Jason has not yet finished the code review

[jason-c-kwan]

The issue is that @jason-c-kwan has not yet finished the code review, and his progress has also been rather slow. To help others contribute to the code review, the following is a list of files that are either completed or in progress. Issues are mentioned where one was created, so if there is something with a check mark and no issue, it is probably OK. If you are reviewing something, perhaps leave a comment.

Key:
👀 - in progress
✔️ - done
⭐ - currently being looked at

• autometa.py ✔️
• autometa/__main__.py ✔️ issue [dev branch] Issues with autometa/__main__.py #60
• autometa/binning/recursive_dbscan.py ✔️ issue [dev branch] Issues with autometa/binning/recursive_dbscan.py #52
• autometa/common/coverage.py ✔️ issue [Dev branch] Issues with autometa/common/coverage.py #21
• autometa/common/kmers.py ✔️ issue [Dev branch] Issues with autometa/common/kmers.py #17
• autometa/common/mag.py ✔️ issue [dev branch] Issues with autometa/common/mag.py #53
• autometa/common/markers.py ✔️ issue [dev branch] Issues with autometa/common/markers.py #44
• autometa/common/metagenome.py ✔️ issue [dev branch] Issues with autometa/common/metagenome.py #54
• autometa/common/utilities.py ✔️ issue [dev branch] Issues with autometa/common/utilities.py #40
• autometa/common/external/bedtools.py ✔️ issue [Dev branch] Issues with autometa/common/external/bedtools.py #18
• autometa/common/external/bowtie.py ✔️ issue [Dev branch] Issues with autometa/common/external/bowtie.py #20
• autometa/common/external/diamond.py ✔️ issue [Dev branch] Issues with autometa/common/external/diamond.py #36
• autometa/common/external/hmmer.py ✔️ issue [dev branch] Issues with autometa/common/external/hmmer.py #43
• autometa/common/external/prodigal.py ✔️ issue [Dev branch] Issues with autometa/common/external/prodigal.py #16
• autometa/common/external/samtools.py ✔️ issue [Dev branch] Issues with autometa/common/external/samtools.py #19
• autometa/config/__init__.py ✔️ issue [dev branch] Issues with autometa/config/__init__.py #58
• autometa/config/databases.py ✔️ issue [dev branch] Issues with autometa/config/databases.py #59
• autometa/config/environ.py ✔️ issue [dev branch] Issues with autometa/config/environ.py #55
• autometa/config/project.py ✔️ issue [dev branch] Issues with autometa/config/project.py #56
• autometa/config/user.py ✔️ issue [dev branch] Issues with autometa/config/user.py #57
• autometa/taxonomy/lca.py ✔️ issue [dev branch] Issues with autometa/taxonomy/lca.py #41
• autometa/taxonomy/majority_vote.py ✔️ issue [dev branch] Issued with autometa/taxonomy/majority_vote.py #42
• autometa/taxonomy/ncbi.py ✔️ issue [Dev branch] Issues with autometa/taxonomy/ncbi.py #33

[jason-c-kwan]

Can I close this now, or are there other files I need to review?

[jason-c-kwan]

OK, seems like there are some extras:

• autometa/common/exceptions.py
• autometa/common/external/work_queue.py
• autometa/datasets/__init__.py <- not much in this one yet.

And there are tons of old scripts in the validation folder.

Which of the above are ready to be reviewed? They way I've been doing a eulerian tour of the code, I don't think these have been referenced from the other scripts yet, although perhaps I missed references to exceptions.py.

[evanroyrees]

None of the above are ready to be reviewed at this time