Merge pull request #225 from KumarLabJax/bug/fix-jabs-cli-in-singularity-image

Bug/fix jabs cli in singularity image

Author: bergsalex

README.md

@@ -130,8 +130,8 @@ https://doi.org/10.5281/zenodo.16697331
 
 ## Singularity/Linux
 
-We supply a tested pair of singularity definition files. The [first vm](vm/behavior-classifier-vm.def) is intended for command-line use on 
-compute clusters when scaling inferences. The [second vm](vm/behavior-classifier-vm-gui.def) is designed for interacting with the GUI in a portable 
+We supply a tested pair of singularity definition files. The [first vm](vm/headless.def) is intended for command-line use on 
+compute clusters when scaling inferences. The [second vm](vm/gui.def) is designed for interacting with the GUI in a portable 
 environment. Please inspect the definition files for related linux packages to run the software.
 
 ## JABS Project Portability

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "jabs-behavior-classifier"
-version = "0.36.0"
+version = "0.36.1"
 description = ""
 readme = "README.md"
 requires-python = ">=3.10,<3.14"

uv.lock

@@ -1,11 +1,9 @@
 # build like:
-#   singularity build --fakeroot JABS-GUI.sif behavior-classifier-vm-gui.def
+#   singularity build --fakeroot JABS-GUI.sif gui.def
 
 Bootstrap: docker
 From: ghcr.io/astral-sh/uv:python3.13-bookworm
 
-%environment
-    export UV_SYSTEM_PYTHON=1
 
 %setup
     mkdir -p ${SINGULARITY_ROOTFS}/behavior-classifier
@@ -21,14 +19,29 @@ From: ghcr.io/astral-sh/uv:python3.13-bookworm
 
 %post
     # GUI libraries
-    apt-get update && apt-get install -y qt6-base-dev libglu1-mesa-dev libgl1-mesa-glx alsa-utils libnss3 libxkbfile1 'libxcb*'
+    apt-get update && apt-get install -y \
+        qt6-base-dev \
+        libglu1-mesa-dev \
+        libgl1-mesa-glx \
+        alsa-utils \
+        libnss3 \
+        libxkbfile1 \
+        'libxcb*' &&
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
     # Note that libxcb is wildcarded because it wasn't very clear which xcb library was missing, so we can just grab them all
 
-    # Run unittests to ensure build environment should work as intended
+    export UV_SYSTEM_PYTHON=1
+    export UV_PYTHON=/usr/local/bin/python
+
     cd /behavior-classifier/
     uv sync --locked --compile-bytecode --no-editable
+
+    # Run unittests to ensure build environment should work as intended
     uv run pytest tests
 
+    uv build && python3 -m pip install dist/*.whl
+
     # Cleanup
     rm -R /behavior-classifier
 

vm/behavior-classifier-vm-gui.def vm/gui.defvm/behavior-classifier-vm-gui.def renamed to vm/gui.def

@@ -1,11 +1,9 @@
 # build like:
-#   singularity build --fakeroot behavior-classifier.sif behavior-classifier-vm.def
+#   singularity build --fakeroot behavior-classifier.sif headless.def
 
 Bootstrap: docker
 From: ghcr.io/astral-sh/uv:python3.13-bookworm
 
-%environment
-    export UV_SYSTEM_PYTHON=1
 
 %setup
     mkdir -p ${SINGULARITY_ROOTFS}/behavior-classifier
@@ -20,11 +18,14 @@ From: ghcr.io/astral-sh/uv:python3.13-bookworm
     exec jabs-classify "$@"
 
 %post
-    # Run unittests to ensure build environment should work as intended
-    # skip tests of GUI components that will fail since this Singularity image does not support the JABS gui
     cd /behavior-classifier/
     uv sync --locked --compile-bytecode --no-editable
+
+    # Run unittests to ensure build environment should work as intended
+    # skip tests of GUI components that will fail since this Singularity image does not support the JABS gui
     uv run pytest --ignore=tests/test_search_bar_widget.py  tests
 
+    uv build && python3 -m pip install dist/*.whl
+
     # Cleanup
     rm -R /behavior-classifier