Parallel get env

[joshqsumner]

Describe your changes
Not all parallel clusters have a simple option to fetch the conda environment that the original call to plantcv-run-workflow happened in. This is particularly a problem through jupyterconfig on the datascience jupyter server where there is no conda env active but it should also be relevant to PBS clusters, etc. This adds some logic in run_parallel to find the conda env if the sys.executable path includes a conda/miniforge directory and add activation commands to the job_script_prologue if the prologue is empty.

Type of update
This is a new feature.

Associated issues
Closes #1869

Additional context
This is probably difficult to test on the remote, I so far do not have any good ideas about rearranging the logic or modifying the tests to cover this. Monkeypatch works to mock sys.executable so splitting this into a helper function I can test the helper easily.

For the reviewer
See this page for instructions on how to review the pull request.

• PR functionality reviewed in a Jupyter Notebook
• All tests pass
• Test coverage remains 100%
• Documentation tested
• New documentation pages added to plantcv/mkdocs.yml
• Changes to function input/output signatures added to updating.md
• Code reviewed
• PR approved

[deepsource-io]

DeepSource Code Review

We reviewed changes in dd09c4f...0ae03c2 on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

See full review on DeepSource ↗

PR Report Card

Overall Grade

Security   Reliability   Complexity   Hygiene

Code Review Summary

Analyzer	Status	Updated (UTC)	Details
Python		Feb 25, 2026 2:23p.m.	Review ↗
Test coverage		Feb 25, 2026 2:23p.m.	Review ↗

Code Coverage Summary

Language	Line Coverage (New Code)	Line Coverage (Overall)
Aggregate	100% [✓ above threshold]	100%
Python	100% [✓ above threshold]	100%

➟ Additional coverage metrics may have been reported. See full coverage report ↗

[Copilot]

Pull request overview

Adds automatic detection of the active Conda environment when running plantcv.parallel.run_parallel, and injects activation commands into Dask job scripts when a prologue is not provided—targeting HPC/Jupyter setups where getenv is insufficient.

Changes:

• Add _check_for_conda helper and call it from run_parallel to set cluster_config["job_script_prologue"] automatically.
• Add a unit test for the Conda-detection helper using monkeypatch on sys.executable.
• Document the behavior in the parallel configuration docs.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
plantcv/parallel/run_parallel.py	Adds Conda environment detection and config mutation to inject worker prologue activation.
tests/parallel/test_run_parallel.py	Introduces a unit test validating prologue generation from a mocked Conda-like sys.executable.
docs/parallel_config.md	Documents that PlantCV will attempt to auto-populate job_script_prologue when not provided.

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