v0.3.0 - A light in the dark

Kerblam! Version 0.3.0 - "A light in the dark"

This version fixes a few bugs an adds pipeline descriptions when you execute kerblam run without a pipeline.
The tutorial has a section describing this change. It will look something like this:

Error: No runtime specified. Available runtimes:
	🐋 heatmaps :: Generate the general heatmap for all transporters
	 process_tcga_metadata
	 gen_test_data :: Make the test expression data from the TCGA/GTEX dataset

What's Changed

• Add kerblam! Shields badge by @MrHedmad in #34
  • You can now add a snazzy badge with the kerblam! rocket and the version of Kerblam! of your project (all manually updated for now).
• Show the list of available pipes even when none are typed by @MrHedmad in #35
  • This means that kerblam run with no specified pipeline shows you the list of available pipes, just like you get when you misspell a pipeline. No more kerblam run asd to see the list!
• build(deps): bump h2 from 0.3.22 to 0.3.24 by @dependabot in #39
• Switching profiles correctly updates the file access metadata by @MrHedmad in #36
  • When you used a --profile, make did not realize that anything had changed. Now it does, as you'd expect it.
• Available pipes message includes description by @MrHedmad in #41
  • The main feature of this release. See the tutorial above to learn how it works.

Full Changelog: v0.2.1...v0.3.0

Install kerblam 0.3.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/MrHedmad/kerblam/releases/download/v0.3.0/kerblam-installer.sh | sh

Download kerblam 0.3.0

File	Platform	Checksum
kerblam-aarch64-apple-darwin.tar.xz	macOS Apple Silicon	checksum
kerblam-x86_64-apple-darwin.tar.xz	macOS Intel	checksum
kerblam-x86_64-unknown-linux-gnu.tar.xz	Linux x64	checksum

v0.2.1 - The --version version

What's Changed

• Add a --version flag to print version string by @MrHedmad in #30
• Fix wrong remote data files path by @MrHedmad in #32

Full Changelog: v0.2.0...v0.2.1

Install kerblam 0.2.1

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/MrHedmad/kerblam/releases/download/v0.2.1/kerblam-installer.sh | sh

Download kerblam 0.2.1

File	Platform	Checksum
kerblam-aarch64-apple-darwin.tar.xz	macOS Apple Silicon	checksum
kerblam-x86_64-apple-darwin.tar.xz	macOS Intel	checksum
kerblam-x86_64-unknown-linux-gnu.tar.xz	Linux x64	checksum

v0.2.0 - The nice things update

There are a lot of features that I noticed are immediately nice to have. This update brings many of them to Kerblam! to make it much more ergonomic to use.
It also includes quite a bit of fixes and some important under-the-hood changes.

What's Changed

• Add version compatibility check by @MrHedmad in #23
  • Kerblam! now complains if the version under meta > version is not the same as the current Kerblam! version, to save you some headaches due to incompatibility.
• Show available pipes on failed run/package command by @MrHedmad in #24
  • Kerblam! now shows you all the pipes it can find if you type a pipe that does not exist when you kerblam run or kerblam package. This should save a bunch of time if you cannot remember if the pipe was name execute, compute or calculate.
• Add --keep-remote option to 'data clean' by @MrHedmad in #29
  • Sometimes it's good to quickly start over. With kerblam data clean --keep-remote you can cleanup all generated data but keep the remote files so you don't have to re-fetch them before running again.
• Issue #11 should be fixed now, but testing is still required (@MrHedmad in c8ea705).
  • This means that setting paths in the kerblam.toml file should be working as intended.
• Add a way to force running locally (@MrHedmad in 87c39f0)
  • If you have a dockerfile does not mean you want to use it all the time. kerblam run --local skips using the container and runs the pipeline locally, even if a corresponding dockerfile is found. This should be useful during development.

Full Changelog: v0.1.0...v0.2.0

Install kerblam 0.2.0

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://github.com/MrHedmad/kerblam/releases/download/v0.2.0/kerblam-installer.sh | sh

Download kerblam 0.2.0

File	Platform	Checksum
kerblam-aarch64-apple-darwin.tar.xz	macOS Apple Silicon	checksum
kerblam-x86_64-apple-darwin.tar.xz	macOS Intel	checksum
kerblam-x86_64-unknown-linux-gnu.tar.xz	Linux x64	checksum

Kerblam! v0.1.0 - The beginning

This is the first release of Kerblam! Expect bugs and missing features. Your feedback is highly appreciated!

Features:

• kerblam new can be used to create a new kerblam! project. Kerblam! asks you if you want to use some common programming languages and sets up a proper .gitignore and pre-commit hooks for you.
• kerblam data fetches remote data and saves it locally, manages local data and can clean it up, preserving only files that must be preserved. It also shows you how much local data is on the disk, how much data is remote and how much disk space you can free without losing anything important.
• kerblam package packages your pipeline and exports a docker image for execution later. It's useful for reproducibility purposes as the docker image is primed for execution, bundling the kerblam! executable, execution files and non-remote data in the blob itself.
• kerblam run executes the analysis for you, by choosing your makefiles and dockerfiles appropriately and building docker containers as needed. Optionally, allows test data or alternative data to be used instead of real data, in order to test your pipelines.
• kerblam ignore can edit your .gitignore file by adding files, folders and GitHub's recommended ignores for specific languages in just one command.

Known issues:
Please see the issues to learn more about missing features and bugs. The most prominent issues are listed here:

• ❗ #11 : Some paths specified in kerblam.toml might not be respected by Kerblam! Especially regarding
  the ./src, ./src/pipes and ./src/dockerfiles directories.
• #13 and #8 : Default profiles without the need for configuration would be nice.
• #12 : kerblam run does not list available pipes when you specify a pipe that is not available.

Thank you for checking Kerblam! out! If you'd like to support the project, please leave a star. I really appreciate it.