C. Titus Brown

``` /Users/t/miniconda3/envs/py37/lib/python3.7/runpy.py:125: RuntimeWarning: 'spacegraphcats.cdbg.index_cdbg_by_kmer' found in sys.modules after import of package 'spacegraphcats.cdbg', but prior to execution of 'spacegraphcats.cdbg.index_cdbg_by_kmer'; this may result in unpredictable behaviour ```

https://codecov.io/gh/spacegraphcats/spacegraphcats/branch/latest * utils/bgzf stuff is largely uncovered, but that's ok - it should be exempted * bcalm_to_gxt2 - the pendant removal stuff is uncovered * much of the catlas code...

``` cli.add_command(run) cli.add_command(build) cli.add_command(search) cli.add_command(check) cli.add_command(showconf) cli.add_command(info) cli.add_command(init) ``` also document other extra commands that are useful - `dump_contigs`, `extract_reads`, and others.

deal with lockfiles better

5

see #220. we could include an `--unlock` command in spacegraphcats command line, or ...?

fix/check spacegraphcats/catlas/gxt_to_gml.py ref #345

do cDBG node IDs need to be ordinal?

1

in #345 commit 122d034, I re-re-re discovered that our code currently requires (and enforces!) that cDBG contig IDs be ordinal, going from 0..N-1 with no gaps in the sequence. The...

how does snakemake locking work, anyway?

2

a loong time ago, I ran into problems with running spacegraphcats from within snakemake, which led to contending locks, which led to me using `--nolock` a lot. but I think...

it'd be nice to have a clear plan for: * logging commands that are run * being consistent about what goes to stdout and what goes to stderr

in progress: https://github.com/conda-forge/staged-recipes/pull/13042 we need to remove khmer as a dependency, OR package khmer for conda-forge, before this can move forward; khmer is currently on bioconda. see issue #334

khmer is currently used in two places -- * the sequence hashing in general * in `evaluate_overhead` the former should be something we can remove once sourmash supports fast sequence...