Merge pull request #3 from NREL/feature/jit-support

Feature/jit support

Author: c-randall

.github/workflows/ci.yml

@@ -44,16 +44,14 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Spell check
-        run: |
-          pip install codespell
-          codespell --config .github/linters/.codespellrc
-          
+      - name: Install nox
+        run: pip install nox
+
       - name: Code format
-        run: |
-          pip install flake8
-          flake8 --config .github/linters/.flake8 src
-          flake8 --config .github/linters/.flake8 tests
+        run: nox -s linter
+
+      - name: Spell check
+        run: nox -s codespell          
 
   test:
     name: (Test ${{ matrix.python-version }}, ${{ matrix.os }})
@@ -73,33 +71,27 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup conda/python
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Setup Python and SUNDIALS
+        uses: mamba-org/setup-micromamba@v2
         with:  # ci_environment.yml specifies sundials version to compile
-          auto-update-conda: true
-          miniconda-version: latest
           environment-file: environments/ci_environment.yml
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sun
-          channels: conda-forge
-          conda-remove-defaults: "true"
+          create-args: python=${{ matrix.python-version }}
 
       - name: Verify environment
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Install scikit-sundae
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          python -m pip install --upgrade nox
+          pip install .[tests]
 
       - name: List info
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
                 
       - name: Pytest
-        run: |
-          pip install pandas pytest
-          pytest .
+        run: nox -s tests -- no-reports

.github/workflows/release.yml

@@ -87,24 +87,19 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup conda/python
-        uses: conda-incubator/setup-miniconda@v3
-        with:  # ci_environment.yml specifies sundials version to compile against
-          auto-update-conda: true
-          miniconda-version: latest
+      - name: Setup Python and SUNDIALS
+        uses: mamba-org/setup-micromamba@v2
+        with:  # ci_environment.yml specifies sundials version to compile
           environment-file: environments/ci_environment.yml
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sun
-          channels: conda-forge
-          conda-remove-defaults: "true"
+          create-args: python=${{ matrix.python-version }}
 
       - name: Install build
         run: pip install build
 
       - name: List info
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Set up environment variables for MacOS
         if: runner.os == 'macOS'
@@ -153,9 +148,9 @@ jobs:
         env:  # Remove known SUNDIALS header and lib paths
           DYLD_LIBRARY_PATH:
         run: |
-          conda uninstall sundials
-          conda create -n test python=${{ matrix.python-version }}
-          conda activate test
+          micromamba remove sundials
+          micromamba create -n test python=${{ matrix.python-version }}
+          micromamba activate test
 
           python -m pip install --upgrade pip
           pip install wheels/*.whl -v
@@ -188,16 +183,11 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup conda/python
-        uses: conda-incubator/setup-miniconda@v3
-        with:  # ci_environment.yml specifies sundials version to compile against
-          auto-update-conda: true
-          miniconda-version: latest
+      - name: Setup Python and SUNDIALS
+        uses: mamba-org/setup-micromamba@v2
+        with:  # ci_environment.yml specifies sundials version to compile
           environment-file: environments/ci_environment.yml
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sun
-          channels: conda-forge
-          conda-remove-defaults: "true"
+          create-args: python=${{ matrix.python-version }}
 
       - name: Install build
         run: pip install build

CHANGELOG.md

@@ -3,8 +3,10 @@
 ## [Unreleased](https://github.com/NREL/scikit-sundae/)
 
 ### New Features
+- Changed signature inspections to support decorated `jit` functions ([PR #3](https://github.com/NREL/scikit-sundae/pull/3))
 
 ### Optimizations
+- Use `micromamba` instead of `miniconda` in CI ([PR #3](https://github.com/NREL/scikit-sundae/pull/3))
 
