Csub silently ignores extra env

[alexdremov]

Before, csub was just ignoring extra env from .env file, which is unexpected and leads to bugs

[Copilot]

Pull request overview

This PR aims to stop csub from silently ignoring additional .env variables by ensuring the container runtime environment includes the full .env contents (not just a fixed subset).

Changes:

• Build literal_env by merging the full parsed .env dict with runtime overrides (HOME, NB_UID, etc.).
• Adjust how environment flags are added to the generated runai submit command.

Comments suppressed due to low confidence (1)

csub.py:120

• literal_env is now built as env | {...}, which pulls in all keys from the .env file, including secret values (e.g., WANDB_API_KEY, HF_TOKEN, GITHUB_TOKEN, etc.). If these are passed through --environment KEY=value, the secret values will end up in the generated command line / logs instead of being sourced from the Kubernetes secret. Consider filtering secret keys out of the dict passed to add_env_flags, and continue injecting secrets via add_secret_env_flags (using EXTRA_SECRET_KEYS to extend the secret key set).

    literal_env = env | {
        "HOME": f"/home/{env['LDAP_USERNAME']}",
        "NB_USER": env["LDAP_USERNAME"],
        "NB_UID": run_uid,
        "NB_GROUP": env["LDAP_GROUPNAME"],
        "NB_GID": run_gid,
        "WORKING_DIR": working_dir,
        "SCRATCH_HOME": scratch_home,
        "SCRATCH_HOME_ROOT": scratch_root,
        "EPFML_LDAP": env["LDAP_USERNAME"],
        "HF_HOME": hf_home,
        "UV_PYTHON_VERSION": env.get("UV_PYTHON_VERSION", "3.11"),
        "TZ": env.get("TZ", "Europe/Zurich"),
        # Keep runtime shell and tool caches available when using `runai exec`
        "GIT_CONFIG_GLOBAL": f"{scratch_home}/.gitconfig",
        "UV_CACHE_DIR": f"{scratch_home}/.cache/uv",
        "UV_PYTHON_INSTALL_DIR": f"{scratch_home}/.uv",
    }

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

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