Remove orphaned setup-env.sh script
This script was not referenced anywhere in the codebase and used an outdated approach for credential management. Current workflow bakes credentials into Docker image from .env file in project root.
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@@ -1,9 +1,6 @@
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# Copy this file to .env and fill in your credentials
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# The .env file will be baked into the Docker image during build
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# Required for Claude Code if not using via subscription.
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ANTHROPIC_API_KEY=your_anthropic_api_key_here
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# Optional: Twilio credentials for SMS notifications
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TWILIO_ACCOUNT_SID=your_twilio_account_sid
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TWILIO_AUTH_TOKEN=your_twilio_auth_token
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@@ -11,7 +8,7 @@ TWILIO_FROM_NUMBER=+1234567890
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TWILIO_TO_NUMBER=+0987654321
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# Optional: Custom conda installation (for academic/lab environments)
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# Example: CONDA_PREFIX=/vol/biomedic3/username/miniconda3
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# Example: CONDA_PREFIX=/path/to/miniconda3
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CONDA_PREFIX=
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# Optional: Additional conda directories (space-separated list)
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@@ -19,7 +16,7 @@ CONDA_PREFIX=
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# Automatic detection:
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# - Paths with "*env*" are added to CONDA_ENVS_DIRS (for environments)
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# - Paths with "*pkg*" are added to CONDA_PKGS_DIRS (for package cache)
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# Example: CONDA_EXTRA_DIRS="/vol/biomedic3/username/.conda/envs /vol/biomedic3/username/conda_envs /vol/biomedic3/username/.conda/pkgs /vol/biomedic3/username/conda_pkgs /homes/username/.conda/envs"
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# Example: CONDA_EXTRA_DIRS="/vol/lab/username/.conda/envs /vol/lab/username/conda_envs /vol/lab/username/.conda/pkgs /vol/lab/username/conda_pkgs"
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CONDA_EXTRA_DIRS=
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# Optional: System packages to install in Docker container (space-separated)
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