Drew T. Doering comments

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                                            Drew T. Doering

create_db() does not parse directives from GFF files starting in v0.11.0

Hey @daler, getting back around to this now! I pasted your `test_issue_213` function into a new script, and am getting the same results as you on the latest `v0.12` tag...

create_db() does not parse directives from GFF files starting in v0.11.0

For the sake of completeness, here is the script (`gffutils_debug.py`) that I'm running your test with: ```python #!/usr/bin/env python import sys import os import tempfile from textwrap import dedent gffutils_git_path...

[Linting] Add option to ignore something

Running into something similar -- I have a rule that only uses `awk` and thus does not require a conda env, but the linter fails because that rule doesn't have...

Is the designed behaviour to update incrementally? If so, how can a user 'skip' versions?

FWIW, I just used `updateR` and it took me from R v3.5.0 straight to R v3.6.0, which skips v3.5.1, 3.5.2, and 3.5.3. This is from RStudio v1.2.1335 running on MacOS...

Is the designed behaviour to update incrementally? If so, how can a user 'skip' versions?

Ah, gotcha, that's interesting. And yeah, I have no reason to believe that calling `R` from a terminal session would behave differently than opening the stand-alone R app, but who...

Add an `--include all` option to `datasets download genome`

Adding another reason -- since many GenBank bacterial genomes only have annotations in GenBank format (and no GFF), the `--include all` option would be very useful when used with the...

Host mirror of the datasets cli code here

Any updates on this? It would be nice to be able to have multiple avenues to address bugs and errors when they arise: 1. Submit an issue here and wait...

Host mirror of the datasets cli code here

This is wonderful news, thank you so much for following up!