initial pixi implementation

Author: martin-springer

.github/workflows/nbval.yaml

@@ -18,23 +18,20 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - uses: prefix-dev/setup-pixi@v0.8.3
       with:
-        python-version: "3.12"
-    - name: Install notebook environment
+        environments: dev
+    - name: Execute notebook
       run: |
-        python -m pip install --upgrade pip wheel
-        pip install --timeout=300 -r requirements.txt -r docs/notebook_requirements.txt .[test]
-    - name: Run notebook and check output
+        pixi run -e dev jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=600 --output ${{ matrix.notebook-file }} docs/${{ matrix.notebook-file }}
+    - name: Validate notebook output
       run: |
         # --nbval-sanitize-with:  pre-process text to remove irrelevant differences (e.g. warning filepaths)
-        pytest --nbval --nbval-sanitize-with docs/nbval_sanitization_rules.cfg docs/${{ matrix.notebook-file }}
-    - name: Run notebooks again, save files
+        pixi run -e dev pytest --nbval --nbval-lax --nbval-sanitize-with docs/nbval_sanitization_rules.cfg docs/${{ matrix.notebook-file }}
+    - name: Convert notebook to HTML
       run: |
-        pip install nbconvert[webpdf]
         mkdir docs/artifacts
-        jupyter nbconvert --to html --execute --ExecutePreprocessor.timeout=600 --allow-errors --output artifacts/${{ matrix.notebook-file }}.html docs/${{ matrix.notebook-file }}
+        pixi run -e dev jupyter nbconvert --to html --output artifacts/${{ matrix.notebook-file }}.html docs/${{ matrix.notebook-file }}
     - name: Upload artifacts
       uses: actions/upload-artifact@v4
       with:

.github/workflows/pytest.yaml

@@ -9,26 +9,60 @@ on:
 
 
 jobs:
-  build:
+  validate-envs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: prefix-dev/setup-pixi@v0.8.3
+      with:
+        environments: core default dev
+        frozen: true
+    - name: Validate core environment
+      run: pixi run -e core python -c "import rdtools; print(rdtools.__version__)"
+    - name: Validate default environment
+      run: pixi run python -c "import rdtools; import jupyter; print('default OK')"
+    - name: Validate dev environment
+      run: pixi run -e dev python -c "import rdtools; import pytest; import jupyter; print('dev OK')"
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        environment: [dev-py310, dev-py311, dev-py312, dev-py313, dev-py314]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: prefix-dev/setup-pixi@v0.8.3
+      with:
+        environments: ${{ matrix.environment }}
+    - name: Test with pytest (${{ matrix.environment }})
+      run: pixi run -e ${{ matrix.environment }} test
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  test-min:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: prefix-dev/setup-pixi@v0.8.3
+      with:
+        environments: dev-min
+    - name: Test with pytest (minimum versions)
+      run: pixi run -e dev-min test
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
+  test-latest:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
-        env: [
-          '-r requirements.txt .[test]',
-          '-r requirements-min.txt .[test]',
-          '--upgrade --upgrade-strategy=eager .[test]'
-        ]
-        exclude:
-          - python-version: "3.10"
-            env: '-r requirements-min.txt .[test]'
-          - python-version: "3.11"
-            env: '-r requirements-min.txt .[test]'
-          - python-version: "3.12"
-            env: '-r requirements-min.txt .[test]'
-          - python-version: "3.13"
-            env: '-r requirements-min.txt .[test]'
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
       fail-fast: false
 
     steps:
@@ -37,13 +71,12 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install ${{ matrix.env }}
+    - name: Install latest versions
       run: |
         python -m pip install --upgrade pip wheel
-        pip install --timeout=300 ${{ matrix.env }}
-    - name: Test with pytest ${{ matrix.env }}
-      run: |
-        python -m pytest --cov=./ --cov-report=xml
+        pip install --timeout=300 --upgrade --upgrade-strategy=eager .[test]
+    - name: Test with pytest (latest)
+      run: python -m pytest --cov=rdtools --cov-report=xml
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4
       env:

.github/workflows/requirements.yaml

@@ -11,6 +11,7 @@
 .coveralls.yml
 .coverage
 .coverage.*
+coverage.xml
 htmlcov/
 
 # ignore test cache
@@ -38,5 +39,8 @@ rdtools.egg-info*
 
 *.pickle
 
+# pixi environments (local, not committed)
+.pixi/
+
 # ignore vscode settings
 .vscode/

