nanomesh 0.2.0

Creates 3d meshes from microscopy experimental data

nanomesh

Creates 3d meshes from microscopy experimental data.

Documentation: https://nanomesh.readthedocs.io/en/latest/

Installation

If you use conda, create a new environment:

conda create -n nanomesh python=3.8
conda activate nanomesh

Install nanomesh:

git clone https://github.com/hpgem/nanomesh.git
cd nanomesh
pip install .

Note, to enable the IPython widgets:

jupyter nbextension enable --py widgetsnbextension

Note, if you are using Jupyter lab:

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets itkwidgets

With pygalmesh (linux only)

To use some of the additional functionality depending on pygalmesh, first install the dependencies for pygalmesh (CGAL and EIGEN3)

sudo apt-get install libcgal-dev libeigen3-dev

The instructions are the same as above, except specify with_pygalmesh as option to trigger the installation of pygalmesh. Currently this installs our fork.

pip install .[with_pygalmesh]

Development

Install nanomesh using the development dependencies:

pip install -e .[develop] -c constraints.txt

Running the tests:

pytest

Linting/checks:

pre-commit

Building the docs:

make html --directory docs

License

Copyright (c) 2020,

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Credits

This package was created with Cookiecutter and the NLeSC/python-template.