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https://github.com/cryoem-uoft/cryosparc-tools
Python library that enables scripting access to CryoSPARC, a cryo-EM software package.
https://github.com/cryoem-uoft/cryosparc-tools
c cryo-em cryosparc cryosparc-tools high-performance-computing image-processing molecular-biology python
Last synced: 7 days ago
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Python library that enables scripting access to CryoSPARC, a cryo-EM software package.
- Host: GitHub
- URL: https://github.com/cryoem-uoft/cryosparc-tools
- Owner: cryoem-uoft
- License: bsd-3-clause
- Created: 2022-06-22T20:46:37.000Z (over 2 years ago)
- Default Branch: develop
- Last Pushed: 2025-01-03T23:03:35.000Z (7 days ago)
- Last Synced: 2025-01-03T23:27:08.291Z (7 days ago)
- Topics: c, cryo-em, cryosparc, cryosparc-tools, high-performance-computing, image-processing, molecular-biology, python
- Language: Python
- Homepage: https://tools.cryosparc.com
- Size: 28.6 MB
- Stars: 30
- Watchers: 6
- Forks: 8
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# 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="[email protected]" \
CRYOSPARC_PASSWORD="password123" \
jupyter notebook
```
Find examples in `docs/examples` directory
## License
cryosparc-tools is licensed under the BSD-3-Clause license.