.gitignore

@@ -25,17 +25,43 @@ command line:
 pip install rdtools
 ```
 
+Optional extras are available:
+
+```
+pip install rdtools[notebooks]  # Jupyter and notebook dependencies
+pip install rdtools[test]       # pytest, coverage, flake8
+pip install rdtools[dev]        # notebooks + test combined
+```
+
+Alternatively, RdTools uses [pixi](https://pixi.sh) for reproducible
+environment management. To get started with pixi:
+
+```
+pixi install          # default environment (core + notebooks)
+pixi run lab          # launch Jupyter Lab
+```
+
+For development, use the `dev` environment which includes both notebook
+and test dependencies:
+
+```
+pixi shell -e dev     # activate the dev environment
+pixi run -e dev test  # run pytest with coverage
+pixi run -e dev nbval # validate notebooks
+pixi run -e dev lab   # launch Jupyter Lab
+```
+
 For API documentation and full examples, please see the [documentation](https://rdtools.readthedocs.io).
 
-RdTools currently is tested on Python 3.9+.
+RdTools currently is tested on Python 3.10+.
 
 ## Citing RdTools
 
 To cite RdTools, please use the following along with the version number
 and the specific DOI coresponding to that version from [Zenodo](https://doi.org/10.5281/zenodo.1210316):
 
--  Michael G. Deceglie, Kevin Anderson,  Adam Shinn, Ambarish Nag, Mark Mikofski,
-   Martin Springer, Jiyang Yan, Kirsten Perry, Sandra Villamar, Will Vining,
+-  Michael G. Deceglie, Martin Springer, Kevin Anderson,  Adam Shinn, Kirsten Perry, Ambarish Nag,
+   Mark Mikofski, Jiyang Yan, Sandra Villamar, Will Vining,
    Gregory Kimball, Daniel Ruth, Noah Moyer, Quyen Nguyen, Dirk Jordan,
    Matthew Muller, and Chris Deline, RdTools, version {insert version}, Computer Software,
    https://github.com/NatLabRockies/rdtools. DOI:{insert DOI}

README.md

@@ -16,7 +16,7 @@
     "1. Import and preliminary calculations: In this step data is imported and augmented to enable analysis with RdTools. **No RdTools functions are used in this step. It will vary depending on the particulars of your dataset.**  \n",
     "2. Analysis with RdTools: This notebook illustrates the use of the TrendAnalysis API with two new features: `label='center'` and `multi_yoy=True`. Because we are implementing this with the `rdtools.TrendAnalysis` object-oriented API, it requires passing kwargs to `degradation_year_on_year` as a dictionary in the `TrendAnalysis.sensor_analysis(yoy_kwargs={})` input.\n",
     "\n",
-    "For a consistent experience, we recommend installing the packages and versions documented in `docs/notebook_requirements.txt`. This can be achieved in your environment by running `pip install -r docs/notebook_requirements.txt` from the base directory. (RdTools must also be separately installed.) This notebook was tested in python 3.12.\n",
+    "For a consistent experience, we recommend using [pixi](https://pixi.sh) to set up the notebook environment. From the base directory, run `pixi run -e notebooks lab` to launch JupyterLab with all required packages. Alternatively, install manually with `pip install rdtools[notebooks]`. This notebook was tested in python 3.13.\n",
     "\n",
     "This notebook works with data from the NREL PVDAQ `[4] NREL x-Si #1` system. This notebook automatically downloads and locally caches the dataset used in this example. The data can also be found on the DuraMAT Datahub (https://datahub.duramat.org/dataset/pvdaq-time-series-with-soiling-signal).\n"
    ]
@@ -228,7 +228,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -247,7 +247,7 @@
    ],
    "source": [
     "# Provide additional timestamp information for the YoY slopes including the left and right timestamps that were used to calculate the slope.\n",
-    "# The index is set to  equal dt_center because we passed label='center' in the yoy_kwargs. \n",
+    "# The index is set to  equal dt_center because we passed label='center' in the yoy_kwargs.\n",
     "print(calc_info['YoY_times'].head().to_markdown())"
    ]
   },
@@ -457,9 +457,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [conda env:rdtools_dev]",
+   "display_name": "rdtools_313-nb",
    "language": "python",
-   "name": "conda-env-rdtools_dev-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -471,7 +471,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.13.11"
   }
  },
  "nbformat": 4,

docs/Multi-year_on_year_example.ipynb

@@ -7,7 +7,7 @@
     "# TrendAnalysis object-oriented example\n",
     "\n",
     "\n",
-    "This juypter notebook is intended to demonstrate the RdTools analysis workflow as implemented with the `rdtools.TrendAnalysis` object-oriented API. For a consistent experience, we recommend installing the packages and versions documented in `docs/notebook_requirements.txt`. This can be achieved in your environment by running `pip install -r docs/notebook_requirements.txt` from the base directory. (RdTools must also be separately installed.) This notebook was tested in python 3.12.\n",
+    "This juypter notebook is intended to demonstrate the RdTools analysis workflow as implemented with the `rdtools.TrendAnalysis` object-oriented API. For a consistent experience, we recommend using [pixi](https://pixi.sh) to set up the notebook environment. From the base directory, run `pixi run -e notebooks lab` to launch JupyterLab with all required packages. Alternatively, install manually with `pip install rdtools[notebooks]`. This notebook was tested in python 3.13.\n",
     "\n",
     "The calculations consist of two phases:\n",
     "\n",

docs/TrendAnalysis_example.ipynb

@@ -7,7 +7,7 @@
     "# TrendAnalysis with satellite data\n",
     "\n",
     "\n",
-    "This juypter notebook is intended to demonstrate how to use the RdTools analysis workflow as implemented with the `rdtools.TrendAnalysis` object-oriented API with satellite weather/irradiance data, such as NSRDB, instead of ground-based sensor data. For a consistent experience, we recommend installing the packages and versions documented in `docs/notebook_requirements.txt`. This can be achieved in your environment by running `pip install -r docs/notebook_requirements.txt` from the base directory. (RdTools must also be separately installed.) This notebook was tested in python 3.12.\n",
+    "This juypter notebook is intended to demonstrate how to use the RdTools analysis workflow as implemented with the `rdtools.TrendAnalysis` object-oriented API with satellite weather/irradiance data, such as NSRDB, instead of ground-based sensor data. For a consistent experience, we recommend using [pixi](https://pixi.sh) to set up the notebook environment. From the base directory, run `pixi run -e notebooks lab` to launch JupyterLab with all required packages. Alternatively, install manually with `pip install rdtools[notebooks]`. This notebook was tested in python 3.13.\n",
     "\n",
     "The calculations consist of two phases:\n",
     "\n",