Package: c-sar-denarius
c-sar-denariusProvides a simple interface over results generated byc-sarusingmkdocs-material.MasterDevelopPublicationsCommandsmarkdownserverInstallationPypiDocker and SingularityDevelopment environmentPython envUpdating licence headersLICENSEPublicationsPlease 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)CommandsBasic command line information is provided by running the bare command:$c-sar-denarius
Usage:c-sar-denarius[OPTIONS]COMMAND[ARGS]...

Options:--versionShowtheversionandexit.--helpShowthismessageandexit.

Commands:markdownGenerate(orextendexisting)c-sar-denariussitefroma...serverServetheresultofapre-existingtargetarea.Each subcommand has more detailed documentation.markdownThis command will generate or extend an existing target location using data from thec-sarresults folder.Please see--helpon the subcommand for details of the options.serverProvides 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--helpon the subcommand for details of the options.InstallationPypipipinstallc-sar-denarius# for basic server componentspipinstallhttps://github.com/elfgoh/sauth/archive/15dbca865332e7b83ccf5d9d227d0321a88132ca.tar.gzDocker and SingularityThere are pre-built images containing this codebase onquay.io.  When pulling an image you must specify
the version there is nolatest.The docker images are known to work correctly after import into a singularity image.Development environmentThis allows you to run all appropriate pre-commit tests.pre-commitPlease install a pre-commit to your user environment (not a venv):curlhttps://pre-commit.com/install-local.py|python3-# may need to add to PATHPython envpython3-mvenvvenvsourcevenv/bin/activate

pipinstall-rtests/test-requirements.txt

pythonsetup.pydevelop# so bin scripts can find module# If this is merged and pypi available move sauth into setup.py# https://github.com/Granitosaurus/sauth/pull/1pipinstallhttps://github.com/elfgoh/sauth/archive/15dbca865332e7b83ccf5d9d227d0321a88132ca.tar.gz# enable pre-commit hookspre-commitinstallUpdating licence headersPlease useskywalking-eyes.Expected workflow:# recent build, change to apache/skywalking-eyes:0.2.0 once releasedexportDOCKER_IMG=ghcr.io/apache/skywalking-eyes/license-eyeCheck state before modifying.licenserc.yaml:docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header checkYou should get some 'valid' here, those without a header as 'invalid'Modify.licenserc.yamlApply the changes:docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header fixAdd/commit changesThe check is executed in the CI pipeline which will fail if expected files are missing the license.DO NOTedit the header in the files, please modify the date component ofcontentin.licenserc.yaml.  The only files needing manual update being:README.mdIf you need to make more extensive changes to the license carefully test the pattern is functional.LICENSECopyright (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’.