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chrispile-1.2.4
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مشاهده بیشترتوضیحات
Syntactic sugar for running ChRIS apps locally
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | chrispile-1.2.4 |
| نام | chrispile |
| نسخه کتابخانه | 1.2.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Jennings Zhang |
| ایمیل نویسنده | Jennings.Zhang@childrens.harvard.edu |
| آدرس صفحه اصلی | https://github.com/FNNDSC/chrispile |
| آدرس اینترنتی | https://pypi.org/project/chrispile/ |
| مجوز | MIT |
#  ChRISPile
[](https://pypi.org/project/chrispile/)
[](https://github.com/FNNDSC/chrispile/blob/master/LICENSE)
[](https://github.com/FNNDSC/chrispile/actions)
Syntactical sugar for running ChRIS plugins locally.
## Abstract
`chrispile` generates wrapper scripts around `docker run` (or `podman run`).
These scripts automatically locate mount points for the position arguments
`/incoming` and `/outgoing` for
[ChRIS plugin apps](https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/About-Plugins#plugin-definition).
Additionally, the wrapper sets sane defaults for running the container.
### Background
Traditionally, `docker run` is a very verbose command with user-unfriendly defaults.
Of course there are good reasons for this design (security isolation)
but it is tedious and confusing to work with.
- the default user is `root` so you will need `sudo` to remove `outputdir`.
- container timezone is UTC
- stopped containers occupy disk space
- GPU is invisible
- user needs to specify image name and command
- folders containing data need to be typed out
`chrispile` aims to hide this complexity from users.
WARNING: it is not a good idea to use `chrispile` unless you understand why it is helpful. You gotta learn the basics: [what is docker?](https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Introduction-to-Docker)
### Example
```bash
mkdir data output
cp scan.nii.gz data
chrispile run -- fnndsc/pl-fetal-brain-mask:1.0.0 --inputPathFilter scan.nii.gz data output
```
The command above is translated to:
```bash
docker run
# clean up the stopped container after it exists
--rm
# run as yourself so that the output is readable+writable by you
--user $(id -u):$(id -g)
# if plugin meta specifies min_gpu_limit, GPU is enabled
# GPU support is detected as --runtime=nvidia (legacy) or --gpus all (native)
--gpus all
# set the timezone in case your plugin logs timestamps
-v /etc/localtime:/etc/localtime:ro
# resolve input and output paths
# SELinux label flag ':z' is appended to volume options if necessary
-v /home/jenni/data:/incoming:ro -v /home/jenni/output:rw
# container image name and command
fnndsc/pl-fetal-brain-mask:1.0.0 fetal_brain_mask
# user specified options
--inputPathFilter scan.nii.gz
# volume mountpoints
/incoming /outgoing
```
## Installation
```bash
pip install chrispile
```
## Usage
```
$ chrispile --help
usage: chrispile [-h] [-V] {run,api,install,list,uninstall} ...
Generate wrapper scripts around docker or podman run to easily run ChRIS plugins
optional arguments:
-h, --help show this help message and exit
info:
-V, --version show program's version number and exit
subcommands:
{run,api,install,list,uninstall}
run run a ChRIS plugin
api query the system for information
install install a ChRIS plugin as an executable
list list installed ChRIS plugins
uninstall uninstall a ChRIS plugin
```
### Run Plugin
```
$ chrispile run --help
usage: chrispile run [--dry-run] [--reload-from] -- dock_image [args ...] inputdir/ outputdir/
positional arguments:
dock_image container image of the ChRIS plugin
args arguments to pass to the ChRIS plugin
optional arguments:
-h, --help show this help message and exit
-d, --dry-run print command to run withour running it
-e src, --reload-from src
mount given host directory as source folder for rapid development
```
#### Run Example
```
docker pull fnndsc/pl-simpledsapp:2.0.0
# setup test data
mkdir input output
touch input/{a,b,c}
```
##### Dry Run
```
$ chrispile run --dry-run -- fnndsc/pl-simpledsapp:2.0.0 --dummyFloat 3.5 input output
docker run --rm --user 1000:1003 \
-v /etc/localtime:/etc/localtime:ro \
-v /home/chris/input:/incoming:ro \
-v /home/chris/output:/outgoing:rw \
fnndsc/pl-simpledsapp:2.0.0 simpledsapp \
--dummyFloat 3.5 \
/incoming /outgoing
```
##### Real Run
```
$ chrispile run -- fnndsc/pl-simpledsapp:2.0.0 --dummyFloat 3.5 input output
_ _ _
(_) | | | |
___ _ _ __ ___ _ __ | | ___ __| |___ __ _ _ __ _ __
/ __| | '_ ` _ \| '_ \| |/ _ \/ _` / __|/ _` | '_ \| '_ \
\__ \ | | | | | | |_) | | __/ (_| \__ \ (_| | |_) | |_) |
|___/_|_| |_| |_| .__/|_|\___|\__,_|___/\__,_| .__/| .__/
| | | | | |
|_| |_| |_|
Version: 2.0.0
Sleeping for 0
Creating new file... /outgoing/b
Creating new file... /outgoing/a
Creating new file... /outgoing/c
```
###### Check Outputs
```
$ ls -lh output
total 0
-rw-r--r-- 1 chris grantlab 0 Feb 13 22:21 a
-rw-r--r-- 1 chris grantlab 0 Feb 13 22:21 b
-rw-r--r-- 1 chris grantlab 0 Feb 13 22:21 c
$ rm -rv output
removed 'output/b'
removed 'output/a'
removed 'output/c'
removed directory 'output'
```
##### Run With Live Code
Mount the source code directory into the installed library's location
within the container for a convenient developer experience.
The container will run changes you've made to the code without having
to rebuild the docker image.
```bash
chrispile run --reload-from ~/Github/pl-simpledsapp/simpledsapp \
-- fnndsc/pl-simpledsapp:2.0.0 --dummyFloat 3.2 input output
```
### Install Plugin
```bash
docker pull fnndsc/pl-brainmgz:2.0.3
chrispile install fnndsc/pl-brainmgz:2.0.3
docker pull fnndsc/pl-lungct:latest
chrispile install fnndsc/pl-lungct:latest
```
Now you can simply run
```bash
mkidr out
lungct out
```
### Uninstall Plugin
```
$ chrispile list
lungct
simpledsapp
med2img.py
$ chrispile uninstall lungct
```
## Planned Features
- [x] Github Actions build matrix to test docker and podman separately
- [ ] store repeated `$(chrispile api ...)` calls as variables in bash script
- [ ] `chrispile create` as an alias for [cookiecutter-chrisapp](https://github.com/FNNDSC/cookiecutter-chrisapp)
- [ ] `chrispile run --clobber` deletes the `/outgoing` directory before start
- [ ] `chrispile install` from https://chrisstore.co and pulls for you
- [ ] `chrispile list` also shows container image tags
- [ ] `chrispile uninstall --rm` also runs `docker rmi`
نیازمندی
| مقدار | نام |
|---|---|
| - | pyyaml |
| - | jinja2 |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl chrispile-1.2.4:
pip install chrispile-1.2.4.whl
نصب پکیج tar.gz chrispile-1.2.4:
pip install chrispile-1.2.4.tar.gz