merged w/ main

carbonplan · Mar 12, 2024 · 63d31fa · 63d31fa
2 parents e24aeb4 + 9d1d0cd
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,6 +1,10 @@
 version: 2
 updates:
-  - package-ecosystem: 'github-actions'
-    directory: '/'
+  - package-ecosystem: "github-actions"
+    directory: "/"
     schedule:
-      interval: 'monthly'
+      interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"
diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml
@@ -0,0 +1,50 @@
+name: codspeed-benchmarks
+
+on:
+  # Run on pushes to the main branch
+  push:
+    branches:
+      - "main"
+  # Run on pull requests
+  pull_request:
+  # `workflow_dispatch` allows CodSpeed to trigger backtest
+  # performance analysis in order to generate initial data.
+  workflow_dispatch:
+
+jobs:
+  benchmarks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Miniconda
+        uses: conda-incubator/[email protected]
+        with:
+          auto-activate-base: true
+          activate-environment: "" # base environment
+          channels: conda-forge,nodefaults
+          channel-priority: strict
+
+      - name: Install dependencies
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          # Preprend $CONDA/bin to $PATH so that conda's python is used over system python
+          echo $CONDA/bin >> $GITHUB_PATH
+          conda install --solver=libmamba dask python=3.10 \
+                        esmpy>=8.2.0 mpich netcdf4 numpy pip pooch pydantic>=1.10 pyproj \
+                        pytest pytest-cov pytest-mypy rasterio rioxarray scipy sparse>=0.13.0 \
+                        xarray xarray-datatree>=0.0.11 xesmf zarr cf_xarray>=0.8.0
+          python -m pip install -U pytest-codspeed setuptools
+          python -m pip install -e . --no-deps
+
+      - name: Run benchmarks
+        uses: CodSpeedHQ/[email protected]
+        with:
+          run: |
+            conda list
+            python -c "import ndpyramid; print(ndpyramid.__version__)"
+            python -m pytest --codspeed
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -9,7 +9,7 @@ on:
       - main
   workflow_dispatch:
   schedule:
-    - cron: '0 0 * * *' # Daily “At 00:00”
+    - cron: "0 0 * * *" # Daily “At 00:00”
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -23,20 +23,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10'] #TODO: add 3.11 once sparse/numba support it
+        python-version: ["3.9", "3.10"] #TODO: add 3.11 once sparse/numba support it
     timeout-minutes: 20
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout
+        uses: actions/checkout@v4
+
       - name: Install Conda environment from environment.yml
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
+          # environment-file is not assumed anymore
           environment-file: ci/environment.yml
-          cache-downloads: true
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python-version }}
+          # now called cache-environment
+          cache-environment: true
 
       - name: Install package
         run: |
@@ -49,7 +53,7 @@ jobs:
         run: |
           python -m pytest
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           file: ./coverage.xml
           fail_ci_if_error: false
diff --git a/.github/workflows/pypi-release.yaml b/.github/workflows/pypi-release.yaml
@@ -13,7 +13,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: 3.9
@@ -39,7 +39,7 @@ jobs:
           else
             echo "✅ Looks good"
           fi
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
@@ -48,11 +48,11 @@ jobs:
     needs: build-artifacts
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: 3.9
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
@@ -73,12 +73,12 @@ jobs:
     if: github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/[email protected].11
+        uses: pypa/[email protected].12
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

diff --git a/.gitignore b/.gitignore
@@ -71,6 +71,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/generated/
 
 # PyBuilder
 target/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -15,18 +15,68 @@ repos:
       - id: debug-statements
       - id: mixed-line-ending
 
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.0.292'
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
     hooks:
-      - id: ruff
-        args: ['--fix']
+      - id: pyupgrade
+        args:
+          - "--py39-plus"
+
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
 
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.8
+    rev: v0.3.9
     hooks:
       - id: blackdoc
 
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.2.1"
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+        args:
+          [
+            "--extra-keys",
+            "metadata.celltoolbar metadata.kernelspec",
+            "metadata.language_info.codemirror_mode.version",
+            "metadata.language_info.pygments_lexer",
+            "metadata.language_info.version",
+            "metadata.toc",
+            "metadata.notify_time",
+            "metadata.varInspector",
+            "cell.metadata.heading_collapsed",
+            "cell.metadata.hidden",
+            "cell.metadata.code_folding",
+            "cell.metadata.tags",
+            "cell.metadata.init_cell",
+          ]
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.1
+    hooks:
+      - id: nbqa-ruff
+        args: ["--fix"]
+      - id: nbqa-isort
+        args: ["--profile=black"]
+        additional_dependencies: [isort==5.6.4]
+      - id: nbqa-black
+      - id: nbqa-pyupgrade
+        args: ["--py39-plus"]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: 'mambaforge-4.10'
+    python: "mambaforge-4.10"
 
