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Added venv creation script based on Jeff Mast's GMD install script.
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‎install-ampl/ampl-venv.sh‎

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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cd $DIR
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# --- begin: must be sourced guard ---
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(return 0 2>/dev/null) || {
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echo "b This script must be sourced, not executed."
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echo " Use: source ${BASH_SOURCE[0]} or . ${BASH_SOURCE[0]}"
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exit 1
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}
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# --- end: must be sourced guard ---
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PY_VER=3.10
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PY_VER_STR="${PY_VER//./}"
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# load system python module
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echo module load python/$PY_VER
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module load python/$PY_VER || return 1
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# activate the venv
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VENV=$(realpath venvs/ampl-py${PY_VER_STR}-venv/bin/activate) || return 1
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echo "Activating ampl-py${PY_VER_STR}-venv @ $VENV"
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source venvs/ampl-py${PY_VER_STR}-venv/bin/activate || return 1
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‎install-ampl/create_venv.sh‎

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#!/bin/bash
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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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cd $DIR
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VENV_ID=ampl
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SYNC_PACKAGES=0
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PATH=~/.local/bin:$PATH
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UV_CMD=$(which uv)
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if [ "$UV_CMD" = "" ]; then
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curl -LsSf https://astral.sh/uv/install.sh | sh
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fi
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OPTIONS=(
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"python/3.10" "Python 3.10 " off
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"python/3.11" "Python 3.11 [deepchem support questionable]" off
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)
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# Show checklist and capture selected values
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CHOICES=$(dialog --clear --title "Select Options" \
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--checklist "Use SPACE to select/unselect, ENTER to confirm:" 20 60 10 \
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"${OPTIONS[@]}" \
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3>&1 1>&2 2>&3)
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dialog --clear \
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--title "Sync Packages" \
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--yesno "Do you want to sync packages in the venvs?" 8 60
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response=$?
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if [[ $response -eq 0 ]]; then
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SYNC_PACKAGES=1
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else
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SYNC_PACKAGES=0
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fi
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clear # remove dialog UI
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# CHOICES is a quoted space-separated list of values, e.g. "build" "limits"
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# Remove quotes and loop
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for choice in $CHOICES; do
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# Remove surrounding quotes
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val="${choice%\"}"
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val="${val#\"}"
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module_name=$val
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python_version="${val#*/}"
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python_version_str="${python_version//./}"
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venv_name="${VENV_ID}-py${python_version_str}-venv"
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module load $module_name
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if [ ! -e $(pwd)/venvs/$venv_name ]; then
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uv venv --python $(which python3) $(pwd)/venvs/$venv_name
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fi
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if [ $SYNC_PACKAGES -eq 1 ]; then
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./uv-sync.sh $python_version
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fi
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done
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‎install-ampl/pyproject.toml‎

