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https://github.com/czbiohub-sf/compmicro-ndutils-env

Shared ndutils environment for maintained by the CompMicro platform

https://github.com/czbiohub-sf/compmicro-ndutils-env

Science Score: 26.0%

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    Scientific vocabulary similarity
    Low similarity (11.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Shared ndutils environment for maintained by the CompMicro platform

Basic Info
  • Host: GitHub
  • Owner: czbiohub-sf
  • License: bsd-3-clause
  • Language: Dockerfile
  • Default Branch: main
  • Homepage:
  • Size: 57.6 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 1
  • Open Issues: 3
  • Releases: 15
Created over 1 year ago · Last pushed 11 months ago
Metadata Files
Readme Contributing License

README.md

compmicro-ndutils-env

This repo contains an environment definition and automated build for the "ndutils" Python environment used for analysis of N-dimensional microscopy data. The environment is maintained by the Computational Microscopy platform at the Chan Zuckerberg Biohub - San Francisco and is available on the bruno high performance compute cluster.

Loading the environment on bruno

If you have access to bruno you can load this shared environment using

sh module load anaconda comp_micro conda activate ndutils

Checking the environment version

This environment is versioned, and a list of previous versions is available under Releases.

You can check the version of the installed environment using the env_version command, using with "pip list", or with "pip show".

``` $ env_version ndutils 0.2.0.dev3

$ pip list | grep ndutils ndutils 0.2.0.dev3

$ pip show ndutils Name: ndutils Version: 0.2.0.dev3 Summary: ndutils compute environment for computational microscopy at CZBiohub SF ... ```

Installation

You can install your own copy of this environment in the following ways. See the available releases at https://github.com/czbiohub-sf/compmicro-ndutils-env/releases.

Pip

python3 -m pip install git+https://github.com/czbiohub-sf/compmicro-ndutils-env.git@v${RELEASE_VERSION}

Conda

git clone git@github.com:czbiohub-sf/compmicro-ndutils-env.git cd compmicro-ndutils-env git checkout v${RELEASE_VERSION} conda env create --file=environment.yml

Docker

A docker image is automatically built using GitHub actions whenever a version tag is pushed. See the GitHub-hosted compmicro-ndutils-env Docker repository.

To pull and run a Docker image: docker run ghcr.io/czbiohub-sf/compmicro-ndutils-env:v${RELEASE_VERSION}

Apptainer

To run an Apptainer container created from the Docker image: apptainer run docker://ghcr.io/czbiohub-sf/compmicro-ndutils-env:v${RELEASE_VERSION}

Or to run a bash shell in Apptainer: apptainer exec docker://ghcr.io/czbiohub-sf/compmicro-ndutils-env:$v{RELEASE_VERSION} bash

Contributing

We welcome contributions! Please see the Contributing guide

Owner

  • Name: Chan Zuckerberg Biohub San Francisco
  • Login: czbiohub-sf
  • Kind: organization
  • Location: San Francisco

GitHub Events

Total
  • Create event: 33
  • Issues event: 3
  • Release event: 13
  • Delete event: 21
  • Issue comment event: 5
  • Push event: 46
  • Public event: 1
  • Pull request event: 6
Last Year
  • Create event: 33
  • Issues event: 3
  • Release event: 13
  • Delete event: 21
  • Issue comment event: 5
  • Push event: 46
  • Public event: 1
  • Pull request event: 6

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 3
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 3
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 1 day
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ziw-liu (2)
Pull Request Authors
  • ieivanov (2)
  • edyoshikun (1)
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Dependencies

.github/workflows/docker-build-test-and-push.yml actions
  • actions/checkout v4 composite
  • docker/build-push-action v6 composite
  • docker/login-action v3 composite
  • docker/setup-buildx-action v3 composite
.github/workflows/test-conda-install.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v3 composite
.github/workflows/test-pip-install.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v3 composite
Dockerfile docker
  • ubuntu 22.04 build
pyproject.toml pypi
requirements.txt pypi
  • napari *
  • napari-animation *
environment.yml conda
  • pip
  • python 3.10.*