From ff7d91757687636edb697eb63f45a7de9564419b Mon Sep 17 00:00:00 2001 From: Daniel Franco Date: Mon, 16 Sep 2024 11:09:41 +0200 Subject: [PATCH] Update to 3.5.2 version --- biapy/__init__.py | 2 +- biapy/utils/env/Dockerfile | 8 ++++---- biapy/utils/env/Dockerfile_CUDA10.2 | 6 +++--- pyproject.toml | 2 +- templates/classification/2d_classification.yaml | 2 +- templates/classification/2d_classification_rgb.yaml | 2 +- templates/classification/3d_classification.yaml | 2 +- templates/denoising/2d_denoising.yaml | 2 +- templates/denoising/3d_denoising.yaml | 2 +- templates/detection/2d_detection.yaml | 2 +- templates/detection/3D_cell_detection_zarr_tutorial.yaml | 2 +- templates/detection/3d_detection.yaml | 2 +- templates/image-to-image/2d_image-to-image.yaml | 2 +- templates/image-to-image/3d_image-to-image.yaml | 2 +- .../instance_segmentation/2d_instance_segmentation.yaml | 2 +- .../instance_segmentation/3d_instance_segmentation.yaml | 2 +- templates/self-supervised/2d_self-supervised.yaml | 2 +- templates/self-supervised/3d_self-supervised.yaml | 2 +- .../semantic_segmentation/2d_semantic_segmentation.yaml | 2 +- .../semantic_segmentation/3d_semantic_segmentation.yaml | 2 +- templates/semantic_segmentation/wound_segmentation.yaml | 2 +- templates/super-resolution/2d_super-resolution.yaml | 2 +- templates/super-resolution/2d_super-resolution_rgb.yaml | 2 +- templates/super-resolution/3d_super-resolution.yaml | 2 +- 24 files changed, 29 insertions(+), 29 deletions(-) diff --git a/biapy/__init__.py b/biapy/__init__.py index eb5dd5da..97f43be7 100644 --- a/biapy/__init__.py +++ b/biapy/__init__.py @@ -1,4 +1,4 @@ -__version__ = "3.5.1" +__version__ = "3.5.2" import argparse import os diff --git a/biapy/utils/env/Dockerfile b/biapy/utils/env/Dockerfile index 69af8ec0..71436adc 100755 --- a/biapy/utils/env/Dockerfile +++ b/biapy/utils/env/Dockerfile @@ -31,14 +31,14 @@ RUN conda update -qy conda \ SHELL ["conda", "run", "-n", "BiaPy_env", "/bin/bash", "-c"] # Install BiaPy -RUN pip install biapy==3.4.3 +RUN pip install biapy==3.5.2 # Install Pytorch 2.2.0 + CUDA 11.8 -RUN pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu118 -RUN pip install timm torchmetrics +RUN pip install torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118 +RUN pip install timm pytorch-msssim torchmetrics[image] # Clone BiaPy, as running it with python -c "" stops the container with no error after a few seconds running -RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.4.3 /installations/BiaPy +RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.5.2 /installations/BiaPy # To remove CuDNN issue WORKDIR /installations/miniconda3/envs/BiaPy_env/lib/python3.10/site-packages/nvidia/cuda_nvrtc/lib/ diff --git a/biapy/utils/env/Dockerfile_CUDA10.2 b/biapy/utils/env/Dockerfile_CUDA10.2 index 1ea0b995..5e8a305e 100755 --- a/biapy/utils/env/Dockerfile_CUDA10.2 +++ b/biapy/utils/env/Dockerfile_CUDA10.2 @@ -32,14 +32,14 @@ RUN conda update -qy conda \ SHELL ["conda", "run", "-n", "BiaPy_env", "/bin/bash", "-c"] # Install BiaPy -RUN pip install biapy==3.4.3 +RUN pip install biapy==3.5.2 # Install Pytorch 1.12.1 + CUDA 10.2 RUN conda install pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=10.2 -c pytorch -RUN pip install timm torchmetrics +RUN pip install timm pytorch-msssim torchmetrics[image] # Clone BiaPy, as running it with python -c "" stops the container with no error after a few seconds running -RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.4.3 /installations/BiaPy +RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.5.2 /installations/BiaPy # To remove CuDNN issue WORKDIR /installations/miniconda3/envs/BiaPy_env/lib/python3.10/site-packages/nvidia/cuda_nvrtc/lib/ diff --git a/pyproject.toml b/pyproject.toml index b285f3cd..5f31e126 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "biapy" -version = "3.5.1" +version = "3.5.2" description = "BiaPy: Bioimage analysis pipelines in Python" readme = "README.md" requires-python = ">=3.10" diff --git a/templates/classification/2d_classification.yaml b/templates/classification/2d_classification.yaml index 0323f5d5..fedd357d 100644 --- a/templates/classification/2d_classification.yaml +++ b/templates/classification/2d_classification.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/classification/2d_classification_rgb.yaml b/templates/classification/2d_classification_rgb.yaml index 82053b45..958aba55 100644 --- a/templates/classification/2d_classification_rgb.yaml +++ b/templates/classification/2d_classification_rgb.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/classification/3d_classification.yaml b/templates/classification/3d_classification.yaml index bd324206..11858656 100644 --- a/templates/classification/3d_classification.yaml +++ b/templates/classification/3d_classification.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/denoising/2d_denoising.yaml b/templates/denoising/2d_denoising.yaml index 8e351b60..92b97be3 100644 --- a/templates/denoising/2d_denoising.yaml +++ b/templates/denoising/2d_denoising.