bump_version.sh

#!/usr/bin/env bash
# bump_version.sh — update version.py, commit, and tag a new emapper release.
#
# Usage:
#   ./bump_version.sh [BUMP] [OPTIONS]
#
# BUMP types:
#   pre      — increment pre-release counter:  3.0.0-beta1 → 3.0.0-beta2
#              if not currently on a pre-release, starts at label1:  3.0.0 → 3.0.0-beta1
#   release  — drop pre-release suffix:        3.0.0-beta3 → 3.0.0
#   patch    — (default) increment patch:      3.0.0 → 3.0.1  /  3.0.0-beta1 → 3.0.1
#   minor    — increment minor, reset patch:   3.0.0 → 3.1.0
#   major    — increment major, reset rest:    3.0.0 → 4.0.0
#   X.Y.Z[-preN] — set an exact version string
#
# Options:
#   --pre-label LABEL   pre-release label to use with 'pre' bump (default: beta)
#   --db-version X.Y.Z  set __DB_VERSION__ (default: 7.0.0)
#   --yes               skip confirmation prompt
#
# After a successful tag the script prints the git push commands to run.
# It does NOT push automatically — review the tag first.

set -euo pipefail

REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
VERSION_FILE="$REPO_ROOT/eggnogmapper/version.py"

# ── defaults ──────────────────────────────────────────────────────────────────
BUMP="patch"
DB_VERSION="7.0.0"
PRE_LABEL="beta"
AUTO_YES=0

# ── parse args ────────────────────────────────────────────────────────────────
while [[ $# -gt 0 ]]; do
    case "$1" in
        --db-version)  DB_VERSION="$2";  shift 2 ;;
        --pre-label)   PRE_LABEL="$2";   shift 2 ;;
        --yes)         AUTO_YES=1;       shift   ;;
        patch|minor|major|pre|release) BUMP="$1"; shift ;;
        [0-9]*.*)  BUMP="$1"; shift ;;   # exact version e.g. 3.0.0-beta1
        *) echo "Unknown argument: $1" >&2; exit 1 ;;
    esac
done

# ── read current version ──────────────────────────────────────────────────────
[[ -f "$VERSION_FILE" ]] || { echo "ERROR: $VERSION_FILE not found." >&2; exit 1; }

CURRENT="$(grep "__VERSION__" "$VERSION_FILE" | cut -d"'" -f2)"
[[ -n "$CURRENT" ]] || { echo "ERROR: could not parse __VERSION__ from $VERSION_FILE" >&2; exit 1; }

NOVEL_FAMS_VERSION="$(grep "__NOVEL_FAMS_DB_VERSION__" "$VERSION_FILE" | cut -d"'" -f2)"

# split into base (X.Y.Z) and optional pre-release suffix (betaN)
if [[ "$CURRENT" =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)-([a-zA-Z]+)([0-9]+)$ ]]; then
    VMAJ="${BASH_REMATCH[1]}"
    VMIN="${BASH_REMATCH[2]}"
    VPAT="${BASH_REMATCH[3]}"
    CUR_LABEL="${BASH_REMATCH[4]}"
    CUR_NUM="${BASH_REMATCH[5]}"
elif [[ "$CURRENT" =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then
    VMAJ="${BASH_REMATCH[1]}"
    VMIN="${BASH_REMATCH[2]}"
    VPAT="${BASH_REMATCH[3]}"
    CUR_LABEL=""
    CUR_NUM=""
else
    echo "ERROR: cannot parse version '$CURRENT'" >&2; exit 1
fi

# ── compute new version ───────────────────────────────────────────────────────
case "$BUMP" in
    pre)
        if [[ -n "$CUR_LABEL" ]]; then
            # already on a pre-release — increment the number
            NEW_VERSION="${VMAJ}.${VMIN}.${VPAT}-${CUR_LABEL}$((CUR_NUM + 1))"
        else
            # start a new pre-release series
            NEW_VERSION="${VMAJ}.${VMIN}.${VPAT}-${PRE_LABEL}1"
        fi
        ;;
    release)
        # drop the pre-release suffix to produce a stable release
        NEW_VERSION="${VMAJ}.${VMIN}.${VPAT}"
        ;;
    patch)
        NEW_VERSION="${VMAJ}.${VMIN}.$((VPAT + 1))"
        ;;
    minor)
        NEW_VERSION="${VMAJ}.$((VMIN + 1)).0"
        ;;
    major)
        NEW_VERSION="$((VMAJ + 1)).0.0"
        ;;
    *)
        # exact version string passed directly
        NEW_VERSION="$BUMP"
        ;;
esac

TAG="v${NEW_VERSION}"

# ── confirm ───────────────────────────────────────────────────────────────────
echo "=================================================="
echo "  current  : $CURRENT"
echo "  new      : $NEW_VERSION  (tag: $TAG)"
echo "  db       : $DB_VERSION"
echo "  novel db : $NOVEL_FAMS_VERSION  (unchanged)"
echo "=================================================="

if [[ "$AUTO_YES" == "0" ]]; then
    read -rp "Proceed? [y/N] " CONFIRM
    [[ "${CONFIRM,,}" == "y" ]] || { echo "Aborted."; exit 0; }
fi

# ── write version.py ──────────────────────────────────────────────────────────
cat > "$VERSION_FILE" <<EOF
#autogenerated during release process. Do not modify
__VERSION__='${NEW_VERSION}'
__DB_VERSION__='${DB_VERSION}'
__NOVEL_FAMS_DB_VERSION__='${NOVEL_FAMS_VERSION}'
EOF

echo "Written: $VERSION_FILE"

# ── commit and tag ────────────────────────────────────────────────────────────
git -C "$REPO_ROOT" add eggnogmapper/version.py
git -C "$REPO_ROOT" commit -m "chore: release ${TAG}"
git -C "$REPO_ROOT" tag "$TAG"

echo ""
echo "Done. Commit and tag '${TAG}' created."
echo ""
echo "To publish:"
echo "  git -C $REPO_ROOT push && git -C $REPO_ROOT push --tags"
echo ""
echo "To build Apptainer image:"
echo "  cd $REPO_ROOT/apptainer && ./build.sh"
echo "  # or for a dev image: ./build.sh --local"