From 3436028f571957cb2c5c45fbcbd08a8c37252962 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Sat, 28 Sep 2024 18:56:14 +0200
Subject: [PATCH] [pyproject] Pin clapper; Remove pixi system-requirements
(default is fine)
---
pixi.lock | 10372 +++++-----------
pyproject.toml | 7 +-
src/mednet/scripts/classify/evaluate.py | 2 +-
.../scripts/classify/saliency/completeness.py | 2 +-
.../scripts/classify/saliency/generate.py | 2 +-
.../classify/saliency/interpretability.py | 2 +-
src/mednet/scripts/classify/saliency/view.py | 2 +-
src/mednet/scripts/config.py | 4 +-
src/mednet/scripts/detect/evaluate.py | 2 +-
src/mednet/scripts/experiment.py | 4 +-
src/mednet/scripts/predict.py | 4 +-
src/mednet/scripts/preprocess.py | 2 +-
.../scripts/segment/dump_annotations.py | 4 +-
src/mednet/scripts/segment/evaluate.py | 2 +-
src/mednet/scripts/segment/view.py | 2 +-
src/mednet/scripts/train.py | 2 +-
src/mednet/scripts/upload.py | 2 +-
17 files changed, 3078 insertions(+), 7339 deletions(-)
diff --git a/pixi.lock b/pixi.lock
index 660b25cd..8979a5a3 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -7,7 +7,7 @@ environments:
linux-64:
- conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.4.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.6.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_4.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.0.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h2ec8cdc_2.conda
@@ -25,7 +25,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.3-h5888daf_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.16.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.16.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.14.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.1.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/hatch-1.12.0-pyhd8ed1ab_0.conda
@@ -35,21 +35,20 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.27.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/hyperlink-21.0.0-pyhd3deb0d_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.8-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.4.0-pyha770c72_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-8.4.0-hd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.5.0-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.5-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.classes-3.4.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.context-5.3.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.functools-4.0.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jeepney-0.8.0-pyhd8ed1ab_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.3.0-pyha804496_0.conda
- - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.4.1-pyha804496_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.1.0-h77fa898_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h69a702a_1.conda
- - conda: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.3-h315aac3_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.82.1-h2ff4ddf_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
@@ -70,20 +69,20 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-hba22ea6_2.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pexpect-4.9.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pkginfo-1.10.0-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.3.2-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.3.6-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.6-hc5c86c4_1_cpython.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/readme_renderer-44.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/requests-toolbelt-1.0.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/rfc3986-2.0.0-pyhd8ed1ab_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.7.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.8.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/secretstorage-3.3.3-py312h7900ff3_3.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_0.conda
@@ -91,21 +90,21 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-w-1.0.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.13.2-pyha770c72_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/trove-classifiers-2024.7.2-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/trove-classifiers-2024.9.12-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/twine-5.1.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.12.2-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.2-pyhd8ed1ab_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.3-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/userpath-1.7.0-pyhd8ed1ab_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/linux-64/uv-0.4.9-h0f3a69f_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/uv-0.4.17-h0f3a69f_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.1.2-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.26.4-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.26.6-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py312hef9b889_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
