Merge pull request #445 from Dana-Farber-AIOS/dev

v 3.0.1. PyTorch changes.

Author: jamesgwen

.github/workflows/tests-linux.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
     timeout-minutes: 60 # add a timeout
 
     steps:
@@ -83,14 +83,27 @@ jobs:
         sudo df -h
         sudo du -h
         
+    # - name: free disk space
+    #   run: |
+    #     sudo swapoff -a
+    #     sudo rm -f /swapfile
+    #     sudo apt clean
+    #     docker rmi $(docker image ls -aq)
+    #     sudo df -h
+    #     sudo du -h
+
     - name: free disk space
       run: |
         sudo swapoff -a
         sudo rm -f /swapfile
-        sudo apt clean
-        docker rmi $(docker image ls -aq)
-        sudo df -h
-        sudo du -h
+        sudo apt-get clean
+        if [ "$(docker image ls -aq)" ]; then
+          docker rmi $(docker image ls -aq)
+        else
+          echo "No Docker images to remove."
+         fi
+         sudo df -h
+         sudo du -h
 
     # - name: Check Coverage Command
     #   run: |

.github/workflows/tests-windows.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: [ "3.9", "3.10"]
     timeout-minutes: 120
 
     steps:

environment.yml

@@ -6,7 +6,7 @@ channels:
 
 dependencies:
     - python<=3.10
-    - pip==23.3.2
+    - pip==25.0.1
     - numpy==1.23.5
     - scipy<=1.11.4
     - scikit-image<=0.22.0

pathml/_version.py

@@ -3,4 +3,4 @@
 License: GNU GPL 2.0
 """
 
-__version__ = "3.0.0"
+__version__ = "3.0.1"

requirements/environment_test.yml

@@ -6,13 +6,13 @@ channels:
 
 dependencies:
     - python<=3.10
-    - pip==23.3.2
+    - pip==25.0.1
     - numpy==1.23.5
     - scipy<=1.11.4
     - scikit-image<=0.22.0
     - matplotlib<=3.8.2
     - openjdk<=18.0.0
-    - pytorch==1.13.1
+    - pytorch==2.6.0
     - h5py==3.10.0
     - dask<=2023.12.1
     - pydicom==2.4.4

requirements/requirements_torch.txt

@@ -1,2 +1 @@
---extra-index-url https://download.pytorch.org/whl/cu116
-torch==1.13.1+cu116
+torch==2.6.0

setup.py

@@ -10,7 +10,7 @@
 
 version = about["__version__"]
 
-dependency_links = ["https://download.pytorch.org/whl/cu116"]
+dependency_links = ["https://download.pytorch.org/whl/cu124"]
 
 setuptools.setup(
     name="pathml",
@@ -40,7 +40,7 @@
         "dask[distributed]",
         "anndata>=0.7.6",
         "scanpy==1.9.6",
-        "torch==1.13.1",
+        "torch==2.6.0",
         "opencv-contrib-python==4.8.1.78",
         "python-bioformats==4.0.7",
         "python-javabridge==4.0.3",

tests/preprocessing_tests/test_tilestitcher.py

@@ -1,7 +1,7 @@
 """
- Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine
- License: GNU GPL 2.0
- """
+Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine
+License: GNU GPL 2.0
+"""
 
 import glob
 import os