File size: 4,213 Bytes
3a6a916 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 | #!/usr/bin/env bash
# Create the conda env used by Datasets/prepare_atlas.ipynb and prepare_benchmark.ipynb.
#
# Usage:
# bash create_env.sh
# FORCE_RECREATE=1 bash create_env.sh
# CONDA_ENVS_PREFIX=/path/to/.conda/envs bash create_env.sh
#
# Then:
# conda activate cyflow_datasets
# # in Jupyter / Cursor: kernel "Python (cyflow_datasets)"
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
DATASETS_DIR="$(cd "${SCRIPT_DIR}/.." && pwd)"
YML_PATH="${SCRIPT_DIR}/environment.yml"
ENV_NAME="${ENV_NAME:-cyflow_datasets}"
FORCE_RECREATE="${FORCE_RECREATE:-0}"
echo "========================================================================"
echo " CREATE DATASETS ENVIRONMENT: ${ENV_NAME}"
echo "========================================================================"
echo "Setup dir : ${SCRIPT_DIR}"
echo "Datasets dir : ${DATASETS_DIR}"
echo ""
load_conda() {
if command -v module >/dev/null 2>&1; then
echo ">>> Loading cluster modules (anaconda3)..."
module load anaconda3/2023.09-0/none-none 2>/dev/null || module load anaconda3 || true
fi
if ! command -v conda >/dev/null 2>&1; then
for conda_sh in \
"${HOME}/miniforge3/etc/profile.d/conda.sh" \
"${HOME}/mambaforge/etc/profile.d/conda.sh" \
"${HOME}/miniconda3/etc/profile.d/conda.sh" \
"/opt/anaconda3/etc/profile.d/conda.sh" \
"/opt/miniconda3/etc/profile.d/conda.sh"
do
if [[ -f "${conda_sh}" ]]; then
# shellcheck source=/dev/null
source "${conda_sh}"
break
fi
done
fi
if ! command -v conda >/dev/null 2>&1; then
echo "ERROR: conda not found. Install Miniforge/Anaconda or load the anaconda module."
exit 1
fi
# Ensure `conda activate` works in this non-interactive shell.
eval "$(conda shell.bash hook)"
echo " conda: $(command -v conda)"
echo ""
}
env_exists() {
conda env list | awk '{print $1}' | grep -qx "$1"
}
prepare_yml() {
local dest="$1"
if [[ -n "${CONDA_ENVS_PREFIX:-}" ]]; then
grep -vE '^[[:space:]]*prefix:' "${YML_PATH}" > "${dest}"
echo "prefix: ${CONDA_ENVS_PREFIX%/}/${ENV_NAME}" >> "${dest}"
echo ">>> Using prefix ${CONDA_ENVS_PREFIX%/}/${ENV_NAME}"
else
cp "${YML_PATH}" "${dest}"
fi
}
load_conda
if [[ "${FORCE_RECREATE}" == "1" ]] && env_exists "${ENV_NAME}"; then
echo ">>> FORCE_RECREATE: removing existing env '${ENV_NAME}'"
conda env remove -n "${ENV_NAME}" -y
echo ""
fi
if env_exists "${ENV_NAME}"; then
echo ">>> Environment '${ENV_NAME}' already exists (skip conda create)"
echo " Set FORCE_RECREATE=1 to rebuild."
else
tmp_yml="$(mktemp "${TMPDIR:-/tmp}/cyflow_datasets_XXXXXX.yml")"
prepare_yml "${tmp_yml}"
echo ">>> Creating '${ENV_NAME}' from environment.yml"
conda env create -n "${ENV_NAME}" -f "${tmp_yml}"
rm -f "${tmp_yml}"
echo " Created: ${ENV_NAME}"
fi
echo ""
echo ">>> Registering Jupyter kernel"
conda activate "${ENV_NAME}"
python -m ipykernel install --user \
--name "${ENV_NAME}" \
--display-name "Python (${ENV_NAME})"
echo ""
echo ">>> Smoke-test imports (cwd=${DATASETS_DIR})"
cd "${DATASETS_DIR}"
python - <<'PY'
import importlib
mods = [
"numpy", "pandas", "scipy", "sklearn", "yaml",
"matplotlib", "seaborn", "anndata", "scanpy",
"fcsparser", "scyan", "pytometry", "tableone",
"huggingface_hub", "openpyxl", "utils_datasets",
]
failed = []
for name in mods:
try:
importlib.import_module(name)
print(f" ok {name}")
except Exception as exc:
failed.append((name, exc))
print(f" FAIL {name}: {exc}")
if failed:
raise SystemExit(1)
print("All imports succeeded.")
PY
echo ""
echo "========================================================================"
echo " Activate: conda activate ${ENV_NAME}"
echo " Notebooks: Datasets/prepare_atlas.ipynb"
echo " Datasets/prepare_benchmark.ipynb"
echo " Kernel : Python (${ENV_NAME})"
echo "========================================================================"
echo "Done."
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