Description:

cryosparctools 4.6.0

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: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.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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