 ### Bug Fixes
 

README.md

@@ -100,9 +100,9 @@ For convenience, we also provide the following for your BibTex:
 ```
 
 ## Acknowledgements
-scikit-SUNDAE was originally inspired by [scikits.odes](https://scikits-odes.readthedocs.io/) which also offers Python bindings to SUNDIALS. The API for scikit-SUNDAE was mostly adopted from scikits.odes; however, all of our source code is original. If you are comparing the two:
+scikit-SUNDAE was originally inspired by [scikits-odes](https://scikits-odes.readthedocs.io/) which also offers Python bindings to SUNDIALS. The API for scikit-SUNDAE was mostly adopted from scikits-odes; however, all of our source code is original. If you are comparing the two:
 
-1. **scikits.odes:** includes iterative solvers and some optional solvers (e.g., LAPACK). The package only provides source distributions, so users must configure and compile SUNDAILS on their own.
+1. **scikits-odes:** includes iterative solvers and some optional solvers (e.g., LAPACK). The package only provides source distributions, so users must configure and compile SUNDAILS on their own.
 2. **scikit-SUNDAE:** includes more flexible events function capabilities (e.g., direction detection and terminal flags), scipy-like output, and provides both binary and source distributions. Iterative and optional solvers are not available.
 
 Our binary distributions include pre-compiled dynamic SUNDIALS libraries. These are self-contained and will not affect other, existing installations you may already have. To be in compliance with SUNDIALS distribution requirements, all scikit-SUNDAE distributions include a copy of the [SUNDIALS license](https://github.com/LLNL/sundials/blob/main/LICENSE).

docs/jupyter_execute/4ac9fb6696fe831a1e43e8f3befd4a7a2eb462ff634d84e144e077bdbed7c1eb.png

@@ -21,8 +21,8 @@ sksundae
 
    Documentation is accessible via Python's ``help()`` function which prints
    docstrings from a package, module, function, class, etc. You can also access
-   the documentation by visiting the website, hosted through GitHub pages. The
-   website includes search functionality and more detailed examples.
+   the documentation by visiting the website, hosted on Read the Docs. The website
+   includes search functionality and more detailed examples.
 
    .. rubric:: Acknowledgements
 
@@ -34,10 +34,10 @@ sksundae
    many packages, DAE solvers are not as prevalent.
 
    scikit-SUNDAE started out as a lighter-weight and easy-to-install alternative
-   to `scikits.odes`_, which similarly provides SUNDIALS bindings, but requires
+   to `scikits-odes`_, which similarly provides SUNDIALS bindings, but requires
    building from source. The goal was to offer a simpler installation process,
    with binary distributions that are consistent across major platforms (PyPI and
-   conda). While scikit-SUNDAE's API was mostly modeled after scikits.odes, we
+   conda). While scikit-SUNDAE's API was mostly modeled after scikits-odes, we
    want to point out that our codebase was written from scratch and that this is
    a separate, independent package. During development we prioritized:
 
@@ -52,7 +52,7 @@ sksundae
    Lawrence Livermore National Security and Southern Methodist University. All
    rights reserved.
 
-   .. _scikits.odes: https://scikits-odes.readthedocs.io
+   .. _scikits-odes: https://scikits-odes.readthedocs.io
    .. _conda-forge: https://anaconda.org/conda-forge/sundials
    .. _scipy.integrate: https://docs.scipy.org/doc/scipy/reference/integrate.html
    .. _SUNDIALS license: https://github.com/LLNL/sundials/blob/main/LICENSE

docs/jupyter_execute/52fdfa81d9f85145a87de576c6e53776accd4ccd35fbffc90545a337e3d220f7.png

@@ -47,7 +47,7 @@ Project Origins
 ---------------
 scikit-SUNDAE was written by researchers at the **National Renewable Energy Laboratory (NREL)** primarily to solve physics-based battery models. Modeling in Python typically allows for rapid development and makes codebases more shareable. However, there was an identified gap in Python's numerical computing ecosystem: the lack of accessible DAE solvers. While ODE solvers are widely available in many packages, DAE solvers are not as prevalent.
 