osx-arm64:
- - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.4.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.6.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_4.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.0.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-python-1.1.0-py312hde4cb15_2.conda
@@ -120,7 +119,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.2-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.16.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.16.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.14.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.1.0-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/hatch-1.12.0-pyhd8ed1ab_0.conda
@@ -130,15 +129,14 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.27.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/hyperlink-21.0.0-pyhd3deb0d_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.8-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.4.0-pyha770c72_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-8.4.0-hd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.5.0-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.5-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.classes-3.4.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.context-5.3.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.functools-4.0.0-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.3.0-pyh534df25_0.conda
- - conda: https://conda.anaconda.org/conda-forge/osx-arm64/libcxx-18.1.8-h3ed4263_7.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.4.1-pyh534df25_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/libcxx-19.1.0-ha82da77_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libexpat-2.6.3-hf9b8971_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libffi-3.4.2-h3422bc3_5.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/libsqlite-3.46.1-hc14010f_0.conda
@@ -153,37 +151,37 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/pathspec-0.12.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pexpect-4.9.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pkginfo-1.10.0-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.3.2-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.3.6-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2
- conda: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.6-h739c21a_0_cpython.conda
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.6-h739c21a_1_cpython.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/python_abi-3.12-5_cp312.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.2-h92ec313_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/readme_renderer-44.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.3-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/rfc3986-2.0.0-pyhd8ed1ab_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.7.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/rich-13.8.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.13.2-pyha770c72_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/trove-classifiers-2024.7.2-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/trove-classifiers-2024.9.12-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/twine-5.1.1-pyhd8ed1ab_0.conda
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- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h8827d51_1.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.2-pyhd8ed1ab_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.3-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/userpath-1.7.0-pyhd8ed1ab_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/osx-arm64/uv-0.4.9-hd3a8144_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/uv-0.4.17-hd3a8144_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.1.2-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.26.4-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.26.6-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/xz-5.2.6-h57fd34a_0.tar.bz2
- - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.2-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.23.0-py312h15fbf35_1.conda
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda
cuda:
@@ -196,29 +194,29 @@ environments:
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size: 2562
timestamp: 1578324546067
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license: MIT AND Apache-2.0
license_family: Apache
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license: BSD-3-Clause
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license: BSD-3-Clause
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license: BSD-3-Clause
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noarch: python
