pytest errors

[iimog]

Hi @rvosa,

As part of my review, I tried running the test suite. However, simply running pytest after the installation results in:

=========================== short test summary info ============================
FAILED tests/arise/test_arise.py::test_arise_coi - SystemExit: 1
FAILED tests/bge/test_bge.py::test_bge_coi - SystemExit: 1
======== 2 failed, 1 passed, 2 skipped, 2 warnings in 467.62s (0:07:47) ========

Full log: pytest-vanilla.log

The log indicates that a Galaxy domain and API credentials are required to run the tests. This should be clearly stated. However even with valid credentials for usegalaxy.org and usegalaxy.eu the tests still fail.

Running the first test individually revealed that the required app is not installed:

$ pytest tests/arise/test_arise.py
============================================================ test session starts ============================================================
platform linux -- Python 3.14.5, pytest-9.0.3, pluggy-1.6.0
rootdir: /tank/home/iimog/orga/reviews/2026/joss/barcode_validator/barcode_validator
configfile: pyproject.toml
collected 1 item                                                                                                                            

tests/arise/test_arise.py F                                                                                                           [100%]

[...]
ERROR    barcode_validator.cli:cli.py:124 Validation failed: Tool 'Identify reads with blastn and find taxonomy' not found
[...]

I'm not very familiar with Galaxy, but it appears that I'm unable to install the tool on any of these instances. When I search on the instance for the "barcode validator" tool, I don't get any results. On the Galaxy Tool Shed, I get two results (rvosa/barcode_validator_structural and rvosa/suite_barcode_validator). But installing them on a Galaxy instance appears to require admin privileges.

Does this mean, I need to find an instance with this tool installed or host my own, in order to even run the tests for barcode_validator?

[rvosa]

Hi @iimog, thanks for checking this. I will need to make some changes because these tests are specific for our own Galaxy instance and should simply be skipped if you don't have access. Furthermore, this should be documented better. Bear with me while I deal with this.