-scikit-SUNDAE started out as a replacement for `scikits.odes <https://scikits-odes.readthedocs.io>`_, which also provides SUNDIALS bindings, but requires building from source. The goal was to offer a simpler installation process, with binary distributions that are consistent across major platforms (PyPI and conda).
+scikit-SUNDAE started out as a replacement for `scikits-odes <https://scikits-odes.readthedocs.io>`_, which also provides SUNDIALS bindings, but requires building from source. The goal was to offer a simpler installation process, with binary distributions that are consistent across major platforms (PyPI and conda).
 
 Roadmap and Future Directions
 -----------------------------

docs/jupyter_execute/67de17182b118574299ee7e6b9ceb6007a00234a90ac238352b935d0c535c2df.png

@@ -97,7 +97,7 @@ Installing scikit-SUNDAE from source is recommended only in the following cases:
 
 .. note:: 
 
-    Please be aware that we do not provide installation support for users compiling or against custom SUNDIALS builds. Our package is built and tested against releases available on conda-forge, and we cannot guarantee compatibility with custom builds. We simply include this in the installation instructions for those interested. However, you are on your own if the package does not compile against your custom-configured SUNDIALS. In you experience issues, we recommend compiling against SUNDIALS releases from conda-forge instead, which we do provide support for. 
+    Please be aware that we do not provide installation support for users compiling against custom SUNDIALS builds. Our package is built and tested against releases available on conda-forge, and we cannot guarantee compatibility with custom builds. We simply include this in the installation instructions for those interested. However, you are on your own if the package does not compile against your custom configuration. In you experience issues, we recommend compiling against SUNDIALS releases from conda-forge instead, which we provide support for. 
 
 Instructions
 ^^^^^^^^^^^^

docs/jupyter_execute/6d817044928ebbaf1835b92d5d5d4b64234959af9202990d7bc4f46891cb0667.png

@@ -34,11 +34,11 @@ Acknowledgements
 ================
 We extend our appreciation to the developers and maintainers of the SUNDIALS project for their exceptional work in creating a robust, reliable, and open-source suite of solvers. Full details on the SUNDIALS license and copyright information can be found `here <https://github.com/LLNL/sundials/blob/main/LICENSE>`_.
 
-We also acknowledge the `scikits.odes <https://scikits-odes.readthedocs.io/>`_ package, which similarly provides Python bindings to SUNDIALS. While scikit-SUNDAE's API was largely modeled after scikits.odes to maintain a familiar structure, it is important to note that scikit-SUNDAE is an independently developed package, sharing no source code with scikits.odes.
+We also acknowledge the `scikits-odes <https://scikits-odes.readthedocs.io/>`_ package, which similarly provides Python bindings to SUNDIALS. While scikit-SUNDAE's API was largely modeled after scikits-odes to maintain a familiar structure, it is important to note that scikit-SUNDAE is an independently developed package, sharing no source code with scikits-odes.
 
-If you are comparing scikits.odes to scikit-SUNDAE, you should consider the following differences:
+If you are comparing scikits-odes to scikit-SUNDAE, you should consider the following differences:
 
-* **scikits.odes** includes iterative solvers and some optional solvers (e.g., LAPACK). The package only provides source distributions, so users must configure and compile SUNDAILS on their own.
+* **scikits-odes** includes iterative solvers and some optional solvers (e.g., LAPACK). The package only provides source distributions, so users must configure and compile SUNDAILS on their own.
 * **scikit-SUNDAE** provides more flexible events function capabilities (e.g., direction detection and terminal flags), scipy-like output, and provides both binary and source distributions. Users not already familiar with SUNDIALS will likely prefer scikit-SUNDAE due to the streamlined installation process.
 
