sdrf-pipelines
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bigbio
A repository to convert SDRF proteomics files into pipelines config files
I propose that tis project adopts some of the standard Python development tools to make contributions easier and reduce some of the burden of new contributors. * `black` and `black-disable-checker`...
@ypriverol Do you have a set of SDRF files for experiments of all different kinds of expected flavors? If not we should systematically generate SDRF example files with all the...
It would be better to not manually work with path strings but use the modern `pathlib` instead. https://github.com/bigbio/sdrf-pipelines/blob/837af51f360e81d5b9b6b10a21698fc4c7a3c582/sdrf_pipelines/parse_sdrf.py#L124
A good example can be found here: https://github.com/mduclehcm/rome/blob/master/.git-blame-ignore-revs More context here: https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view
Developers need to run tests locally and it would be nice to have documentation about how to run the tests in this repo during package development.
It would be nice to have links to the most relevant repositories and resources related to `sdrf-pipelines` in the `README.md`. e.g. to the https://github.com/bigbio/proteomics-metadata-standard repo. There is already a link...
The test for empty rows is probably good enough if these rows are at the beginning or end of the file, but it is not sufficient for the case when...
Thoroughly check the input of the public API. e.g. checking if the `template` string supplied to the `SdrfDataFrame .validate` method is in the `ALL_TEMPLATES` variable defined in `sdrf_schema.py` and if...
There is a good discussion to be had about how permissive or strict a parser for a file standard should be and if it is permissive which errors in the...
When looking at the `sdrf-pipelines` package there are many different terms that have a range of meanings and uses. The string `sdrf-pipelines` is only used for the installation and the...