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nplinker

A python framework for microbial natural products data mining by integrating genomics and metabolomics data

https://github.com/nplinker/nplinker

Science Score: 64.0%

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
    1 of 14 committers (7.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.1%) to scientific vocabulary

Keywords

data-harmonization data-integration genomics metabolomics multi-omics-integration

Keywords from Contributors

mass-spectrometry fuzzy-matching fuzzy-search similarity-measures word2vec
Last synced: 6 months ago · JSON representation ·

Repository

A python framework for microbial natural products data mining by integrating genomics and metabolomics data

Basic Info
Statistics
  • Stars: 20
  • Watchers: 5
  • Forks: 13
  • Open Issues: 15
  • Releases: 19
Topics
data-harmonization data-integration genomics metabolomics multi-omics-integration
Created over 7 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.dev.md

nplinker developer documentation

If you're looking for user documentation, go here.

Code editor

We use Visual Studio Code (VS Code) as code editor.

The VS Code Profile for this project is vscode/nplinker.code-profile, which contains the settings, extensions and snippets for the project.

To use the profile, you must first import it by clicking the following menus: Code -> Settings -> Profiles -> Import Profile.... Then select the file vscode/nplinker.code-profile to import the profile. VS Code will take a while to install the extensions and apply the settings. Want more info? See vscode profiles guide.

If you want to add more settings, you can update the workspace settings, see the guide for more info.

Setup

We use Python 3.11 for development environment.

```shell

Create a virtual environment

conda create -n npl-dev python=3.11

activate virtual environment

conda activate npl-dev

Clone the repository

git clone https://github.com/NPLinker/nplinker.git cd nplinker

install development dependencies

pip install -e ".[dev]"

install non-pypi dependencies

install-nplinker-deps ```

Running the tests

Run unit tests with ```shell pytest

or

pytest -n 2 tests/unit `` Parallel testing is supported withpytest-xdistplugin. To run tests in parallel, use the-noption, e.g.-n 2to run tests in parallel with 2 CPUs. By default,pytest` will use all available CPUs to run the tests in parallel.

Run integration tests with shell pytest -n 0 tests/integration -n 0 means no parallel testing.

Test coverage

In addition to just running the tests to see if they pass, they can be used for coverage statistics, i.e. to determine how much of the package's code is actually executed during tests. In an activated virtual environment with the development tools installed, inside the package directory, run:

shell coverage run

This runs tests and stores the result in a .coverage file. To see the results on the command line, run

shell coverage report

coverage can also generate output in HTML and other formats; see coverage help for more information.

Linting and formatting

We use ruff for linting, sorting imports and formatting code. The configurations of ruff are set in pyproject.toml file.

Running the linters and formatters requires an activated virtual environment with the development tools installed.

```shell

Lint all files in the current directory.

ruff check .

Lint all files in the current directory, and fix any fixable errors.

ruff check . --fix

Format all files in the current directory

ruff format .

Format a single python file

ruff format filename.py ```

Static typing

We use inline type annotation for static typing rather than stub files (i.e. .pyi files).

Since Python 3.11 is used as dev environment (older NPLinker must support Python version ≥3.9), you may see various typing issues at runtime. Here is a guide to solve the potential runtime issues.

By default, we use from __future__ import annotations at module level to stop evaluating annotations at function definition time (see PEP 563), which would solve most of compatibility issues between different Python versions. Make sure you're aware of the caveats.

We use Mypy as static type checker:

```

install mypy

pip install mypy

run mypy

mypy src/nplinker ```

Mypy configurations are set in pyproject.toml file.

For more info about static typing and mypy, see: - Static typing with Python - Mypy doc

Docs

We use MkDocs and its theme Material for MkDocs to generate documentations. The configurations of MkDocs are set in mkdocs.yml file.

To watch the changes of current doc in real time, run: ```shell mkdocs serve

or to watch src and docs directories

mkdocs serve -w docs -w src ``` Then open your browser and go to http://127.0.0.1:8000/.

Publishing the docs

Documentation is published to GitHub Pages using mike, which also manages versioning on the gh-pages branch.

Deploying a new version

To deploy version 2.0 of the docs and mark it as the latest, run:

bash make deploy-docs version=2.0

This command does the following:

  • Fetches the latest README from the nplinker-webapp repository.
  • Builds and deploys the documentation to the gh-pages branch.
  • Updates the latest alias to point to this version.
  • Creates a commit on the gh-pages branch to record the deployment.

If you want to undo a deployment, you can run:

bash mike delete 2.0

Previewing the docs

  • To preview all committed versions from gh-pages, use:

bash mike serve

  • To preview your local, uncommitted changes, use:

bash make build-docs

make build-docs will also update the webapp README before serving the docs.

Versioning

Updating the version of the NPLinker package is done with make command update-version, e.g.

shell make update-version CURRENT_VERSION=0.0.1 NEW_VERSION=0.0.2

This command will update the version in the following files: - src/nplinker/__init__.py - pyproject.toml - CITATION.cff

Making a release

This section describes how to make a release in 2 parts:

  1. Create Github release
  2. Publish to Pypi

(1/2) Create Github release

We use the Github action Draft or publish Github release to create a Github release.

Click the right corner Run workflow button, then fill in the current version number and new version number, and choose publish to publish Github release, then click the Run workflow button.

The action will first update the version with the command make update-version. Then it will generate a release notes and update the CHANGELOG.md file with the notes. After that, the action will commit and push the changes. In the end, the action will create a Github release with the new version number and create a tag for the release.

After the action is finished successfully, you can go to the release page to check the release.

This repository uses the GitHub-Zenodo integration, the new Github release will trigger Zenodo into making a snapshot of the repository and sticking a DOI on it. Check the Zenodo page to see the new snapshot.

(2/2) Publish to Pypi

You can publish the package to pypi with the following steps:

```shell

Go to your local nplinker repository

cd path-to-nplinker-repo

Clean the repository

make clean

Build the source distribution and the wheel

make build

Publish to pypi

make release ```

After publishing to pypi, you can check the pypi page to see the new version.

