fix(utils): improve ecosystem path portability

README.md

@@ -136,7 +136,7 @@ only after reviewing the build results and registry target.
 ### Run coverage across all repos
 ```bash
 bash run_coverage.sh
-# Output: ~/Desktop/machine/out/coverage/
+# Output: ${OMNIBIOAI_ROOT:-<ecosystem-root>}/out/coverage/
 ```
 
 ### Update all GitHub repo descriptions and topics
@@ -257,7 +257,7 @@ Test files live in `tests/`; `pytest.ini` only collects from there.
 These are the intended schedules, not an installer. Confirm that each
 referenced repository and script exists on the target machine before adding
 entries to crontab. Most scripts assume the default root
-`~/Desktop/machine`; use their documented arguments or environment variables
+`${OMNIBIOAI_ROOT:-<ecosystem-root>}`; use their documented arguments or environment variables
 where available when deploying on another host.
 
 | Time | Script | Purpose |

backup-system-state.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 # backup-system-state.sh — Daily backup of spark-70f0's non-git system state
 #
 # Backs up: every real .env file across the ecosystem repos, a fresh
@@ -41,7 +42,7 @@
 
 set -euo pipefail
 
-MACHINE_DIR="/home/manish/Desktop/machine"
+MACHINE_DIR="$OMNIBIOAI_ROOT"
 BACKUP_DIR="${MACHINE_DIR}/work/backups/system-state"
 REPO_DIR="/home/manish/.omnibioai-system-backups-repo"
 PASSPHRASE_FILE="/home/manish/.omnibioai-config-backup-passphrase"

build-all-new.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 # build-all-new.sh
 
-BASE=/home/manish/Desktop/machine
+BASE="$OMNIBIOAI_ROOT"
 REGISTRY=ghcr.io/omnibioai
 
 declare -A SERVICES=(

build_all_tools.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 set -e
 
-MACHINE_DIR="$HOME/Desktop/machine"
+MACHINE_DIR="$OMNIBIOAI_ROOT"
 ECR="068155050939.dkr.ecr.us-east-1.amazonaws.com/omnibioai"
 REGION="us-east-1"
 JOB_QUEUE="arn:aws:batch:us-east-1:068155050939:job-queue/omnibioai-jq"

build_cython.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 # OmniBioAI Cython compilation script
 # Compiles all HIGH priority files across all repos
 # Run before building Docker images
 
 set -e
-MACHINE=~/Desktop/machine
+MACHINE="$OMNIBIOAI_ROOT"
 LOG=$MACHINE/out/cython_build.log
 mkdir -p $MACHINE/out
 

build_omnibioai_ecosystem.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 # utils/build_omnibioai_ecosystem.sh
 #
 # Orchestrates a full ecosystem build:
@@ -8,11 +9,11 @@
 #   4. Build and (re)start omnibioai-studio via docker compose
 #
 # Usage: bash omnibioai-utils/build_omnibioai_ecosystem.sh [root_dir]
-# Default root: ~/Desktop/machine
+# Default root: "$OMNIBIOAI_ROOT"
 
 set -euo pipefail
 
-ROOT="${1:-$HOME/Desktop/machine}"
+ROOT="${1:-$OMNIBIOAI_ROOT}"
 
 RED='\033[0;31m'
 GREEN='\033[0;32m'
@@ -153,4 +154,4 @@ export REDIS_ACL_POLICY_PATH="${REDIS_ACL_POLICY_PATH:-$STUDIO_DIR/config/redis/
 
 ok "✓ omnibioai-studio built and running."
 echo ""
-echo -e "${BOLD}${GREEN}All 4 steps completed successfully.${RESET}"
+echo -e "${BOLD}${GREEN}All 4 steps completed successfully.${RESET}"

check_platform_workflows.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 #
 # check_platform_workflows.sh
 #
@@ -29,7 +30,7 @@
 
 set -uo pipefail
 
-MACHINE_DIR="${1:-$HOME/Desktop/machine}"
+MACHINE_DIR="${1:-$OMNIBIOAI_ROOT}"
 # Falls back to the gh CLI's own stored credentials (gh auth login) when
 # GH_TOKEN isn't exported -- cron runs with a minimal environment, so this
 # is what lets this script work unattended instead of failing silently

check_unpushed_work.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 # check_unpushed_work.sh
 #
 # Cross-repo health check: scans every git repo under ROOT for uncommitted
@@ -20,7 +21,7 @@
 
 set -uo pipefail
 
-ROOT="/home/manish/Desktop/machine"
+ROOT="$OMNIBIOAI_ROOT"
 JSON_OUT=""
 QUIET=false
 
