From 7915f51835b4d1d0699b98e66dd3a9a0722f5dc1 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Mon, 3 Jul 2023 16:29:03 -0700 Subject: [PATCH 1/7] update install instructions, cleanup pixi.toml to avoid duplicate info, fix doc building in nix --- .github/workflows/dev_envs.yml | 40 +- .gitignore | 3 + dev.yml | 12 + doc/conf.py | 5 + doc/developer.md | 60 +- flake.nix | 2 + pixi.lock | 8317 ++++++++++++++++++++++++++++++++ pixi.toml | 15 + pyproject.toml | 5 +- 9 files changed, 8428 insertions(+), 31 deletions(-) create mode 100644 dev.yml create mode 100644 pixi.lock create mode 100644 pixi.toml diff --git a/.github/workflows/dev_envs.yml b/.github/workflows/dev_envs.yml index ec8958619b..5831a4e108 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 +26,31 @@ 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@v0.5.1 + with: + pixi-version: v0.13.0 + cache: 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: @@ -34,7 +60,6 @@ jobs: uses: actions/cache@v4 env: CACHE_NUMBER: 0 - with: path: ~/conda_pkgs_dir key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} @@ -42,20 +67,11 @@ 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/dev.yml b/dev.yml new file mode 100644 index 0000000000..a596bf87bc --- /dev/null +++ b/dev.yml @@ -0,0 +1,12 @@ +name: sourmash_dev +channels: + - conda-forge +dependencies: + - clangdev = ">=16.0.6,<17.1" + - cxx-compiler = ">=1.7.0,<1.8" + - git = "2.41.0.*" + - libclang = ">=16.0.6,<17.1" + - pandoc = "3.1.3.*" + - python = "3.10.*" + - rust = ">=1.76.0,<1.77" + - 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..ab879609a2 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 `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/flake.nix b/flake.nix index 69d3acb5dc..2606a08f3a 100644 --- a/flake.nix +++ b/flake.nix @@ -126,6 +126,8 @@ cargo-codspeed cargo-semver-checks nixpkgs-fmt + + pixi ]; shellHook = '' diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000000..7457287f17 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,8317 @@ +version: 4 +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/linux-64/binutils-2.40-hdd6e379_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-hf600244_0.conda + - 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libgcc-ng >=12 + - libstdcxx-ng >=12 + - libzlib >=1.2.13,<1.3.0a0 + license: BSD-3-Clause + license_family: BSD + size: 545199 + timestamp: 1693151163452 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 0000000000..e7f53c022a --- /dev/null +++ b/pixi.toml @@ -0,0 +1,15 @@ +[project] +name = "sourmash" +channels = ["conda-forge"] +platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64", "win-64"] + +[dependencies] +clangdev = ">=16.0.6,<17.1" +cxx-compiler = ">=1.7.0,<1.8" +git = "2.41.0.*" +libclang = ">=16.0.6,<17.1" +pandoc = "3.1.3.*" +python = "3.10.*" +rust = ">=1.76.0,<1.77" +tox = ">=4.11.0,<5" +conda = ">=23.11.0,<23.12" diff --git a/pyproject.toml b/pyproject.toml index bf5df8eb18..12276ebfd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -116,12 +116,13 @@ demo = [ "ipython", ] doc = [ - "sphinx>=4.4.0,<8", + "sphinx>=6,<8", "myst-parser==3.0.1", - "Jinja2==3.1.4", + "Jinja2", "alabaster", "sphinxcontrib-napoleon", "nbsphinx", + "sphinx-design==0.5.0", "ipython", "docutils>=0.17.1,<0.22", ] From 333b9cdad024cde4b1bcc590d504923ea9e3196b Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Tue, 5 Mar 2024 10:00:17 -0800 Subject: [PATCH 2/7] fix dev.yml syntax --- dev.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/dev.yml b/dev.yml index a596bf87bc..f758240046 100644 --- a/dev.yml +++ b/dev.yml @@ -2,11 +2,11 @@ name: sourmash_dev channels: - conda-forge dependencies: - - clangdev = ">=16.0.6,<17.1" - - cxx-compiler = ">=1.7.0,<1.8" - - git = "2.41.0.*" - - libclang = ">=16.0.6,<17.1" - - pandoc = "3.1.3.*" - - python = "3.10.*" - - rust = ">=1.76.0,<1.77" - - tox = ">=4.11.0,<5" + - clangdev >=16.0.6,<17.1 + - cxx-compiler >=1.7.0,<1.8 + - git 2.41.0.* + - libclang >=16.0.6,<17.1 + - pandoc 3.1.3.* + - python 3.10.