From 3a644709ff48a81eb8e9e6f3c641c29a76ea7e9f Mon Sep 17 00:00:00 2001 From: Alex Kerney Date: Tue, 12 Aug 2025 12:05:56 -0400 Subject: [PATCH 1/2] Use pixi to manage environment Sets up Pixi to manage environment for local development, which should also help avoid 429 errors from Anaconda in Github Actions. See https://github.com/oceanhackweek/oceanhackweek.github.io/actions/runs/16913851668/job/47922502166?pr=357 --- .github/workflows/check_sphinx_build.yml | 17 +- .github/workflows/deploy-docs.yml | 9 +- .gitignore | 2 + _InstructionSiteUpdates.md | 12 +- environment.yml | 20 - pixi.lock | 2852 ++++++++++++++++++++++ pixi.toml | 30 + 7 files changed, 2902 insertions(+), 40 deletions(-) delete mode 100644 environment.yml create mode 100644 pixi.lock create mode 100644 pixi.toml diff --git a/.github/workflows/check_sphinx_build.yml b/.github/workflows/check_sphinx_build.yml index 6466c4a1..5b673bf2 100644 --- a/.github/workflows/check_sphinx_build.yml +++ b/.github/workflows/check_sphinx_build.yml @@ -18,21 +18,20 @@ jobs: with: submodules: true - - name: Install Conda environment from environment.yml - uses: mamba-org/setup-micromamba@0dea6379afdaffa5d528b3d1dabc45da37f443fc # v2.0.4 + - uses: prefix-dev/setup-pixi@v0.8.14 with: - environment-file: environment.yml - cache-environment: true + pixi-version: v0.51.0 + cache: true - name: Build documentation shell: bash -l {0} run: | - make html + pixi run html - # - name: Check links - # shell: bash -l {0} - # run: | - # make linkcheck + - name: Check links + shell: bash -l {0} + run: | + pixi run linkcheck # workaround https://github.com/actions/upload-artifact/issues/38 - name: tarball diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index a569454f..e86cfe66 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -11,17 +11,16 @@ jobs: with: submodules: true - - name: Install Conda environment from environment.yml - uses: mamba-org/setup-micromamba@v2.0.0 + - uses: prefix-dev/setup-pixi@v0.8.14 with: - environment-file: environment.yml - cache-environment: true + pixi-version: v0.51.0 + cache: true - name: Build documentation shell: bash -l {0} run: | - make html + pixi run html - name: Deploy uses: JamesIves/github-pages-deploy-action@3.7.1 diff --git a/.gitignore b/.gitignore index 2cff7cc9..f3d5bafd 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,5 @@ _config_localdev.yml _build **/.ipynb_checkpoints/* __pycache__ + +.pixi diff --git a/_InstructionSiteUpdates.md b/_InstructionSiteUpdates.md index 4952f678..7d4e474e 100644 --- a/_InstructionSiteUpdates.md +++ b/_InstructionSiteUpdates.md @@ -56,14 +56,14 @@ It is worth noting that we are using the `source` branch as the base for this re #### Environment -There is a pre-configured conda environment in `environment.yml`. -To use it, `conda env create --file environment.yml`, then activate with `conda activate ohw-site`. +There is a pre-configured conda environment in `pixi.toml`. +To use it, prefix commands with `pixi run` to make sure the environment is up to date. #### Commands -- `make live` - The environment is setup with [sphinx-autobuild](https://pypi.org/project/sphinx-autobuild/) which will update open browsers when files are saved. The site will be available at [http://127.0.0.1:8000/](http://127.0.0.1:8000/). -- `make html` - Launch a one off build of HTML output. -- `make clean` - Clean all the build directories. This can be useful as Sphinx tries to do incremental builds, and sometimes it will end up out of sync. +- `pixi run live` - The environment is setup with [sphinx-autobuild](https://pypi.org/project/sphinx-autobuild/) which will update open browsers when files are saved. The site will be available at [http://127.0.0.1:8000/](http://127.0.0.1:8000/). +- `pixi run html` - Launch a one off build of HTML output. +- `pixi run clean` - Clean all the build directories. This can be useful as Sphinx tries to do incremental builds, and sometimes it will end up out of sync. - `git pull upstream source` to bring in any changes from the main repo. ### Writing and Linking Pages @@ -210,7 +210,7 @@ After you create a PR, Netlify will build the site and make a comment with a lin While most pages follow the same structure in the repo, as they do on the website, there are a few additional files to be aware of: - `conf.pd` - This is the Sphinx configuration file. -- `environment.yml` - The conda environment needed to build the website. +- `pixi.toml` - The conda environment needed to build the website. - `requirements.txt` - A pip installable environment to build the website. This is mainly used by Netlify to create previews of Pull Requests. It is generated with `pip list --format=freeze > requirements.txt` - `posts.md` - A stub page that is replaced when blog posts are generated. - `_build/` - Automatically generated output from Sphinx. diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 15e5b350..00000000 --- a/environment.yml +++ /dev/null @@ -1,20 +0,0 @@ -name: ohw-site -channels: - - conda-forge -dependencies: - - python>=3.8,<3.9 - # website/blog building - - myst-nb>=0.16.0 - - sphinx>= 5.0.2 - - jupytext - - pre-commit - # - sphinx-panels - - ablog>=0.10.26 - - sphinx-autobuild>=2021.3.14 - - pydata-sphinx-theme>=0.9.0 - - ipywidgets>=7.7.1 - - sphinx-design>=0.2.0 - # computation - - numpy>=1.23.1 - - pandas>=1.4.3 - - xarray>=2022.3.0 diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..3f9e1912 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,2852 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + packages: + osx-arm64: + - 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-[target.osx-arm64.dependencies] python = ">=3.8,<3.9" myst-nb = ">=0.16.0" sphinx = ">=5.0.2"