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Developer Guide

Thank you for contributing to MolecularFingerprints.jl. This guide outlines the technical workflow for setting up your local environment, managing dependencies, and validating your changes.

Engineering Standards

Before opening a Pull Request (PR), please review our CONTRIBUTING.md.

Local Environment Setup

To modify the source code, you must clone the repository and instantiate its dependencies. This ensures your local environment exactly matches the project's Manifest.toml.

# Clone the repository
git clone https://github.com/LukaszSztukiewicz/MolecularFingerprints.jl
cd MolecularFingerprints.jl

# Launch Julia with the project environment active
julia --project=.

Inside the Julia REPL, synchronize your environment:

using Pkg
Pkg.instantiate()  # Downloads all dependencies specified in Project.toml

Testing

We use the standard Julia Test library. Our test suite is located in the test/ directory.

Running Tests

There are two primary ways to run the suite. The first is preferred for rapid iteration:

  1. From the REPL (Active Development):
pkg> test
  1. From the Terminal (CI Emulation):
julia --project -e 'using Pkg; Pkg.test()'

Managing Test Dependencies

The tests reside in their own environment (test/Project.toml). If your new tests require a new package (e.g., BenchmarkTools):

pkg> activate test
pkg> add BenchmarkTools
pkg> dev .  # Ensure the test environment points to the local source code

Documentation Workflow

Documentation is built using Documenter.jl. To preview your changes to docstrings or .md files locally, use the provided build script.

Building Locally

  1. Enter the docs environment:
julia --project=docs/
  1. Run the build script:
using Pkg
Pkg.instantiate()
include("docs/make.jl")

This generates the HTML files in docs/build/. Open index.html in your browser to preview.

Continuous Integration (CI)

When you push a branch to GitHub, our GitHub Actions pipeline automatically triggers:

  • Unit Tests: Executed across multiple Julia versions (current stable and LTS) and OS platforms (Linux, macOS, Windows).
  • Code Coverage: Reports are sent to Codecov to ensure no regressions in test coverage.
  • Documentation Preview: A temporary version of the docs is built to verify formatting.

Updating Dependencies

If you need to update the package dependencies to a newer version:

pkg> activate .
pkg> update
pkg> activate test
pkg> update

Always commit the updated Manifest.toml files to ensure other developers stay in sync.