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[project]
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name = "ampl"
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version = "1.0"
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# NOTE:
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# * deepchem only works with python <= 3.10 (and possibly 3.11)
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# - seems to install in python 3.11 but website says suports only
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# python <= 3.10
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# - does not work with python 3.12+ due to tensorflow-addons dependency
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# which is no longer supported and only has support up to python 3.11
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# * ampl only works with python 3.9, 3.10, 3.11 (due to deepchem)
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# - encoders / decoders need python 3.9
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# - everthing else works with python 3.9 and 3.10 (and possibly 3.11)
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# * this will install on python 3.12 but won't have deepchem
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requires-python = ">=3.9,<3.13"
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# Dependencies for all Python versions
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dependencies = [
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"setuptools",
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"pip",
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# core dependencies
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"torch_cluster",
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"torch_scatter",
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"torch_sparse",
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"torch_spline_conv",
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"torch-geometric",
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# deepchem 2.8.0 deps [NOTE: may not work on python >= 3.11]
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"deepchem[torch,tensorflow]==2.8.0; python_version >= '3.10' and python_version < '3.12'",
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# deepchem[tensorflow] deps
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"tensorflow-cpu==2.14.0; python_version >= '3.10' and python_version < '3.12'",
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# atomsci-ampl deps [need to be added to atomsci-ampl]
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"molvs",
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"xgboost",
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"umap-learn",
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"imbalanced-learn",
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"ipykernel",
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"ipython",
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"pytest",
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"seaborn",
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"matplotcheck",
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# code repos
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"atomsci-ampl; python_version >= '3.10' and python_version < '3.12'",
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"atomsci-clients",
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# rdkit
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"rdkit>=2024.3.5; python_version >= '3.10'",
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"numpy<2",
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# python specific versions [dgl / pyg dependent]
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"dgl==2.1.0; python_version >= '3.10'",
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"pyg_lib==0.3.1; python_version >= '3.10' and python_version < '3.12'",
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"pyg_lib==0.4.0; python_version >= '3.12'",
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"torch==2.1.2+cpu; python_version >= '3.10' and python_version < '3.12'",
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"torch==2.3.1+cpu; python_version >= '3.12'"
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]
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[tool.uv]
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allow-insecure-host = [
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"download.pytorch.org",
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"data.dgl.ai",
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"data.pyg.org"
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]
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[[tool.uv.index]]
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name = "pytorch"
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url = "https://download.pytorch.org/whl/cpu/torch_stable.html"
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format = "flat"
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[[tool.uv.index]]
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name = "dgl"
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url = "https://data.dgl.ai/wheels/repo.html"
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format = "flat"
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[[tool.uv.index]]
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# NOTE: pyg libraries for torch >= 2.2 seem to have GLIBC incompatibilities on LC
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name = "pyg_lib_py312"
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url = "https://data.pyg.org/whl/torch-2.3.1+cpu.html"
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format = "flat"
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[[tool.uv.index]]
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name = "pyg_lib_py310"
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url = "https://data.pyg.org/whl/torch-2.1.2+cpu.html"
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format = "flat"
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[tool.uv.sources]
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# code repos
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atomsci-ampl = [
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{ git = "https://github.com/ATOMScience-org/AMPL.git", rev = "py310", marker = "python_version >= '3.10'"}
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]
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atomsci-clients = { git = "ssh://git@czgitlab.llnl.gov:7999/atom/clients.git", rev = "master" }
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# dgl
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dgl = { index = "dgl" }
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# torch
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torch = { index = "pytorch" }
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pyg_lib = [
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{ index = "pyg_lib_py310", marker = "python_version >= '3.10' and python_version < '3.12'" },
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{ index = "pyg_lib_py312", marker = "python_version >= '3.12'" },
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]
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torch_cluster = [
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{ index = "pyg_lib_py310", marker = "python_version >= '3.10' and python_version < '3.12'" },
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{ index = "pyg_lib_py312", marker = "python_version >= '3.12'" },
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]
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torch_scatter = [
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{ index = "pyg_lib_py310", marker = "python_version >= '3.10' and python_version < '3.12'" },
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{ index = "pyg_lib_py312", marker = "python_version >= '3.12'" },
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]
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torch_sparse = [
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{ index = "pyg_lib_py310", marker = "python_version >= '3.10' and python_version < '3.12'" },
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{ index = "pyg_lib_py312", marker = "python_version >= '3.12'" },
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]
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torch_spline_conv = [
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{ index = "pyg_lib_py310", marker = "python_version >= '3.10' and python_version < '3.12'" },
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{ index = "pyg_lib_py312", marker = "python_version >= '3.12'" },
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]
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‎install-ampl/uv-sync.sh‎

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DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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cd $DIR
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PATH=~/.local/bin:$PATH
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UV_CMD=$(which uv)
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if [ "$UV_CMD" = "" ]; then
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curl -LsSf https://astral.sh/uv/install.sh | sh
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fi
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. ampl-venv.sh || exit 1
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# NOTE add --refresh to get latest version of repos
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uv sync --active
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