Merge pull request #5 from AllenNeuralDynamics/feat-partition-smartsp…

…im-job Feat partition smartspim job
AllenNeuralDynamics · Aug 16, 2024 · d296db3 · d296db3
2 parents c063564 + bed9369
commit d296db3
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Showing 23 changed files with 3,186 additions and 1,636 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "aind-smartspim-data-transformation"
 description = "Generated from aind-library-template"
 license = {text = "MIT"}
-requires-python = ">=3.9"
+requires-python = ">=3.9.2"
 authors = [
     {name = "Allen Institute for Neural Dynamics"}
 ]
@@ -49,7 +49,7 @@ version = {attr = "aind_smartspim_data_transformation.__version__"}
 
 [tool.black]
 line-length = 79
-target_version = ['py36']
+target_version = ['py39']
 exclude = '''
 
 (

diff --git a/scripts/singularity_build.def b/scripts/singularity_build.def
@@ -6,17 +6,10 @@ From: python:3.10-bullseye
     cp -R . ${SINGULARITY_ROOTFS}/aind-smartspim-data-transformation
 
 %post
-    # Installing dask mpi
-    wget https://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
-    tar xfz mpich-3.2.tar.gz
-    rm mpich-3.2.tar.gz
-    mkdir mpich-build
-    cd mpich-build
-    ../mpich-3.2/configure --disable-fortran 2>&1 | tee c.txt
-    make 2>&1 | tee m.txt
-    make install 2>&1 | tee mi.txt
-    cd ..
-
+    curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+    unzip awscliv2.zip
+    rm awscliv2.zip
+    ./aws/install
     cd ${SINGULARITY_ROOTFS}/aind-smartspim-data-transformation
-    pip install . mpi4py dask_mpi --no-cache-dir
+    pip install . --no-cache-dir
     rm -rf ${SINGULARITY_ROOTFS}/aind-smartspim-data-transformation
diff --git a/src/aind_smartspim_data_transformation/_shared/__init__.py b/src/aind_smartspim_data_transformation/_shared/__init__.py
diff --git a/src/aind_smartspim_data_transformation/_shared/types.py b/src/aind_smartspim_data_transformation/_shared/types.py
diff --git a/src/aind_smartspim_data_transformation/compress/dask_utils.py b/src/aind_smartspim_data_transformation/compress/dask_utils.py