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FROM mambaorg/micromamba:1.5-focal-cuda-11.7.1 | ||
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USER root | ||
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RUN apt update && apt install -y git && apt clean | ||
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USER $MAMBA_USER | ||
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COPY --chown=$MAMBA_USER:$MAMBA_USER ./environment.yml /home/env.yaml | ||
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RUN micromamba install -y -n base -f /home/env.yaml && \ | ||
micromamba clean --all --yes |
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{ | ||
"name": "httomo", | ||
"image": "gcr.io/diamond-pubreg/httomo/dev:0.0.1", | ||
"workspaceMount": "src=${localWorkspaceFolder},dst=/httomo,type=bind", | ||
"workspaceFolder": "/httomo", | ||
// Please fill in: | ||
// - `HTTOMOLIB_LOCAL_REPO` and `HTTOMOLIBGPU_LOCAL_REPO` with your local | ||
// git repos of httomolib and httomolibgpu respectively | ||
// - `LOCAL_OUT` with a directory that supports parallel I/O (any directory | ||
// on a local drive will be sufficient) | ||
"mounts": [ | ||
"src=HTTOMOLIB_LOCAL_REPO,dst=/httomolib,type=bind", | ||
"src=HTTOMOLIBGPU_LOCAL_REPO,dst=/httomolibgpu,type=bind", | ||
"src=LOCAL_OUT,dst=/httomo/output_dir,type=bind", | ||
], | ||
"containerUser": "root", | ||
"securityOpt": [ "label=disable" ], | ||
"postCreateCommand": "micromamba run -n base pip install -e /httomolib /httomolibgpu /httomo", | ||
"customizations": { | ||
"vscode": { | ||
"extensions": [ | ||
"ms-python.python", | ||
"ms-pyright.pyright", | ||
"charliermarsh.ruff", | ||
] | ||
} | ||
}, | ||
"settings": { | ||
"python.analysis.typeCheckingMode": "strict", | ||
} | ||
} |
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name: httomo | ||
channels: | ||
- astra-toolbox | ||
- conda-forge | ||
- httomo | ||
- anaconda | ||
dependencies: | ||
- astra-toolbox::astra-toolbox | ||
- conda-forge::click>=8.1.3 | ||
- conda-forge::cupy | ||
- conda-forge::h5py=*=*mpi_mpich* | ||
- conda-forge::hdf5plugin | ||
- conda-forge::mpi4py | ||
- conda-forge::pyyaml | ||
- conda-forge::numpy<1.24 | ||
- conda-forge::nvtx | ||
- conda-forge::python | ||
- conda-forge::plumbum | ||
- anaconda::ipython | ||
- conda-forge::tomopy | ||
- httomo::larix | ||
- httomo::tomobar |