added new examples to notebook 17

setup.cfg → .flake8

@@ -18,7 +18,3 @@ import-order-style = smarkets
 statistics = True
 count = True
 verbose = 1
-# format = [%(code)s] %(text)s @ %(path)s:%(row)d:%(col)d
-
-[codespell]
-ignore-words-list = pres,nd

.github/workflows/draft-pdf.yml

@@ -6,15 +6,15 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
           # This should be the path to the paper within your repo.
           paper-path: docs/JOSS2/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v3
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/main.yml

@@ -1,17 +1,23 @@
 name: Tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
 
 jobs:
   Linting:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.7
+          python-version: "3.9"
       - name: Linting
         run: |
           pip install pre-commit
@@ -23,30 +29,32 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: ["3.8", "3.10"]
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip install -r requirements-dev.txt
-        pip install sympy # needed for notebook 9, but not required for pysindy
+        pip install --upgrade pip
+        pip install .[dev,miosr,cvxpy]
     - name: Build the docs
       # Not exactly how RTD does it, but close.
       run: |
+        sudo apt-get update -y
         sudo apt-get install pandoc
+        pip install .[docs]
         cd docs
         python -m sphinx -T -E -W -b html -d _build/doctrees . _build/html
         cd ..
     - name: Test with pytest
       run: |
-        pytest test --cov=pysindy --cov-report=xml
+        coverage run --source=pysindy -m pytest test  && coverage xml
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -55,7 +63,7 @@ jobs:
         pip install papermill
         cd examples
         papermill --report-mode 1_feature_overview.ipynb out.json
-    - uses: actions/cache@v1
+    - uses: actions/cache@v3
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-dev.txt') }}

.github/workflows/release.yml

@@ -10,17 +10,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v1
+        uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.7
-      - name: Install dependencies
-        run: pip install wheel
+          python-version: "3.9"
+      - name: Install Build
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
       - name: Build package
-        run: python setup.py sdist bdist_wheel
+        run: python -m build .
       - name: Upload package
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@v1.8.5
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -3,6 +3,7 @@ dist
 *.egg-info
 commit-msg
 todo
+poetry.lock
 
 # Environments
 .env

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
   rev: 5.0.4
   hooks:
     - id: flake8
-      args: ["--config=setup.cfg"]
+      args: ["--config=.flake8"]
 -   repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.9.0
     hooks:
@@ -34,11 +34,12 @@ repos:
     hooks:
     - id: sphinx-lint
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
+    rev: v2.2.4
     hooks:
     -   id: codespell
         types_or: [python, rst, markdown]
-        args: ["-L hist"]
+        additional_dependencies: [tomli]
+        args: ["--toml", "pyproject.toml"]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:

.readthedocs.yml

@@ -4,6 +4,9 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  version: 3.7
+  version: 3.8
   install:
-    - requirements: requirements-dev.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.rst

@@ -38,7 +38,7 @@ The approximation problem to be solved can then be compactly written as
 
 Each row of this matrix equation corresponds to one coordinate function of ``f(x)``.
 SINDy employs sparse regression techniques to find a solution ``Xi`` with sparse column vectors.
-For a more in-depth look at the mathematical foundations of SINDy, please see our `introduction to SINDy <https://pysindy.readthedocs.io/en/latest/examples/2_introduction_to_sindy.html>`__.
+For a more in-depth look at the mathematical foundations of SINDy, please see our `introduction to SINDy <https://pysindy.readthedocs.io/en/latest/examples/2_introduction_to_sindy/example.html>`__.
 
 Relation to PySINDy
 ^^^^^^^^^^^^^^^^^^^
@@ -93,7 +93,7 @@ which prints the following
   x' = -2.000 x
   y' = 1.000 y
 
-PySINDy provides numerous other features not shown here. We recommend the `feature overview <https://pysindy.readthedocs.io/en/latest/examples/1_feature_overview.html>`__ section of the documentation for a more exhaustive summary of additional features.
+PySINDy provides numerous other features not shown here. We recommend the `feature overview <https://pysindy.readthedocs.io/en/latest/examples/1_feature_overview/example.html>`__ section of the documentation for a more exhaustive summary of additional features.
 
 Installation
 ------------
@@ -121,23 +121,41 @@ Then, to install the package, run
 
   pip install .
 
