks.py           | 2 +-
 scripts/submit_train_test_split.py       | 2 +-
 scripts/submit_wsi_mapping.py            | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/scripts/submit_annotation_masks.py b/scripts/submit_annotation_masks.py
index 86c3953..43d7be7 100644
--- a/scripts/submit_annotation_masks.py
+++ b/scripts/submit_annotation_masks.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m preprocessing.annotation_masks +experiment=...",
diff --git a/scripts/submit_fix_mask_icc_profile.py b/scripts/submit_fix_mask_icc_profile.py
index ccd53ee..6b5bbce 100644
--- a/scripts/submit_fix_mask_icc_profile.py
+++ b/scripts/submit_fix_mask_icc_profile.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m preprocessing.fix_mask_icc_profile +experiment=...",
diff --git a/scripts/submit_qc.py b/scripts/submit_qc.py
index 1506461..8eadf81 100644
--- a/scripts/submit_qc.py
+++ b/scripts/submit_qc.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m preprocessing.qc +experiment=...",
diff --git a/scripts/submit_remap_annotation_masks.py b/scripts/submit_remap_annotation_masks.py
index eceb0cd..edf4e3f 100644
--- a/scripts/submit_remap_annotation_masks.py
+++ b/scripts/submit_remap_annotation_masks.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m preprocessing.remap_annotation_masks +experiment=...",
diff --git a/scripts/submit_tiling.py b/scripts/submit_tiling.py
index b1c1ff9..7b20eb0 100644
--- a/scripts/submit_tiling.py
+++ b/scripts/submit_tiling.py
@@ -8,7 +8,7 @@
     memory="64Gi",
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run -m preprocessing.tiling +experiment=...",
diff --git a/scripts/submit_tissue_masks.py b/scripts/submit_tissue_masks.py
index 2386b85..12f6a24 100644
--- a/scripts/submit_tissue_masks.py
+++ b/scripts/submit_tissue_masks.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m preprocessing.tissue_masks +experiment=...",
diff --git a/scripts/submit_train_test_split.py b/scripts/submit_train_test_split.py
index 7a19085..b36f94b 100644
--- a/scripts/submit_train_test_split.py
+++ b/scripts/submit_train_test_split.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m split.train_test_split +experiment=...",
diff --git a/scripts/submit_wsi_mapping.py b/scripts/submit_wsi_mapping.py
index fdc38bf..d09f30e 100644
--- a/scripts/submit_wsi_mapping.py
+++ b/scripts/submit_wsi_mapping.py
@@ -9,7 +9,7 @@
     gpu=None,
     public=False,
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/tissue-classification.git workdir",
+        "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
         "uv run python -m preprocessing.wsi_mapping",

From 0a616daa8ae90cc45941be9770bc448302ba4dd1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:13:52 +0200
Subject: [PATCH 3/9] fix: remove mk-docs

---
 .github/workflows/mkdocs-build.yml | 11 -----------
 1 file changed, 11 deletions(-)
 delete mode 100644 .github/workflows/mkdocs-build.yml

diff --git a/.github/workflows/mkdocs-build.yml b/.github/workflows/mkdocs-build.yml
deleted file mode 100644
index 7cc105b..0000000
--- a/.github/workflows/mkdocs-build.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: MkDocs Build (RationAI Standard)
-on:
-  push:
-    branches: ["master"]
-  pull_request:
-    branches: ["master"]
-  workflow_dispatch:
-
-jobs:
-  run:
-    uses: RationAI/.github/.github/workflows/mkdocs-build.yml@main

From 41699e0f0268135f1ad89123cd5bab3bf2dd60bb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:16:21 +0200
Subject: [PATCH 4/9] fix: remove pytest

---
 .github/workflows/pytest.yml | 11 -----------
 1 file changed, 11 deletions(-)
 delete mode 100644 .github/workflows/pytest.yml

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
deleted file mode 100644
index 3cef152..0000000
--- a/.github/workflows/pytest.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: Pytest (RationAI Standard)
-on:
-  push:
-    branches: ["master"]
-  pull_request:
-    branches: ["master"]
-  workflow_dispatch:
-
-jobs:
-  run:
-    uses: RationAI/.github/.github/workflows/pytest.yml@main

From 380feadd1a7ababff64537b71afd2764313112a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:18:51 +0200
Subject: [PATCH 5/9] fix: add init to silence mypy

