File size: 4,758 Bytes
e8d350a | 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 | #!/usr/bin/env bash
# Domestic-server pipeline:
# 1. Read configs/<env>/env.yml
# 2. mamba env create -n <env> -f env.yml (uses ~/.condarc mirrors)
# 3. If editable.txt non-empty: pip install -e <path> for each entry (source must be present)
# 4. conda-pack the new env into out/<env>.tar.gz (matches local pipeline)
#
# Idempotent: skips envs whose tarball already exists. Failure-tolerant.
# Parallel via xargs -P. Per-env status in state.tsv, failures in failed.txt.
#
# Required env vars:
# CONFIGS_DIR e.g. /home/user/mmsci/configs
# OUT_DIR e.g. /home/user/mmsci/conda_packs
# EDITABLE_SRC e.g. /home/user/mmsci/editable_sources (root containing editable source trees; optional)
# MAMBA_BIN e.g. /opt/conda/bin/mamba (default: 'mamba' on PATH)
# CONDA_PACK e.g. /opt/conda/bin/conda-pack (default: 'conda-pack' on PATH)
# JOBS parallel envs (default 4)
# LIST optional file of env names; default = all dirs under CONFIGS_DIR
set -uo pipefail
: "${CONFIGS_DIR:?CONFIGS_DIR required}"
: "${OUT_DIR:?OUT_DIR required}"
EDITABLE_SRC="${EDITABLE_SRC:-}"
MAMBA_BIN="${MAMBA_BIN:-mamba}"
CONDA_PACK="${CONDA_PACK:-conda-pack}"
JOBS="${JOBS:-4}"
LIST_FILE="${LIST:-}"
LOG_DIR="$OUT_DIR/_logs"
STATE="$OUT_DIR/build.state.tsv"
FAILED="$OUT_DIR/build.failed.txt"
mkdir -p "$OUT_DIR" "$LOG_DIR"
[[ -s "$STATE" ]] || printf "env\tstatus\tphase\tseconds\tsize_bytes\n" > "$STATE"
if [[ -z "$LIST_FILE" ]]; then
LIST_FILE="$OUT_DIR/_envs.txt"
find "$CONFIGS_DIR" -mindepth 1 -maxdepth 1 -type d -printf '%f\n' | sort > "$LIST_FILE"
fi
total=$(wc -l < "$LIST_FILE")
echo "[$(date +%T)] building $total envs, JOBS=$JOBS"
echo " configs: $CONFIGS_DIR"
echo " out: $OUT_DIR"
echo " mamba: $MAMBA_BIN"
echo " pack: $CONDA_PACK"
echo " editable_src: ${EDITABLE_SRC:-(none)}"
export CONFIGS_DIR OUT_DIR EDITABLE_SRC MAMBA_BIN CONDA_PACK LOG_DIR STATE FAILED
build_one() {
local env="$1"
local conf="$CONFIGS_DIR/$env"
local yml="$conf/env.yml"
local edit="$conf/editable.txt"
local meta="$conf/meta.json"
local dst="$OUT_DIR/$env.tar.gz"
local log="$LOG_DIR/$env.log"
: > "$log"
if [[ -s "$dst" ]]; then
echo "[skip] $env already packed"
printf "%s\tskip\t-\t0\t%s\n" "$env" "$(stat -c %s "$dst")" >> "$STATE"
return 0
fi
if [[ ! -s "$yml" ]]; then
echo "[missing-yml] $env"
printf "%s\tfail\tmissing_yml\t0\t0\n" "$env" >> "$STATE"
echo "$env missing_yml" >> "$FAILED"
return 1
fi
local t0=$(date +%s)
echo "[create] $env" | tee -a "$log"
if ! "$MAMBA_BIN" env create -n "$env" -f "$yml" -y >>"$log" 2>&1; then
local dt=$(( $(date +%s) - t0 ))
echo "[FAIL create] $env after ${dt}s (see $log)"
printf "%s\tfail\tcreate\t%s\t0\n" "$env" "$dt" >> "$STATE"
echo "$env create" >> "$FAILED"
return 1
fi
# editable installs (pip install -e <path>)
if [[ -s "$edit" && -n "$EDITABLE_SRC" ]]; then
while IFS=$'\t' read -r egg_name src_path; do
[[ -z "$src_path" ]] && continue
# remap original path -> EDITABLE_SRC/<env>/<basename>
local remap="$EDITABLE_SRC/$env/$(basename "$src_path")"
if [[ ! -d "$remap" ]]; then
echo "[editable-missing] $env: $remap" | tee -a "$log"
continue
fi
echo "[editable] $env: pip install -e $remap" | tee -a "$log"
if ! "$MAMBA_BIN" run -n "$env" pip install -e "$remap" >>"$log" 2>&1; then
echo "[FAIL editable] $env: $remap" | tee -a "$log"
fi
done < "$edit"
fi
# pack
echo "[pack] $env" | tee -a "$log"
if ! "$CONDA_PACK" -n "$env" -o "$dst" --compress-level=4 -j 8 \
--ignore-missing-files --ignore-editable-packages --force >>"$log" 2>&1; then
local dt=$(( $(date +%s) - t0 ))
echo "[FAIL pack] $env after ${dt}s"
printf "%s\tfail\tpack\t%s\t0\n" "$env" "$dt" >> "$STATE"
echo "$env pack" >> "$FAILED"
rm -f "$dst"
return 1
fi
local dt=$(( $(date +%s) - t0 ))
local sz=$(stat -c %s "$dst")
echo "[done] $env -> $(numfmt --to=iec "$sz") in ${dt}s"
printf "%s\tdone\t-\t%s\t%s\n" "$env" "$dt" "$sz" >> "$STATE"
}
export -f build_one
cat "$LIST_FILE" | xargs -n1 -P "$JOBS" -I{} bash -c 'build_one "$@"' _ {}
echo "[$(date +%T)] all done"
echo "summary:"
awk -F'\t' 'NR>1{c[$2]++} END{for(k in c)printf " %-8s %4d\n",k,c[k]}' "$STATE"
echo "total tarballs: $(ls "$OUT_DIR"/*.tar.gz 2>/dev/null | wc -l)"
echo "total size: $(du -shc "$OUT_DIR"/*.tar.gz 2>/dev/null | tail -1 | cut -f1)"
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