 scikit-SUNDAE was authored by the National Renewable Energy Laboratory (NREL), operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE). The views expressed in the project and documentation do not necessarily represent the views of the DOE or the U.S. Government.

docs/jupyter_execute/721f67fdb932b7a33615860b9dcddd09b01eb72e5adda3ecee09563eaa62f0e7.png

@@ -5,9 +5,11 @@
 
 import nox
 
+nox.options.sessions = []
+
 
 @nox.session(name='cleanup', python=False)
-def run_cleanup(_):
+def run_cleanup(_) -> None:
     """Use os/shutil to remove some files/directories"""
 
     if os.path.exists('.coverage'):
@@ -20,14 +22,16 @@ def run_cleanup(_):
 
 
 @nox.session(name='linter', python=False)
-def run_flake8(session):
+def run_flake8(session: nox.Session) -> None:
     """
     Run flake8 with the github config file
 
     Use the optional 'format' argument to run autopep8 prior to the linter.
 
     """
 
+    session.run('pip', 'install', '--upgrade', '--quiet', 'flake8')
+
     if 'format' in session.posargs:
         session.run('autopep8', '.', '--in-place', '--recursive',
                     '--global-config=.github/linters/.flake8')
@@ -36,7 +40,7 @@ def run_flake8(session):
 
 
 @nox.session(name='codespell', python=False)
-def run_codespell(session):
+def run_codespell(session: nox.Session) -> None:
     """
     Run codespell with the github config file
 
@@ -45,16 +49,17 @@ def run_codespell(session):
 
     """
 
-    command = ['codespell', '--config=.github/linters/.codespellrc']
+    session.run('pip', 'install', '--upgrade', '--quiet', 'codespell')
 
+    command = ['codespell', '--config=.github/linters/.codespellrc']
     if 'write' in session.posargs:
         command.insert(1, '-w')
 
     session.run(*command)
 
 
 @nox.session(name='spellcheck', python=False)
-def run_spellcheck(session):
+def run_spellcheck(session: nox.Session) -> None:
     """
     Run codespell with docs files included
 
@@ -74,7 +79,7 @@ def run_spellcheck(session):
 
 
 @nox.session(name='tests', python=False)
-def run_pytest(session):
+def run_pytest(session: nox.Session) -> None:
     """
     Run pytest and generate test/coverage reports
 
@@ -84,14 +89,21 @@ def run_pytest(session):
 
     """
 
-    command = [
-        'pytest',
-        '--cov=src/sksundae',
-        '--cov-report=html:reports/htmlcov',
-        '--cov-report=xml:reports/coverage.xml',
-        '--junitxml=reports/junit.xml',
-        'tests/',
-    ]
+    if 'no-reports' in session.posargs:
+        command = [
+            'pytest',
+            '--cov=src/sksundae',
+            'tests/',
+        ]
+    else:
+        command = [
+            'pytest',
+            '--cov=src/sksundae',
+            '--cov-report=html:reports/htmlcov',
+            '--cov-report=xml:reports/coverage.xml',
+            '--junitxml=reports/junit.xml',
+            'tests/',
+        ]
 
     for arg in session.posargs:
         if arg.startswith('parallel='):
@@ -105,7 +117,7 @@ def run_pytest(session):
 
 
 @nox.session(name='badges', python=False)
-def run_genbadge(session):
+def run_genbadge(session: nox.Session) -> None:
     """Run genbadge to make test/coverage badges"""
 
     session.run(
@@ -122,7 +134,7 @@ def run_genbadge(session):
 
 
 @nox.session(name='docs', python=False)
-def run_sphinx(session):
+def run_sphinx(session: nox.Session) -> None:
     """
     Run spellcheck and then use sphinx to build docs
 
@@ -148,7 +160,7 @@ def run_sphinx(session):
 
 
 @nox.session(name='pre-commit', python=False)
-def run_pre_commit(session):
+def run_pre_commit(session: nox.Session) -> None:
     """
     Run all linters/tests and make new badges
 
@@ -165,7 +177,7 @@ def run_pre_commit(session):
 
 
 @nox.session(name='rebuild', python=False)
-def run_build_ext(session):
+def run_build_ext(session: nox.Session) -> None:
     """
     Rebuilds the Cython extensions in place
 
@@ -177,4 +189,5 @@ def run_build_ext(session):
 
     """
 
+    session.run('pip', 'install', '--upgrade', '--quiet', 'cython')
     session.run('python', 'setup.py', 'build_ext', '--inplace')