Steve Moss

Ported tests to nose and need to test against both ensembl and ensemblgenomes REST APIs.

tests fail under certain conditions

1

getInfoSpecies returns two different lengths strings - need to investigate why.

ValueError: cannot convert float NaN to integer

7

I'm trying to run `hagfish_extract` and am getting the following error: ``` [smoss@biolserva pacbio_assembly]$ hagfish_extract pbreads_to_pbasm_blasr.sorted.bam /home/smoss/.local/lib/python2.7/site-packages/numpy/core/_methods.py:59: RuntimeWarning: Mean of empty slice. warnings.warn("Mean of empty slice.", RuntimeWarning) /home/smoss/.local/lib/python2.7/site-packages/numpy/core/_methods.py:71: RuntimeWarning: invalid...

We have a Kyverno policy in our cluster that requires use of the `app.kubernetes.io/name`, `app.kubernetes.io/instance` and `app.kubernetes.io/version` labels, as per https://kubernetes.io/docs/concepts/overview/working-with-objects/common-labels/. We also need to add some annotations for access...

## Priority: Low (Enhancement) ### Issue Retry behavior is currently hardcoded with `max_attempts = 5` and a fixed backoff strategy. Different use cases might need different retry configurations. ### Current...

## Priority: Low (Infrastructure) ### Improvements #### 1. Add .python-version File For tools like pyenv, mise, asdf: ```bash echo "3.12" > .python-version ``` #### 2. Add py.typed Marker For PEP...

## Priority: Low (Documentation) ### Issues #### 1. Missing Class-Level Documentation The `EnsemblRest` class lacks comprehensive docstring explaining: - Rate limiting behavior (15 req/sec) - Retry logic (up to 5...

## Priority: Medium ### Issue Most tests are marked with `@pytest.mark.live`, meaning they hit the actual Ensembl REST API. This makes: - Local development slower - Tests dependent on external...

## Priority: Low (Enhancement) ### Issue The `EnsemblRest` class creates a `requests.Session` but doesn't provide a clean way to close it, which can lead to resource leaks in long-running applications....

## Priority: Low (Enhancement) ### Issue The API configuration dictionary uses generic `dict[str, Any]` types, which doesn't provide type safety or IDE autocomplete for API endpoint definitions. ### Current Code...