Revert "Adopt pixi for environment management and modernize CI (#493)"

This reverts commit dec571e.

Author: martin-springer

.github/workflows/nbval.yaml

@@ -18,16 +18,23 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: prefix-dev/setup-pixi@v0.8.3
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        environments: dev
-    - name: Validate notebook output
+        python-version: "3.12"
+    - name: Install notebook environment
       run: |
-        pixi run -e dev pytest --nbval --nbval-sanitize-with docs/nbval_sanitization_rules.cfg docs/${{ matrix.notebook-file }}
-    - name: Convert notebook to HTML
+        python -m pip install --upgrade pip wheel
+        pip install --timeout=300 -r requirements.txt -r docs/notebook_requirements.txt .[test]
+    - name: Run notebook and check output
       run: |
+        # --nbval-sanitize-with:  pre-process text to remove irrelevant differences (e.g. warning filepaths)
+        pytest --nbval --nbval-sanitize-with docs/nbval_sanitization_rules.cfg docs/${{ matrix.notebook-file }}
+    - name: Run notebooks again, save files
+      run: |
+        pip install nbconvert[webpdf]
         mkdir docs/artifacts
-        pixi run -e dev jupyter nbconvert --to html --output artifacts/${{ matrix.notebook-file }}.html docs/${{ matrix.notebook-file }}
+        jupyter nbconvert --to html --execute --ExecutePreprocessor.timeout=600 --allow-errors --output artifacts/${{ matrix.notebook-file }}.html docs/${{ matrix.notebook-file }}
     - name: Upload artifacts
       uses: actions/upload-artifact@v4
       with:

.github/workflows/pytest.yaml

@@ -9,60 +9,24 @@ on:
 
 
 jobs:
-  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 }}
+  build:
 
-  test-latest:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        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: "3.11"
+            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]'
       fail-fast: false
 
     steps:
@@ -71,12 +35,13 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install latest versions
+    - name: Install ${{ matrix.env }}
       run: |
         python -m pip install --upgrade pip wheel
-        pip install --timeout=300 --upgrade --upgrade-strategy=eager .[test]
-    - name: Test with pytest (latest)
-      run: python -m pytest --cov=rdtools --cov-report=xml
+        pip install --timeout=300 ${{ matrix.env }}
+    - name: Test with pytest ${{ matrix.env }}
+      run: |
+        python -m pytest --cov=./ --cov-report=xml
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4
       env:

.github/workflows/requirements.yaml

@@ -0,0 +1,29 @@
+name: requirements
+
+on:
+  push:
+    branches:
+    - master
+    - development
+  pull_request:
+
+
+jobs:
+  requirements:
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install notebook environment
+      run: |
+        python -m pip install --upgrade pip wheel
+        pip install --timeout=300 -r requirements.txt -r docs/notebook_requirements.txt

.gitignore

@@ -11,7 +11,6 @@
 .coveralls.yml
 .coverage
 .coverage.*
-coverage.xml
 htmlcov/
 
 # ignore test cache
@@ -39,9 +38,5 @@ rdtools.egg-info*
 
 *.pickle
 
-# pixi environments (local, not committed)
-.pixi/*
-!.pixi/config.toml
-
 # ignore vscode settings
 .vscode/

.pixi.lnk

@@ -25,43 +25,17 @@ 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 3.10+.
+RdTools currently is tested on Python 3.9+.
 
 ## 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, Martin Springer, Kevin Anderson,  Adam Shinn, Kirsten Perry, Ambarish Nag,
-   Mark Mikofski, Jiyang Yan, Sandra Villamar, Will Vining,
+-  Michael G. Deceglie, Kevin Anderson,  Adam Shinn, Ambarish Nag, Mark Mikofski,
+   Martin Springer, Jiyang Yan, Kirsten Perry, 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 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",
+    "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",
     "\n",
     "This notebook works with data from system 4 of the PVDAQ dataset [1]. 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",
     "\n",
@@ -230,7 +230,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -459,9 +459,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "rdtools_313-nb",
+   "display_name": "Python [conda env:rdtools_dev]",
    "language": "python",
-   "name": "python3"
+   "name": "conda-env-rdtools_dev-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -473,7 +473,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.12.11"
   }
  },
  "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 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",
+    "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",
     "\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 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",
+    "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",
     "\n",
     "The calculations consist of two phases:\n",
     "\n",

docs/TrendAnalysis_example_NSRDB.ipynb

@@ -7,7 +7,7 @@
     "# Degradation and soiling example\n",
     "\n",
     "\n",
-    "This jupyter notebook is intended to the RdTools trend analysis workflow using the functional API.  In addition, the notebook demonstrates the effects of changes in the workflow. 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]`. These environments and examples are tested with Python 3.13.\n",
+    "This jupyter notebook is intended to the RdTools trend analysis workflow using the functional API.  In addition, the notebook demonstrates the effects of changes in the workflow. For a consistent experience, we recommend installing the specific versions of packages used to develop this notebook. This can be achieved in your environment by running `pip install -r requirements.txt` followed by `pip install -r docs/notebook_requirements.txt` from the base directory. (RdTools must also be separately installed.) These environments and examples are tested with Python 3.12.\n",
     "\n",
     "The calculations consist of several steps illustrated here:\n",
     "<ol start=\"0\">\n",
@@ -94371,7 +94371,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "rdtools_313-nb",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -94385,7 +94385,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,