@@ -127,4 +128,4 @@ fi
 if [ "$UNPUSHED_COUNT" -gt 0 ]; then
     exit 1
 fi
-exit 0
+exit 0

clock_count.sh

@@ -1,22 +1,23 @@
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 cloc \
-  ~/Desktop/machine/omnibioai \
-  ~/Desktop/machine/omnibioai-landing \
-  ~/Desktop/machine/omnibioai-api-gateway \
-  ~/Desktop/machine/omnibioai-tes \
-  ~/Desktop/machine/omnibioai_sdk \
-  ~/Desktop/machine/omnibioai-rag \
-  ~/Desktop/machine/omnibioai-toolserver \
-  ~/Desktop/machine/omnibioai-model-registry \
-  ~/Desktop/machine/omnibioai-dev-hub \
-  ~/Desktop/machine/omnibioai-policy-engine \
-  ~/Desktop/machine/omnibioai-security-audit \
-  ~/Desktop/machine/omnibioai-hpc-policy-engine \
-  ~/Desktop/machine/omnibioai-auth \
-  ~/Desktop/machine/omnibioai-tool-images \
-  ~/Desktop/machine/omnibioai-control-center \
-  ~/Desktop/machine/omnibioai-workflow-bundles \
-  ~/Desktop/machine/omnibioai-studio \
-  ~/Desktop/machine/omnibioai-lims \
+  "$OMNIBIOAI_ROOT"/omnibioai \
+  "$OMNIBIOAI_ROOT"/omnibioai-landing \
+  "$OMNIBIOAI_ROOT"/omnibioai-api-gateway \
+  "$OMNIBIOAI_ROOT"/omnibioai-tes \
+  "$OMNIBIOAI_ROOT"/omnibioai_sdk \
+  "$OMNIBIOAI_ROOT"/omnibioai-rag \
+  "$OMNIBIOAI_ROOT"/omnibioai-toolserver \
+  "$OMNIBIOAI_ROOT"/omnibioai-model-registry \
+  "$OMNIBIOAI_ROOT"/omnibioai-dev-hub \
+  "$OMNIBIOAI_ROOT"/omnibioai-policy-engine \
+  "$OMNIBIOAI_ROOT"/omnibioai-security-audit \
+  "$OMNIBIOAI_ROOT"/omnibioai-hpc-policy-engine \
+  "$OMNIBIOAI_ROOT"/omnibioai-auth \
+  "$OMNIBIOAI_ROOT"/omnibioai-tool-images \
+  "$OMNIBIOAI_ROOT"/omnibioai-control-center \
+  "$OMNIBIOAI_ROOT"/omnibioai-workflow-bundles \
+  "$OMNIBIOAI_ROOT"/omnibioai-studio \
+  "$OMNIBIOAI_ROOT"/omnibioai-lims \
   --exclude-dir=node_modules,.venv,__pycache__,migrations,htmlcov,.git,obsolete,locale,data,work,uploads,downloads,results,output,cache,logs,tmp \
   --exclude-ext=json,lock,svg,min.js,map,po,pot,txt,csv,log,sql \
   --include-lang=Python,JavaScript,TypeScript,CSS,HTML,Shell,R,Dockerfile,YAML,Groovy,JSX,SCSS \

ecosystem_status.sh

@@ -1,8 +1,9 @@
 #!/usr/bin/env bash
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/ecosystem_path.sh"
 # utils/ecosystem_status.sh
 # Check git status for all repos in the OmniBioAI ecosystem
 # Usage: bash utils/ecosystem_status.sh [root_dir]
-# Default root: ~/Desktop/machine
+# Default root: $OMNIBIOAI_ROOT
 
 SCRIPT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
 DEFAULT_ROOT="$(cd -- "$SCRIPT_DIR/.." && pwd)"
@@ -128,4 +129,4 @@ if [ "$non_main" -gt 0 ]; then
         fi
     done
     echo ""
-fi
+fi