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You can get the latest development branch with:
git clone https://github.com/sourmash-bio/sourmash.git
sourmash runs under Python 3.10 and later.
We recommend using conda for setting up an environment for developing
new features, running tests and code quality checks.
Here are some suggestions on how to set them up
:::{note} You only need one of these, no need to install them all! :::
::::{tab-set}
:::{tab-item} conda
Follow the installation instructions for
installing Miniforge3 (a conda distribution that uses
the conda-forge channel by default).
Once conda is installed, run
conda env create -n sourmash_dev --file dev.yml
to create an environment called sourmash_dev containing the programs needed
for development.
Once the environment is created, you can activate it for development with
conda activate sourmash_dev
:::
:::{tab-item} pixi
Follow the installation instructions for
installing pixi.
To activate the new environment, run
pixi shell
and proceed to the "Running tests and checks" section.
:::
:::{tab-item} nix
Follow the installation instructions for setting up Nix in your system (Linux or macOS).
Once Nix is installed, run
nix develop
to start an environment ready for running tests and checks.
:::
:::{tab-item} General instructions
As long as you have tox and a Rust compiler available,
you can skip conda, pixi, or nix.
For Rust, we suggest using rustup to install the Rust environment:
curl https://sh.rustup.rs -sSf | sh
And for tox you can use pipx for
installing it without interfering with other Python environments:
pipx install tox
We suggest working on sourmash in a virtualenv; e.g. from within the
cloned repository (and after installing tox and Rust), you can do:
tox -e dev
. .tox/dev/bin/activate
Finally, you can also explicitly install all the Python dependencies for sourmash by running
pip install -r requirements.txt
(but they are already installed in the virtualenv created with tox -e dev).
To update rust to the latest version, use rustup update.
To update your Python dependencies to the latest required for sourmash, you can run pip install -r requirements.txt.
:::
::::
We use tox for managing dependencies and
running tests and checks during development.
tox -l lists available tasks.
You can run tests by invoking make test in the sourmash directory;
tox -e py310 will run the Python tests with Python 3.10,
and cargo test will run the Rust tests.
We use pre-commit to run automatic checks and fixes
when developing sourmash. You can run it with
tox -e fix_lint
which prints a "hint" at the end of the run with instructions to set it up to
run automatically every time you run git commit.
We use GitHub Actions for continuous integration.
Code coverage can be viewed interactively at codecov.io.
Please see the docs README for information on how we write and build the sourmash docs.
There are three main components in the sourmash repo:
- Python module (in
src/sourmash/) - The command-line interface (in
src/sourmash/cli) - The Rust core library (in
src/core)
pyproject.toml has all the configuration to prepare a Python package containing these
three components.
First it compiles the Rust core component into a shared library,
which is wrapped by cffi and exposed to the Python module.
These steps are executed by maturin,
a modern PEP 517-compatible build backend for Python projects containing Rust
extensions.
A short description of the high-level files and dirs in the sourmash repo:
.
