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cryosparc-tools

PyPI Python package

Toolkit for interfacing with CryoSPARC. Read the documentation at 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
    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
    python3 -m venv .venv
    source .venv/bin/activate  # macOS / Linux
    # OR
    .venv\Scripts\activate.bat  # Windows
    
  3. Install dev dependencies and build native modules
    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:

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:40000 or cryoem0:40000 (can alias cryoem0 to 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_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.

Metadata

Release files for cryosparc-tools 4.4.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for cryosparc-tools 4.4.1
File Size Uploaded
cryosparc-tools-4.4.1.tar.gz 336.2 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for cryosparc-tools 4.4.1
File
cryosparc_tools-4.4.1-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.10 PyPy 3.10 7.3 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.9 PyPy 3.9 7.3 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.9 PyPy 3.9 7.3 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.8 PyPy 3.8 7.3 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.8 PyPy 3.8 7.3 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.7 PyPy 3.7 7.3 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.7 PyPy 3.7 7.3 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp312-cp312-win_arm64.whl CPython 3.12 CPython 3.12 Windows ARM64 Details
cryosparc_tools-4.4.1-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
cryosparc_tools-4.4.1-cp312-cp312-musllinux_1_1_x86_64.whl CPython 3.12 CPython 3.12 Linux musl 1.1+ x86-64 Details
cryosparc_tools-4.4.1-cp312-cp312-musllinux_1_1_aarch64.whl CPython 3.12 CPython 3.12 Linux musl 1.1+ ARM64 Details
cryosparc_tools-4.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
cryosparc_tools-4.4.1-cp312-cp312-macosx_10_9_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.9+ x86-64 Details
cryosparc_tools-4.4.1-cp312-cp312-macosx_10_9_universal2.whl CPython 3.12 CPython 3.12 macOS 10.9+ universal2 (ARM64, x86-64) Details
cryosparc_tools-4.4.1-cp311-cp311-win_arm64.whl CPython 3.11 CPython 3.11 Windows ARM64 Details
cryosparc_tools-4.4.1-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
cryosparc_tools-4.4.1-cp311-cp311-musllinux_1_1_x86_64.whl CPython 3.11 CPython 3.11 Linux musl 1.1+ x86-64 Details
cryosparc_tools-4.4.1-cp311-cp311-musllinux_1_1_aarch64.whl CPython 3.11 CPython 3.11 Linux musl 1.1+ ARM64 Details
cryosparc_tools-4.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
cryosparc_tools-4.4.1-cp311-cp311-macosx_10_9_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
cryosparc_tools-4.4.1-cp311-cp311-macosx_10_9_universal2.whl CPython 3.11 CPython 3.11 macOS 10.9+ universal2 (ARM64, x86-64) Details
cryosparc_tools-4.4.1-cp310-cp310-win_arm64.whl CPython 3.10 CPython 3.10 Windows ARM64 Details
cryosparc_tools-4.4.1-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
cryosparc_tools-4.4.1-cp310-cp310-musllinux_1_1_x86_64.whl CPython 3.10 CPython 3.10 Linux musl 1.1+ x86-64 Details
cryosparc_tools-4.4.1-cp310-cp310-musllinux_1_1_aarch64.whl CPython 3.10 CPython 3.10 Linux musl 1.1+ ARM64 Details
cryosparc_tools-4.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp310-cp310-macosx_11_0_arm64.whl CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
cryosparc_tools-4.4.1-cp310-cp310-macosx_10_9_x86_64.whl CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details
cryosparc_tools-4.4.1-cp310-cp310-macosx_10_9_universal2.whl CPython 3.10 CPython 3.10 macOS 10.9+ universal2 (ARM64, x86-64) Details
cryosparc_tools-4.4.1-cp39-cp39-win_arm64.whl CPython 3.9 CPython 3.9 Windows ARM64 Details
cryosparc_tools-4.4.1-cp39-cp39-win_amd64.whl CPython 3.9 CPython 3.9 Windows x86-64 Details
cryosparc_tools-4.4.1-cp39-cp39-musllinux_1_1_x86_64.whl CPython 3.9 CPython 3.9 Linux musl 1.1+ x86-64 Details
cryosparc_tools-4.4.1-cp39-cp39-musllinux_1_1_aarch64.whl CPython 3.9 CPython 3.9 Linux musl 1.1+ ARM64 Details
cryosparc_tools-4.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp39-cp39-macosx_11_0_arm64.whl CPython 3.9 CPython 3.9 macOS 11.0+ ARM64 Details
cryosparc_tools-4.4.1-cp39-cp39-macosx_10_9_x86_64.whl CPython 3.9 CPython 3.9 macOS 10.9+ x86-64 Details
cryosparc_tools-4.4.1-cp39-cp39-macosx_10_9_universal2.whl CPython 3.9 CPython 3.9 macOS 10.9+ universal2 (ARM64, x86-64) Details
cryosparc_tools-4.4.1-cp38-cp38-win_amd64.whl CPython 3.8 CPython 3.8 Windows x86-64 Details
cryosparc_tools-4.4.1-cp38-cp38-musllinux_1_1_x86_64.whl CPython 3.8 CPython 3.8 Linux musl 1.1+ x86-64 Details
cryosparc_tools-4.4.1-cp38-cp38-musllinux_1_1_aarch64.whl CPython 3.8 CPython 3.8 Linux musl 1.1+ ARM64 Details
cryosparc_tools-4.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp38-cp38-macosx_11_0_arm64.whl CPython 3.8 CPython 3.8 macOS 11.0+ ARM64 Details
cryosparc_tools-4.4.1-cp38-cp38-macosx_10_9_x86_64.whl CPython 3.8 CPython 3.8 macOS 10.9+ x86-64 Details
cryosparc_tools-4.4.1-cp38-cp38-macosx_10_9_universal2.whl CPython 3.8 CPython 3.8 macOS 10.9+ universal2 (ARM64, x86-64) Details
cryosparc_tools-4.4.1-cp37-cp37m-win_amd64.whl CPython 3.7 CPython 3.7 pymalloc Windows x86-64 Details
cryosparc_tools-4.4.1-cp37-cp37m-musllinux_1_1_x86_64.whl CPython 3.7 CPython 3.7 pymalloc Linux musl 1.1+ x86-64 Details
cryosparc_tools-4.4.1-cp37-cp37m-musllinux_1_1_aarch64.whl CPython 3.7 CPython 3.7 pymalloc Linux musl 1.1+ ARM64 Details
cryosparc_tools-4.4.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-64 Details
cryosparc_tools-4.4.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ ARM64 Details
cryosparc_tools-4.4.1-cp37-cp37m-macosx_10_9_x86_64.whl CPython 3.7 CPython 3.7 pymalloc macOS 10.9+ x86-64 Details

Total release size: 52.1 MB

Release files / cryosparc-tools-4.4.1.tar.gz

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5.0.1

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5.0.0

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4.6.1

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