| Name | cryosparc-tools JSON |
| Version |
4.6.1
JSON |
| download |
| home_page | None |
| Summary | Toolkit for interfacing with CryoSPARC |
| upload_time | 2024-11-13 16:40:40 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | Copyright 2024 Structura Biotechnology Inc. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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)
## Getting Help and Reporting Bugs
For usage questions and general discussion about `cryosparc-tools` scripts and functions, please post to the [CryoSPARC discussion forum](https://discuss.cryosparc.com/c/scripting) under the Scripting category.
If you would like to request or propose a feature, change or fix for `cryosparc-tools` source code, please either [report an issue](https://github.com/cryoem-uoft/cryosparc-tools/issues/new) or [submit a pull request](https://github.com/cryoem-uoft/cryosparc-tools/compare).
See [CONTRIBUTING.md](CONTRIBUTING.md) for full details.
## 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 --recursive https://github.com/cryoem-uoft/cryosparc-tools.git
cd cryosparc-tools
git lfs pull
```
2. (Optional) Create and activate a virtual environment
```sh
python3 -m venv .venv
source .venv/bin/activate # macOS / Linux
# OR
.venv\Scripts\activate.bat # Windows
```
3. Install dev dependencies and build native modules
```sh
pip install -U pip wheel
pip install -e ".[dev]"
```
4. Install pre-commit hooks
```
pre-commit install
```
### Re-compile native module
Recompile native modules after making changes to C code:
```sh
python -m setup build_ext -i
```
## 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 `cryoem0:40000` (can alias `cryoem0` to localhost)
Clean previous build artefacts:
```sh
rm -rf cryosparc/*.so build dist *.egg-info
```
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.
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"description": "# cryosparc-tools\n\n[](https://pypi.org/project/cryosparc-tools/)\n[](https://github.com/cryoem-uoft/cryosparc-tools/actions/workflows/python-package.yml)\n\nToolkit for interfacing with CryoSPARC. Read the documentation at\n[tools.cryosparc.com](https://tools.cryosparc.com)\n\n## Getting Help and Reporting Bugs\n\nFor usage questions and general discussion about `cryosparc-tools` scripts and functions, please post to the [CryoSPARC discussion forum](https://discuss.cryosparc.com/c/scripting) under the Scripting category.\n\nIf you would like to request or propose a feature, change or fix for `cryosparc-tools` source code, please either [report an issue](https://github.com/cryoem-uoft/cryosparc-tools/issues/new) or [submit a pull request](https://github.com/cryoem-uoft/cryosparc-tools/compare).\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for full details.\n\n## Development\n\n### Prerequisites\n\n- Git and Git LFS\n- Python >= 3.7\n- Miniconda3\n- C compiler such as GCC or Clang\n\n### Set Up\n\n1. Clone this repository\n ```sh\n git clone --recursive https://github.com/cryoem-uoft/cryosparc-tools.git\n cd cryosparc-tools\n git lfs pull\n ```\n2. (Optional) Create and activate a virtual environment\n ```sh\n python3 -m venv .venv\n source .venv/bin/activate # macOS / Linux\n # OR\n .venv\\Scripts\\activate.bat # Windows\n ```\n3. Install dev dependencies and build native modules\n ```sh\n pip install -U pip wheel\n pip install -e \".[dev]\"\n ```\n4. Install pre-commit hooks\n ```\n pre-commit install\n ```\n\n### Re-compile native module\n\nRecompile native modules after making changes to C code:\n\n```sh\npython -m setup build_ext -i\n```\n\n## Build Packages for Publishing\n\nInstall build dependencies\n\n```sh\npip install -e \".[build]\"\n```\n\nRun the build\n\n```sh\npython -m build\n```\n\nPackages for the current architecture and python version are added to the\n`dist/` directory.\n\n## Build Documentation\n\nDocumentation is located in the `docs` directory and is powered by [Jupyter Book](https://jupyterbook.org/en/stable/intro.html).\n\nTo build the docs, install build dependencies\n\n```sh\npip install -e \".[build]\"\n```\n\nThen run Jupyter Book\n\n```sh\njupyter-book build docs\n```\n\nSite will be be built into the `docs/_build/html` directory.\n\n**Note:** Jupyter Book is not configured to re-run example notebooks upon build\nsince the notebooks require an active CryoSPARC instance to run.\n\nSee the [Run Example Notebooks](#run-example-notebooks) section for instructions\non how to run the notebooks.\n\nInline 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).\n\n## Run Example Notebooks\n\nThe Jupyter notebooks in the example documentation require additional\ndependencies to execute, including the following system configuration:\n\n- Nvidia GPU and driver\n- [Miniconda](https://docs.conda.io/en/latest/miniconda.html) installed\n- CryoSPARC running at `localhost:40000` or `cryoem0:40000` (can alias `cryoem0` to localhost)\n\nClean previous build artefacts:\n\n```sh\nrm -rf cryosparc/*.so build dist *.egg-info\n```\n\nInstall dependencies into a new conda environment:\n\n```sh\nconda create -n cryosparc-tools-example -c conda-forge \\\n python=3 numpy==1.18.5 \\\n pyqt=5 libtiff wxPython=4.1.1 adwaita-icon-theme\nconda activate cryosparc-tools-example\npip install -U pip\npip install nvidia-pyindex matplotlib~=3.4.0 pandas==1.1.4 notebook\npip install \"cryolo[c11]\"\npip install -e \".[build]\"\n```\n\nRun the notebook server with the following environment variables:\n\n- `CRYOSPARC_LICENSE_ID` with Structura-issued CryoSPARC license\n- `CRYOSPARC_EMAIL` with a CryoSPARC user account email\n- `CRYOSPARC_PASSWORD` with a CryoSPARC user account password\n\nYou may also need to include `LD_LIBRARY_PATH` which includes the location of\nCUDA Toolkit and cuDNN runtime libraries (e.g., `~/miniconda3/envs/tools/lib/python3.8/site-packages/nvidia/*/lib`).\n\n```\nCRYOSPARC_LICENSE_ID=\"xxxxxxxx-xxxx-xxxx-xxxxxxxxxxxx\" \\\nCRYOSPARC_EMAIL=\"ali@example.com\" \\\nCRYOSPARC_PASSWORD=\"password123\" \\\njupyter notebook\n```\n\nFind examples in `docs/examples` directory\n\n## License\n\ncryosparc-tools is licensed under the BSD-3-Clause license.\n",
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