test: add unit tests

[deliaBlue]

Closes #52

In order to add a test for filter_multimappers.py the following changes had been made:

• Create the test
• Create the test files (input and output files)
• modify the script to stop if the file is empty and fix count_indels and find_best_alignments calls
• Add dependencies in both the environment.yml and environment.dev.yml
• Add test in CI.yml
• Add coverage file

[uniqueg]

Oh, I'm really sorry @deliaBlue. I had reviewed this on Saturday, and was wondering why you didn't respond. But now I've seen that I hadn't actually submitted the review. Sorry about that 🙈

[uniqueg]

See individual comments.

[uniqueg]

Sorry for adding a whole bunch of new comments 🙈

[deliaBlue]

Regarding the token option you mention here, If you open the codecov link in the CI, you will see the warning unusable report. If you click on download you will see this:

<Error>
<Code>ExpiredToken</Code>
<Message>The provided token has expired.</Message>
<Details>
Request signature expired at: 2023-04-27T09:14:19+00:00
</Details>
</Error>

I thought that maybe adding the token it would fix this; it did not. I'll take a look at it later.

[uniqueg]

Regarding the token option you mention here, If you open the codecov link in the CI, you will see the warning unusable report. If you click on download you will see this:

<Error>
<Code>ExpiredToken</Code>
<Message>The provided token has expired.</Message>
<Details>
Request signature expired at: 2023-04-27T09:14:19+00:00
</Details>
</Error>

I thought that maybe adding the token it would fix this; it did not. I'll take a look at it later.

But did you actually try without a token? Whenever I saw this the token was there. The thing is that I think the tokens are scoped to each repository, so you can't use an organization-scoped CodeCov token. And indeed, such a token is not defined:

So I suggest that you first try without a token, and if/when it turns out that we really need a token, I will create one on CodeCov and set it here as a repository secret (I don't think that you have the permissions to do that, but you can try).

[deliaBlue]

I try it without the token and still obtain the same.
Also, as you can see, I tried to "fix the path" adding the correct one on the codecov.yml as explained here but still obtain the "unusable report" error and in fact, when checking the "unusable report" the path to the coverage file is not changed, I'm not quite sure the error is in the path but I cannot argue any other option; I cannot see where the problem is.

[deliaBlue]

I'll proceed on deleting the coverage call. This issue can be addressed in #74 .