-If you do not have pip you can instead use
+If you do not have root access, you should add the ``--user`` option to the above lines.
+
+Caveats
+^^^^^^^
+
+To run the unit tests, or example notebooks, you should install the dev-dependencies with:
 
 .. code-block:: bash
 
-  python setup.py install
+  pip install pysindy[dev]
 
-If you do not have root access, you should add the ``--user`` option to the above lines.
+or if you are installing from a local copy
 
-Caveats
-^^^^^^^
-If you would like to use the ``SINDy-PI`` optimizer, the ``Trapping SINDy`` optimizer (TrappingSR3), or the other SR3 optimizations with inequality constraints, you will also need to install the cvxpy package, e.g. with ``pip install cvxpy``.
+.. code-block:: bash
+
+  pip install .[dev]
+
+To build a local copy of the documentation, you should install the docs-dependencies with:
+
+.. code-block:: bash
+
+  pip install pysindy[docs]
+
+If you are looking to use convex optimization provided by `cvxpy <https://github.com/cvxpy/cvxpy>`__, then you have to install
+
+.. code-block:: bash
+
+    pip install pysindy[cvxpy]
 
-To run the unit tests, example notebooks, or build a local copy of the documentation, you should install the additional dependencies in ``requirements-dev.txt``
+to utilize Mixed-Integer Optimized Sparse Regression (MIOSR) via `GurobiPy <https://pypi.org/project/gurobipy/>`__, you
+require
 
 .. code-block:: bash
 
-  pip install -r requirements-dev.txt
+    pip install pysindy[miosr]
 
 
 Documentation
@@ -178,32 +196,58 @@ You can optimize your notebook for testing by checking ``__name__``.  When our t
 
 Contributing code
 ^^^^^^^^^^^^^^^^^
-We welcome contributions to PySINDy. To contribute a new feature please submit a pull request. To get started we recommend installing the packages in ``requirements-dev.txt`` via
+We welcome contributions to PySINDy. To contribute a new feature please submit a pull request. To get started we recommend installing an editable ``dev`` version from a local clone via
 
 .. code-block:: bash
 
-    pip install -r requirements-dev.txt
+    pip install -e .[dev]
 
 This will allow you to run unit tests and automatically format your code. To be accepted your code should conform to PEP8 and pass all unit tests. Code can be tested by invoking
 
 .. code-block:: bash
 
     pytest
 
-We recommend using ``pre-commit`` to format your code. Once you have staged changes to commit
+We recommend using ``pre-commit`` to format your code. The easiest approach is to install pre-commit via
+
+.. code-block:: bash
+
+    pre-commit install
+
+After which pre-commit will automatically check all future commits. Once you have staged changes to commit
 
 .. code-block:: bash
 
     git add path/to/changed/file.py
 
-you can run the following to automatically reformat your staged code
+Pre-commit will then automatically run all checks against your committed code. If you want to trigger this manually, you can run the following to automatically reformat your staged code
 
 .. code-block:: bash
 
     pre-commit
 
 Note that you will then need to re-stage any changes ``pre-commit`` made to your code.
 
+Building documentation requires the ``docs`` dependencies, which can be installed with either
+
+.. code-block:: bash
+
+    pip install pysindy[docs]
+
+or with
+
+.. code-block:: bash
+
+    pip install .[docs]
+
+for a local clone of the repository. Once installed, run
+
+.. code-block:: bash
+
+    python -m sphinx -TEb html -d _build/doctrees -D language=en . ./build
+
+Or check the build step in the most recent CI run or [RTD build](https://readthedocs.org/projects/pysindy/builds/).
+
 There are a number of SINDy variants and advanced functionality that would be great to implement in future releases:
 
 1. Bayesian SINDy, for instance that from Hirsh, Seth M., David A. Barajas-Solano, and J. Nathan Kutz. "Sparsifying Priors for Bayesian Uncertainty Quantification in Model Discovery." arXiv preprint arXiv:2107.02107 (2021).

examples/11_SSR_FROLS_examples.ipynb

@@ -11,7 +11,7 @@
     "Jupyter notebook written by Alan Kaptanoglu and Jared Callaham.\n",
     "\n",
     "An interactive version of this notebook is available on binder\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7?filepath=examples/11_SSR_FROLS_examples.ipynb)"
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7.3?filepath=examples/11_SSR_FROLS_examples.ipynb)"
    ]
   },
   {

examples/13_ensembling.ipynb

@@ -6,12 +6,12 @@
    "source": [
     "# Ensembling Feature Overview\n",
     "Ensembling is a fancy name for sub-sampling the data and generating $n_\\text{models}$ from regressing onto each of these sub-samples. In practice this helps to robustify the regressions against outliers and other issues. We highly recommend checking out the following paper for understanding the usefulness of these methods against noisy data: \n",
-    "#### Fasel, Urban, et al. \"Ensemble-SINDy: Robust sparse model discovery in the low-data, high-noise limit, with active learning and control.\" arXiv preprint arXiv:2111.10992 (2021). https://arxiv.org/abs/2111.10992\n",
+    "#### Fasel, U., Kutz, J. N., Brunton, B. W., & Brunton, S. L. (2022). Ensemble-SINDy: Robust sparse model discovery in the low-data, high-noise limit, with active learning and control. Proceedings of the Royal Society A, 478(2260), 20210904. https://arxiv.org/abs/2111.10992\n",
     "\n",
     "This notebook provides an overview of the basic and advanced functionality of using ensemble methods in PySINDy. Ensembling robustifies the SINDy method. Written by Alan Kaptanoglu and Urban Fasel. \n",
     "\n",
     "An interactive version of this notebook is available on binder\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7?filepath=examples/13_ensembling.ipynb)\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7.3?filepath=examples/13_ensembling.ipynb)\n",
     "\n",
     "There are many variants of ensembling/subsampling strategies and post-processing methods. We will show the following useful variants below: <br> <br>\n",
     "Ensembling: <br>\n",

