diff --git a/pyproject.toml b/pyproject.toml index 4f61e34..56d04d7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ warn_unused_configs = true no_implicit_reexport = true [tool.bumpver] -current_version = "1.4.0" +current_version = "2.0.0" 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 858067b..7b17bd6 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = slide2vec -version = 1.4.0 +version = 2.0.0 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 3e8d9f9..8c0d5d5 100644 --- a/slide2vec/__init__.py +++ b/slide2vec/__init__.py @@ -1 +1 @@ -__version__ = "1.4.0" +__version__ = "2.0.0" diff --git a/slide2vec/configs/conch.yaml b/slide2vec/configs/conch.yaml index e5f0bcf..ce4ae76 100644 --- a/slide2vec/configs/conch.yaml +++ b/slide2vec/configs/conch.yaml @@ -1,6 +1,6 @@ -csv: "/data/temporary/clement/notebooks/discern/prostate-bladder-breast-debug.csv" # path to csv containing slide paths +csv: "/data/temporary/clement/discern/multi-organ-1k.csv" # path to csv containing slide paths -output_dir: "output" # output directory +output_dir: "/data/temporary/clement/discern/slide2vec" # output directory visualize: true @@ -12,7 +12,7 @@ tiling: model: level: "tile" # level at which to extract the features ("tile", "region" or "slide") name: "conch" - batch_size: 1 + batch_size: 32 speed: fp16: true # use mixed precision during model inference