Use SQLAlchemy>2 and replaced alchy with sqlservice

[4.7] - 2024-05-22

Added

• github actions to publish the repo to PyPI and publish mkdocs on new release event

Changed

• Replace ruamel.yaml with pyyaml lib
• Updated GitHub actions
• Replaced alchy lib with sqlservice
• Unfreeze SQLAlchemy

Fixed

• Add missing brew path to GitHub action. It has been removed from PATH variable in Ubuntu
• Badges on README page

Chanjo 3.0.0

A brand new release of Chanjo is upon us 🎉

This version integrates with Sambamba and drops Pysam/Samtools as a dependency. It also expands on the possibilities to directly calculate coverage metrics from the command line! Please refer to the updated documentation and the CHANGELOG for more on what's new - enjoy!

And a big thanks to @moonso who is joining as a new core contributor for this release 😄

Get started by:

$ pip install --upgrade chanjo

Beta of the next major release of Chanjo

We have really done a lot of work to clean up the interface
You can now directly query the database for interesting coverage metrics
We rely on Sambamba to generate coverage stats from BAM files

Public release (DOI)

Chanjo can now be referenced in scientific journals using DOI.

New sample table

Chanjo will now automatically keep track of which cutoff you used for completeness, creation dates, and source BAM file for each sample.

Also the docs have been updated with info on SQL structure

Multi sample support

Chanjo is now able to handle multiple samples and store them in the same SQLite database. This is great for comparing different samples and keeping all coverage annotations in one place.

A lot of (breaking) changes has had to be made to get to this point. Do check out the updated "chanjo-autopilot" help text if you plan on using the CLI.

I've now also limited Chanjo in scope: it will be focused on reading coverage data and annotating elements. Everything else downstream will be handled by a separate, although, connected package. Announcement later :)

Lastly Chanjo now extends the SQL schema structure found in my own new Elemental DB project.

Base level resolution

1. Read depth levels are now persisted in the SQLite database as a compressed BLOB. This is useful in the off chance that full base-level resolution is needed.

NOTICE: I've now decided the focus for Chanjo which will be threefold: 1. Setting up a datastore of elements, 2. Getting coverage data as a list of read depths, 3. Annotating elements with relevant coverage metrics.

Stay tuned to find out more about project integrating with Chanjo downstream!

Significant speed improvements!

1. Significant speed improvements running the "autopilot"
2. New SQL methods for calculating averages and count number of passing elements
3. Extended documentation, API docs are working again
4. Updated CLI for the "autopilot"

Making progress on all fronts

• Lot's of updates to the documentation
• Transcripts and genes can persist coverage + completeness in SQLite
• Coverage + completeness calculated with autopilot
• Bugs fixed in autopilot
• You will soon be able to do aggregate calculations on coverage/completeness across elements
• Web REST API removed

And the release of official Chanjo wallpapers!

The first glorious release

Chanjo is now somewhat feature complete and ready to be tested out and installed. I release it as beta for now without making any promises the API will be super stable.

If you notice any bugs, any information you can give me would be greatly appreciated.

Be sure to read the documentation to get started.