chore: update .gitattributes for artefact data handling

- Applying black formatting.

Author: BenjaminIsaac0111

.gitattributes

@@ -1,2 +1,22 @@
+# Force LF line endings for all text files
 * text=auto eol=lf
 
+# Explicitly handle Python files
+*.py text eol=lf
+
+# Handle configuration files
+*.yaml text eol=lf
+*.json text eol=lf
+*.toml text eol=lf
+*.md text eol=lf
+
+# Mark data artifacts as binary to prevent corruption
+*.csv binary
+*.sqlite binary
+*.h5 binary
+*.pth binary
+*.pt binary
+*.pkl binary
+
+# Large data and logs should definitely be binary
+*.log text eol=lf

.gitignore

@@ -182,9 +182,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
 #  you could uncomment the following to ignore the entire vscode folder
 # .vscode/
 
@@ -213,9 +213,73 @@ checkpoints/
 checkpoints_full/
 results/
 results_long_run/
+runs/
+vscode/
+.agent/
 
 # Images
 *.png
 *.jpg
 *.jpeg
 *.svg
+docs/research_proposal.tex
+.vscode/settings.json
+hest_data/.gitattributes
+hest_data/HEST_v1_3_0.csv
+hest_data/README.md
+hest_data/cellvit_seg/INT1_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT1_cellvit_seg.parquet
+hest_data/cellvit_seg/INT10_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT10_cellvit_seg.parquet
+hest_data/cellvit_seg/INT11_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT11_cellvit_seg.parquet
+hest_data/cellvit_seg/INT12_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT12_cellvit_seg.parquet
+hest_data/cellvit_seg/INT13_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT13_cellvit_seg.parquet
+hest_data/cellvit_seg/INT16_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT16_cellvit_seg.parquet
+hest_data/cellvit_seg/INT19_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT19_cellvit_seg.parquet
+hest_data/cellvit_seg/INT20_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT20_cellvit_seg.parquet
+hest_data/cellvit_seg/INT21_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/INT21_cellvit_seg.parquet
+hest_data/cellvit_seg/INT1_cellvit_seg.geojson
+hest_data/cellvit_seg/INT10_cellvit_seg.geojson
+hest_data/cellvit_seg/INT11_cellvit_seg.geojson
+hest_data/cellvit_seg/INT12_cellvit_seg.geojson
+hest_data/cellvit_seg/INT13_cellvit_seg.geojson
+hest_data/cellvit_seg/INT16_cellvit_seg.geojson
+hest_data/cellvit_seg/INT19_cellvit_seg.geojson
+hest_data/cellvit_seg/INT20_cellvit_seg.geojson
+hest_data/cellvit_seg/INT21_cellvit_seg.geojson
+hest_data/cellvit_seg/TENX175_cellvit_seg.geojson
+hest_data/cellvit_seg/TENX175_cellvit_seg.geojson.zip
+hest_data/cellvit_seg/TENX175_cellvit_seg.parquet
+hest_data/metadata/TENX175.json
+hest_data/patches/TENX175.h5
+hest_data/st/TENX175.h5ad
+hest_data/tissue_seg/TENX175_contours.geojson
+hest_data/wsis/TENX175.tif
+.idea/.gitignore
+.idea/csv-editor.xml
+.idea/deployment.xml
+.idea/jupyter-settings.xml
+.idea/misc.xml
+.idea/modules.xml
+.idea/SpatialTranscriptFormer.iml
+.idea/vcs.xml
+.idea/inspectionProfiles/profiles_settings.xml
+.idea/inspectionProfiles/Project_Default.xml
+.idea/runConfigurations/STF_Compute_Pathways.xml
+.idea/runConfigurations/STF_Train_PrimaryPathway.xml
+.gemini/settings.json
+.gemini/agents/literature-search.md
+.gemini/agents/test-triage.md
+
+# Large Data Artifacts
+global_genes_stats.csv
+*.sqlite
+HEST_v1_3_0.csv
+global_genes.json

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+
+-   repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+    -   id: black
+        language_version: python3

config.yaml

@@ -12,7 +12,7 @@ training:
   batch_size: 8
   learning_rate: 0.0001
   output_dir: "./runs"
-  
+
 # MSigDB Pathway Settings
 pathways:
   default_collection: "hallmarks"

docs/TESTING.md

@@ -24,7 +24,7 @@ Or using the provided PowerShell script:
   - Sample filtering logic (by Organ, Disease, Technology).
   - Pattern generation for HEST subsets.
   - Unzipping logic for segmentation files.
-  
+
 - `tests/test_splitting_logic.py`: Tests for `splitting.py`. Verifies:
   - Patient-level splitting (train/val/test).
   - Leakage prevention (ensuring patients don't overlap between splits).