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- lame >=3.100,<3.101.0a0
- libass >=0.17.3,<0.17.4.0a0
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license: GPL-2.0-or-later
license_family: GPL
purls:
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name: ffmpeg
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subdir: linux-64
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- libva >=2.22.0,<3.0a0
- libvpx >=1.14.1,<1.15.0a0
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- libzlib >=1.3.1,<2.0a0
- openh264 >=2.4.1,<2.4.2.0a0
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license_family: GPL
purls:
- pkg:pypi/ffmpeg
- size: 9897550
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name: ffmpeg
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- md5: 20bb671f432f0d6b327c9517547e9840
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+ build: gpl_h8657690_705
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+ url: https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-7.0.2-gpl_h8657690_705.conda
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- dav1d >=1.2.1,<1.2.2.0a0
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- lame >=3.100,<3.101.0a0
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license: GPL-2.0-or-later
license_family: GPL
purls:
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- size: 8643313
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name: ffmpeg
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+ build: gpl_he9820c9_105
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subdir: osx-arm64
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- md5: 1d4bd3eb115ec469609beb7fa164bf6b
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license_family: BSD
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- libsqlite >=3.46.1,<4.0a0
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- license: MIT
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- purls:
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name: libgdal-fits
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+ build: h248c7bc_5
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- - libstdcxx >=13
- license: MIT
- license_family: MIT
purls:
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name: libgdal-fits
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subdir: linux-64
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+ url: https://conda.anaconda.org/conda-forge/linux-64/libgdal-fits-3.9.2-h2db6552_5.conda
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license: MIT
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- license_family: MIT
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subdir: osx-arm64
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- md5: bb7a5ffe703108d0d460af0c5b0167f0
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/libgdal-grib-3.9.2-h6d3d72d_5.conda
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license: MIT
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- - libstdcxx >=13
- license: MIT
- license_family: MIT
purls:
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name: libgdal-grib
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subdir: linux-64
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license: MIT
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- license: MIT
- license_family: MIT
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- size: 578034
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name: libgdal-hdf4
version: 3.9.2
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subdir: osx-arm64
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license: MIT
- license_family: MIT
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- license: MIT
- license_family: MIT
purls:
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subdir: linux-64
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license: MIT
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- license: MIT
- license_family: MIT
- purls:
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name: libgdal-hdf5
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+ build: h2def128_5
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subdir: osx-arm64
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license: MIT
- license_family: MIT
purls:
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subdir: linux-64
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license: MIT
- license_family: MIT
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license: MIT
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+ - libtiff >=4.7.0,<4.8.0a0
- libwebp-base >=1.4.0,<2.0a0
- libzlib >=1.3.1,<2.0a0
- numpy >=1.19,<3
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license_family: Apache
purls:
- pkg:pypi/libopencv
- size: 21796713
