| #!/usr/bin/env bash |
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| set -euo pipefail |
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| 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}" |
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| echo "========================================================================" |
| echo " CREATE DATASETS ENVIRONMENT: ${ENV_NAME}" |
| echo "========================================================================" |
| echo "Setup dir : ${SCRIPT_DIR}" |
| echo "Datasets dir : ${DATASETS_DIR}" |
| echo "" |
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| load_conda() { |
| if command -v module >/dev/null 2>&1; then |
| echo ">>> Loading cluster modules (anaconda3)..." |
| module load anaconda3/2023.09-0/none-none 2>/dev/null || module load anaconda3 || true |
| fi |
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| if ! command -v conda >/dev/null 2>&1; then |
| for conda_sh in \ |
| "${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 "${conda_sh}" ]]; then |
| |
| source "${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 |
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| |
| eval "$(conda shell.bash hook)" |
| echo " conda: $(command -v conda)" |
| echo "" |
| } |
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| env_exists() { |
| conda env list | awk '{print $1}' | grep -qx "$1" |
| } |
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| 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 |
| } |
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| load_conda |
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| 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 |
|
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| 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}") |
|
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| if failed: |
| raise SystemExit(1) |
| print("All imports succeeded.") |
| PY |
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| 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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|