 # Build documentation in the doc/ directory with Sphinx
 sphinx:

diff --git a/README.md b/README.md
@@ -1,24 +1,20 @@
-<p align='left'>
-  <a href='https://carbonplan.org/#gh-light-mode-only'>
-    <img
-      src='https://carbonplan-assets.s3.amazonaws.com/monogram/dark-small.png'
-      height='48px'
-    />
-  </a>
-  <a href='https://carbonplan.org/#gh-dark-mode-only'>
-    <img
-      src='https://carbonplan-assets.s3.amazonaws.com/monogram/light-small.png'
-      height='48px'
-    />
-  </a>
+<p align="left" >
+<a href='https://carbonplan.org'>
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://carbonplan-assets.s3.amazonaws.com/monogram/light-small.png">
+  <img alt="CarbonPlan monogram." height="48" src="https://carbonplan-assets.s3.amazonaws.com/monogram/dark-small.png">
+</picture>
+</a>
 </p>
 
 # ndpyramid
 
 A small utility for generating ND array pyramids using Xarray and Zarr.
 
 [![CI](https://github.com/carbonplan/ndpyramid/actions/workflows/main.yaml/badge.svg)](https://github.com/carbonplan/ndpyramid/actions/workflows/main.yaml)
-![MIT License](https://badgen.net/badge/license/MIT/blue)
+![PyPI](https://img.shields.io/pypi/v/ndpyramid)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/ndpyramid.svg)](https://anaconda.org/conda-forge/ndpyramid)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 # installation
 
@@ -74,8 +70,8 @@ See the docstrings for more details about input parameters and options.
 
 ## license
 
-All the code in this repository is [MIT](https://choosealicense.com/licenses/mit/) licensed, but we request that you please provide attribution if reusing any of our digital content (graphics, logo, articles, etc.).
+All the code in this repository is [MIT](https://choosealicense.com/licenses/mit/)-licensed, but we request that you please provide attribution if reusing any of our digital content (graphics, logo, articles, etc.).
 
 ## about us
 
-CarbonPlan is a non-profit organization that uses data and science for climate action. We aim to improve the transparency and scientific integrity of climate solutions with open data and tools. Find out more at [carbonplan.org](https://carbonplan.org/) or get in touch by [opening an issue](https://github.com/carbonplan/ndpyramid/issues/new) or [sending us an email](mailto:[email protected]).
+CarbonPlan is a nonprofit organization that uses data and science for climate action. We aim to improve the transparency and scientific integrity of climate solutions with open data and tools. Find out more at [carbonplan.org](https://carbonplan.org/) or get in touch by [opening an issue](https://github.com/carbonplan/ndpyramid/issues/new) or [sending us an email](mailto:[email protected]).
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -10,17 +10,21 @@ dependencies:
   - numpy
   - pip
   - pooch
+  - pre-commit
   - pydantic>=1.10
   - pyproj
   - pytest
   - pytest-cov
   - pytest-mypy
   - rasterio
   - rioxarray
+  - s3fs
   - scipy
   - sparse>=0.13.0
   - xarray
   - xarray-datatree>=0.0.11
   - xesmf
   - zarr
   - cf_xarray>=0.8.0
+  - pip:
+      - pytest-codspeed
diff --git a/codecov.yml b/codecov.yml
@@ -5,8 +5,8 @@ codecov:
 comment: false
 
 ignore:
-  - 'tests/*.py'
-  - 'setup.py'
+  - "tests/*.py"
+  - "setup.py"
 
 coverage:
   precision: 2

diff --git a/docs/conf.py b/docs/conf.py
@@ -27,9 +27,11 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = ['myst_parser',
-            'sphinx.ext.autodoc',
-            'sphinx.ext.autosummary',]
+extensions = [
+    'myst_parser',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+]
 
 autosummary_generate = True
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -5,10 +5,6 @@ ndpyramid
 
 A small utility for generating ND array pyramids using Xarray and Zarr.
 
-.. toctree::
-   :hidden:
-   self
-
 .. toctree::
     :maxdepth: 1
     :hidden:
@@ -30,3 +26,4 @@ A small utility for generating ND array pyramids using Xarray and Zarr.
     :caption: Reference
 
     API <api>
+    schema