Merge pull request #116 from hci-unihd/plantseg_napari

Major refactor of all PlantSeg process and add support for napari as viewer
kreshuklab · Jan 20, 2023 · a76354f · a76354f
2 parents 77097dd + 698f663
commit a76354f
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diff --git a/.github/workflows/build-deploy-on-conda.yml b/.github/workflows/build-deploy-on-conda.yml
@@ -13,29 +13,38 @@ jobs:
     - name: Print PlantSeg version name
       run: |
         echo $RELEASE_VERSION
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: 3.8
-    - name: Add conda to system path
+        auto-activate-base: true
+        activate-environment: ""
+        channels: local,conda-forge,defaults
+        channel-priority: false
+
+    - shell: bash -l {0}
       run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Build PlantSeg
+        conda info --envs
+    - name: Build PlantSeg using Boa
+      shell: bash -l {0}
       run: |
-          conda install -q conda-build
-          conda build -c conda-forge -c awolny conda-recipe
-    - name: Install dependencies
+          conda config --set allow_conda_downgrades true
+          conda install conda=4.12.0 -y
+          conda install --yes -c conda-forge mamba
+          mamba install -q boa
+          mamba mambabuild -c conda-forge -c awolny conda-recipe
+    - name: Create PlantSeg env
       run: |
-        conda install -c conda-forge -c awolny --use-local plantseg
+          mamba create -n plant-seg -c local -c conda-forge -c awolny plantseg pytest
     - name: Run pytest
+      shell: bash -l {0}
       run: |
-        conda install pytest
+        conda activate plant-seg
         pytest
+        conda deactivate
     - name: Deploy on conda
       if: ${{ startsWith( github.ref, 'refs/tags/') && success() }}
       env:
         ANACONDA_SECRET: ${{ secrets.ANACONDA_TOKEN }}
+      shell: bash -l {0}
       run: |
-        conda install -q anaconda-client
+        mamba install -q anaconda-client
         anaconda -t $ANACONDA_SECRET upload $CONDA/conda-bld/**/plantseg-*.tar.bz2
diff --git a/Documentation-GUI/Data-Processing.md b/Documentation-GUI/Data-Processing.md
diff --git a/Documentation-GUI/Predictions.md b/Documentation-GUI/Predictions.md
diff --git a/Documentation-GUI/README.md b/Documentation-GUI/README.md
diff --git a/Documentation-GUI/Segmentation.md b/Documentation-GUI/Segmentation.md
diff --git a/Documentation-GUI/images/3datlas_leaf_raw.png b/Documentation-GUI/images/3datlas_leaf_raw.png
diff --git a/Documentation-GUI/images/3datlas_root_raw.png b/Documentation-GUI/images/3datlas_root_raw.png
diff --git a/Documentation-GUI/images/cnn-predictions.png b/Documentation-GUI/images/cnn-predictions.png
diff --git a/Documentation-GUI/images/confocal.png b/Documentation-GUI/images/confocal.png
diff --git a/Documentation-GUI/images/cos_root_mc_raw.png b/Documentation-GUI/images/cos_root_mc_raw.png
diff --git a/Documentation-GUI/images/main_figure.png b/Documentation-GUI/images/main_figure.png
diff --git a/Documentation-GUI/images/main_figure_nologo.png b/Documentation-GUI/images/main_figure_nologo.png
diff --git a/Documentation-GUI/images/meristem.png b/Documentation-GUI/images/meristem.png
diff --git a/Documentation-GUI/images/plantseg_overview.png b/Documentation-GUI/images/plantseg_overview.png
diff --git a/Documentation-GUI/images/preprocessing.png b/Documentation-GUI/images/preprocessing.png
diff --git a/Documentation-GUI/images/segmentation.png b/Documentation-GUI/images/segmentation.png
diff --git a/Documentation-GUI/images/tum_ovules_mc_raw.png b/Documentation-GUI/images/tum_ovules_mc_raw.png