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Update environment.yml from a Prepared Instance

After running a backpack, the conda environment that was actually built and used may differ from what is written in software/environment.yml — packages may have been resolved to different versions, transitive dependencies may have been pulled in, or you may have installed extra packages during an interactive session.

floability backpack update-env exports the Conda environment recorded by an instance and writes concrete versions back into the backpack.

See also: Create Your First Backpack for how to set up the initial environment.yml.

When to use this

  • You ran a backpack and want to pin the exact versions that worked.
  • You installed packages interactively during a session and want to capture them.
  • You want to share a backpack with a fully reproducible environment spec.

Prerequisites

  • An instance with usable recorded environment metadata. This includes a successfully prepared (ready) instance and a completed or interrupted run whose environment preparation succeeded. A failed or incomplete instance without that metadata is rejected.
  • conda available on PATH.

Two modes

Full replacement (default)

Exports every package installed in the instance environment and uses that as the new dependency list. The backpack's name field and any floability-specific fields (e.g. post_install_script) are preserved; the prefix field from the export is dropped automatically.

floability backpack update-env --from-instance <name-or-path>

Run from inside the backpack directory, or pass an explicit path:

floability backpack update-env --from-instance fi_cms-physics_20260410-104122_a1b2c3d4 ./cms-physics

Versions-only

Only updates the version of packages already listed in environment.yml. Structure, channels, package selection, post_install_script, and all other fields are left exactly as you wrote them.

floability backpack update-env --from-instance <name-or-path> --versions-only

Use this when your environment.yml is carefully curated and you only want to lock in the versions that were actually resolved, rather than expanding it to include every transitive dependency.

Identifying the instance

Pass either a registered short name or a full path:

# by short name (from `floability instance list`)
floability backpack update-env --from-instance fi_cms-physics_20260410-104122_a1b2c3d4

# by path
floability backpack update-env --from-instance /path/to/floability-base-dir/fi_cms-physics_20260410-104122_a1b2c3d4

To find the latest instance quickly:

floability instance latest
floability backpack update-env --from-instance $(floability instance latest)

What changes on disk

File Action
software/environment.yml Overwritten with the updated spec
software/old-environment.yml Backup of the previous environment.yml

The backup lets you diff or roll back if needed:

diff software/old-environment.yml software/environment.yml

Example: full replacement

Before (hand-written spec):

name: cms-physics
channels:
  - conda-forge
dependencies:
  - python=3.10
  - numpy
  - coffea
  - pip:
    - fastjet==3.4.2.1
post_install_script: install_taskvine.sh

After running update-env:

name: cms-physics
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1
  - python=3.10.14
  - numpy=1.26.4
  - coffea=2024.4.0
  - ...
  - pip:
    - fastjet==3.4.2.1
    - coffea==2024.4.0
post_install_script: install_taskvine.sh

Note: name is preserved from the original backpack file, not taken from the conda export. post_install_script is also carried over.

Example: versions-only

Before:

name: cms-physics
channels:
  - conda-forge
dependencies:
  - python=3.10
  - numpy
  - coffea
  - pip:
    - fastjet==3.4.2.1
post_install_script: install_taskvine.sh

After running update-env --versions-only (only the version specs change):

name: cms-physics
channels:
  - conda-forge
dependencies:
  - python=3.10.14
  - numpy=1.26.4
  - coffea=2024.4.0
  - pip:
    - fastjet==3.4.2.1
post_install_script: install_taskvine.sh

The package list stays exactly what you defined. Only the version strings are filled in from what was actually installed.

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