Add planemo test workflow with bioconda dependency installation

[Copilot]

• Explore repository structure and understand existing CI/CD setup
• Review existing planemo-lint.yml workflow
• Review monophylizer.xml tool definition and tests
• Create new GitHub Actions workflow for planemo test with bioconda
• Configure workflow to install perl-bio-monophylizer from bioconda
• Configure workflow to run planemo test monophylizer.xml
• Validate workflow syntax
• Refactor to use planemo's conda_auto_install feature
• Improve shell configuration for error handling
• Remove redundant Python version specification
• Final code review
• Security check with CodeQL - no vulnerabilities found
• Remove defaults channel from conda configuration per feedback
• Fix conda environment activation issue by using conda-managed Python and named environment
• Add debugging step to show actual test output on failure for troubleshooting

Original prompt

Add to the CI/CD a step where perl-bio-monophylizer is installed from bioconda and then used to run planemo test monophylizer.xml as a unit test under the same conditions as the planemo linter

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[rvosa]

@copilot don't use the conda defaults channel

[Copilot]

@copilot don't use the conda defaults channel

Removed defaults channel from conda configuration in commit e3dc4bd. The workflow now only uses conda-forge and bioconda channels.

[rvosa]

@copilot the planemo tests are failing. Something seems to be going wrong with activating the conda environment.

[Copilot]

@copilot the planemo tests are failing. Something seems to be going wrong with activating the conda environment.

Fixed the conda environment activation issue in commit f5d9f5e. The problem was mixing setup-python and setup-miniconda actions. Now using conda-managed Python with a named environment ('planemo') that properly activates with the bash -el shell configuration.

[rvosa]

@copilot the planemo test keeps failing and it says exactly 30 lines are wrong (which is the expected number of lines). Can we see the output that is being produced? I want to see if it could be a line breaks issue or sth.

[Copilot]

@copilot the planemo test keeps failing and it says exactly 30 lines are wrong (which is the expected number of lines). Can we see the output that is being produced? I want to see if it could be a lin...

Added debugging output in commit b5983f7 that will display the actual test output on failure, including:

• The generated output file content
• Line count comparison
• Hex dump of the last characters (to detect line ending issues)
• Full diff between expected and actual output

This will help identify if it's a line breaks issue or other formatting problem. The debug output will appear in the CI logs when the test fails.

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