c-sar-denarius

Provides a simple interface over results generated by c-sar using mkdocs-material.

Master	Develop

• Publications
• Commands
  • markdown
  • server
• Installation
  • Pypi
  • Docker and Singularity
• Development environment
  • Python env
  • Updating licence headers
• LICENSE

Publications

Please contact the following for appropriate referencing methods:

• Keiran Raine (kr2@sanger.ac.uk)
• Clare Pacini (cp16@sanger.ac.uk)
• Victoria Offord (vo1@sanger.ac.uk)

Commands

Basic command line information is provided by running the bare command:

$ c-sar-denarius
Usage: c-sar-denarius [OPTIONS] COMMAND [ARGS]...

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  markdown  Generate (or extend existing) c-sar-denarius site from a...
  server    Serve the result of a pre-existing target area.

Each subcommand has more detailed documentation.

markdown

This command will generate or extend an existing target location using data from the c-sar results folder.

Please see --help on the subcommand for details of the options.

server

Provides a basic webserver on the current host to serve the generated site. Basic authentication is provided for use on an internal network, but this is only intended for use by a small number of users. Consider using a more robust server for long term presentation of data.

Please see --help on the subcommand for details of the options.

Installation

Pypi

pip install c-sar-denarius
# for basic server components
pip install https://github.com/elfgoh/sauth/archive/15dbca865332e7b83ccf5d9d227d0321a88132ca.tar.gz

Docker and Singularity

There are pre-built images containing this codebase on quay.io. When pulling an image you must specify the version there is no latest.

The docker images are known to work correctly after import into a singularity image.

Development environment

This allows you to run all appropriate pre-commit tests.

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

Python env

python3 -m venv venv
source venv/bin/activate

pip install -r tests/test-requirements.txt

python setup.py develop # so bin scripts can find module
# If this is merged and pypi available move sauth into setup.py
# https://github.com/Granitosaurus/sauth/pull/1
pip install https://github.com/elfgoh/sauth/archive/15dbca865332e7b83ccf5d9d227d0321a88132ca.tar.gz

# 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.md

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-denarius.

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’.