udpate scripts

PORTABILITY_PATH_INVENTORY.md

@@ -0,0 +1,7 @@
+# Path portability inventory
+
+Active utility defaults now resolve through `ecosystem_path.sh`: `OMNIBIOAI_ROOT` takes precedence, otherwise the parent of this repository is used. Positional root arguments remain supported where they existed.
+
+The obsolete `Desktop/machine` references found in active utilities were replaced in the build, backup, coverage, startup, sync, sweep, audit, and data helper scripts. Historical cron examples, generated `build-results.txt`, migration notes, test fixtures, and PubMed archival documentation retain their original paths as records of past runs. Ordinary identifiers and unrelated prose were left unchanged.
+
+Validation covers default resolution, an override containing spaces, Bash syntax, Python compilation, and `git diff --check`. No backup, restore, sync, build, deployment, or stack-start command was executed.

ecosystem_path.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+# Shared portable ecosystem path resolution for utility scripts.
+# OMNIBIOAI_ROOT wins; otherwise derive the ecosystem root from this checkout.
+if [[ -z "${OMNIBIOAI_UTILS_DIR:-}" ]]; then
+  OMNIBIOAI_UTILS_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+fi
+omni_resolve_root() {
+  if [[ -n "${OMNIBIOAI_ROOT:-}" ]]; then printf '%s\n' "$OMNIBIOAI_ROOT"; return; fi
+  printf '%s\n' "$(cd "$OMNIBIOAI_UTILS_DIR/.." && pwd)"
+}
+OMNIBIOAI_ROOT="$(omni_resolve_root)"
+export OMNIBIOAI_ROOT

omnibioai-up.sh

@@ -1,13 +1,14 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -euo pipefail
 
 SESSION="omnibioai"
 
 # Base paths (repos)
-OMNI_CORE=~/Desktop/machine/omnibioai
-OMNI_TES=~/Desktop/machine/omnibioai-tes
-OMNI_TOOL=~/Desktop/machine/omnibioai-toolserver
-OMNI_LIMS=~/Desktop/machine/omnibioai-lims
+OMNI_CORE="$OMNIBIOAI_ROOT"/omnibioai
+OMNI_TES="$OMNIBIOAI_ROOT"/omnibioai-tes
+OMNI_TOOL="$OMNIBIOAI_ROOT"/omnibioai-toolserver
+OMNI_LIMS="$OMNIBIOAI_ROOT"/omnibioai-lims
 
 # Optional: load your env (uncomment + set the right file if you use one)
 # [ -f ~/.bashrc ] && source ~/.bashrc

prepare_hipaa_audit.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -uo pipefail
 
-ROOT="${1:-$HOME/Desktop/machine}"
+ROOT="${1:-$OMNIBIOAI_ROOT}"
 
 echo
 echo "=============================================================="

pubmed/create_new_chunks.py

@@ -8,8 +8,8 @@
 from pathlib import Path
 from datetime import datetime
 
-DATA_DIR = Path("/home/manish/Desktop/machine/data/PubMed/Abstracts")
-STATE_FILE = Path("/home/manish/Desktop/machine/data/PubMed/sync_state.json")
+DATA_DIR = Path(os.path.join(os.environ.get("OMNIBIOAI_ROOT", str(Path(__file__).resolve().parents[2])), "data", "PubMed", "Abstracts"))
+STATE_FILE = Path(os.path.join(os.environ.get("OMNIBIOAI_ROOT", str(Path(__file__).resolve().parents[2])), "data", "PubMed", "sync_state.json"))
 CHUNK_SIZE = 500000
 
 def get_updated_pmids():

pubmed/reindex_one_shard.py

@@ -1,3 +1,4 @@
+import os
 #!/usr/bin/env python3
 
 """
@@ -22,7 +23,7 @@
 # Configuration
 SHARD = "_general_corpus_chunk100"
 
-PUBMED_DIR = Path("/home/manish/Desktop/machine/data/PubMed")
+PUBMED_DIR = Path(os.path.join(os.environ.get("OMNIBIOAI_ROOT", str(Path(__file__).resolve().parents[2])), "data", "PubMed"))
 
 INPUT_DIR = PUBMED_DIR / "Abstracts" / SHARD
 STAGING_DIR = PUBMED_DIR / "Index" / "_reindex_staging" / SHARD

pubmed/reindex_one_shard_ollama.py

@@ -1,3 +1,4 @@
+import os
 #!/usr/bin/env python3
 
 """
@@ -18,7 +19,7 @@
 SHARD = "_general_corpus_chunk100"
 
 PUBMED_DIR = Path(
-    "/home/manish/Desktop/machine/data/PubMed"
+    os.path.join(os.environ.get("OMNIBIOAI_ROOT", str(Path(__file__).resolve().parents[2])), "data", "PubMed")
 )
 
 INPUT_DIR = PUBMED_DIR / "Abstracts" / SHARD

pubmed/run_chunks.sh

@@ -1,11 +1,12 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)/ecosystem_path.sh"
 # run_chunks.sh
 # Runs embedding_engine.py over each _general_corpus_chunk* study,
 # capping concurrency to avoid repeating the OOM/swap situation.
 