- timestamp: 1723437479548
-- kind: conda
- name: libopencv
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- build: headless_py312h7bc6ef4_3
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- subdir: osx-arm64
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- license: Apache-2.0
- license_family: Apache
- purls:
- - pkg:pypi/libopencv
- size: 21816750
- timestamp: 1723437420883
+ size: 21813754
+ timestamp: 1726971473525
- kind: conda
name: libopencv
version: 4.10.0
- build: headless_py312h7bc6ef4_3
- build_number: 3
+ build: headless_py312haa779ad_4
+ build_number: 4
subdir: osx-arm64
- url: https://conda.anaconda.org/conda-forge/osx-arm64/libopencv-4.10.0-headless_py312h7bc6ef4_3.conda
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- md5: 3326a89908c2e00e29224c7b1b573d0d
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/libopencv-4.10.0-headless_py312haa779ad_4.conda
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- libasprintf >=0.22.5,<1.0a0
- libcblas >=3.9.0,<4.0a0
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- libiconv >=1.17,<2.0a0
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- - libopenvino-tensorflow-lite-frontend >=2024.3.0,<2024.3.1.0a0
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- libprotobuf >=4.25.3,<4.25.4.0a0
- - libtiff >=4.6.0,<4.7.0a0
+ - libtiff >=4.7.0,<4.8.0a0
- libwebp-base >=1.4.0,<2.0a0
- libzlib >=1.3.1,<2.0a0
- numpy >=1.19,<3
@@ -16260,105 +13777,51 @@ packages:
license_family: Apache
purls:
- pkg:pypi/libopencv
- size: 21816750
- timestamp: 1723437420883
-- kind: conda
- name: libopencv
- version: 4.10.0
- build: qt6_py311h4743a55_603
- build_number: 603
- subdir: linux-64
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- license: Apache-2.0
- license_family: Apache
- purls:
- - pkg:pypi/libopencv
- size: 30424392
- timestamp: 1723434362104
+ size: 21853376
+ timestamp: 1726971451962
- kind: conda
name: libopencv
version: 4.10.0
- build: qt6_py312h6ebf6f7_603
- build_number: 603
+ build: qt6_py311h22e9e49_604
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subdir: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libopencv-4.10.0-qt6_py312h6ebf6f7_603.conda
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- md5: ec62936b199ec07a713c6b7f9c0f76f3
+ url: https://conda.anaconda.org/conda-forge/linux-64/libopencv-4.10.0-qt6_py311h22e9e49_604.conda
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- hdf5 >=1.14.3,<1.14.4.0a0
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- libasprintf >=0.22.5,<1.0a0
- libcblas >=3.9.0,<4.0a0
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- libjpeg-turbo >=3.0.0,<4.0a0
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- libprotobuf >=4.25.3,<4.25.4.0a0
- - libstdcxx-ng >=12
- - libtiff >=4.6.0,<4.8.0a0
+ - libstdcxx >=13
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- libwebp-base >=1.4.0,<2.0a0
- libzlib >=1.3.1,<2.0a0
- numpy >=1.19,<3
@@ -16368,51 +13831,51 @@ packages:
license_family: Apache
purls:
- pkg:pypi/libopencv
- size: 30358816
- timestamp: 1723433882910
+ size: 30797757
+ timestamp: 1726968759247
- kind: conda
name: libopencv
version: 4.10.0
- build: qt6_py312h6ebf6f7_603
- build_number: 603
+ build: qt6_py312h01efb12_604
+ build_number: 604
subdir: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libopencv-4.10.0-qt6_py312h6ebf6f7_603.conda
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- md5: ec62936b199ec07a713c6b7f9c0f76f3
+ url: https://conda.anaconda.org/conda-forge/linux-64/libopencv-4.10.0-qt6_py312h01efb12_604.conda
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- freetype >=2.12.1,<3.0a0
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- hdf5 >=1.14.3,<1.14.4.0a0
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- libasprintf >=0.22.5,<1.0a0
- libcblas >=3.9.0,<4.0a0
- - libgcc-ng >=12
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- libprotobuf >=4.25.3,<4.25.4.0a0
- - libstdcxx-ng >=12
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- libwebp-base >=1.4.0,<2.0a0
- libzlib >=1.3.1,<2.0a0
- numpy >=1.19,<3
@@ -16422,436 +13885,436 @@ packages:
license_family: Apache
purls:
- pkg:pypi/libopencv
- size: 30358816
- timestamp: 1723433882910
+ size: 30825773
+ timestamp: 1726969093815
- kind: conda
name: libopenvino
- version: 2024.3.0
- build: h2da1b83_0
- subdir: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/libopenvino-2024.3.0-h2da1b83_0.conda
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- md5: bb7a2589859c7475e38c1af677e16698
+ version: 2024.4.0
+ build: h49f535f_0
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+ url: https://conda.anaconda.org/conda-forge/osx-arm64/libopenvino-2024.4.0-h49f535f_0.conda
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+ - tbb >=2021.13.0
purls:
- pkg:pypi/libopenvino
- size: 5329666
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+ size: 3942341
