Commit c599bb85 authored by Ana Cukarska's avatar Ana Cukarska
Browse files

Merge branch 'update-python-3-12' into 'master' 

Updating to python 3.12

See merge request !129
parents e4907dc9 bdd1fd71

CONTRIBUTORS

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@@ -2,6 +2,7 @@ Software maintainer 
-------------------

# Ordered alphabetically by last name.

Last name, First name; <email>; Years of contribution

Cukarska, Ana; <ana.cukarska@tum.de>; 2026-

Dietrich, Felix; <felix.dietrich@tum.de>; 2019-

Lehmberg, Daniel; <daniel.lehmberg@hm.edu>; 2019-

Makefile

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@@ -148,7 +148,7 @@ install_deps: venv 
#install_devdeps: @ Install (or update) development dependencies in virtual environment specifed in file "requirements-dev.txt".

install_devdeps: venv

	$(ACTIVATE_VENV); \

	python -m pip install --upgrade pip wheel setuptools twine; \

	python -m pip install --upgrade pip wheel setuptools importlib twine; \

	python -m pip install -r requirements-dev.txt



#install_docdeps: @ Install non-Python dependencies to build datafold's documentation (requires admin rights or set, DOCKER_ENVIRONMENT=true).
@@ -157,14 +157,14 @@ ifeq ($(OS),Linux) 
ifeq ($(IS_DOCKER),) # true if IS_DOCKER is empty

	@# TODO this could be improved to avoid statement duplication... only sudo changes

	sudo apt-get update \

	&& wget "https://github.com/jgm/pandoc/releases/download/3.1.5/pandoc-3.1.5-1-amd64.deb" \

	&& sudo apt -y --no-install-recommends install ./pandoc-3.1.5-1-amd64.deb \

	&& wget "https://github.com/jgm/pandoc/releases/download/3.9/pandoc-3.9-1-amd64.deb" \

	&& sudo apt -y --no-install-recommends install ./pandoc-3.9-1-amd64.deb \

	&& sudo apt -y --no-install-recommends install $(_DOCDEPS) \

	&& rm -f pandoc-3.1.5-1-amd64.deb;

	&& rm -f pandoc-3.9-1-amd64.deb;

else # in docker "sudo" is not available and everything is executed with root

	apt-get update \

	&& wget "https://github.com/jgm/pandoc/releases/download/3.1.5/pandoc-3.1.5-1-amd64.deb" \

	&& apt -y --no-install-recommends install ./pandoc-3.1.5-1-amd64.deb \

	&& wget "https://github.com/jgm/pandoc/releases/download/3.9/pandoc-3.9-1-amd64.deb" \

	&& apt -y --no-install-recommends install ./pandoc-3.9-1-amd64.deb \

	&& apt -y --no-install-recommends install $(_DOCDEPS);

endif

else # OS = Windows

README.rst

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@@ -35,7 +35,7 @@ The package includes: 
  model can handle a sparse kernel matrix and allows setting an arbitrary kernel,

  including the standard Gaussian kernel,

  `continuous k-nearest neighbor kernel <https://arxiv.org/abs/1606.02353>`__, or

  `dynamics-adapted cone kernel <https://cims.nyu.edu/~dimitris/files/Giannakis15_cone_kernels.pdf>`__.

  `dynamics-adapted cone kernel <https://epubs.siam.org/doi/10.1137/140954544>`__.

* Cross-validation. The method ``EDMDCV`` allows model parameters to be optimized with

  cross-validation splittings that account for the temporal order in time series data.

* Methods to perform Model Predictive Control (MPC) with Koopman operator-based methods (

datafold/appfold/tests/test_edmd.py

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@@ -766,7 +766,7 @@ class EDMDTest(unittest.TestCase): 


        diff = inverse_dict - self.sine_wave_tsc

        # sort out the removed rows from Takens (NaN values)

        self.assertTrue((diff.dropna() < 1e-14).all().all())

        self.assertTrue((diff.dropna() < 1e-14).to_numpy().all())



        if plot:

            ax = self.sine_wave_tsc.plot()
@@ -805,7 +805,7 @@ class EDMDTest(unittest.TestCase): 


        diff = inverse_dict - self.sine_wave_tsc

        # sort out the removed rows from Takens (NaN values)

        self.assertTrue((diff.dropna() < 1e-14).all().all())

        self.assertTrue((diff.dropna() < 1e-14).to_numpy().all())



        # test that the fit_param dmd__store_generator_matrix was really passed to the

        # DMD model.

datafold/dynfold/tests/test_dmd.py

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@@ -726,7 +726,7 @@ class DMDTest(unittest.TestCase): 


        # also fails if there are changes in the implementation that includes small

        # numerical noise

        self.assertLessEqual(np.abs(score_dmd - score_gdmd), 9.81e-11)

        self.assertLessEqual(np.abs(score_dmd - score_gdmd), 9.81e-10)



        if plot:

            print(score_dmd)
@@ -898,7 +898,9 @@ class DMDTest(unittest.TestCase): 
        expected = DMDStandard().fit(harmonic)

        actual = DMDStandard().fit(combined, sample_weights=weights)



        nptest.assert_array_equal(expected.eigenvalues_, actual.eigenvalues_)

        nptest.assert_almost_equal(

            expected.eigenvalues_, actual.eigenvalues_, decimal=16

        )



    def test_resdmd(self):

        dim = 7