[Biopython-dev] Changing run_tests.py (Galaxy package inspired)

[Tiago Rodrigues Antao]

Just to make sure we are on the same page:

--check-dependencies would raise as an error:
MissingExternalDependencyError
MissingPythonDependencyError
and a new
MissingProprietaryDependencyError subclass of 
MissingExternalDependencyError

--check-free-dependencies would raise
MissingExternalDependencyError
MissingPythonDependencyError

On Wed, 11 May 2016, Peter Cock wrote:

> On Wed, May 11, 2016 at 4:36 PM, Tiago Rodrigues Antao <tra at popgen.net> wrote:
>> Hi,
>>
>> For simplicity I am including Python libraries as dependencies. I do not see
>> a use case for separation, or is there?
>>
>
> There is a use case.
>
> We have two exceptions here, MissingExternalDependencyError
> is the base class used for external applications etc, while subclass
> MissingPythonDependencyError also subclasses ImportError - so
> that you can catch it with:
>
> try:
>    from Bio import XXX
> except ImportError:
>    print("Sad face")
>
> Then in run_tests.py we look for MissingExternalDependencyError
> (and its subclasses) as things that we will skip with a warning.
>
> Peter
>