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container_template

https://github.com/precimed/container_template

Science Score: 67.0%

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
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: precimed
  • License: gpl-3.0
  • Language: Shell
  • Default Branch: main
  • Size: 88.9 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 3
  • Releases: 2
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Project container_template

This is a template repository for Singularity/Dockerfile containers/images and build scripts

Build status

License DOI Documentation Status Flake8 lint Dockerfile lint Container build Container build push Use this Template

Citation

If you use this material for scientific publications, please cite it as follows:

Espen Hagen, Bayram Cevdet Akdeniz, Alexandr Frei. (2022). precimed/container_template: container_template-0.1.0rc0 (v0.1.0rc0). Zenodo. https://doi.org/10.5281/zenodo.7244728

Getting started

To use these codes, do not clone or fork this repository, but click the green Use this template button above.

You may then create a new repository on a GitHub organization or user account (<user>) under a new project name (<project>), that can be cloned by issuing in a terminal application

git clone git@github.com:<user>/<project>.git cd <project>

The codes may then be adapted further to suit the requirements of the project, as described next

Setup-requirements

After cloning the template repository as described above a few requirements must be in place. Some scripts rely on Python with some packages available in the Python environment.

One convenient way to set up a Python environment is Conda, available via Miniconda or Miniforge. Assuming one of these Python distributions is installed, issue the following to create a new Python environment using conda:

conda create -n <container_template> python=3 pip # create environment named <container_template> conda activate <container_template> # activates enviromnent <container_template> pip install -r setup-requirements.txt

Initial setup

To set up your own project from this template, issue in the terminal:

python scripts/init.py

The script is interactive, and will prompt the user for some info. It will modify certain files in the <project> directory and also replace this README file. Some files may also be renamed. Remember to commit and push the changes after running the setup script (scripts/init.py):

git add <file1> <file2> ... git commit -m "initial setup" git push

The remaining codes may then be added to and be modified further to suit the requirements of the <project>. See the updated project README.md file for further instructions.

Owner

  • Name: precimed
  • Login: precimed
  • Kind: organization

Citation (citation.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Hagen"
    given-names: "Espen"
    orcid: "https://orcid.org/0000-0002-1321-5970"
  - family-names: "Cevdet Akdeniz"
    given-names: "Bayram"
    orcid: "https://orcid.org/0000-0002-9493-3105"
  - family-names: "Frei"
    given-names: "Oleksandr"
    orcid: "https://orcid.org/0000-0002-6427-2625"

title: "container_template"
version: 0.1.0rc0
doi: "10.5281/zenodo.7244728"
date-released: 2022-10-24
url: "https://github.com/precimed/container_template"

GitHub Events

Total
  • Issues event: 5
  • Delete event: 5
  • Push event: 12
  • Pull request event: 4
  • Create event: 4
Last Year
  • Issues event: 5
  • Delete event: 5
  • Push event: 12
  • Pull request event: 4
  • Create event: 4

Dependencies

.github/workflows/docker.yml actions
  • actions/checkout v1 composite
  • reviewdog/action-hadolint v1 composite
.github/workflows/greetings.yml actions
  • actions/first-interaction v1 composite
.github/workflows/python.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • reviewdog/action-flake8 v3 composite
.github/workflows/stale.yml actions
  • actions/stale v3 composite
.github/workflows/container_build.yml actions
  • actions/checkout v4 composite
  • docker/build-push-action v6 composite
  • docker/login-action v3 composite
  • docker/metadata-action v5 composite
  • docker/setup-buildx-action v3 composite
  • docker/setup-qemu-action v3 composite
.github/workflows/container_build_push.yml actions
  • actions/checkout v4 composite
  • docker/build-push-action v6 composite
  • docker/login-action v3 composite
  • docker/metadata-action v5 composite
  • docker/setup-buildx-action v3 composite
  • docker/setup-qemu-action v3 composite
  • eWaterCycle/setup-apptainer v2 composite
docker/dockerfiles/container_template/Dockerfile docker
  • ubuntu 24.04 build
docker/scripts/environment.yml pypi
docs/source/environment.yml pypi
project-requirements.txt pypi
setup-requirements.txt pypi
test-requirements.txt pypi
  • pytest * test