changed install conda->mamba and changed build of micro_sam pip->mamba

computational-cell-analytics · Apr 11, 2024 · 898e09f · 898e09f
1 parent 1067782
commit 898e09f
Show file tree

Hide file tree

Showing 2 changed files with 77 additions and 9 deletions.
diff --git a/.github/workflows/build_installers.yaml b/.github/workflows/build_installers.yaml
@@ -18,15 +18,19 @@ jobs:
     env:
       PREPARE_SCRIPT: |
         cd deployment
-        conda install -y -c conda-forge constructor
-        conda install -y -c conda-forge ruamel.yaml
-        conda install -y -c conda-forge mamba
-        mamba env create --file=../environment_cpu.yaml
-        conda activate sam
-        cd ../
-        pip install . --no-deps -v
-        cd deployment
-        conda activate base
+        mamba install -y -c conda-forge constructor
+        mamba install -y -c conda-forge ruamel.yaml
+        mamba install -y -c conda-forge mamba
+        mamba install -y -c conda-forge conda-build
+        mamba build recipe
+        # Now we need to create an environment from the package we just built
+        mamba create -n sam ./output/micro_sam-0.4.1.tar.gz
+        # mamba env create --file=../environment_cpu.yaml
+        # conda activate sam
+        # cd ../
+        # pip install . --no-deps -v
+        # cd deployment
+        # conda activate base
       RUN_SCRIPT: |
         python version_getter.py
         mkdir ./${{ matrix.os }}_x86_64
@@ -38,6 +42,7 @@ jobs:
         with:
           ref: ${{ github.ref }}
 
+      # chnage this to set-up with mamba 
       - name: setup conda
         if: matrix.os == 'windows-latest' || matrix.os == 'ubuntu-latest'
         uses: conda-incubator/setup-miniconda@v2
@@ -48,6 +53,12 @@ jobs:
         env:
           ACTIONS_ALLOW_UNSECURE_COMMANDS: true
 
+      - name: Install Mamba
+        # Install mamba after setting up conda
+        shell: bash -el {0}  # adjust shell as needed for your OS
+        run: |
+          conda install -y -c conda-forge mamba
+
       - name: build ${{ matrix.os }}_x86_64
         if: matrix.os == 'windows-latest'
         shell: pwsh

diff --git a/deployment/recipe/meta.yaml b/deployment/recipe/meta.yaml
@@ -0,0 +1,57 @@
+{% set version = "0.4.1" %}
+
+package:
+  name: micro_sam
+  version: {{ version }}
+
+source:
+  path: ../../
+
+build:
+  entry_points:
+    - micro_sam.annotator = micro_sam.sam_annotator.annotator:main
+    - micro_sam.annotator_2d = micro_sam.sam_annotator.annotator_2d:main
+    - micro_sam.annotator_3d = micro_sam.sam_annotator.annotator_3d:main
+    - micro_sam.annotator_tracking = micro_sam.sam_annotator.annotator_tracking:main
+    - micro_sam.image_series_annotator = micro_sam.sam_annotator.image_series_annotator:main
+    - micro_sam.precompute_embeddings = micro_sam.precompute_state:main
+  noarch: python
+  number: 1
+  script: pip install . --no-deps --ignore-installed --no-cache-dir -vvv
+
+requirements:
+  host:
+    - python >=3.8
+    - pip
+  run:
+    - kornia
+    - napari >=0.4.18
+    - pooch
+    - pyqt
+    - python >=3.8
+    - python-elf >=0.4.8
+    - pytorch
+    - segment-anything
+    - torchvision
+    - torch_em
+    - tqdm
+    - zarr
+
+test:
+  imports:
+    - micro_sam
+  source_files:
+    - test/**/*.py
+  commands:
+    - python -m unittest discover -s test -v
+
+about:
+  license: MIT
+  license_file: LICENSE
+  license_family: MIT
+  summary: Segment Anything for Microscopy.
+  home: https://github.com/computational-cell-analytics/micro-sam
+
+extra:
+  recipe-maintainers:
+    - constantinpape