Fabian Egli

nginx.service specs differ from apt-get install

10

While preparing to compile nginx from source with this build script, I realized that there are some differences in the `nginx.service` file produced by it and the one I have...

Do not use assert outside of testing code

16

There are multiple uses of assert inside the production code. This is bad practice because assert is removed when python is run with optimization, e.g. `python -0 some_script_using_biopython.py`. The problem...

- [x] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_. - [x] I have read the...

[WIP] improve error messages for invalid formats

17

This is the start of an attempt to solve #3614. - [x] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND**...

Use of future functionality

1

### Description of the bug The `shutil.copytree` argument [`dirs_exist_ok`](https://docs.python.org/3/library/shutil.html#shutil.copytree) is only available in Python version 3.8+ but nf-core tool still support Python 3.7 https://github.com/nf-core/tools/blob/b5400d84d307343353b6ab09aad204231f74fb0e/nf_core/modules/lint/module_changes.py#L28 Two options: drop Python 3.7 support...

Tests are slow due to too many web queries and limits set by web resources

1

### Description of feature Many tests will pull form the github repo. 55 in total. This means running the tests once already pulls 55 times, running them repeatedly every couple...

### Description of feature PR #1700 grew too big and this is now an issue collecting the information about the adoption to pathlib. #### From PR #1700 - [x] provide...

Cleanup licenses

2

Closes #1712 ## PR checklist - [ ] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated - [ ] If you've fixed a...

Is the licenses functionality still desired/needed?

7

### Description of feature As of #1689 there are too many commented out tests with the following note: ``` # TODO nf-core: Assess and strip out if no longer required...

### Description of feature The `plain` argument needs a description in the docstring.