* + - rust >=1.76.0,<1.77 + - tox >=4.11.0,<5 From 44777154c2a4cfb9199c1077b5b247b45db88ebf Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sat, 6 Apr 2024 19:43:54 -0700 Subject: [PATCH 3/7] re-use pyproject.toml for pixi --- .envrc | 7 +- flake.nix | 2 - pixi.lock | 7880 +++++++++++++++++++++++++++++++++--------------- pixi.toml | 15 - pyproject.toml | 24 + 5 files changed, 5457 insertions(+), 2471 deletions(-) delete mode 100644 pixi.toml 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/flake.nix b/flake.nix index 2606a08f3a..69d3acb5dc 100644 --- a/flake.nix +++ b/flake.nix @@ -126,8 +126,6 @@ cargo-codspeed cargo-semver-checks nixpkgs-fmt - - pixi ]; shellHook = '' diff --git a/pixi.lock b/pixi.lock index 7457287f17..4a2fb132c3 100644 --- a/pixi.lock +++ b/pixi.lock @@ -7,14 +7,22 @@ environments: 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/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-hdd6e379_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-hf600244_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.40-hbdbef99_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py310hc6cd4ac_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/bitarray-2.9.2-py310h2372a71_0.conda + - 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-[dependencies] -clangdev = ">=16.0.6,<17.1" -cxx-compiler = ">=1.7.0,<1.8" -git = "2.41.0.*" -libclang = ">=16.0.6,<17.1" -pandoc = "3.1.3.*" -python = "3.10.*" -rust = ">=1.76.0,<1.77" -tox = ">=4.11.0,<5" -conda = ">=23.11.0,<23.12" diff --git a/pyproject.toml b/pyproject.toml index 12276ebfd3..f1bc1ee4fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -248,3 +248,27 @@ paths.source = [ report.fail_under = 88 run.parallel = true run.plugins = ["covdefaults"] + +[tool.pixi.project] +name = "sourmash" +channels = ["conda-forge"] +platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64", "win-64"] + +[tool.pixi.dependencies] +clangdev = ">=16.0.6,<17.1" +cxx-compiler = ">=1.7.0,<1.8" +git = "2.41.0.*" +libclang = ">=16.0.6,<17.1" +pandoc = "3.1.3.*" +python = "3.10.*" +rust = ">=1.76.0,<1.77" +tox = ">=4.11.0,<5" +# prefer conda deps over PyPI +screed = ">=1.1.2,<2" +cffi = ">=1.14.0" +numpy = "*" +matplotlib = "*" +scipy = "*" +deprecation = ">=2.0.6" +cachetools = ">=4,<6" +bitstring = ">=3.1.9,<5" From 1b800dc73f8bfc63b15c7a9023da4801c5685bb4 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sat, 27 Jul 2024 17:58:06 -0700 Subject: [PATCH 4/7] update pixi action --- .github/workflows/dev_envs.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/dev_envs.yml b/.github/workflows/dev_envs.yml index 5831a4e108..b76bc461a0 100644 --- a/.github/workflows/dev_envs.yml +++ b/.github/workflows/dev_envs.yml @@ -37,10 +37,11 @@ jobs: fetch-depth: 0 - name: set up pixi - uses: prefix-dev/setup-pixi@v0.5.1 + uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.13.0 + pixi-version: v0.26.1 cache: true + frozen: true - name: run tests for 3.10 shell: pixi run bash {0} From 9e713a20fb83b5a4d9b5b1d759c898eace799331 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sat, 27 Jul 2024 21:15:13 -0700 Subject: [PATCH 5/7] update pixi.lock --- pixi.lock | 8362 +++++++++++++++++++++++++++--------------------- pyproject.toml | 9 +- 2 files changed, 4715 insertions(+), 3656 deletions(-) diff --git a/pixi.lock b/pixi.lock index 4a2fb132c3..a8742ca2d9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 4 +version: 5 environments: default: channels: @@ -7,189 +7,193 @@ environments: 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 - 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conda-forge dependencies: - - clangdev >=16.0.6,<17.1 + - clangdev >=16.0.6,<16.1 - cxx-compiler >=1.7.0,<1.8 - git 2.41.0.* - - libclang >=16.0.6,<17.1 + - libclang >=16.0.6,<16.1 - pandoc 3.1.3.* - python 3.10.* - - rust >=1.76.0,<1.77 + - rust >=1.80.0,<1.81 - tox >=4.11.0,<5 From 7f0b40455727273b4a6ec936f995a7d6dc4e38b6 Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sat, 27 Jul 2024 22:43:08 -0700 Subject: [PATCH 7/7] small docs and Makefile fixes --- Makefile | 2 +- doc/developer.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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/doc/developer.md b/doc/developer.md index ab879609a2..3b6d9ff811 100644 --- a/doc/developer.md +++ b/doc/developer.md @@ -71,7 +71,7 @@ to start an environment ready for [running tests and checks](#running-tests-and- :::{tab-item} General instructions As long as you have `tox` and a Rust compiler available, -you can skip `pixi` or `Nix`. +you can skip `conda`, `pixi`, or `nix`. For Rust, we suggest using `rustup` to install the Rust environment: ```