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cellpack-1.0.3
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مشاهده بیشترتوضیحات
algorthim to pack molecular recipes
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cellpack-1.0.3 |
| نام | cellpack |
| نسخه کتابخانه | 1.0.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Megan Riel-Mehan |
| ایمیل نویسنده | meganr@alleninstitute.org |
| آدرس صفحه اصلی | https://github.com/mesoscope/cellpack |
| آدرس اینترنتی | https://pypi.org/project/cellpack/ |
| مجوز | MIT license |
# cellPack
[](https://github.com/mesoscope/cellpack/actions)
[](https://mesoscope.github.io/cellpack/)
[](https://codecov.io/gh/mesoscope/cellpack)
algorithm to pack molecular recipes
### Setup
1. create a virtual env: `conda create -n autopack`
2. `activate autopack`
3. `pip install -e .[dev]`
### Run analysis code
By default analyze will run all packing methods on `cellpack/test-recipes/NM_Analysis_FigureB1.0.json
Examples:
* `analyze -o [PATH/TO/OUTPUT/FOLDER]` will create subfolders for each packing method at your output folder
* To run just one packing method: `analyze -o [PATH/TO/OUTPUT/FOLDER] -p jitter`
* To change the dimension of the packing: `analyze -r cellpack/test-recipes/NM_Analysis_FigureC1.json -o /Users/meganriel-mehan/Dropbox/cellPack/NM_Analysis_C_1 -d 3`
* Turn off plotly plot: `analyze -o [PATH/TO/OUTPUT/FOLDER] -ng` or `analyze -o [PATH/TO/OUTPUT/FOLDER] --no-grid-plot`
### Run conversion code
* To convert to simularium and view at https://staging.simularium.allencell.org/viewer
`convert -r [FULL_PATH_TO_INPUT_RECIPE_FILE] -p [FULL_PATH_TO_PACKING_RESULT] -o [OUTPUT_PATH]`
## Installation
**Stable Release:** `pip install cellpack`<br>
**Development Head:** `pip install git+https://github.com/mesoscope/cellpack.git`
## Documentation
For full package documentation please visit [mesoscope.github.io/cellpack](https://mesoscope.github.io/cellpack).
## Development
See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
### Contributing cheat sheet
1. `pip install -e .[dev]`
This will install your package in editable mode with all the required development
dependencies (i.e. `tox`).
2. `make build`
This will run `tox` which will run all your tests in both Python 3.7
and Python 3.8 as well as linting your code.
3. `make clean`
This will clean up various Python and build generated files so that you can ensure
that you are working in a clean environment.
4. `make docs`
This will generate and launch a web browser to view the most up-to-date
documentation for your Python package.
#### Suggested Git Branch Strategy
1. `main` is for the most up-to-date development, very rarely should you directly
commit to this branch. GitHub Actions will run on every push and on a CRON to this
branch but still recommended to commit to your development branches and make pull
requests to main. If you push a tagged commit with bumpversion, this will also release to PyPI.
2. Your day-to-day work should exist on branches separate from `main`. Even if it is
just yourself working on the repository, make a PR from your working branch to `main`
so that you can ensure your commits don't break the development head. GitHub Actions
will run on every push to any branch or any pull request from any branch to any other
branch.
3. It is recommended to use "Squash and Merge" commits when committing PR's. It makes
each set of changes to `main` atomic and as a side effect naturally encourages small
well defined PR's.
**MIT license**
نیازمندی
| مقدار | نام |
|---|---|
| >=0.4.0 | fire |
| >=3.3.4 | matplotlib |
| >=1.19.2 | numpy |
| ==1.10.10 | panda3d |
| ==2.0.1 | pmw |
| >=1.6.2 | scipy |
| >=1.2.0 | simulariumio |
| >=5.3.1 | plotly |
| ==0.7.2 | pycollada |
| >=0.1.8 | pyembree |
| >=6.2.0 | pymunk |
| >=3.9.34 | trimesh |
| >=0.4.0 | fire |
| >=3.3.4 | matplotlib |
| >=1.19.2 | numpy |
| ==1.10.10 | panda3d |
| ==2.0.1 | pmw |
| >=1.6.2 | scipy |
| >=1.2.0 | simulariumio |
| >=5.3.1 | plotly |
| ==0.7.2 | pycollada |
| >=0.1.8 | pyembree |
| >=6.2.0 | pymunk |
| >=3.9.34 | trimesh |
| >=5.2 | pytest-runner |
| >=19.10b0 | black |
| >=2.1.4 | codecov |
| >=3.8.3 | flake8 |
| >=3.2.1 | flake8-debugger |
| >=5.4.3 | pytest |
| >=2.9.0 | pytest-cov |
| >=0.11 | pytest-raises |
| >=1.0.1 | bump2version |
| >=5.1 | coverage |
| >=7.15.0 | ipython |
| >=0.2.7 | m2r2 |
| >=3.4.3 | Sphinx |
| >=0.5.1 | sphinx-rtd-theme |
| >=3.15.2 | tox |
| >=3.1.1 | twine |
| >=0.34.2 | wheel |
| >=5.2 | pytest-runner |
| >=19.10b0 | black |
| >=2.1.4 | codecov |
| >=3.8.3 | flake8 |
| >=3.2.1 | flake8-debugger |
| >=5.4.3 | pytest |
| >=2.9.0 | pytest-cov |
| >=0.11 | pytest-raises |
| >=1.0.1 | bump2version |
| >=5.1 | coverage |
| >=7.15.0 | ipython |
| >=0.2.7 | m2r2 |
| >=3.4.3 | Sphinx |
| >=0.5.1 | sphinx-rtd-theme |
| >=3.15.2 | tox |
| >=3.1.1 | twine |
| >=0.34.2 | wheel |
| >=5.2 | pytest-runner |
| >=19.10b0 | black |
| >=2.1.4 | codecov |
| >=3.8.3 | flake8 |
| >=3.2.1 | flake8-debugger |
| >=5.4.3 | pytest |
| >=2.9.0 | pytest-cov |
| >=0.11 | pytest-raises |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl cellpack-1.0.3:
pip install cellpack-1.0.3.whl
نصب پکیج tar.gz cellpack-1.0.3:
pip install cellpack-1.0.3.tar.gz