Fixing failing build - Githubissues

streetslab / dimelo

python package for analysis of dimelo-seq & nanopore modified base data

MIT License

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Fixing failing build #21

Closed thekugelmeister closed 2 years ago

thekugelmeister commented 2 years ago

Builds currently fail on test_parse_bam_bedFile and test_parse_bam_region. More than likely, this indicates that the tests themselves are bugged / insufficient / problematic in some way. This PR will remain open, with test fixes pushed intermittently, until the builds pass and reasonable parse_bam tets are implemented.

thekugelmeister commented 2 years ago

In the errors from the failed tests, it looks like the database is not being populated at all: AssertionError: b'' != b'd9f626468e4221a30318639f19dc2cd8a3f00fa6e12a5280c1b58204\n'

Possible causes:

tempfile library does not work as expected on Travis CI build machines
Some other error is happening in database population

thekugelmeister commented 2 years ago

It appears that the problem here is actually in the subprocess call to sqlite3! Not sure why, not sure how to debug it, and not sure what to do about it. Hmm...

thekugelmeister commented 2 years ago

Calling sqlite3 mod_mappings_subset.db .sha3sum on Travis results in the following error: Error: unknown command or invalid arguments: "sha3sum". Enter ".help" for help

Apparently, calling sqlite3 with dot commands does not work in the build environment? That makes no sense to me, unless something is different about the specific version of sqlite3 installed in that environment. This would lead to the question of why the build environment differs from the dev environment.

thekugelmeister commented 2 years ago

Closed in favor of enabling test using github actions