From 272a97fe758b65079862fb1ca03be4946c736427 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sun, 28 Jul 2024 09:20:51 -0700 Subject: [PATCH] Update dev env instructions (#2990) Close #2793 - Add pixi, first mentioned in https://github.com/sourmash-bio/sourmash/issues/2707#issuecomment-1686499578 - Use tabs in docs to help to point out only one option is needed - Default recommendation is conda, add `dev.yml` with dev dependencies --- .envrc | 7 +- .github/workflows/dev_envs.yml | 40 +- .gitignore | 3 + Makefile | 2 +- dev.yml | 12 + doc/conf.py | 5 + doc/developer.md | 60 +- pixi.lock | 12347 +++++++++++++++++++++++++++++++ pyproject.toml | 32 +- 9 files changed, 12476 insertions(+), 32 deletions(-) create mode 100644 dev.yml create mode 100644 pixi.lock diff --git a/.envrc b/.envrc index 3550a30f2d..805772cb0f 100644 --- a/.envrc +++ b/.envrc @@ -1 +1,6 @@ -use flake +#use flake + +PATH=~/.pixi/bin:$PATH + +watch_file pixi.lock +eval "$(pixi shell-hook)" diff --git a/.github/workflows/dev_envs.yml b/.github/workflows/dev_envs.yml index ec8958619b..ebb7474d4a 100644 --- a/.github/workflows/dev_envs.yml +++ b/.github/workflows/dev_envs.yml @@ -3,6 +3,9 @@ on: pull_request: push: branches: [latest] +concurrency: + group: ${{ github.ref }} + cancel-in-progress: ${{ github.ref != 'refs/heads/latest' }} jobs: nix: runs-on: ${{ matrix.os }} @@ -23,8 +26,32 @@ jobs: - run: nix develop --command bash -c "tox -e py310" + pixi: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-14] + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: set up pixi + uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.26.1 + cache: true + frozen: true + + - name: run tests for 3.10 + shell: pixi run bash {0} + run: tox -e py310 + mamba: - runs-on: ubuntu-latest + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-14] steps: - uses: actions/checkout@v4 with: @@ -42,20 +69,11 @@ jobs: - name: setup conda uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca with: - auto-update-conda: true python-version: "3.10" - channels: conda-forge,bioconda - miniforge-variant: Mambaforge miniforge-version: latest - use-mamba: true - mamba-version: "*" + environment-file: dev.yml activate-environment: sourmash_dev auto-activate-base: false - use-only-tar-bz2: true - - - name: install dependencies - shell: bash -l {0} - run: mamba install 'tox>=3.27,<4' tox-conda rust git compilers pandoc libstdcxx-ng - name: run tests for 3.10 shell: bash -l {0} diff --git a/.gitignore b/.gitignore index 7a51026aaa..07af85da86 100644 --- a/.gitignore +++ b/.gitignore @@ -37,3 +37,6 @@ wasm-pack.log # nix .direnv/ result + +# pixi +.pixi/ diff --git a/Makefile b/Makefile index 891b710732..806b8b228f 100644 --- a/Makefile +++ b/Makefile @@ -18,7 +18,7 @@ dist: FORCE $(PYTHON) -m build --sdist test: .PHONY - tox -e py39 + tox -e py310 cargo test doc: .PHONY diff --git a/dev.yml b/dev.yml new file mode 100644 index 0000000000..9a2f582a93 --- /dev/null +++ b/dev.yml @@ -0,0 +1,12 @@ +name: sourmash_dev +channels: + - conda-forge +dependencies: + - clangdev >=16.0.6,<16.1 + - cxx-compiler >=1.7.0,<1.8 + - git 2.41.0.* + - libclang >=16.0.6,<16.1 + - pandoc 3.1.3.* + - python 3.10.* + - rust >=1.80.0,<1.81 + - tox >=4.11.0,<5 diff --git a/doc/conf.py b/doc/conf.py index 43623fcfc5..520b5da692 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -41,6 +41,7 @@ "nbsphinx", "IPython.sphinxext.ipython_console_highlighting", "myst_parser", + "sphinx_design", ] # Add any paths that contain templates here, relative to this directory. @@ -314,3 +315,7 @@ autodoc_mock_imports = ["sourmash.minhash"] myst_heading_anchors = 3 +myst_enable_extensions = [ + "html_admonition", + "colon_fence", +] diff --git a/doc/developer.md b/doc/developer.md index 218f24cab7..3b6d9ff811 100644 --- a/doc/developer.md +++ b/doc/developer.md @@ -12,33 +12,52 @@ git clone https://github.com/sourmash-bio/sourmash.git ``` sourmash runs under Python 3.10 and later. -We recommend using `conda` or `Nix` for setting up an environment for developing +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 =]) +Here are some suggestions on how to set them up -### Using mamba (conda alternative) +:::{note} +You only need one of these, no need to install them all! +::: + +::::{tab-set} + +:::{tab-item} conda Follow the [installation instructions](https://github.com/conda-forge/miniforge#install) for -installing `mambaforge` (a conda distribution that uses -[`mamba`](https://github.com/TheSnakePit/mamba) -and the [`conda-forge`](https://conda-forge.org/) channel by default). +installing `Miniforge3` (a conda distribution that uses +the [`conda-forge`](https://conda-forge.org/) channel by default). -Once `mamba` is installed, run +Once `conda` is installed, run ``` -mamba create -n sourmash_dev 'tox>=3.27,<4' tox-conda rust git compilers pandoc libstdcxx-ng +conda env create -n sourmash_dev --file dev.yml ``` to create an environment called `sourmash_dev` containing the programs needed for development. -To activate the new environment, run +Once the environment is created, you can activate it for development with ``` conda activate sourmash_dev ``` + +::: + +:::{tab-item} pixi + +Follow the [installation instructions](https://github.com/prefix-dev/pixi) for +installing `pixi`. + +To activate the new environment, run +``` +pixi shell +``` and proceed to the ["Running tests and checks"](#running-tests-and-checks) section. -### Using Nix +::: + +:::{tab-item} nix -Follow the [installation instructions](https://nixos.org/manual/nix/stable/#chap-installation) +Follow the [installation instructions](https://zero-to-nix.com/start/install) for setting up Nix in your system (Linux or macOS). Once Nix is installed, run @@ -47,18 +66,22 @@ nix develop ``` to start an environment ready for [running tests and checks](#running-tests-and-checks). -### General instructions +::: + +:::{tab-item} General instructions As long as you have `tox` and a Rust compiler available, -you can skip `mamba` or `Nix`. +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 run + +And for `tox` you can use [pipx](https://pipx.pypa.io/latest/installation/) for +installing it without interfering with other Python environments: ``` -python -m pip install tox +pipx install tox ``` We suggest working on sourmash in a virtualenv; e.g. from within the @@ -74,12 +97,15 @@ pip install -r requirements.txt ``` (but they are already installed in the virtualenv created with `tox -e dev`). -## Updating your developer environment - 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`. +::: + +:::: + + ## Running tests and checks We use [`tox`](https://tox.readthedocs.io) for managing dependencies and diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000000..a8742ca2d9 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,12347 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/noarch/_sysroot_linux-64_curr_repodata_hack-3-h69a702a_16.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils-2.40-h4852527_7.conda + - 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