plantismash

Explore potential Biosynthetic Gene Clusters in plant genomes. This tool is originally sourced from antiSMASH 4.0.

https://github.com/plantismash/plantismash

Science Score: 26.0%

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

  • CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
  • Academic publication links
  • Committers with academic emails
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Explore potential Biosynthetic Gene Clusters in plant genomes. This tool is originally sourced from antiSMASH 4.0.

Basic Info
  • Host: GitHub
  • Owner: plantismash
  • License: agpl-3.0
  • Language: OpenEdge ABL
  • Default Branch: master
  • Homepage:
  • Size: 268 MB
Statistics
  • Stars: 27
  • Watchers: 3
  • Forks: 12
  • Open Issues: 19
  • Releases: 5
Created about 7 years ago · Last pushed 11 months ago
Metadata Files
Readme Contributing License Citation

README-Release.md

antiSMASH release process

This file documents the release process of antiSMASH.

Preparation work

Make sure all relevant pull requests have been merged, and check if any showstopper bugs are still open. Showstopper bugs mainly include regressions from previous versions.

What version number will the new release get?

antiSMASH is using semantic versioning. Unfortunately, semantic versioning focuses on libaries and other things that present APIs, making it an imperfect match for antiSMASH.

Reflecting the basic ideas behind semantic versioning, we should consider our command line the "API" of antiSMASH for now, as antiSMASH is certainly called from many in-house scripts. As a result, we should be increasing the MINOR version if we add new features that have additional command line options, and increase the MAJOR version when we remove command line options.

We should also increase the MINOR version if we add new secondary metabolite classes to be detected. This rule wasn't followed previously, but should be followed for future releases.

Tag the actual release

  • Make sure the CONTRIBUTORS file is up-to-date. Update and commit if necessary.
  • Update the version number in antismash/__init__.py and commit.
  • Grab a list of detailed changes using git shortlog <last-release-tag>.. > changes.txt
  • Edit changes.txt to add some release notes on top.
  • Tag the release using git tag -s -F changes.txt antismash-<MAJOR>-<MINOR>-<PATCH>, filling in the correct values for MAJOR, MINOR and PATCH, of course.
  • Push the changes to bitbucket git push origin master && git push origin master --tags

Post-push work

Now that the git repository contains the new release, a couple of further steps are required.

Create release tarball

This is simply done by calling the appropriate script: ./bash_scripts/create_release_tarball.sh <VERSION> <OUTPUT_DIR>

and verify it looks sane tar tf <OUTPUT_DIR>/antismash-<VERSION>.tar.gz

Upload the tarball to dl.secondarymetabolites.org for testing

scp <OUTPUT_DIR>/antismash-<VERSION>.tar.gz root@dl.secondarymetabolites.org:/vol/downloads/

Update and test install_deb.sh

From the antismash/installer.git repository on bitbucket, update the install_deb.sh file with the current version number. Then, use vagrant up for the respective distro to check the installer script.

Connect your browser to the output page to check if the output looks sane.

Commit and push your changes to the install_deb.sh file if everything is fine.

Upload tarball and installer script to Bitbucket

This is best done in a web browser via the Bitbucket web UI.

Update the docker images

From the antismash/docker.git repository on bitbucket, update the Dockerfile for the standalone image. Bump the version number of the file and adjust the ANTISMASH_VERSION variable.

Then, rebuild the docker image using docker build -t antismash/standalone ., tag the version using docker tag antismash/standalone antismash/standalone:<VERSION>. Test the docker image. If everything works, push it to the Docker Hub by using docker push antismash/standalone && docker push antismash/standalone:<VERSION>.

Then, repeat the process for the other container builds.

Update the download page

In the antismash/websmash.git repository on bitbucket, update all relevant download links in websmash/templates/download.html. Make sure to also adjust the tests to check for the new release string. Run nosetests -v to make sure you got everything right.

Push your changes, and pull from the webserver to roll out the new version.

Send the release announcement to the mailing list

You can reuse the contents of changes.txt for this. Make sure there's a link to the antiSMASH download page in the email.

Add a notification message on the antiSMASH website

Use the smashctl notice tool for this.

Owner

  • Name: plantismash
  • Login: plantismash
  • Kind: organization

GitHub Events

Total
  • Create event: 9
  • Release event: 5
  • Issues event: 12
  • Watch event: 2
  • Delete event: 3
  • Issue comment event: 19
  • Push event: 66
  • Gollum event: 4
  • Pull request event: 6
  • Fork event: 1
Last Year
  • Create event: 9
  • Release event: 5
  • Issues event: 12
  • Watch event: 2
  • Delete event: 3
  • Issue comment event: 19
  • Push event: 66
  • Gollum event: 4
  • Pull request event: 6
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 7
  • Total Committers: 4
  • Avg Commits per committer: 1.75
  • Development Distribution Score (DDS): 0.714
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Hernando Suarez h****1@g****m 2
Satria A Kautsar s****r@w****l 2
PlantiSMASH p****h@b****l 2
Satria A Kautsar s****d@g****m 1
Committer Domains (Top 20 + Academic)

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 11
  • Total pull requests: 2
  • Average time to close issues: 4 months
  • Average time to close pull requests: 1 minute
  • Total issue authors: 11
  • Total pull request authors: 2
  • Average comments per issue: 0.27
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 2
  • Average time to close issues: 7 days
  • Average time to close pull requests: 1 minute
  • Issue authors: 10
  • Pull request authors: 2
  • Average comments per issue: 0.3
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • veritas515nature (1)
  • Joe-Heffer-Shef (1)
  • lomeyet1 (1)
  • qing-xuan-yang (1)
  • daisysotero (1)
  • monian1113 (1)
  • cr12270 (1)
  • isunshine-cc (1)
  • joshpark00 (1)
  • lpereira89 (1)
  • samaralemos (1)
  • jtraverazuara (1)
Pull Request Authors
  • elenadelpup (3)
  • adraismawur (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

modelling_requirements.txt pypi
  • cobra ==0.2.1
  • ez-setup *
  • glpk ==0.3
requirements.txt pypi
  • argparse *
  • backports.lzma *
  • bcbio-gff ==0.6.4
  • biopython ==1.68
  • cssselect *
  • helperlibs *
  • networkx ==1.11
  • numpy *
  • pyExcelerator *
  • pyquery ==1.2.9
  • pysvg *
  • python-louvain ==0.5
  • straight.plugin ==1.4.0