From 4bb2a1ed0722d82acd52baad68b8e1b4b61bc8e5 Mon Sep 17 00:00:00 2001 From: Filipe Fernandes Date: Tue, 19 Nov 2024 20:10:18 +0100 Subject: [PATCH 1/3] use pixi --- environment.yml => .binder/environment.yml | 50 +- .gitattributes | 2 + .github/workflows/metrics.yml | 14 +- .github/workflows/tests.yml | 11 +- .gitignore | 4 + notebooks/README.md | 35 +- pixi.lock | 15808 +++++++++++++++++++ pyproject.toml | 31 + 8 files changed, 15898 insertions(+), 57 deletions(-) rename environment.yml => .binder/environment.yml (89%) create mode 100644 .gitattributes create mode 100644 pixi.lock diff --git a/environment.yml b/.binder/environment.yml similarity index 89% rename from environment.yml rename to .binder/environment.yml index 9204f31..89fa306 100644 --- a/environment.yml +++ b/.binder/environment.yml @@ -1,25 +1,25 @@ -name: ioos-metrics -channels: - - conda-forge -dependencies: - - python=3.13 - - bs4 - - ckanapi - - fake-useragent - - fiscalyear - - geopandas>=0.13.2 - - gliderpy - - html5lib - - joblib - - lxml - - nbclassic - - pandas - - pdfminer.six - - pyarrow - - pyobis - - pytest - - requests - - suds - - pip - - pip: - - git+https://github.com/ioos/ioos_metrics.git +name: ioos-metrics +channels: + - conda-forge +dependencies: + - python=3.12 + - bs4 + - ckanapi + - fake-useragent + - fiscalyear + - geopandas>=0.13.2 + - gliderpy + - html5lib + - joblib + - lxml + - nbclassic + - pandas + - pdfminer.six + - pyarrow + - pyobis + - pytest + - requests + - suds + - pip + - pip: + - git+https://github.com/ioos/ioos_metrics.git diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..07fe41c --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# GitHub syntax highlighting +pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/metrics.yml b/.github/workflows/metrics.yml index c0833a2..7acb399 100644 --- a/.github/workflows/metrics.yml +++ b/.github/workflows/metrics.yml @@ -23,11 +23,11 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 - - name: Setup Micromamba - uses: mamba-org/setup-micromamba@v2 + - uses: actions/checkout@v4 + - name: Setup Pixi + uses: prefix-dev/setup-pixi@v0.8.1 with: - init-shell: bash - environment-file: environment.yml + manifest-path: pyproject.toml - name: echo secrets into a file shell: bash -l {0} @@ -41,10 +41,8 @@ jobs: - name: Collect quarterly GTS and BTN metrics shell: bash -l {0} - run: > - python btn_metrics.py - && python gts_regional_metrics.py - && python gts_atn_metrics.py + run: | + pixi run metrics - name: Get current date run: echo "NOW=$(date -u)" >> ${GITHUB_ENV} diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 038df21..ff49b17 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -12,14 +12,13 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Setup Micromamba - uses: mamba-org/setup-micromamba@v2 + - uses: actions/checkout@v4 + - name: Setup Pixi + uses: prefix-dev/setup-pixi@v0.8.1 with: - init-shell: bash - environment-file: environment.yml - environment-name: TEST + manifest-path: pyproject.toml - name: Tests shell: bash -l {0} run: | - python -m pytest -rxs tests + pixi run tests diff --git a/.gitignore b/.gitignore index 3b35fb9..862e20e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ *.log +updated_metrics.csv .ipynb_checkpoints/ /config.py /website/deploy/asset_inventory.html @@ -8,3 +9,6 @@ dist/ ioos_metrics/_version.py website/deploy/gts_atn.html website/deploy/gts_regional.html +# pixi environments +.pixi +*.egg-info diff --git a/notebooks/README.md b/notebooks/README.md index d0be54f..32a2267 100644 --- a/notebooks/README.md +++ b/notebooks/README.md @@ -1,18 +1,17 @@ -# Run the metrics notebook - -## How to run - -1. Install pixi: https://pixi.sh/dev/#installation -1. Clone this repository: `git clone https://github.com/ioos/ioos_metrics.git` -1. Enter the repository directory: `cd gider_metrics` -1. Create tne enviroment: `conda env create --name METRICS --file environment.yml` -1. Start the notebook: `jupyter nbclassic` - -## You can also try it on mybinder - -[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ioos/ioos_metrics/HEAD?labpath=/notebooks/glider_metrics.ipynb) - - -## Or Google Colab - -[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ioos/ioos_metrics/blob/main/notebooks/glider_metrics.ipynb) +# Run the metrics notebook + +## How to run + +1. Install pixi: https://pixi.sh/dev/#installation +1. Clone this repository: `git clone https://github.com/ioos/ioos_metrics.git` +1. Enter the repository directory: `cd ioos_metrics` +1. Start the notebook: `pixi run notebook` + +## You can also try it on mybinder + +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ioos/ioos_metrics/HEAD?labpath=/notebooks/glider_metrics.ipynb) + + +## Or Google Colab + +[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ioos/ioos_metrics/blob/main/notebooks/glider_metrics.ipynb) diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..558b832 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,15808 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + 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/anyio-4.6.2.post1-pyhd8ed1ab_0.conda + - 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