Deprecate console db#841
Merged
Merged
Conversation
Remove the console module (thin wrapper around rich.Console) and the db module (legacy JCVI database connectors for Sybase/MySQL/PostgreSQL/Oracle). Replace console imports with direct rich.console.Console usage in aws.py, fetch.py, and formats/base.py. Remove the now-unused set_db_opts method from OptionParser. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
variation.deconvolute, assembly.syntenypath, annotation.ahrd, apps.emboss, apps.gbsubmit Relocate reusable code to consuming modules: - CoordsLine, Coords, Overlap_types, get_coords_stats -> formats.blast - CDT class -> compara.pad - ContigFile/ContigLine/ReadLine -> assembly.postprocess - read_interpro -> projects.pineapple - needle/NeedleHeader -> annotation.reformat Also fix remaining utils.console references in formats.fasta and algorithms.ec from prior deprecation. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
utils.ez_setup Relocate reusable code to consuming modules: - Bowtie2 wrappers (BowtieLogFile, check_index, align) -> apps.align - Download utilities (ALL_DOWNLOADERS, get_best_downloader) -> apps.base - LASTZ score conversion functions -> formats.maf Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Contributor
There was a problem hiding this comment.
Pull request overview
This PR removes several legacy/duplicate modules (including the prior Rich console singleton and DB helpers) and consolidates selected functionality into fewer modules (notably downloader logic into apps.base and MUMmer .coords parsing/filtering into formats.blast), updating downstream imports accordingly.
Changes:
- Remove deprecated/legacy modules (console/db/ez_setup, and multiple older command wrappers) and relocate a subset of their functionality into existing modules.
- Consolidate download helpers into
jcvi.apps.baseand move.coordsparsing/filtering intojcvi.formats.blast, updating callers. - Replace imports of the removed console singleton with local
rich.console.Consoleinstances /printhelpers.
Reviewed changes
Copilot reviewed 33 out of 33 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| src/jcvi/variation/deconvolute.py | Removed the legacy FASTQ deconvolution CLI module. |
| src/jcvi/utils/ez_setup.py | Removed downloader-selection helper module (functionality moved elsewhere). |
| src/jcvi/utils/db.py | Removed legacy DB connection/query utilities. |
| src/jcvi/utils/console.py | Removed module-level Rich Console singleton. |
| src/jcvi/utils/aws.py | Replaced import of removed console singleton with a local Console() instance. |
| src/jcvi/projects/pineapple.py | Inlined read_interpro() implementation (previously imported from removed module). |
| src/jcvi/graphics/mummerplot.py | Switched .coords import/filtering to formats.blast (coords_filter). |
| src/jcvi/formats/maf.py | Inlined BLASTZ score conversion helpers previously imported from removed apps.lastz. |
| src/jcvi/formats/fasta.py | Replaced printf import with Console().print. |
| src/jcvi/formats/coords.py | Removed standalone .coords parsing/CLI module (parsing moved into formats.blast). |
| src/jcvi/formats/contig.py | Removed TIGR contig parsing module (logic moved into assembly.postprocess). |
| src/jcvi/formats/cdt.py | Removed CDT/GTR parsing module (logic moved into compara.pad). |
| src/jcvi/formats/blast.py | Added .coords parsing/filtering utilities and shared Overlap_types here. |
| src/jcvi/formats/base.py | Replaced console singleton usage in check_exists() with a local Console(). |
| src/jcvi/compara/pad.py | Inlined CDT parsing needed for PAD workflow; removed dependency on formats.cdt. |
| src/jcvi/assembly/syntenypath.py | Removed legacy syntenic path assembly module. |
| src/jcvi/assembly/preprocess.py | Updated imports to use apps.align (bowtie wrappers consolidated there). |
| src/jcvi/assembly/postprocess.py | Inlined contig parsing types (ContigFile, etc.) and switched to read_block. |
| src/jcvi/assembly/goldenpath.py | Updated Overlap_types import to come from formats.blast. |
| src/jcvi/assembly/automaton.py | Updated bowtie align import to use apps.align. |
| src/jcvi/apps/lastz.py | Removed legacy LASTZ wrapper module. |
| src/jcvi/apps/gbsubmit.py | Removed legacy GenBank submission tooling module. |
| src/jcvi/apps/fetch.py | Replaced printf/console singleton usage with a local Console() instance. |
| src/jcvi/apps/emboss.py | Removed EMBOSS wrapper module (needle logic moved into annotation.reformat). |
| src/jcvi/apps/bowtie.py | Removed bowtie wrapper module (logic consolidated into apps.align). |
| src/jcvi/apps/blastplus.py | Removed legacy BLAST+ wrapper module. |
| src/jcvi/apps/base.py | Removed DB option helper; moved downloader selection/implementation into this module. |
| src/jcvi/apps/align.py | Added bowtie2 wrapper utilities (log parsing, index check, alignment wrapper) for backward compatibility. |
| src/jcvi/annotation/reformat.py | Inlined EMBOSS needle logic and removed dependency on deleted apps.emboss. |
| src/jcvi/annotation/automaton.py | Updated bowtie index import to use apps.align. |
| src/jcvi/annotation/ahrd.py | Removed legacy AHRD pipeline utility module. |
| src/jcvi/algorithms/supermap.py | Updated CoordsLine import to come from formats.blast. |
| src/jcvi/algorithms/ec.py | Replaced printf import with Console().print. |
Comments suppressed due to low confidence (1)
src/jcvi/apps/base.py:257
- The PR title suggests only deprecating the console/db utilities, but this change set also removes or relocates substantial functionality (e.g., download helpers, bowtie/lastz-related code, coords/contig/cdt utilities). Please confirm the intended scope and, if this is a larger cleanup, consider updating the PR title/description to match so reviewers/users understand the breaking changes.
def set_downloader(self, downloader=None):
"""
Add --downloader options for given command line program.
"""
downloader_choices = [x[0] for x in ALL_DOWNLOADERS]
self.add_argument(
"--downloader",
default=downloader,
choices=downloader_choices,
help="Use the specified downloader to retrieve resources",
)
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
![chatgpt-codex-connector[bot]](https://avatars.githubusercontent.com/in/1144995?s=60&v=4){kind=small}
There was a problem hiding this comment.
💡 Codex Review
Here are some automated review suggestions for this pull request.
Reviewed commit: 97c9f7cd9a
ℹ️ About Codex in GitHub
Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you
- Open a pull request for review
- Mark a draft as ready
- Comment "@codex review".
If Codex has suggestions, it will comment; otherwise it will react with 👍.
Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".
| return dbfile | ||
|
|
||
|
|
||
| def bowtie_align(args): |
There was a problem hiding this comment.
This commit deletes src/jcvi/apps/bowtie.py and moves the Bowtie2 wrapper into apps/align.py, but main() in apps/align.py still does not register any Bowtie action. Because ActionDispatcher only allows names in the actions tuple, users now have no CLI path for this workflow (jcvi apps.bowtie ... is gone, and jcvi apps.align bowtie_align ... is rejected), which breaks existing alignment pipelines that invoke Bowtie through jcvi commands.
Useful? React with 👍 / 👎.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.