Merge pull request #22 from yb6599/master

CI update

Author: kmanohar

.github/workflows/main.yml

@@ -0,0 +1,85 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CI
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+
+jobs:
+  linting:
+    name: Linting
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Linting
+        run: |
+          pip install pre-commit
+          pre-commit run --all-files
+
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: build
+      run: pip install .
+    - name: test import
+      run: python -c "import pysensors"
+  
+  tests:
+      name: Tests
+      needs: linting
+      runs-on: ubuntu-latest
+      strategy:
+          fail-fast: false
+          max-parallel: 4
+          matrix:
+            python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+      steps:
+        - uses: actions/checkout@v4
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v5
+          with:
+            python-version: ${{ matrix.python-version }}
+        - name: Install dependencies
+          run: |
+            pip install -r requirements-dev.txt
+        - name: Test with pytest
+          run: |
+            pytest tests --cov=pysensors --cov-report=xml
+        - name: Upload coverage to Codecov
+          uses: codecov/codecov-action@v5
+          with:
+            token: ${{ secrets.CODECOV_TOKEN }}
+            file: ./coverage.xml
+        - name: Execute feature notebook with papermill
+          run: |
+            pip install papermill
+            cd examples
+            papermill --report-mode pysensors_overview.ipynb out.json
+        - uses: actions/cache@v4
+          with:
+            path: ~/.cache/pip
+            key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}
+            restore-keys: |
+              ${{ runner.os }}-pip-

.github/workflows/run-tests.yml

@@ -17,6 +17,7 @@ coverage.xml
 
 # virtual environment
 venv/*
+env/*
 
 .ipynb_checkpoints
 */.ipynb_checkpoints/*

.gitignore

@@ -1,22 +1,26 @@
- 
 fail_fast: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v5.0.0
   hooks:
     - id: check-added-large-files
       args: ["--maxkb=775"]
     - id: check-merge-conflict
-- repo: https://github.com/asottile/reorder_python_imports
-  rev: v3.8.2
+- repo: https://github.com/PyCQA/isort
+  rev: 5.12.0
   hooks:
-    - id: reorder-python-imports
-- repo: https://github.com/ambv/black
-  rev: 22.8.0
+    - id: isort
+      args: [--profile=black]
+- repo: https://github.com/psf/black
+  rev: 25.1.0
   hooks:
     - id: black
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.9.2
+-   repo: https://github.com/sphinx-contrib/sphinx-lint
+    rev: v0.6.1
+    hooks:
+    - id: sphinx-lint
+- repo: https://github.com/pycqa/flake8
+  rev: 7.1.1
   hooks:
     - id: flake8
       args: ["--config=setup.cfg"]

.pre-commit-config.yaml

@@ -32,11 +32,11 @@ PySensors provides the ``SSPOR`` (Sparse Sensor Placement Optimization for Recon
 Take representative examples of the types of data to be reconstructed (in this case polynomials)
 
 .. code-block:: python
-  
+
   x = numpy.linspace(0, 1, 1001)
   data = numpy.vander(x, 11).T  # Create an array whose rows are powers of x
 
-feed them to a ``SSPOR`` instance with 10 sensors, and 
+feed them to a ``SSPOR`` instance with 10 sensors, and
 
 .. code-block:: python
 
@@ -265,7 +265,7 @@ References
 
 .. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.02828/status.svg
     :target: https://doi.org/10.21105/joss.02828
-    
+
 .. |Zenodo| image:: https://zenodo.org/badge/260577702.svg
     :target: https://zenodo.org/badge/latestdoi/260577702
 

README.rst

@@ -14,4 +14,4 @@
 
 
    PySensors @ PyPI <https://pypi.org/project/python-sensors/>
-   Issue Tracker <https://github.com/dynamicslab/pysensors/issues>
+   Issue Tracker <https://github.com/dynamicslab/pysensors/issues>

docs/index.rst

@@ -1,15 +1,13 @@
-from pkg_resources import DistributionNotFound
-from pkg_resources import get_distribution
+from importlib.metadata import PackageNotFoundError, distribution
 
 try:
-    __version__ = get_distribution("python-sensors").version
-except DistributionNotFound:
+    __version__ = distribution("python-sensors").version
+except PackageNotFoundError:
     pass
 
 from .classification import SSPOC
 from .reconstruction import SSPOR
 
-
 __all__ = [
     # Modules:
     "basis",

examples/classification.ipynb

@@ -1,6 +1,6 @@
+from ._custom import Custom
 from ._identity import Identity
 from ._random_projection import RandomProjection
 from ._svd import SVD
-from ._custom import Custom
 
-__all__ = ["Identity", "SVD", "RandomProjection","Custom"]
+__all__ = ["Identity", "SVD", "RandomProjection", "Custom"]