c-sar

Master	Develop

• Notes
  • CRISPRcleanR v1.2.1
• Developer notes
  • Version numbers
  • Submodules
  • Changing branches
  • Editing the submodule
  • Updating the submodule
  • pre-commit
  • Updating licence headers
• LICENSE

Notes

CRISPRcleanR v1.2.1

The version of CRISPRcleanR in the GitHub DESCRIPTION does not match the latest release version 1.2.1 which is defined in build/install_R_packages.sh.

Developer notes

Version numbers

The version is in 2 files, please ensure it is updated on each release:

• Dockerfile
• nextflow.config

Submodules

This project has a submodule to make it easier to build the docker image. The initial checkout needs to be done via recursive strategy:

# new checkout
git clone --recurse-submodules git@....git

# existing checkout
cd repo
# update local metadata (new branches etc)
git fetch
# check branch, switch if necessary
git status
# pull any changes
git pull
# populate the submodule
git submodule update --init --recursive

Changing branches

If you change branches you need to make sure the submodule changes with you:

git checkout --recurse-submodules $NEW_BRANCH

Editing the submodule

You can edit a submodule directly in this checkout and commit back to the original repository, however it is generally less confusing to consider the submodule as a read-only component. If you want to push changes made in this way please see the official git documentation linked above.

Updating the submodule

Generally submodules are only updated to specific commits and tags. To change which commit your branch refers to:

cd submodules/rcrispr
git pull
git checkout ${TAG_OR_COMMITREF}
cd ../../
git status
# you will see the submodule is listed as dirty
git commit -m "Updated RCRISPR submodule to ${TAG_OR_COMMITREF}" submodules/rcrispr

pre-commit

Please install a pre-commit to your user environment (not a venv):

curl https://pre-commit.com/install-local.py | python3 -
# may need to add to PATH

# in repo folder, enable pre-commit hooks
pre-commit install

Updating licence headers

Please use skywalking-eyes.

Expected workflow:

# recent build, change to apache/skywalking-eyes:0.2.0 once released
export DOCKER_IMG=ghcr.io/apache/skywalking-eyes/license-eye

1. Check state before modifying .licenserc.yaml:
   • docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header check
   • You should get some 'valid' here, those without a header as 'invalid'
2. Modify .licenserc.yaml
3. Apply the changes:
   • docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header fix
4. Add/commit changes

The check is executed in the CI pipeline which will fail if expected files are missing the license.

DO NOT edit the header in the files, please modify the date component of content in .licenserc.yaml. The only files needing manual update being:

• README.Rmd

If you need to make more extensive changes to the license carefully test the pattern is functional.

LICENSE

Copyright (c) 2021 Genome Research Ltd

Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>

This file is part of C-SAR.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.

1. The usage of a range of years within a copyright statement contained within
this distribution should be interpreted as being equivalent to a list of years
including the first and last year specified and all consecutive years between
them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
2009, 2011-2012’ should be interpreted as being identical to a statement that
reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
2009, 2010, 2011, 2012’.