Owner

  • Name: NPLinker
  • Login: NPLinker
  • Kind: organization

Natural product (NP) genome and metabolome mining

Citation (CITATION.cff) 

# YAML 1.2
---
cff-version: "1.1.0"
title: "NPLinker"
authors:
  -
    given-names: Cunliang
    family-names: Geng
    affiliation: "Netherlands eScience Center"
    orcid: "https://orcid.org/0000-0002-1409-8358"
  -
    given-names: Giulia
    family-names: Crocioni
    affiliation: "Netherlands eScience Center"
  -
    given-names:  Simon
    family-names:  Rogers
  -
    given-names:  Andrew
    family-names:  Ramsay
  -
    given-names:  Katherine
    family-names:  Duncan
  -
    given-names:  Justin
    family-names:  van
  -
    given-names:  Grímur
    family-names:  Hjörleifsson
  -
    given-names:  Sylvia
    family-names:  Soldatou
  -
    given-names:  Florian
    family-names:  Huber
  -
    given-names:  Joe
    family-names:  Wandy
  -
    given-names:  Ronan
    family-names:  Daly
  -
    given-names:  Joris
    family-names:  Louwen
  -
    given-names:  Marnix
    family-names:  Medema
version: "2.0.0-beta.1"
repository-code: "https://github.com/NPLinker/nplinker"
keywords:
  - Genome
  - Metabolome
  - Natural Products
  - Data Mining
message: "If you use this software, please cite it using these metadata."
license: Apache-2.0

GitHub Events

Total
  • Create event: 37
  • Release event: 1
  • Issues event: 21
  • Watch event: 3
  • Delete event: 37
  • Issue comment event: 108
  • Push event: 102
  • Pull request review comment event: 63
  • Pull request review event: 81
  • Pull request event: 72
  • Fork event: 2
Last Year
  • Create event: 37
  • Release event: 1
  • Issues event: 21
  • Watch event: 3
  • Delete event: 37
  • Issue comment event: 108
  • Push event: 102
  • Pull request review comment event: 63
  • Pull request review event: 81
  • Pull request event: 72
  • Fork event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 907
  • Total Committers: 14
  • Avg Commits per committer: 64.786
  • Development Distribution Score (DDS): 0.416
Top Committers
Name Email Commits
Andrew Ramsay a****y@u****m 530
Simon Rogers s****s@g****m 98
Andrew Ramsay g****b@a****t 73
louwe015 j****n@w****l 60
Grimur Hjorleifsson g****h@g****m 43
louwenjjr j****n@h****m 28
florian-huber 3****r@u****m 19
Andrew Ramsay a****w@a****t 18
Cunliang Geng c****g@e****l 14
Andrew Ramsay a****y@g****m 10
dependabot[bot] 4****]@u****m 9
CunliangGeng C****g@u****m 2
Helge Hecht h****t@r****z 2
Rónán Daly r****y@g****k 1
Committer Domains (Top 20 + Academic)
andrewramsay.net: 2 glasgow.ac.uk: 1 recetox.muni.cz: 1 esciencecenter.nl: 1 wur.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 97
  • Total pull requests: 220
  • Average time to close issues: 6 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 20
  • Total pull request authors: 10
  • Average comments per issue: 3.0
  • Average comments per pull request: 2.03
  • Merged pull requests: 197
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 14
  • Pull requests: 73
  • Average time to close issues: 3 months
  • Average time to close pull requests: 8 days
  • Issue authors: 6
  • Pull request authors: 6
  • Average comments per issue: 1.21
  • Average comments per pull request: 1.81
  • Merged pull requests: 57
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • CunliangGeng (41)
  • gcroci2 (12)
  • andrewramsay (8)
  • hechth (8)
  • louwenjjr (5)
  • liannette (4)
  • justinjjvanderhooft (2)
  • jeep3 (2)
  • MenusGarg (2)
  • sdrogers (2)
  • AMao-0512 (1)
  • ialas (1)
  • shendricks464 (1)
  • wkipandula (1)
  • adraismawur (1)
Pull Request Authors
  • CunliangGeng (223)
  • liannette (16)
  • adraismawur (8)
  • gcroci2 (7)
  • hechth (7)
  • dependabot[bot] (6)
  • louwenjjr (4)
  • rtlortega (4)
  • grimur (1)
  • sdrogers (1)
Top Labels
Issue Labels
GEN (12) MET (7) enhancement (6) IO-format (4) docs (4) Tracker-issue (3) bug (2) packaging (2) dashboard (2) scoring (2) data-format (1) question (1)
Pull Request Labels
dependencies (6) docs (4) GEN (3) github_actions (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 185 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 12
  • Total maintainers: 1
pypi.org: nplinker

Natural Products Linker

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 185 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 13.3%
Stargazers count: 15.6%
Average: 20.0%
Dependent repos count: 21.5%
Downloads: 39.6%
Maintainers (1)
CunliangGeng
Last synced: 7 months ago

Dependencies

.github/workflows/build.yml actions
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.github/workflows/markdown-link-check.yml actions
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.github/workflows/publish_gh_release.yml actions
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  • stefanzweifel/git-auto-commit-action v4 composite
.github/workflows/publish_to_pypi.yml actions
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pyproject.toml pypi
setup.py pypi
.github/workflows/format-typing-check.yml actions
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.github/workflows/sonar-cloud.yml actions
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.github/workflows/scorecard.yml actions
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