install_requirements.sh

#!/usr/bin/env bash
set -euo pipefail

# ────────────────────────────────
# helper: coloured echo
# ────────────────────────────────
info () { printf "\e[1;34m%s\e[0m\n" "$*"; }
warn () { printf "\e[1;33m%s\e[0m\n" "$*"; }
err  () { printf "\e[1;31m%s\e[0m\n" "$*"; }

# ────────────────────────────────
# 0) make sure basic CLI tools are present
# ────────────────────────────────
REQUIRED=(curl unzip)        # extend here if you hit new gaps (e.g. tar bzip2)
MISSING=()
for cmd in "${REQUIRED[@]}"; do
    command -v "$cmd" &>/dev/null || MISSING+=("$cmd")
done
if ((${#MISSING[@]})); then
    warn "🔧  Installing missing system packages: ${MISSING[*]}"
    sudo apt-get update -qq
    sudo apt-get install -y "${MISSING[@]}"
fi

# ────────────────────────────────
# 1) download Kang 2018 dataset
# ────────────────────────────────
info "📥  Downloading tutorial data from Zenodo …"
mkdir -p data
ZIP_PATH="data/zenodo_perturbations_ECCB2025.zip"

curl -L -o "$ZIP_PATH" \
     "https://zenodo.org/records/15745452/files/zenodo_perturbations_ECCB2025.zip?download=1"

# extract *only* .h5ad files from the inner folder, strip path (-j)
info "📂  Extracting .h5ad files …"
unzip -j -qq "$ZIP_PATH" 'zenodo_perturbations_ECCB2025/*.h5ad' -d data/

# drop macOS resource forks such as ._kang_2018.h5ad
find data -type f -name '._*' -delete

rm "$ZIP_PATH"
info "   ✔️  data/ now contains: $(ls data/*.h5ad | wc -l)  H5AD files."

# ────────────────────────────────
# 2) (optional) show system Python / Pip
# ────────────────────────────────
if command -v python >/dev/null; then
    info "$(python --version) @ $(which python)"
else
    warn "No system Python found (that’s fine, Miniconda will provide one)."
fi
if command -v pip >/dev/null;   then
    info "$(pip --version) @ $(which pip)"
fi

# ────────────────────────────────
# 3) install  ▸ or ▸  reuse  Conda / Mamba / Micromamba
# ────────────────────────────────
MINICONDA_DIR="$HOME/miniconda3"
CONDA_BIN=""           # will hold the full path to conda | mamba | micromamba

# 3a) first preference – look for any tool already on the current $PATH
for CANDIDATE in conda mamba micromamba; do
    if command -v "$CANDIDATE" &>/dev/null; then
        CONDA_BIN=$(command -v "$CANDIDATE")
        break
    fi
done

# 3b) second preference – even if *not* on $PATH, reuse ~/miniconda3 if it exists
if [[ -z $CONDA_BIN && -x "$MINICONDA_DIR/bin/conda" ]]; then
    CONDA_BIN="$MINICONDA_DIR/bin/conda"
    export PATH="$MINICONDA_DIR/bin:$PATH"
fi

# 3c) OPTIONAL extra-safety – bail out if the directory is half-installed
if [[ -d $MINICONDA_DIR && -z $CONDA_BIN ]]; then
    err "Found existing $MINICONDA_DIR but no usable Conda executable.
⇢  Please delete or rename the folder, then re-run this script."
    exit 1
fi

# 3d) install Miniconda only if we still have no package manager
if [[ -z $CONDA_BIN ]]; then
    info "🚀  No Conda/Mamba detected – installing Miniconda under  $MINICONDA_DIR …"

    case "$(uname -s)-$(uname -m)" in
        Darwin-arm64*)  URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh" ;;
        Darwin-*)       URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh" ;;
        Linux-*)        URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"  ;;
        *)              err "❌  Unsupported platform.  Windows users: run via WSL 2."; exit 1 ;;
    esac

    curl -fsSL "$URL" -o /tmp/miniconda.sh
    bash /tmp/miniconda.sh -b -u -p "$MINICONDA_DIR"
    rm  /tmp/miniconda.sh

    CONDA_BIN="$MINICONDA_DIR/bin/conda"
fi

# 3e) initialise the selected tool for *this* shell and future log-ins
CONDA_BASE="$($CONDA_BIN info --base)"
if [[ $CONDA_BIN == *"micromamba"* ]]; then
    eval "$($CONDA_BIN shell hook -s bash)"
else
    source "$CONDA_BASE/etc/profile.d/conda.sh"
fi
grep -qxF "source \"$CONDA_BASE/etc/profile.d/conda.sh\""  "$HOME/.bashrc" \
  || echo "source \"$CONDA_BASE/etc/profile.d/conda.sh\"" >>"$HOME/.bashrc"

# load the appropriate shell hook
if [[ $CONDA_BIN == *"micromamba"* ]]; then
    eval "$($CONDA_BIN shell hook -s bash)"
else
    eval "$($CONDA_BIN shell.bash hook)"
fi

# choose the right front-end command once and reuse it
if command -v conda &>/dev/null; then
    ACTIVATOR=conda          # Conda or Mamba
else
    ACTIVATOR=$(basename "$CONDA_BIN")   # micromamba
fi

$ACTIVATOR activate base

# ────────────────────────────────
# 4) create tutorial environments *sequentially*
# ────────────────────────────────
export CONDA_EXTRACT_THREADS=1   # avoid rare multi-process extract crashes
info "⏳  Creating Conda environments (scgen & scpram) …"
for YAML in envs/environment_scgen.yml envs/environment_scpram.yml; do
    ENV_NAME=$(grep '^name:' "$YAML" | awk '{print $2}')
    info "   ➡️  Creating environment: $ENV_NAME"
    if "$CONDA_BIN" info --envs | grep -qE "^\s*$ENV_NAME\s"; then
        info "   ✔️  Environment $ENV_NAME already exists – skipping."
    else
        "$CONDA_BIN" env create -f "$YAML" || { err "Environment $ENV_NAME failed."; exit 1; }
    fi
done
info "   ✔️  Environments ready."

# ────────────────────────────────
# 5) optional: launch notebooks
# ────────────────────────────────
read -rp "▶️  Launch scGen notebook now? [y/N] " run
if [[ $run =~ ^[Yy]$ ]]; then
    $ACTIVATOR activate scgen
    jupyter-lab 1_scGen/scGen_Tutorial_ECCB2025.ipynb
    $ACTIVATOR deactivate
fi

read -rp "▶️  Launch scPRAM notebook now? [y/N] " run
if [[ $run =~ ^[Yy]$ ]]; then
    $ACTIVATOR activate scpram
    jupyter-lab 2_scPRAM/scPRAM_Tutorial_ECCB2025.ipynb
    $ACTIVATOR deactivate
fi

info "🥳  Setup finished – happy analysing!"