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This pull-request is an proposal to add GitHub Actions CI (Continous Integration). When the CI (Continous Integration) is enabled for this repository, it is much easy for people to contribute by sending pull-requests. And you can check it easier.
The pull request is working in progress (WIP).
The logic is to use the Docker container, replace the MItoHiFi source from the one installed in the Docker container with the target commit or pull-request's source, and test it. There are 2 test cases, test with small reads file, and configs file. These are tested at #30 .
The reads FASTA test data
ilDeiPorc1.reads.small.fa
that I added in this pull request is not real data, but what I picked up the first 20045 lines from the real data fileilDeiPorc1.reads.fa
. Because currently the entire process with the real datailDeiPorc1.reads.fa
took around 75 minutes. It's too long as a total running time in CI.I confirmed the MItoHifi stable version in the container passed and worked with the reads FASTA file
ilDeiPorc1.reads.small.fa
at #30 (comment) . So, I think the test cases with the test data file is still better than no tests.There is one problem that I can not solve around the
fetch.py
get_num_seqs
method. The method expects the*.trnas
files exist in the current working directory. But I don't see the files. See the debug log in the `fetch.py.For the error in CI, I assume there is a specific logic in the MitoHifi master branch from the latest stable version or a specific logic to install MitoHifi to set in the container.
@jgnunes What do you think about adding the GitHub Actions CI?
Do you know what's wrong? Here is the CI log.
https://github.com/marcelauliano/MitoHiFi/actions/runs/3324184394/jobs/5495438314#step:7:45
MitoHiFi/fetch.py
Lines 19 to 41 in c225acb
Note I modified the
fetch.py
temporarily to show the debug log in this CI result. But I will remove the modification eventually by rebasing the commit.Examples
For the GitHub Actions CI, I introduce other project cases.