diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 1e60a3f3300..1aaa04b654c 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: bbdba7762d98ab5e33b2739d850c8034fb4a270a611f78498151cbf856de1886 +# input_hash: 31d323d670a8deec16e2186403aa54ab8464102ac712829e12e62d80bc50f272 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 @@ -12,7 +12,8 @@ https://conda.anaconda.org/conda-forge/linux-64/git-lfs-3.4.0-ha770c72_0.conda#8 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_1.conda#acfb4817400db5804030a3a7ef7909a1 https://conda.anaconda.org/conda-forge/noarch/nomkl-1.0-h5ca1d4c_0.tar.bz2#9a66894dfd07c4510beb6b3f9672ccc0 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-3_cp38.conda#2f3f7af062b42d664117662612022204 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda#c2e2630ddb68cf52eec74dc7dfab20b5 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_1.conda#8bb001683321dcbde117a7337b5aace7 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d @@ -31,7 +32,7 @@ https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f 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-https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.conda#b6a0939e7b6b3a854b8c8f04606da1a7 +https://conda.anaconda.org/conda-forge/osx-64/pygraphviz-1.11-py311hc6eba27_0.conda#fed0a15be9e09c83aba369a5049655c1 +https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.4.21-pyhd8ed1ab_0.conda#673319f48d9b160c8056783d301e090c https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.7.3-pyhd8ed1ab_0.conda#969249eb7c2f7a9b820520a355dc7d04 https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.8.0-pyhd8ed1ab_0.conda#1dba1a577df2625a24667612a069e91c https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.2.0-pyhd8ed1ab_0.conda#38589f4104d11f2a59ff01a9f4e3bfb3 @@ -301,8 +293,23 @@ https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.8.0-pyhd8ed1ab_0.conda https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda#67e0fe74c156267d9159e9133df7fd37 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda#80bb1cc3b540790cb5afecd73c2d4d1f https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.0.0-pyhb4ecaf3_1.conda#a0be31e9bd84d6eae87cdbf74c56b90b -https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.3-pyhd8ed1ab_0.conda#0dbaa7d08d3d79b2a1a4dd6a02cc4581 https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.3-pyhd8ed1ab_0.conda#1f2d368cde97926b5e351d1a0286bb1e https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.8.0-pyhd8ed1ab_0.conda#518b05adab6cfe6ea249319932d9d4a3 https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917 +https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.3-pyhd8ed1ab_0.conda#0dbaa7d08d3d79b2a1a4dd6a02cc4581 +https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.5.0-pyhd8ed1ab_0.tar.bz2#3c275d7168a6a135329f4acb364c229a +https://conda.anaconda.org/conda-forge/noarch/recommonmark-0.7.1-pyhd8ed1ab_0.tar.bz2#b3becf9905b8c7ba839072f65e693253 +https://conda.anaconda.org/conda-forge/noarch/sphinx-automodapi-0.16.0-pyh6ff6d48_0.conda#c2dfb5d38d19546cf818d75801c21ed0 +https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.14.0-pyhd8ed1ab_0.conda#b3788794f88c9512393032e448428261 +https://conda.anaconda.org/conda-forge/noarch/sphinx-jsonschema-1.19.1-pyhd8ed1ab_0.tar.bz2#d340bddca07283d3362b0e46b1791568 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.7-pyhd8ed1ab_0.conda#aebfabcb60c33a89c1f9290cab49bc93 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.6.1-pyhd8ed1ab_1.conda#109cf3a7c844834267057e80b4f4eae3 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.5-pyhd8ed1ab_0.conda#ebf08f5184d8eaa486697bc060031953 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.4-pyhd8ed1ab_0.conda#a9a89000dfd19656ad004b937eeb6828 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda#914897066d5873acfb13e75705276ad1 +https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.conda#b6a0939e7b6b3a854b8c8f04606da1a7 +https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-1.3.0-pyha770c72_0.conda#a615c369167e508293d8409973b34863 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.6-pyhd8ed1ab_0.conda#cf5c9649272c677a964a7313279e3a9b +https://conda.anaconda.org/conda-forge/noarch/sphinx-5.3.0-pyhd8ed1ab_0.tar.bz2#f9e1fcfe235d655900bfeb6aee426472 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0.conda#0612e497d7860728f2cda421ea2aec09 diff --git a/tardis/io/atom_data/base.py b/tardis/io/atom_data/base.py index 