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cryosparc-tools-4.2.0
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Toolkit for interfacing with CryoSPARC
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cryosparc-tools-4.2.0 |
| نام | cryosparc-tools |
| نسخه کتابخانه | 4.2.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | "Structura Biotechnology Inc." <info@structura.bio> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/cryosparc-tools/ |
| مجوز | - |
# cryosparc-tools
[](https://pypi.org/project/cryosparc-tools/)
[](https://github.com/cryoem-uoft/cryosparc-tools/actions/workflows/python-package.yml)
Toolkit for interfacing with CryoSPARC. Read the documentation at
[tools.cryosparc.com](https://tools.cryosparc.com)
## Development
### Prerequisites
- Git and Git LFS
- Python >= 3.7
- Miniconda3
- C compiler such as GCC or Clang
### Set Up
1. Clone this repository
```sh
git clone https://github.com/cryoem-uoft/cryosparc-tools.git
cd cryosparc-tools
git lfs pull
```
2. Create and activate a conda environment named "tools" with the desired python version. See the Run Example Notebooks section to install an environment
```sh
conda create -n tools python=3.7 -c conda-forge
conda activate tools
```
3. Install dev dependencies and build native modules
```sh
pip install -U pip wheel
pip install -e ".[dev]"
```
### Re-compile native module
Recompile native modules after making changes to C code:
```sh
make
```
## Build Packages for Publishing
Install build dependencies
```sh
pip install -e ".[build]"
```
Run the build
```sh
python -m build
```
Packages for the current architecture and python version are added to the
`dist/` directory.
## Build Documentation
Documentation is located in the `docs` directory and is powered by [Jupyter Book](https://jupyterbook.org/en/stable/intro.html).
To build the docs, install build dependencies
```sh
pip install -e ".[build]"
```
Then run Jupyter Book
```sh
jupyter-book build docs
```
Site will be be built into the `docs/_build/html` directory.
**Note:** Jupyter Book is not configured to re-run example notebooks upon build
since the notebooks require an active CryoSPARC instance to run.
See the [Run Example Notebooks](#run-example-notebooks) section for instructions
on how to run the notebooks.
Inline source documentation is compiled to HTML via [Sphinx](https://www.sphinx-doc.org/en/master/index.html) and uses [Google Style Python docstrings](https://www.sphinx-doc.org/en/master/usage/extensions/example_google.html#example-google).
## Run Example Notebooks
The Jupyter notebooks in the example documentation require additional
dependencies to execute, including the following system configuration:
- Nvidia GPU and driver
- [Miniconda](https://docs.conda.io/en/latest/miniconda.html) installed
- CryoSPARC running at `localhost:40000` or `cryoem5:40000` (can alias `cryoem5` to localhost)
Clean previous build artefacts:
```sh
make clean
```
Install dependencies into a new conda environment:
```sh
conda create -n cryosparc-tools-example -c conda-forge \
python=3 numpy==1.18.5 \
pyqt=5 libtiff wxPython=4.1.1 adwaita-icon-theme
conda activate cryosparc-tools-example
pip install -U pip
pip install nvidia-pyindex matplotlib~=3.4.0 pandas==1.1.4 notebook
pip install "cryolo[c11]"
pip install -e ".[build]"
```
Run the notebook server with the following environment variables:
- `CRYOSPARC_LICENSE_ID` with Structura-issued CryoSPARC license
- `CRYOSPARC_EMAIL` with a CryoSPARC user account email
- `CRYOSPARC_PASSWORD` with a CryoSPARC user account password
You may also need to include `LD_LIBRARY_PATH` which includes the location of
CUDA Toolkit and cuDNN runtime libraries (e.g., `~/miniconda3/envs/tools/lib/python3.8/site-packages/nvidia/*/lib`).
```
CRYOSPARC_LICENSE_ID="xxxxxxxx-xxxx-xxxx-xxxxxxxxxxxx" \
CRYOSPARC_EMAIL="ali@example.com" \
CRYOSPARC_PASSWORD="password123" \
jupyter notebook
```
Find examples in `docs/examples` directory
## License
cryosparc-tools is licensed under the BSD-3-Clause license.
نیازمندی
| مقدار | نام |
|---|---|
| ~=1.15 | numpy |
| ~=0.6 | python-snappy |
| >=3.7 | typing-extensions |
| - | build |
| - | autodocsumm |
| - | cython |
| - | jupyter-book |
| - | build |
| - | black |
| - | cython |
| - | httpretty |
| - | pyright |
| - | pytest-benchmark |
| - | pytest-xdist[psutil] |
| - | pytest |
| - | ruff |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl cryosparc-tools-4.2.0:
pip install cryosparc-tools-4.2.0.whl
نصب پکیج tar.gz cryosparc-tools-4.2.0:
pip install cryosparc-tools-4.2.0.tar.gz