 set -euo pipefail
 
-PARENT="/home/manish/Desktop/machine/omnibioai-data/PubMed/Abstracts"
+PARENT="$OMNIBIOAI_ROOT/omnibioai-data/PubMed/Abstracts"
 CHUNK_PREFIX="_general_corpus_chunk"
 MAX_CONCURRENT=1   # tune based on observed RSS per chunk; start conservative
 EMBED_MODEL="pubmedbert"

pubmed/split_general_corpus.sh

@@ -1,12 +1,13 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)/ecosystem_path.sh"
 # split_general_corpus.sh
 # Splits _general_corpus/*.json into chunk subdirectories of CHUNK_SIZE files each,
 # so ragbio.embeddings.embedding_engine can be run per-chunk via --study <chunk_name>
 # without any code changes.
 
 set -euo pipefail
 
-SRC="/home/manish/Desktop/machine/omnibioai-data/PubMed/Abstracts/_general_corpus"
+SRC="$OMNIBIOAI_ROOT/omnibioai-data/PubMed/Abstracts/_general_corpus"
 PARENT="$(dirname "$SRC")"
 CHUNK_SIZE=500000
 CHUNK_PREFIX="_general_corpus_chunk"

run_coverage.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
-MACHINE=~/Desktop/machine
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
+MACHINE="$OMNIBIOAI_ROOT"
 OUT=$MACHINE/out/coverage
 mkdir -p $OUT
 find $MACHINE -name "coverage.json" -exec chmod 666 {} \; 2>/dev/null
@@ -107,7 +108,7 @@ merged = {
     }
 }
 
-out = os.path.expanduser("~/Desktop/machine/out/coverage/omnibioai.json")
+out = os.path.join(os.environ.get("OMNIBIOAI_ROOT", ""), "out/coverage/omnibioai.json")
 with open(out, "w") as f:
     json.dump(merged, f, indent=2)
 print(f"  ✅ omnibioai merged: {total_covered}/{total_stmts} = {total_pct:.2f}%")
@@ -121,7 +122,7 @@ echo ""
 python3 - <<'EOF'
 import json, os, glob
 
-out_dir   = os.path.expanduser("~/Desktop/machine/out/coverage")
+out_dir   = os.path.join(os.environ.get("OMNIBIOAI_ROOT", ""), "out/coverage")
 SKIP      = {"omnibioai-services.json", "omnibioai-plugins.json"}
 THRESHOLD = 90.0
 

start-all-uis.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -e
-BASE=$HOME/Desktop/machine
+BASE="$OMNIBIOAI_ROOT"
 echo 'Starting OmniBioAI backend APIs...'
 
 # Workflow bundles backend

start_all.sh

@@ -1,11 +1,12 @@
 #!/bin/bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -e
 
 echo "=============================="
 echo "Starting OmniBioAI stack"
 echo "=============================="
 
-ROOT=~/Desktop/machine
+ROOT="$OMNIBIOAI_ROOT"
 
 # ----------------------------
 # Start omnibioai-tes

start_stack_tmux.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -euo pipefail
 
-ROOT="$HOME/Desktop/machine"
+ROOT="$OMNIBIOAI_ROOT"
 UTILS="$ROOT/utils/kill_port.sh"
 
 # Ports

sweep_all_repos.sh

@@ -1,12 +1,13 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -uo pipefail
 
 # Scans every sibling repo under MACHINE_DIR for leftover ghcr.io/man4ish
 # references, using the same logic as update_ghcr_refs.sh (dry-run only,
 # same exclusions for release/, obsolete/, node_modules/, work/, *.log etc).
 # Prints a per-repo summary so you can decide where to actually apply the fix.
 
-MACHINE_DIR="${1:-$HOME/Desktop/machine}"
+MACHINE_DIR="${1:-$OMNIBIOAI_ROOT}"
 UPDATE_SCRIPT="$(cd "$(dirname "$0")" && pwd)/update_ghcr_refs.sh"
 
 if [ ! -f "$UPDATE_SCRIPT" ]; then
@@ -73,4 +74,4 @@ else
     echo "      Review: bash $UPDATE_SCRIPT ${MACHINE_DIR}/${r}"
     echo "      Apply:  bash $UPDATE_SCRIPT ${MACHINE_DIR}/${r} --apply"
   done
-fi
+fi

sync_all_repos.sh

@@ -1,9 +1,10 @@
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 
 #!/usr/bin/env bash
 
 set -u
 
-ROOT="${1:-$HOME/Desktop/machine}"
+ROOT="${1:-$OMNIBIOAI_ROOT}"
 
 REPOS=(
     "omnibioai-api-gateway"

test_split_on_sample.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -euo pipefail
 
-SRC_REAL="${SRC_REAL:-/home/manish/Desktop/machine/omnibioai-data/PubMed/Abstracts/_general_corpus}"
+SRC_REAL="${SRC_REAL:-$OMNIBIOAI_ROOT/omnibioai-data/PubMed/Abstracts/_general_corpus}"
 SAMPLE_SIZE=20
 TEST_ROOT="/tmp/gc_split_test_$$"
 SRC="${TEST_ROOT}/_general_corpus"

tests/test_ecosystem_path.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+repo="$(cd "$(dirname "$0")/.." && pwd)"
+expected="$(cd "$repo/.." && pwd)"
+actual="$(env -u OMNIBIOAI_ROOT bash -c 'source "$1/ecosystem_path.sh"; printf "%s" "$OMNIBIOAI_ROOT"' _ "$repo")"
+[[ "$actual" == "$expected" ]]
+override="$(OMNIBIOAI_ROOT="/tmp/root with spaces" bash -c 'source "$1/ecosystem_path.sh"; printf "%s" "$OMNIBIOAI_ROOT"' _ "$repo")"
+[[ "$override" == "/tmp/root with spaces" ]]