From a168996b170ef3f872ac6bfe612dacd41b3bab01 Mon Sep 17 00:00:00 2001
From: clemsgrs <clementnet@outlook.com>
Date: Mon, 2 Mar 2026 20:04:12 +0000
Subject: [PATCH] Bump version to 2.0.2

---
 pyproject.toml                   |  2 +-
 setup.cfg                        |  2 +-
 slide2vec/__init__.py            |  2 +-
 slide2vec/configs/pathojepa.yaml | 29 +++++++++++++++++++++--------
 4 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 57f56a9..9e07486 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ warn_unused_configs = true
 no_implicit_reexport = true
 
 [tool.bumpver]
-current_version = "2.0.1"
+current_version = "2.0.2"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false       # We do version bumping in CI, not as a commit
 tag = false          # Git tag already exists — we don't auto-tag
diff --git a/setup.cfg b/setup.cfg
index 7f7b10e..9aaf0fe 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = slide2vec
-version = 2.0.1
+version = 2.0.2
 description = Embedding of whole slide images with Foundation Models
 author = Clément Grisi
 platforms = unix, linux, osx, cygwin, win32
diff --git a/slide2vec/__init__.py b/slide2vec/__init__.py
index 010388e..7b7db65 100644
--- a/slide2vec/__init__.py
+++ b/slide2vec/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "2.0.1"
+__version__ = "2.0.2"
 
 import sys
 import os
diff --git a/slide2vec/configs/pathojepa.yaml b/slide2vec/configs/pathojepa.yaml
index 3c2afc3..b4d0ef3 100644
--- a/slide2vec/configs/pathojepa.yaml
+++ b/slide2vec/configs/pathojepa.yaml
@@ -1,23 +1,29 @@
-csv: ""
+# csv: "/data/pathology/projects/clement/leopard/csvs/dev-slide2vec.csv"
+# csv: "/data/pathology/projects/clement/leopard/csvs/tcga/tcga-slide2vec.csv"
+# csv: "/data/pathology/projects/clement/leopard/csvs/test-slide2vec.csv" 
+# csv: "/data/pathology/projects/clement/leopard/csvs/cologne-slide2vec.csv"
+csv: "/data/pathology/projects/clement/leopard/csvs/brazil-slide2vec-august-2025-revision.csv"
 
-visualize: true
-
-output_dir: "output" # output directory
+output_dir: "/data/pathology/projects/clement/discern/pathojepa/slide2vec"
+visualize: false
 
 tiling:
   params:
     spacing: 0.5 # spacing at which to tile the slide, in microns per pixel
     tolerance: 0.05 # tolerance for matching the spacing (float between 0 and 1)
-    tile_size: 224 # PathoJEPA inference target tile size
+    tile_size: 2048 # PathoJEPA inference target tile size
     min_tissue_percentage: 0.1 # threshold used to filter out tiles with too little tissue
+  seg_params:
+    downsample: 64
   filter_params:
-    ref_tile_size: 224
+    ref_tile_size: 256
 
 model:
-  level: "tile" # set to "region" to run region-level inference with this tile encoder
+  level: "region" # set to "region" to run region-level inference with this tile encoder
   name: "pathojepa"
   arch: "vit_small"
-  pretrained_weights: "/path/to/pathojepa/checkpoint.pth.tar"
+  pretrained_weights: "/data/pathology/projects/clement/discern/pathojepa/runs/dmky8lh7/jepa-pathorob-latest.pth.tar"
+  input_size: 224
   patch_size: 256 # region-unrolling size when model.level == "region"
   token_size: 16 # ViT patch size used by PathoJEPA
   normalize_embeddings: false
@@ -25,3 +31,10 @@ model:
 
 speed:
   fp16: false
+
+wandb:
+  enable: true
+  project: "leopard"
+  username: "clemsg"
+  exp_name: "features"
+  tags: ["features", "dev", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]