---
 preprocessing/__init__.py | 0
 split/__init__.py         | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 preprocessing/__init__.py
 create mode 100644 split/__init__.py

diff --git a/preprocessing/__init__.py b/preprocessing/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/split/__init__.py b/split/__init__.py
new file mode 100644
index 0000000..e69de29

From 9c633651472a0b4ddfbf7858fe58001063efd35e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:30:01 +0200
Subject: [PATCH 6/9] fix: apply more typing issues

---
 preprocessing/qc.py     | 2 +-
 preprocessing/tiling.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/preprocessing/qc.py b/preprocessing/qc.py
index 0367ff8..a1e9f4f 100644
--- a/preprocessing/qc.py
+++ b/preprocessing/qc.py
@@ -63,7 +63,7 @@ async def qc_main(
         ),
     ]
 
-    async with rationai.AsyncClient() as client:
+    async with rationai.AsyncClient() as client:  # type: ignore[attr-defined]
         tasks = []
 
         for group, use_wb in processing_groups:
diff --git a/preprocessing/tiling.py b/preprocessing/tiling.py
index a2ff426..b85d341 100644
--- a/preprocessing/tiling.py
+++ b/preprocessing/tiling.py
@@ -1,7 +1,7 @@
 import re
 import tempfile
 from pathlib import Path
-from typing import Any
+from typing import Any, cast
 
 import hydra
 import mlflow
@@ -237,7 +237,7 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
 
         df_slides, df_tiles = tiling(
             df=split_df,
-            class_mapping=OmegaConf.to_container(config.class_mapping, resolve=True),
+            class_mapping=cast(dict[str, list[str]], OmegaConf.to_container(config.class_mapping, resolve=True)),
             tile_extent=config.tile_size,
             stride=config.stride,
             mpp=config.mpp,

From 065ce3b7414c75cc50f4d7d8ed5d5323736fc077 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:34:12 +0200
Subject: [PATCH 7/9] feat: configure Gemini

---
 .gemini/config.yml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 .gemini/config.yml

diff --git a/.gemini/config.yml b/.gemini/config.yml
new file mode 100644
index 0000000..7da814d
--- /dev/null
+++ b/.gemini/config.yml
@@ -0,0 +1,8 @@
+code_review:
+  instructions: |
+    Review code changes and provide feedback as short bullet points only.
+    - No introductory or closing sentences
+    - One bullet per issue
+    - Each bullet: what is wrong and how to fix it, nothing more
+    - Skip compliments and summaries
+    - If there is nothing to flag, say only: "LGTM"

From 07107c96c881e0ce64f1a9e7d34102dab2476ecb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Wed, 22 Apr 2026 20:34:37 +0200
Subject: [PATCH 8/9] fix: format

---
 preprocessing/tiling.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/preprocessing/tiling.py b/preprocessing/tiling.py
index b85d341..46df81a 100644
--- a/preprocessing/tiling.py
+++ b/preprocessing/tiling.py
@@ -237,7 +237,10 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
 
         df_slides, df_tiles = tiling(
             df=split_df,
-            class_mapping=cast(dict[str, list[str]], OmegaConf.to_container(config.class_mapping, resolve=True)),
+            class_mapping=cast(
+                "dict[str, list[str]]",
+                OmegaConf.to_container(config.class_mapping, resolve=True),
+            ),
             tile_extent=config.tile_size,
             stride=config.stride,
             mpp=config.mpp,

From 0828e3d9539b91d6bf919b9d4b5e0bb7ab33271d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vojt=C4=9Bch=20C=C3=ADfka?= <550433@mail.muni.cz>
Date: Thu, 23 Apr 2026 20:22:46 +0200
Subject: [PATCH 9/9] fix: typo

---
 scripts/submit_tiling.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/submit_tiling.py b/scripts/submit_tiling.py
index 7b20eb0..89f2cea 100644
--- a/scripts/submit_tiling.py
+++ b/scripts/submit_tiling.py
@@ -11,7 +11,7 @@
         "git clone https://github.com/RationAI/tissue-classification.git workdir",
         "cd workdir",
         "uv sync",
-        "uv run -m preprocessing.tiling +experiment=...",
+        "uv run python -m preprocessing.tiling +experiment=...",
     ],
     storage=[storage.secure.DATA],
 )