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scipion-ed

Basic data and protocols objects for Electron Diffraction processing within Scipion

https://github.com/scipion-ed/scipion-ed

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Basic data and protocols objects for Electron Diffraction processing within Scipion

Basic Info
  • Host: GitHub
  • Owner: scipion-ed
  • License: gpl-3.0
  • Language: Python
  • Default Branch: devel
  • Size: 121 KB
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 0
  • Open Issues: 3
  • Releases: 4
Created almost 7 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.rst 

scipion-ed
==========

**scipion-ed** is the base plugin defining the Domain for Electron Diffraction image processing.


Installation
------------

For using scipion-ed, we need to have a working Python 3 environment (e.g via virtualenv or conda).
After that, we might easily install by:

.. code-block:: bash

    pip install scipion-ed scipion-ed-dials


Development
-----------

For development, we probably want to download the source code and install from there. In that way
changes can be made and we can test it quickly. We also need a working Python 3 environment and we
recommend to create a development folder to download the source code.

.. code-block:: bash

    # Create a folder for the installation
    mkdir scipion-ed-dev
    cd scipion-ed-dev

    # Then we can install scipion-ed by:
    git clone git@github.com:scipion-ed/scipion-ed.git
    python -m pip install -e scipion-ed  # Install in the environment as development

    # And also install the plugins
    git clone git@github.com:scipion-ed/scipion-ed-dials.git
    python -m pip install -e scipion-ed-dials  # Install in the environment as development


Publishing the package to PyPI
..............................

In order to make scipion-ed available to install with `pip install scipion-ed`,
we need to:

.. code-block:: bash

    python install twine restructuredtext-lint
    cd scipion-ed

    # It might be a good idea to check the README.rst before uploading:
    rst-lint README.rst

    python setup.py sdist
    twine upload dist/scipion-ed-3.0.1.tar.gz

Running tests (TO BE UPDATED)
.............................

.. code-block:: bash

    cd scipion-ed
    cd pwed/tests
    python -m unittest discover

    # To visualize the test project you need to specify SCIPION_DOMAIN and SCIPION_VERSION
    export SCIPION_DOMAIN=scipion-ed/pwed
    export SCIPION_VERSION=3.0.0

    python scipion-pyworkflow/pyworkflow/apps/pw_project.py TestEdBaseProtocols



Python 3 environments
.....................

For development, we probably want to download the source code and install from there. In that way
changes can be made and we can test it quickly.

We also need a working Python 3 environment and we recommend to create a development folder to download the source code.

.. code-block:: bash

    # Create a clean virtual environment
    python -m virtualenv --python=python3 env
    source env/bin/activate

It is also possible to use a conda environment.

.. code-block:: bash

    # Create the environment
    conda create -n sped-dev python=3.8 pip
    conda activate sped-dev

Troubleshooting
---------------

If you get "error: command 'x86_64-linux-gnu-gcc' failed with exit status 1" you may need to install python3-dev:
sudo apt install python3-dev -y


Tkinter with Python3
....................


Tkinter with Conda
..................


.. image:: https://zenodo.org/badge/189014932.svg
   :target: https://zenodo.org/badge/latestdoi/189014932

Owner

  • Name: scipion-ed
  • Login: scipion-ed
  • Kind: organization

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Scipion-ED base plugin
message: >-
  If you use this software, please cite it using
  these metadata.
type: software
authors:
  - given-names: Viktor E.G.
    family-names: Bengtsson
    email: viktor.e.g.bengtsson@gmail.com
    orcid: "https://orcid.org/0000-0002-6020-9178"
  - given-names: José Miguel
    family-names: de la Rosa-Trevin
    email: delarosatrevin@scilifelab.se
    affiliation: >-
      Department of Biochemistry and Biophysics,
      Science for Life Laboratory, Stockholm
      University, Stockholm
    orcid: "https://orcid.org/0000-0002-3320-1269"
identifiers:
  - type: doi
    value: 10.5281/zenodo.6035770
repository-code: "https://github.com/scipion-ed/scipion-ed"
license: GPL-3.0
commit: 28d4cac
version: v3!1.0.0
date-released: "2022-04-04"

GitHub Events

Total
Last Year

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 119
  • Total Committers: 3
  • Avg Commits per committer: 39.667
  • Development Distribution Score (DDS): 0.176
Top Committers
Name Email Commits
ViktorEGBengtsson v****n@m****e 98
Jose Miguel de la Rosa Trevin d****n@g****m 17
Viktor E.G. Bengtsson v****n@g****m 4
Committer Domains (Top 20 + Academic)
mmk.su.se: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 5
  • Total pull requests: 5
  • Average time to close issues: 3 days
  • Average time to close pull requests: 2 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ViktorEGBengtsson (5)
Pull Request Authors
  • ViktorEGBengtsson (5)
Top Labels
Issue Labels
enhancement (4) wontfix (2) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 10 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 10
  • Total maintainers: 2
pypi.org: scipion-ed

Base pyworkflow plugin for Electron Diffraction image processing

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 10 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Stargazers count: 23.1%
Average: 24.6%
Forks count: 29.8%
Downloads: 38.4%
Maintainers (2)
delarosatrevin vbeng
Last synced: 7 months ago

Dependencies

requirements.txt pypi
  • scipion-pyworkflow *
setup.py pypi
  • requirements *
requirements-dev.txt pypi
  • black * development
  • flake8 * development
  • pre-commit * development
  • pyupgrade * development