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How-To Guides

Install dependencies​

It is recommended to use Conda (and conda-forge) for managing dependencies.

  1. Install Miniconda
  2. Install conda-build for installing local conda packages
  3. Create and activate environment with dependencies: 
    conda create -n arraymorph
    conda activate arraymorph
    conda install -n arraymorph cmake conda-forge::hdf5=1.14.2 conda-forge::aws-sdk-cpp conda-forge::azure-core-cpp conda-forge::azure-storage-blobs-cpp conda-forge::h5py

Install ArrayMorph via Conda​

Option 1: Build and Install from Source​

Clone the repository and build the conda package locally:

 git clone https://github.com/ICICLE-ai/arraymorph.git
 cd arraymorph/arraymorph
 conda build -c conda-forge .
 conda install -n arraymorph arraymorph --use-local -c conda-forge

Option 2: Install from Pre-built Local Package​

We provide a pre-built conda package in the arraymorph_channel directory. Install it directly using:

git clone https://github.com/ICICLE-ai/arraymorph.git
cd arraymorph/arraymorph_channel
conda index .
conda install -n arraymorph arraymorph -c file://$(pwd) -c conda-forge

Install ArryMorph from source code​

Build ArrayMorph​

git clone https://github.com/ICICLE-ai/arraymorph.git
cd arraymorph/arraymorph
cmake -B ./build -S . -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
cd build
make

Enable VOL plugin:​

export HDF5_PLUGIN_PATH=/path/to/arraymorph/arraymorph/build/src
export HDF5_VOL_CONNECTOR=arraymorph

Configure Environment for Cloud Access​

Create a JSON configuration file named config at ~/.arraymorph with the following settings based on your cloud provider:

AWS Configuration:​

{
    "STORAGE_PLATFORM": "S3",
    "BUCKET_NAME": "XXXXX",
    "AWS_ACCESS_KEY_ID": "XXXXX",
    "AWS_SECRET_ACCESS_KEY": "XXXXX",
    "AWS_REGION": "us-east-2"
}

Azure Configuration:​

{
    "STORAGE_PLATFORM": "Azure",
    "BUCKET_NAME": "XXXXX",
    "AZURE_STORAGE_CONNECTION_STRING": "XXXXX"
}

S3-compatible object store configuration (MinIO, Ceph, Garage):​

Set AWS_ENDPOINT_URL_S3, AWS_USE_PATH_STYLE, and AWS_SIGNED_PAYLOADS to match the requirements of most self-hosted S3-compatible stores:

{
    "STORAGE_PLATFORM": "S3",
    "BUCKET_NAME": "XXXXX",
    "AWS_ENDPOINT_URL_S3": "XXXXX",
    "AWS_S3_ADDRESSING_STYLE": "path",
    "AWS_ACCESS_KEY_ID": "XXXXX",
    "AWS_SECRET_ACCESS_KEY": "XXXXX",
    "AWS_REGION": "XXXXX",
    "AWS_USE_PATH_STYLE": "true",
    "AWS_USE_TLS": "true",
    "AWS_SIGNED_PAYLOADS": "true"
}

Enable ArrayMorph with h5py in Python​

To enable ArrayMorph when using h5py, import the arraymorph package BEFORE importing h5py:

import arraymorph
import h5py
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