+ timestamp: 1726763749725
- kind: conda
name: libopenvino
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- build: h5c9529b_0
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license_family: MIT
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license_family: MIT
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license: MIT
license_family: MIT
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license: MIT
license_family: MIT
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name: xorg-libxrender
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subdir: linux-64
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license_family: MIT
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+ md5: f9545ef8a367db7b2bb45a66650a752d
depends:
- __glibc >=2.17,<3.0.a0
- idna >=2.0
@@ -27812,16 +23609,16 @@ packages:
license_family: Apache
purls:
- pkg:pypi/yarl
- size: 153157
- timestamp: 1725946291968
+ size: 156552
+ timestamp: 1727511333203
- kind: conda
name: yarl
- version: 1.11.1
+ version: 1.13.1
build: py312h024a12e_0
subdir: osx-arm64
- url: https://conda.anaconda.org/conda-forge/osx-arm64/yarl-1.11.1-py312h024a12e_0.conda
- sha256: c24ec0a51e317722cfc36962cb1965714ac0647bfa0ac1fb4955321928285082
- md5: a68a333a9ffc093575682fa747e38947
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/yarl-1.13.1-py312h024a12e_0.conda
+ sha256: 3dd43c0c56f7ebce7fc1a7458b3677e8bae1ffd3e69de5f33900fad5316a48be
+ md5: 7f735d412c81c48ac9c784004d23ee64
depends:
- __osx >=11.0
- idna >=2.0
@@ -27833,16 +23630,16 @@ packages:
license_family: Apache
purls:
- pkg:pypi/yarl
- size: 139226
- timestamp: 1725946411244
+ size: 141664
+ timestamp: 1727511334341
- kind: conda
name: yarl
- version: 1.11.1
+ version: 1.13.1
build: py312h66e93f0_0
subdir: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/yarl-1.11.1-py312h66e93f0_0.conda
- sha256: a8f342aad4759f9305e629d414eabecd1ca687faa12da2c9c3f46efeb91e4e79
- md5: 5b5d6f3f65bdc30844eb0a919147c15d
+ url: https://conda.anaconda.org/conda-forge/linux-64/yarl-1.13.1-py312h66e93f0_0.conda
+ sha256: d184281da96ccaf01d044146b73a50513d554889b1f1efb1f1a40675e74d40df
+ md5: 2df2598fb30eaccaf8717bac238d4e49
depends:
- __glibc >=2.17,<3.0.a0
- idna >=2.0
@@ -27854,78 +23651,64 @@ packages:
license_family: Apache
purls:
- pkg:pypi/yarl
- size: 152128
- timestamp: 1725946293010
+ size: 154923
+ timestamp: 1727511288063
- kind: conda
name: zfp
version: 1.0.1
- build: ha84d530_1
- build_number: 1
+ build: h1c5d8ea_2
+ build_number: 2
subdir: osx-arm64
- url: https://conda.anaconda.org/conda-forge/osx-arm64/zfp-1.0.1-ha84d530_1.conda
- sha256: 55fd874ea43a96880a79fd18cde5e7a61b234d9065fe4c5b423dfbc09e5d1bf2
- md5: 588dc431a2f805060225549c4c99225e
+ url: https://conda.anaconda.org/conda-forge/osx-arm64/zfp-1.0.1-h1c5d8ea_2.conda
+ sha256: 814af9f9429cca403aa308cef46455e745284fb1ecbad83a5722bfc58db8b11a
+ md5: 8066eb9d5acdbaf825cf8cf689517a33
depends:
- __osx >=11.0
- - libcxx >=16
- - llvm-openmp >=16.0.6
+ - libcxx >=17
+ - llvm-openmp >=17.0.6
license: BSD-3-Clause
license_family: BSD
purls:
- pkg:pypi/zfp
- size: 196636
- timestamp: 1719230614632
+ size: 200112
+ timestamp: 1726925701356
- kind: conda
name: zfp
version: 1.0.1
- build: hac33072_1
- build_number: 1
+ build: h5888daf_2
+ build_number: 2
subdir: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/zfp-1.0.1-hac33072_1.conda
- sha256: 0f39a8089dd152419ec98d437f3910811fe0150261481a4e5a45bcbba5f318e2
- md5: df96b7266e49529d82de467b23977452
+ url: https://conda.anaconda.org/conda-forge/linux-64/zfp-1.0.1-h5888daf_2.conda
+ sha256: 0dfafc75c72f308c0200836f2b973766cdcb8741b1ab61e0b462a34dd6b6ad20
+ md5: e0409515c467b87176b070bff5d9442e
depends:
+ - __glibc >=2.17,<3.0.a0
- _openmp_mutex >=4.5
- - libgcc-ng >=12
- - libstdcxx-ng >=12
+ - libgcc >=13
+ - libstdcxx >=13
license: BSD-3-Clause
license_family: BSD
purls:
- pkg:pypi/zfp
- size: 276454
- timestamp: 1719230451754
-- kind: conda
- name: zipp
- version: 3.20.1
- build: pyhd8ed1ab_0
- subdir: noarch
- noarch: python
- url: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda
- sha256: 30762bd25b6fc8714d5520a223ccf20ad4a6792dc439c54b59bf44b60bf51e72
- md5: 74a4befb4b38897e19a107693e49da20
- depends:
- - python >=3.8
- license: MIT
- license_family: MIT
- size: 21110
- timestamp: 1724731063145
+ size: 279120
+ timestamp: 1726925529897
- kind: conda
name: zipp
- version: 3.20.1
+ version: 3.20.2
build: pyhd8ed1ab_0
subdir: noarch
noarch: python
- url: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.1-pyhd8ed1ab_0.conda
- sha256: 30762bd25b6fc8714d5520a223ccf20ad4a6792dc439c54b59bf44b60bf51e72
- md5: 74a4befb4b38897e19a107693e49da20
+ url: https://conda.anaconda.org/conda-forge/noarch/zipp-3.20.2-pyhd8ed1ab_0.conda
+ sha256: 1e84fcfa41e0afdd87ff41e6fbb719c96a0e098c1f79be342293ab0bd8dea322
+ md5: 4daaed111c05672ae669f7036ee5bba3
