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Merged
vojtech-cifka merged 9 commits into from
Apr 27, 2026
Merged

chore: migrate CI from GitLab to GitHub Actions #2

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80ba54f
feat: add workflows
vojtech-cifka Apr 22, 2026
fd19a47
chore: point to the github repo
vojtech-cifka Apr 22, 2026
0a616da
fix: remove mk-docs
vojtech-cifka Apr 22, 2026
41699e0
fix: remove pytest
vojtech-cifka Apr 22, 2026
380fead
fix: add init to silence mypy
vojtech-cifka Apr 22, 2026
9c63365
fix: apply more typing issues
vojtech-cifka Apr 22, 2026
065ce3b
feat: configure Gemini
vojtech-cifka Apr 22, 2026
07107c9
fix: format
vojtech-cifka Apr 22, 2026
0828e3d
fix: typo
vojtech-cifka Apr 23, 2026
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8 changes: 8 additions & 0 deletions .gemini/config.yml
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@@ -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"
11 changes: 11 additions & 0 deletions .github/workflows/python-lint.yml
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@@ -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
6 changes: 0 additions & 6 deletions .gitlab-ci.yml
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This file was deleted.

Empty file added preprocessing/__init__.py
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2 changes: 1 addition & 1 deletion preprocessing/qc.py
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Expand Up @@ -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:
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7 changes: 5 additions & 2 deletions preprocessing/tiling.py
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@@ -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
Expand Down Expand Up @@ -237,7 +237,10 @@ 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,
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2 changes: 1 addition & 1 deletion scripts/submit_annotation_masks.py
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Expand Up @@ -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=...",
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2 changes: 1 addition & 1 deletion scripts/submit_fix_mask_icc_profile.py
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Expand Up @@ -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=...",
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2 changes: 1 addition & 1 deletion scripts/submit_qc.py
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Expand Up @@ -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=...",
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2 changes: 1 addition & 1 deletion scripts/submit_remap_annotation_masks.py
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Expand Up @@ -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=...",
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4 changes: 2 additions & 2 deletions scripts/submit_tiling.py
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Expand Up @@ -8,10 +8,10 @@
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",
Comment thread
vojtech-cifka marked this conversation as resolved.
"cd workdir",
"uv sync",
"uv run -m preprocessing.tiling +experiment=...",
"uv run python -m preprocessing.tiling +experiment=...",
],
storage=[storage.secure.DATA],
)
2 changes: 1 addition & 1 deletion scripts/submit_tissue_masks.py
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Expand Up @@ -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=...",
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2 changes: 1 addition & 1 deletion scripts/submit_train_test_split.py
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Expand Up @@ -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=...",
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2 changes: 1 addition & 1 deletion scripts/submit_wsi_mapping.py
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Expand Up @@ -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",
Expand Down
Empty file added split/__init__.py
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