examples/14_cavity_flow.ipynb

@@ -25,7 +25,7 @@
     "This Jupyter notebook example is written by Jared Callaham and demonstrates the use of SINDy to learn a model for the quasiperiodic dynamics in a shear-driven cavity at Re=7500, following [Callaham, Brunton, and Loiseau (2021)](https://arxiv.org/abs/2106.02409).  It will focus on working through a relatively involved fluid dynamics example, rather than comparing optimizers, libraries, etc.  This example also includes some other more advanced SINDy \"tricks\" like using dynamic mode decomposition to rotate the generalized coordinates and co-opting some of the SINDy infrastructure to perform nonlinear dimensionality reduction.\n",
     "\n",
     "An interactive version of this notebook is available on binder\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7?filepath=examples/14_cavity_flow.ipynb)\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7.3?filepath=examples/14_cavity_flow.ipynb)\n",
     "\n",
     "As in the cylinder wake example (see notebook 3), the reduced-order model appproximates the 2D time-varying velocity field $\\mathbf{u}(\\mathbf{x}, t)$ with the POD expansion\n",
     "$$\n",

examples/15_pysindy_lectures.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "This notebook is a summary of the PySINDy YouTube lectures found [here](https://www.youtube.com/playlist?list=PLN90bHJU-JLoOfEk0KyBs2qLTV7OkMZ25). \n",
     "An interactive version of this notebook is available on binder\n",
-    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7?filepath=examples/15_pysindy_lectures.ipynb)\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7.3?filepath=examples/15_pysindy_lectures.ipynb)\n",
     "\n",
     "These examples show how to use the SINDy method in practice, addressing the following practical questions:\n",
     "1. How does one choose the thresholding parameter $\\lambda$?\n",
@@ -2229,7 +2229,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -2243,7 +2243,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

examples/16_noise_robustness/16_benchmark_paper.ipynb

@@ -13,7 +13,10 @@
     "\n",
     "In addition, we investigate how Pareto-optimal models generated from sparse system identification methods depend on the dynamical properties of the equations, finding to leading order that the performance of these methods is independent of the dynamical properties of these equations, including the amount of chaos, scale separation, degree of nonlinearity, and, surprisingly, the syntactic complexity.\n",
     " \n",
-    "We will use the dysts database, containingn over 100 chaotic systems. We will investigate a subset of the systems that are polynomially nonlinear, with highest polynomial degree <= 4. All of the following 70 systems are bounded and exhibit strange attractors."
+    "We will use the dysts database, containingn over 100 chaotic systems. We will investigate a subset of the systems that are polynomially nonlinear, with highest polynomial degree <= 4. All of the following 70 systems are bounded and exhibit strange attractors.\n",
+    "\n",
+    "An interactive version of this notebook is available on binder\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7.3?filepath=examples/16_noise_robustness/16_benchmark_paper.ipynb)"
    ]
   },
   {

examples/16_noise_robustness/optimizer_comparison.ipynb

@@ -7,7 +7,10 @@
     "## Full optimizer comparison\n",
     "Notebook written by Lanyue Zhang and Alan Kaptanoglu\n",
     "\n",
-    "This post-processing file takes the results from Pareto-optimal scans of the dysts database with different optimizers and varying amounts of noise, as in the example Jupyter notebook 16_benchmark_paper.ipynb. The primary goal of this notebook is to fully reproduce the results shown in our new system identification benchmark paper."
+    "This post-processing file takes the results from Pareto-optimal scans of the dysts database with different optimizers and varying amounts of noise, as in the example Jupyter notebook 16_benchmark_paper.ipynb. The primary goal of this notebook is to fully reproduce the results shown in our new system identification benchmark paper.\n",
+    "\n",
+    "An interactive version of this notebook is available on binder\n",
+    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dynamicslab/pysindy/v1.7.3?filepath=examples/16_noise_robustness/optimizer_comparison.ipynb)"
    ]
   },
   {

examples/17_parameterized_pattern_formation/.gitignore

@@ -0,0 +1,2 @@
+*.pdf
+data