Updated pyproject.toml and conda environment yaml files (#40)(closes #39)

Author: mese79

.github/workflows/setup_test_publish.yml

@@ -20,7 +20,7 @@ jobs:
         shell: bash -el {0}
 
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.10"]
@@ -29,17 +29,16 @@ jobs:
       - uses: actions/checkout@v4
       # these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
-      - uses: mamba-org/setup-micromamba@v1
+      - uses: mamba-org/setup-micromamba@v2
         env:
           ACTIONS_STEP_DEBUG: false
         with:
           environment-name: ff
           environment-file: env_cpu.yml
           condarc: |
             channels:
-              - pytorch
               - conda-forge
-              - defaults
+              - nodefaults
           init-shell: bash powershell
           cache-downloads: true
           post-cleanup: 'all'
@@ -54,14 +53,18 @@ jobs:
           echo "$(which micromamba)"
           echo "$(which python)"
 
+      - name: pip list
+        run: pip list
+        shell: bash -el {0}
+
       # strategy borrowed from vispy for installing opengl libs on windows
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
         run: |
           micromamba activate ff
           git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
           powershell gl-ci-helpers/appveyor/install_opengl.ps1
-  
+
       - name: Run Tests
         # uses: aganders3/headless-gui@v2.2
         # with:
@@ -70,7 +73,7 @@ jobs:
           micromamba activate ff
           python -m pip install .[dev]
           pytest -v --color=yes --cov=featureforest --cov-report=xml -m "not slow"
-          
+
       - name: Coverage
         uses: codecov/codecov-action@v4
         with:
@@ -115,4 +118,3 @@ jobs:
       - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
-  

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
     hooks:
       - id: ruff  # Run the linter
         types_or: [ python, pyi ]
-        args: [ --fix ]
+        args: [ --fix, --show-fixes ]
       - id: ruff-format  # Run the formatter
         types_or: [ python, pyi ]
   - repo: https://github.com/psf/black

docs/install.md

@@ -14,11 +14,16 @@ mamba env create -f ./env_cpu.yml
 ```
 
 ### Note 
-You need to install `sam-2` which can be installed easily using mamba (or conda). To install `sam-2` using `pip` please refer to the official [sam-2](https://github.com/facebookresearch/sam2) repository.
+You need to install `segment-anything` and `sam-2` which can be installed easily using mamba (or conda). To install `sam-2` using `pip` please refer to the official [sam-2](https://github.com/facebookresearch/sam2) repository.
 
 ## Requirements
-- `python >= 3.10`
-- `numpy==1.24.4`
+- `python>=3.10`
+- `numpy<2.2`
+- `pytorch>=2.3.1`
+- `torchvision>=0.18.1`
+- `timm`
+- `segment-anything`
+- `sam-2`
 - `opencv-python`
 - `scikit-learn`
 - `scikit-image`
@@ -28,12 +33,8 @@ You need to install `sam-2` which can be installed easily using mamba (or conda)
 - `qtpy`
 - `napari`
 - `h5py`
-- `pytorch=2.3.1`
-- `torchvision=0.18.1`
-- `timm=1.0.9`
 - `pynrrd`
-- `segment-anything`
-- `sam-2`
+- `pooch`
 
 ## Installing Only The Plugin
 If you use the provided conda environment yaml files, the plugin will be installed automatically. But in case you already have the environment setup, 
@@ -56,4 +57,4 @@ If you want to install the plugin manually using GPU, please follow the pytorch
 
 
 [conda]: https://conda.io/projects/conda/en/latest/index.html
-[mamba]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html
+[mamba]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html

env_cpu.yml

@@ -1,32 +1,28 @@
 name: featureforest
 channels:
-  - pytorch
   - conda-forge
-  - defaults
+  - nodefaults
 dependencies:
   - python=3.10
-  - pyqt=5.15.10
-  - qtpy
-  - magicgui
+  - numpy<2.2
   - scikit-learn
   - scikit-image
   - scipy
+  - opencv
+  - pyqt
+  - qtpy
   - napari
-  - napari-console
-  - napari-plugin-engine
-  - napari-svg
   - h5py
-  - pytorch=2.3.1
-  - torchvision=0.18.1
+  - pytorch-cpu>=2.5.1
+  - torchvision>=0.20.1
+  - segment-anything
   - sam-2
   - pooch
   - pip
   - pip:
-    - numpy==1.24.4    # timm drops deprecation warnings with newer versions
     - matplotlib
-    - opencv-python
-    - timm==1.0.9
+    - timm
     - pynrrd
     - iopath>=0.1.10
-    - git+https://github.com/facebookresearch/segment-anything.git
-    - git+https://github.com/juglab/featureforest.git
+    - tqdm>=4.66.1
+    - git+https://github.com/juglab/featureforest.git@ms/update/setup

env_gpu.yml

@@ -1,34 +1,29 @@
 name: featureforest
 channels:
-  - pytorch
-  - nvidia
   - conda-forge
-  - defaults
+  - nodefaults
 dependencies:
   - python=3.10
-  - pyqt=5.15.10
-  - qtpy
-  - magicgui
+  - numpy<2.2
   - scikit-learn
   - scikit-image
   - scipy
+  - opencv
+  - pyqt
+  - qtpy
   - napari
-  - napari-console
-  - napari-plugin-engine
-  - napari-svg
   - h5py
-  - pytorch-cuda
-  - pytorch=2.3.1
-  - torchvision=0.18.1
+  - cuda-version>=11.8
+  - pytorch-gpu>=2.5.1
+  - torchvision>=0.20.1
+  - segment-anything
   - sam-2
   - pooch
   - pip
   - pip:
-    - numpy==1.24.4    # timm drops deprecation warnings with newer versions
     - matplotlib
-    - opencv-python
-    - timm==1.0.9
+    - timm
     - pynrrd
     - iopath>=0.1.10
-    - git+https://github.com/facebookresearch/segment-anything.git
+    - tqdm>=4.66.1
     - git+https://github.com/juglab/featureforest.git

pyproject.toml

@@ -43,23 +43,20 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
 dependencies = [
-    "numpy==1.24.4",
+    "numpy<2.2",
     "opencv-python",
     "scikit-learn",
     "scikit-image",
     "matplotlib",
     "pynrrd",
-    "magicgui",
-    "qtpy",
     "napari",
+    "qtpy",
     "h5py",
     "pooch",
     "iopath>=0.1.10",
-    "torch==2.3.1",
-    "torchvision==0.18.1",
-    "timm==1.0.9",
-    "segment-anything-py",
-    # "sam-2 @ git+https://github.com/facebookresearch/sam2.git"
+    "torch>=2.5.1",
+    "torchvision>=0.20.1",
+    "timm",
 ]
 [project.optional-dependencies]
 # development dependencies and tooling
@@ -72,6 +69,7 @@ dev = [
     "sybil",      # doctesting
 ]
 all = ["napari[all]"]
+
 [project.urls]
 homepage = "https://featureforest.github.io/"
 repository = "https://github.com/juglab/featureforest"