Update conda environments and CI

computational-cell-analytics · Dec 20, 2024 · 86fd304 · 86fd304
1 parent 91dc3f7
commit 86fd304
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Showing 5 changed files with 62 additions and 14 deletions.
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -23,6 +23,10 @@ jobs:
         # 3.12 currently not supported due to issues with nifty.
         # python-version: ["3.11", "3.12"]
         python-version: ["3.11"]
+        environment-file:
+            ubuntu-latest: environment_cpu.yaml
+            macos-latest: environment_cpu.yaml
+            windows-latest: environment_cpu_win.yaml
 
     steps:
       - name: Checkout
@@ -31,7 +35,7 @@ jobs:
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: environment_cpu.yaml
+          environment-file: ${{ matrix.environment-file }}
           create-args: >-
             python=${{ matrix.python-version }}
 

diff --git a/environment_cpu.yaml b/environment_cpu.yaml
@@ -1,22 +1,18 @@
 name: sam
 channels:
-    - pytorch
     - conda-forge
 dependencies:
-    - cpuonly
-    # This pin is necessary because later nifty versions have import errors on windows.
-    - nifty =1.2.1=*_4
+    - nifty >=1.2.1
     - imagecodecs
     - magicgui
     - napari >=0.5.0
     - natsort
     - pip
     - pooch
-    - protobuf <5
     - pyqt
     - python-xxhash
     - python-elf >=0.4.8
-    - pytorch >=2.4
+    - pytorch >=2.4 "libtorch=*=cpu*"
     - segment-anything
     - torchvision
     - torch_em >=0.7.0

diff --git a/environment_cpu_win.yaml b/environment_cpu_win.yaml
@@ -0,0 +1,26 @@
+name: sam
+channels:
+    - pytorch
+    - conda-forge
+dependencies:
+    - cpuonly
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
+    - imagecodecs
+    - magicgui
+    - napari >=0.5.0
+    - natsort
+    - pip
+    - pooch
+    - protobuf <5
+    - pyqt
+    - python-xxhash
+    - python-elf >=0.4.8
+    - pytorch >=2.4
+    - segment-anything
+    - torchvision
+    - torch_em >=0.7.0
+    - tqdm
+    - timm
+    - pip:
+        - git+https://github.com/ChaoningZhang/MobileSAM.git
diff --git a/environment_gpu.yaml b/environment_gpu.yaml
@@ -1,23 +1,18 @@
 name: sam
 channels:
-    - pytorch
-    - nvidia
     - conda-forge
 dependencies:
     - imagecodecs
-    # This pin is necessary because later nifty versions have import errors on windows.
-    - nifty =1.2.1=*_4
+    - nifty >=1.2.1
     - magicgui
     - napari >=0.5.0
     - natsort
     - pip
     - pooch
-    - protobuf <5
     - pyqt
     - python-xxhash
     - python-elf >=0.4.8
-    - pytorch >=2.4
-    - pytorch-cuda>=11.7  # you may need to update the cuda version to match your system
+    - pytorch >=2.4 "libtorch=*=cuda*"
     - segment-anything
     - torchvision
     - torch_em >=0.7.0

diff --git a/environment_gpu_win.yaml b/environment_gpu_win.yaml
@@ -0,0 +1,27 @@
+name: sam
+channels:
+    - pytorch
+    - nvidia
+    - conda-forge
+dependencies:
+    - imagecodecs
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
+    - magicgui
+    - napari >=0.5.0
+    - natsort
+    - pip
+    - pooch
+    - protobuf <5
+    - pyqt
+    - python-xxhash
+    - python-elf >=0.4.8
+    - pytorch >=2.4
+    - pytorch-cuda>=11.7  # you may need to update the cuda version to match your system
+    - segment-anything
+    - torchvision
+    - torch_em >=0.7.0
+    - tqdm
+    - timm
+    - pip:
+        - git+https://github.com/ChaoningZhang/MobileSAM.git