depends:
- python >=3.8
license: MIT
license_family: MIT
purls:
- pkg:pypi/zipp
- size: 21110
- timestamp: 1724731063145
+ size: 21409
+ timestamp: 1726248679175
- kind: conda
name: zipp
version: 3.20.2
@@ -27939,8 +23722,6 @@ packages:
- python >=3.8
license: MIT
license_family: MIT
- purls:
- - pkg:pypi/zipp
size: 21409
timestamp: 1726248679175
- kind: conda
@@ -27979,41 +23760,6 @@ packages:
- pkg:pypi/zlib
size: 78260
timestamp: 1716874280334
-- kind: conda
- name: zlib-ng
- version: 2.2.1
- build: h00cdb27_0
- subdir: osx-arm64
- url: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.2.1-h00cdb27_0.conda
- sha256: f6092fbcc88dc46ae0781f41dc8901c84dd8974ba0efdb39f1c31654078c621a
- md5: 2cd592101665c8cec43a35b069740c2b
- depends:
- - __osx >=11.0
- - libcxx >=16
- license: Zlib
- license_family: Other
- purls:
- - pkg:pypi/zlib-ng
- size: 89871
- timestamp: 1719947606865
-- kind: conda
- name: zlib-ng
- version: 2.2.1
- build: he02047a_0
- subdir: linux-64
- url: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.2.1-he02047a_0.conda
- sha256: f555ee579fc1cd5ccf1ef760970c4bc34db8783d3ba5c42c9d50541c924c5b66
- md5: 8fd1654184917db2cb74fc84cb4fff79
- depends:
- - __glibc >=2.17,<3.0.a0
- - libgcc-ng >=12
- - libstdcxx-ng >=12
- license: Zlib
- license_family: Other
- purls:
- - pkg:pypi/zlib-ng
- size: 104865
- timestamp: 1719947458940
- kind: conda
name: zlib-ng
version: 2.2.2
diff --git a/pyproject.toml b/pyproject.toml
index fb5e2cd9..0878b2de 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ classifiers = [
]
dependencies = [
- "clapper",
+ "clapper>=1.3.0",
"click",
"compact-json",
"credible",
@@ -83,11 +83,8 @@ channels = ["conda-forge"]
platforms = ["linux-64", "osx-arm64"]
conda-pypi-map = { "https://conda.anaconda.org/conda-forge" = ".pixi-pytorch-mapping.json" }
-[tool.pixi.system-requirements]
-linux = "4.19.0"
-
[tool.pixi.dependencies]
-clapper = "*"
+clapper = ">=1.3.0"
click = "*"
compact-json = "*"
credible = "*"
diff --git a/src/mednet/scripts/classify/evaluate.py b/src/mednet/scripts/classify/evaluate.py
index 58bc533f..f95d39b3 100644
--- a/src/mednet/scripts/classify/evaluate.py
+++ b/src/mednet/scripts/classify/evaluate.py
@@ -114,7 +114,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
default=False,
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def evaluate(
predictions: pathlib.Path,
output_folder: pathlib.Path,
diff --git a/src/mednet/scripts/classify/saliency/completeness.py b/src/mednet/scripts/classify/saliency/completeness.py
index 36235f1d..f6df6dc7 100644
--- a/src/mednet/scripts/classify/saliency/completeness.py
+++ b/src/mednet/scripts/classify/saliency/completeness.py
@@ -180,7 +180,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
default=True,
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def completeness(
model,
datamodule,
diff --git a/src/mednet/scripts/classify/saliency/generate.py b/src/mednet/scripts/classify/saliency/generate.py
index 9e1cc442..71eecfc9 100644
--- a/src/mednet/scripts/classify/saliency/generate.py
+++ b/src/mednet/scripts/classify/saliency/generate.py
@@ -156,7 +156,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
provided datamodule, skipping any other dataset.""",
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def generate(
model,
datamodule,
diff --git a/src/mednet/scripts/classify/saliency/interpretability.py b/src/mednet/scripts/classify/saliency/interpretability.py
index 9cf032f7..e3edc84c 100644
--- a/src/mednet/scripts/classify/saliency/interpretability.py
+++ b/src/mednet/scripts/classify/saliency/interpretability.py
@@ -106,7 +106,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
default=True,
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def interpretability(
model,
datamodule,
diff --git a/src/mednet/scripts/classify/saliency/view.py b/src/mednet/scripts/classify/saliency/view.py
index 0b4c79f1..0028cefe 100644
--- a/src/mednet/scripts/classify/saliency/view.py
+++ b/src/mednet/scripts/classify/saliency/view.py
@@ -87,7 +87,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
type=click.FloatRange(min=0, max=1),
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def view(
model,
datamodule,
diff --git a/src/mednet/scripts/config.py b/src/mednet/scripts/config.py
index c090117e..da2a1b80 100644
--- a/src/mednet/scripts/config.py
+++ b/src/mednet/scripts/config.py
@@ -37,7 +37,7 @@ def config():
""",
)
-@verbosity_option(logger=logger)
+@verbosity_option(logger=logger, expose_value=False)
def list_(verbose) -> None: # numpydoc ignore=PR01
"""List configuration files installed."""
@@ -119,7 +119,7 @@ def list_(verbose) -> None: # numpydoc ignore=PR01
required=True,
nargs=-1,
)
-@verbosity_option(logger=logger)
+@verbosity_option(logger=logger, expose_value=False)
def describe(name, verbose) -> None: # numpydoc ignore=PR01
"""Describe a specific configuration file."""
