cryosparc-tools
Toolkit for interfacing with CryoSPARC. Read the documentation at 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 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 or submit a pull request.
See CONTRIBUTING.md for full details.
Development
Prerequisites
- Git and Git LFS
- Python >= 3.7
- Miniconda3
- C compiler such as GCC or Clang
Set Up
- Clone this repository
git clone --recursive https://github.com/cryoem-uoft/cryosparc-tools.git cd cryosparc-tools git lfs pull
- (Optional) Create and activate a virtual environment
python3 -m venv .venv source .venv/bin/activate # macOS / Linux # OR .venv\Scripts\activate.bat # Windows
- Install dev dependencies and build native modules
pip install -U pip wheel pip install -e ".[dev]"
- Install pre-commit hooks
pre-commit install
Re-compile native module
Recompile native modules after making changes to C code:
python -m setup build_ext -i
Build Packages for Publishing
Install build dependencies
pip install -e ".[build]"
Run the build
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.
To build the docs, install build dependencies
pip install -e ".[build]"
Then run Jupyter Book
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 section for instructions on how to run the notebooks.
Inline source documentation is compiled to HTML via Sphinx and uses Google Style Python docstrings.
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 installed
- CryoSPARC running at
localhost:40000orcryoem0:40000(can aliascryoem0to localhost)
Clean previous build artefacts:
rm -rf cryosparc/*.so build dist *.egg-info
Install dependencies into a new conda environment:
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_IDwith Structura-issued CryoSPARC licenseCRYOSPARC_EMAILwith a CryoSPARC user account emailCRYOSPARC_PASSWORDwith 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.
1 maintainer
Metadata
1 maintainer
Release files for cryosparc-tools 4.6.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
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|---|---|---|---|
| cryosparc-tools-4.6.1.tar.gz | 346.2 kB | Details |
Built distributions (wheels)
Total release size: 61.5 MB
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Release files / cryosparc_tools-4.6.1-cp39-cp39-win_amd64.whl
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Release files / cryosparc_tools-4.6.1-cp39-cp39-macosx_11_0_arm64.whl
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Release files / cryosparc_tools-4.6.1-cp39-cp39-macosx_10_9_x86_64.whl
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Release files / cryosparc_tools-4.6.1-cp39-cp39-macosx_10_9_universal2.whl
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Release files / cryosparc_tools-4.6.1-cp38-cp38-win_amd64.whl
| Download URL | cryosparc_tools-4.6.1-cp38-cp38-win_amd64.whl |
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Release files / cryosparc_tools-4.6.1-cp38-cp38-musllinux_1_2_x86_64.whl
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Release files / cryosparc_tools-4.6.1-cp38-cp38-musllinux_1_2_aarch64.whl
| Download URL | cryosparc_tools-4.6.1-cp38-cp38-musllinux_1_2_aarch64.whl |
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Release files / cryosparc_tools-4.6.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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twine/5.1.1 CPython/3.10.15
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Release files / cryosparc_tools-4.6.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | cryosparc_tools-4.6.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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Release files / cryosparc_tools-4.6.1-cp38-cp38-macosx_11_0_arm64.whl
| Download URL | cryosparc_tools-4.6.1-cp38-cp38-macosx_11_0_arm64.whl |
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Release files / cryosparc_tools-4.6.1-cp38-cp38-macosx_10_9_x86_64.whl
| Download URL | cryosparc_tools-4.6.1-cp38-cp38-macosx_10_9_x86_64.whl |
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Release files / cryosparc_tools-4.6.1-cp38-cp38-macosx_10_9_universal2.whl
| Download URL | cryosparc_tools-4.6.1-cp38-cp38-macosx_10_9_universal2.whl |
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Release files / cryosparc_tools-4.6.1-cp37-cp37m-win_amd64.whl
| Download URL | cryosparc_tools-4.6.1-cp37-cp37m-win_amd64.whl |
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Release files / cryosparc_tools-4.6.1-cp37-cp37m-musllinux_1_2_x86_64.whl
| Download URL | cryosparc_tools-4.6.1-cp37-cp37m-musllinux_1_2_x86_64.whl |
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Release files / cryosparc_tools-4.6.1-cp37-cp37m-musllinux_1_2_aarch64.whl
| Download URL | cryosparc_tools-4.6.1-cp37-cp37m-musllinux_1_2_aarch64.whl |
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Release files / cryosparc_tools-4.6.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | cryosparc_tools-4.6.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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Release files / cryosparc_tools-4.6.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | cryosparc_tools-4.6.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
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Release files / cryosparc_tools-4.6.1-cp37-cp37m-macosx_10_9_x86_64.whl
| Download URL | cryosparc_tools-4.6.1-cp37-cp37m-macosx_10_9_x86_64.whl |
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