معرفی شرکت ها
c-sar-denarius-1.0.1
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مشاهده بیشتر
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مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Interface overlay for c-sar
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | c-sar-denarius-1.0.1 |
| نام | c-sar-denarius |
| نسخه کتابخانه | 1.0.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Keiran M Raine |
| ایمیل نویسنده | cgphelp@sanger.ac.uk |
| آدرس صفحه اصلی | https://github.com/cancerit/c-sar-denarius |
| آدرس اینترنتی | https://pypi.org/project/c-sar-denarius/ |
| مجوز | AGPL-3.0 |
# c-sar-denarius
Provides a simple interface over results generated by [`c-sar`][csar-repo] using [mkdocs-material][mkdocs-mat].
| Master | Develop |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][circle-master]][circle-base] | [![Develop Badge][circle-develop]][circle-base] |
[](https://github.com/pre-commit/pre-commit)
- [Publications](#publications)
- [Commands](#commands)
- [markdown](#markdown)
- [server](#server)
- [Installation](#installation)
- [Pypi](#pypi)
- [Docker and Singularity](#docker-and-singularity)
- [Development environment](#development-environment)
- [Python env](#python-env)
- [Updating licence headers](#updating-licence-headers)
- [LICENSE](#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:
```bash
$ 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
```bash
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][quay-repo]. 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):
```bash
curl https://pre-commit.com/install-local.py | python3 -
# may need to add to PATH
```
### Python env
```bash
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](https://github.com/apache/skywalking-eyes).
Expected workflow:
```bash
# 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'
1. Modify `.licenserc.yaml`
1. Apply the changes:
- `docker run -it --rm -v $(pwd):/github/workspace $DOCKER_IMG header fix`
1. 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’.
```
<!-- refs -->
[circle-base]: https://circleci.com/gh/cancerit/c-sar-denarius.svg?style=shield
[circle-develop]: https://circleci.com/gh/cancerit/c-sar-denarius.svg?style=shield&branch=dev%3B
[circle-master]: https://circleci.com/gh/cancerit/c-sar-denarius.svg?style=shield&branch=master%3B
[csar-repo]: https://github.com/cancerit/c-sar
[mkdocs-mat]: https://squidfunk.github.io/mkdocs-material/
[quay-repo]: https://quay.io/repository/wtsicgp/c-sar-denarius?tab=tags
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >= 3.9 | Python |
نحوه نصب
نصب پکیج whl c-sar-denarius-1.0.1:
pip install c-sar-denarius-1.0.1.whl
نصب پکیج tar.gz c-sar-denarius-1.0.1:
pip install c-sar-denarius-1.0.1.tar.gz