├── benchmarks/ | Benchmarks for the Python module
├── binder/ | mybinder.org configuration
├── data/ | data used for demos
├── doc/ | the documentation rendered in sourmash.bio
├── include/ | C/C++ header files for using core library
├── src/ |
│ ├── core/ | Code for the core library (Rust)
│ └── sourmash/ | The Python module and CLI code
├── tests/ | Tests for the Python module and CLI
├── utils/ |
├── asv.conf.json | benchmarking config file (for ASV)
├── Cargo.toml | Rust definition for a workspace
├── CITATION.cff | Citation info
├── codemeta.json | Metadata for software discovery
├── CODE_OF_CONDUCT.rst | Code of conduct
├── CONTRIBUTING.md | Instruction for contributing to development
├── LICENSE | License for the repo
├── Makefile | Entry point for most development tasks
├── MANIFEST.in | Describes what files to add to the Python package
├── matplotlibrc | Configuration for matplotlib
├── flake.nix | Nix definitions (package, dev env)
├── shell.nix | Nix config for creating a dev env (backward-compatible)
├── paper.bib | References in the JOSS paper
├── paper.md | JOSS paper content
├── pyproject.toml | Python project definitions (build system and tooling)
├── README.md | Info to get started
├── requirements.txt | Python dependencies for development
└── tox.ini | Configuration for test automation
src/sourmash
├── cli/ | Command-line parsing, help messages and overall infrastucture
├── command_compute.py | compute command implementation
├── command_compute.py | sketch command implementation
├── commands.py | implementation for other CLI commands
├── compare.py | Signature comparison functions
├── _compat.py | Py2/3 compatibility functions
├── exceptions.py | Mapping from core library errors to Python exceptions
├── fig.py | Plotting functions
├── index.py | Index base class and definitions
├── lca/ | LCA index and utility functions
├── logging.py | Logging functions (notify, error, set_quiet)
├── __main__.py | Entry point for the CLI
├── _minhash.py | MinHash sketch implementation (calls the core library)
├── np_utils.py | NumPy utils
├── sbt*.py | SBT implementation
├── search.py | search functions for indices (search, gather)
├── sig | signature manipulation functions
│ └── __main__.py | implementation for `sourmash sig` commands
├── signature_json.py | signature parsing code (to/from JSON)
├── signature.py | signature class and methods
├── sourmash_args.py | convenient shortcuts for CLI usage
└── utils.py | Convenience functions to interact with core library
This is completely defined in src/core to avoid mixing with the code of other components
(and trying to make it easier to reason about changes).
If you're only working on the core,
you don't need to change any files outside this directory.
This is also published to crates.io (the Rust package repository) and NPM, after it is compiled to Webassembly. The GitHub Actions workflow publishes new versions automatically to these repositories.
src/core
├── benches/ | Benchmarks for the core library
├── Cargo.toml | Crate definition and metadata
├── cbindgen.toml | Configuration for cbindgen (the C header generator)
├── examples/ | Examples using the crate API
├── README.md | Containing links to CI, docs and general info about crate.
├── src |
│ ├── cmd.rs | High-level commands (search, index, compute...)
│ ├── errors.rs | All the errors generated by this crate
│ ├── ffi/ | FFI-related functions. They are exported to a C header by cbindgen.
│ ├── from.rs | Conversion methods for other crates
│ ├── index/ | Index methods. An index is a collection of signatures, optimized for searching.
│ ├── lib.rs | Entry point for the library, control the exposed public API.
│ ├── signature.rs | Signature methods. A signature is a collection of sketches.
│ ├── sketch/ | Sketch methods. A sketch is compressed representation of data.
│ └── wasm.rs | Webassembly API.
└── tests/ | Integration tests (using the public API of the crate)
If you change anything in src/core/src/ffi (where the boundary between Rust
and C is defined) you need to regenerate the include/sourmash.h header,
and potentially fix any differences in the Python CFFI layer (which reads the C
header file and expose functionality to Python).
To regenerate the C header, run
$ make include/sourmash.h
This requires cbindgen (and technically a nightly Rust compiler,
but we cheat with RUSTC_BOOTSTRAP=1. For more info check this post).
cbindgen can be installed by running
$ cargo install --force cbindgen
Luiz wrote a blog post describing a PR that changes code at the Python API down to the Rust code library, including some tools for evaluating performance changes.
Versions are tagged in a vMAJOR.MINOR.PATH format,
following the Semantic Versioning convention.
From their definition:
Given a version number MAJOR.MINOR.PATCH, increment the:
MAJOR version when you make incompatible API changes, MINOR version when you add functionality in a backwards compatible manner, and PATCH version when you make backwards compatible bug fixes.
The Python version is not automated,
and must be bumped in pyproject.toml and flake.nix.
For the Rust core library we use rMAJOR.MINOR.PATCH
(note it starts with r, and not v).
The Rust version is not automated,
and must be bumped in src/core/Cargo.toml.
If you are getting an error that contains ImportError: cannot import name 'to_bytes' from 'sourmash.minhash',
then it's likely you need to update Rust and clean up your environment.
Some installation issues can be solved by simply removing the intermediate build files with:
make clean
:maxdepth: 2
release
requirements
storage
release-notes/releases
dev_plugins