diff --git a/src/mednet/scripts/detect/evaluate.py b/src/mednet/scripts/detect/evaluate.py
index 76bbec4e..87b68168 100644
--- a/src/mednet/scripts/detect/evaluate.py
+++ b/src/mednet/scripts/detect/evaluate.py
@@ -89,7 +89,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
default=True,
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def evaluate(
predictions: pathlib.Path,
output_folder: pathlib.Path,
diff --git a/src/mednet/scripts/experiment.py b/src/mednet/scripts/experiment.py
index c6f53520..569fc7ee 100644
--- a/src/mednet/scripts/experiment.py
+++ b/src/mednet/scripts/experiment.py
@@ -6,7 +6,7 @@ import json
from datetime import datetime
import click
-from clapper.click import ConfigCommand, ResourceOption, verbosity_option
+from clapper.click import ConfigCommand, verbosity_option
from clapper.logging import setup
from .train import reusable_options as training_options
@@ -33,7 +33,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
""",
)
@training_options
-@verbosity_option(logger=logger, cls=ResourceOption)
+@verbosity_option(logger=logger, expose_value=False)
@click.pass_context
def experiment(
ctx,
diff --git a/src/mednet/scripts/predict.py b/src/mednet/scripts/predict.py
index b7ff41eb..b2a2e219 100644
--- a/src/mednet/scripts/predict.py
+++ b/src/mednet/scripts/predict.py
@@ -129,9 +129,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
default=-1,
cls=clapper.click.ResourceOption,
)
-@clapper.click.verbosity_option(
- logger=logger, cls=clapper.click.ResourceOption, expose_value=False
-)
+@clapper.click.verbosity_option(logger=logger, expose_value=False)
def predict(
output_folder,
model,
diff --git a/src/mednet/scripts/preprocess.py b/src/mednet/scripts/preprocess.py
index 9e3c8d19..f3074859 100644
--- a/src/mednet/scripts/preprocess.py
+++ b/src/mednet/scripts/preprocess.py
@@ -83,7 +83,7 @@ logger = setup("mednet", format="%(levelname)s: %(message)s")
is_flag=True,
show_default=True,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def preprocess(
output_folder,
model,
diff --git a/src/mednet/scripts/segment/dump_annotations.py b/src/mednet/scripts/segment/dump_annotations.py
index d36c94c6..e28d245a 100644
--- a/src/mednet/scripts/segment/dump_annotations.py
+++ b/src/mednet/scripts/segment/dump_annotations.py
@@ -61,9 +61,7 @@ logger = clapper.logging.setup(
required=True,
cls=clapper.click.ResourceOption,
)
-@clapper.click.verbosity_option(
- logger=logger, cls=clapper.click.ResourceOption, expose_value=False
-)
+@clapper.click.verbosity_option(logger=logger, expose_value=False)
def dump_annotations(
output_folder, model, datamodule, **_
) -> None: # numpydoc ignore=PR01
diff --git a/src/mednet/scripts/segment/evaluate.py b/src/mednet/scripts/segment/evaluate.py
index ee322be7..7908163a 100644
--- a/src/mednet/scripts/segment/evaluate.py
+++ b/src/mednet/scripts/segment/evaluate.py
@@ -133,7 +133,7 @@ __import__("matplotlib").use("agg")
default=True,
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def evaluate(
predictions: pathlib.Path,
output_folder: pathlib.Path,
diff --git a/src/mednet/scripts/segment/view.py b/src/mednet/scripts/segment/view.py
index b357e42f..2edd50d7 100644
--- a/src/mednet/scripts/segment/view.py
+++ b/src/mednet/scripts/segment/view.py
@@ -126,7 +126,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
required=True,
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def view(
predictions: pathlib.Path,
output_folder: pathlib.Path,
diff --git a/src/mednet/scripts/train.py b/src/mednet/scripts/train.py
index 258ddef8..7918515a 100644
--- a/src/mednet/scripts/train.py
+++ b/src/mednet/scripts/train.py
@@ -293,7 +293,7 @@ def reusable_options(f):
""",
)
@reusable_options
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def train(
model,
output_folder,
diff --git a/src/mednet/scripts/upload.py b/src/mednet/scripts/upload.py
index 45b2296a..b8ac30b2 100644
--- a/src/mednet/scripts/upload.py
+++ b/src/mednet/scripts/upload.py
@@ -93,7 +93,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
type=click.IntRange(min=0),
cls=ResourceOption,
)
-@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
+@verbosity_option(logger=logger, expose_value=False)
def upload(
project_path: str,
experiment_folder: pathlib.Path,
--
GitLab