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 # We try to mimic here N2Void project parameters SYSTEM: NUM_CPUS: -1 diff --git a/templates/denoising/3d_denoising.yaml b/templates/denoising/3d_denoising.yaml index 88901da4..63a73366 100644 --- a/templates/denoising/3d_denoising.yaml +++ b/templates/denoising/3d_denoising.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 # We try to mimic here N2Void project parameters SYSTEM: diff --git a/templates/detection/2d_detection.yaml b/templates/detection/2d_detection.yaml index cb6143a2..b2d96e81 100644 --- a/templates/detection/2d_detection.yaml +++ b/templates/detection/2d_detection.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/detection/3D_cell_detection_zarr_tutorial.yaml b/templates/detection/3D_cell_detection_zarr_tutorial.yaml index 4002e452..1c50f7ec 100644 --- a/templates/detection/3D_cell_detection_zarr_tutorial.yaml +++ b/templates/detection/3D_cell_detection_zarr_tutorial.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/detection/3d_detection.yaml b/templates/detection/3d_detection.yaml index 33ec309a..61ca8617 100644 --- a/templates/detection/3d_detection.yaml +++ b/templates/detection/3d_detection.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/image-to-image/2d_image-to-image.yaml b/templates/image-to-image/2d_image-to-image.yaml index 4837a0a0..7cbd043b 100644 --- a/templates/image-to-image/2d_image-to-image.yaml +++ b/templates/image-to-image/2d_image-to-image.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/image-to-image/3d_image-to-image.yaml b/templates/image-to-image/3d_image-to-image.yaml index ff001368..dc41e44d 100644 --- a/templates/image-to-image/3d_image-to-image.yaml +++ b/templates/image-to-image/3d_image-to-image.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/instance_segmentation/2d_instance_segmentation.yaml b/templates/instance_segmentation/2d_instance_segmentation.yaml index c4329bc1..1939034b 100644 --- a/templates/instance_segmentation/2d_instance_segmentation.yaml +++ b/templates/instance_segmentation/2d_instance_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/instance_segmentation/3d_instance_segmentation.yaml b/templates/instance_segmentation/3d_instance_segmentation.yaml index 23c67397..35de6854 100644 --- a/templates/instance_segmentation/3d_instance_segmentation.yaml +++ b/templates/instance_segmentation/3d_instance_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/self-supervised/2d_self-supervised.yaml b/templates/self-supervised/2d_self-supervised.yaml index 477e7144..a6ae11a7 100644 --- a/templates/self-supervised/2d_self-supervised.yaml +++ b/templates/self-supervised/2d_self-supervised.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/self-supervised/3d_self-supervised.yaml b/templates/self-supervised/3d_self-supervised.yaml index 2f4230bc..64215c6c 100644 --- a/templates/self-supervised/3d_self-supervised.yaml +++ b/templates/self-supervised/3d_self-supervised.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/semantic_segmentation/2d_semantic_segmentation.yaml b/templates/semantic_segmentation/2d_semantic_segmentation.yaml index 15e41b77..e3c47e1b 100644 --- a/templates/semantic_segmentation/2d_semantic_segmentation.yaml +++ b/templates/semantic_segmentation/2d_semantic_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/semantic_segmentation/3d_semantic_segmentation.yaml b/templates/semantic_segmentation/3d_semantic_segmentation.yaml index a386f686..28475840 100644 --- a/templates/semantic_segmentation/3d_semantic_segmentation.yaml +++ b/templates/semantic_segmentation/3d_semantic_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/semantic_segmentation/wound_segmentation.yaml b/templates/semantic_segmentation/wound_segmentation.yaml index 0b77a8d4..a00fc882 100644 --- a/templates/semantic_segmentation/wound_segmentation.yaml +++ b/templates/semantic_segmentation/wound_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/super-resolution/2d_super-resolution.yaml b/templates/super-resolution/2d_super-resolution.yaml index f7189b23..c0bfe121 100644 --- a/templates/super-resolution/2d_super-resolution.yaml +++ b/templates/super-resolution/2d_super-resolution.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/super-resolution/2d_super-resolution_rgb.yaml b/templates/super-resolution/2d_super-resolution_rgb.yaml index 470b04d2..eb53945f 100644 --- a/templates/super-resolution/2d_super-resolution_rgb.yaml +++ b/templates/super-resolution/2d_super-resolution_rgb.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1 diff --git a/templates/super-resolution/3d_super-resolution.yaml b/templates/super-resolution/3d_super-resolution.yaml index fba6818e..f80a6aa0 100644 --- a/templates/super-resolution/3d_super-resolution.yaml +++ b/templates/super-resolution/3d_super-resolution.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.1 +# BiaPy version: 3.5.2 SYSTEM: NUM_CPUS: -1