32548134df0..1db66d58e09 100644 --- a/tardis/io/atom_data/base.py +++ b/tardis/io/atom_data/base.py @@ -168,7 +168,7 @@ def from_hdf(cls, fname=None): for name in cls.hdf_names: try: - dataframes[name] = store[name] + dataframes[name] = store.select(name) except KeyError: logger.debug(f"Dataframe does not contain {name} column") nonavailable.append(name) @@ -287,25 +287,33 @@ def __init__( if u.u.cgs == const.u.cgs: atom_data.loc[:, "mass"] = Quantity( atom_data["mass"].values, "u" - ).cgs + ).cgs.value else: - atom_data.loc[:, "mass"] = atom_data["mass"].values * const.u.cgs + atom_data.loc[:, "mass"] = ( + atom_data["mass"].values * const.u.cgs.value + ) # Convert ionization energies to CGS ionization_data = ionization_data.squeeze() - ionization_data[:] = Quantity(ionization_data[:], "eV").cgs + ionization_data[:] = Quantity(ionization_data[:], "eV").cgs.value # Convert energy to CGS - levels.loc[:, "energy"] = Quantity(levels["energy"].values, "eV").cgs + levels.loc[:, "energy"] = Quantity( + levels["energy"].values, "eV" + ).cgs.value # Create a new columns with wavelengths in the CGS units - lines["wavelength_cm"] = Quantity(lines["wavelength"], "angstrom").cgs + lines["wavelength_cm"] = Quantity( + lines["wavelength"], "angstrom" + ).cgs.value # SET ATTRIBUTES self.atom_data = atom_data self.ionization_data = ionization_data self.levels = levels + # Not sure why this is need - WEK 17 Sep 2023 + self.levels.energy = self.levels.energy.astype(np.float64) self.lines = lines # Rename these (drop "_all") when `prepare_atom_data` is removed! @@ -522,7 +530,9 @@ def prepare_atom_data( self.macro_atom_data.loc[:, "destination_level_idx"] = -1 if self.yg_data is not None: - self.yg_data = self.yg_data.loc[self.selected_atomic_numbers] + self.yg_data = self.yg_data.reindex( + self.selected_atomic_numbers, level=0 + ) self.nlte_data = NLTEData(self, nlte_species) diff --git a/tardis/io/model/readers/artis.py b/tardis/io/model/readers/artis.py index d05c917a825..d013867cfde 100644 --- a/tardis/io/model/readers/artis.py +++ b/tardis/io/model/readers/artis.py @@ -1,6 +1,6 @@ import numpy as np from astropy import units as u -from numpy import recfromtxt +import pandas as pd def read_artis_density(fname): @@ -43,13 +43,15 @@ def read_artis_density(fname): "fe52_fraction", "cr48_fraction", ] - artis_model = recfromtxt( + + artis_model = pd.read_csv( fname, - skip_header=2, + skiprows=2, usecols=(0, 1, 2, 4, 5, 6, 7), - unpack=True, - dtype=[(item, np.float64) for item in artis_model_columns], - ) + dtype={item: np.float64 for item in artis_model_columns}, + names=artis_model_columns, + delim_whitespace=True, + ).to_records(index=False) velocity = u.Quantity(artis_model["velocities"], "km/s").to("cm/s") mean_density = u.Quantity(10 ** artis_model["mean_densities_0"], "g/cm^3")[ diff --git a/tardis/io/tests/test_HDFWriter.py b/tardis/io/tests/test_HDFWriter.py index 6aa3758a489..bc7be113880 100644 --- a/tardis/io/tests/test_HDFWriter.py +++ b/tardis/io/tests/test_HDFWriter.py @@ -1,11 +1,8 @@ -import os - import numpy as np import pandas as pd -import pandas.util.testing as pdt import pytest from astropy import units as u -from astropy.tests.helper import assert_quantity_allclose + from numpy.testing import assert_almost_equal, assert_array_almost_equal from tardis.io.util import HDFWriterMixin @@ -61,6 +58,7 @@ def test_complex_obj_write(tmpdir, attr): actual = MockHDF(attr) actual.to_hdf(fname, path="test", overwrite=True) expected = pd.read_hdf(fname, key="/test/mock_hdf/property").values + assert_array_almost_equal(actual.property, expected) @@ -79,7 +77,8 @@ def test_multi_index_write(tmpdir): actual.to_hdf(fname, path="test", overwrite=True) expected = pd.read_hdf(fname, key="/test/mock_hdf/property") expected = pd.MultiIndex.from_tuples(expected.unstack().values) - pdt.assert_almost_equal(actual.property, expected) + # These are multiindex objects, so we need to compare the values + assert np.all(expected.values == actual.property.values) # Test Quantity Objects diff --git a/tardis/io/tests/test_atomic.py b/tardis/io/tests/test_atomic.py index 70de086d9b0..537f3a033ef 100644 --- a/tardis/io/tests/test_atomic.py +++ b/tardis/io/tests/test_atomic.py @@ -49,7 +49,7 @@ def test_atom_data_levels(levels): def test_atom_data_lines(lines): assert_quantity_allclose( - lines.at[(2, 0, 0, 6), "wavelength_cm"] * u.Unit("cm"), + lines.loc[(2, 0, 0, 6), "wavelength_cm"].values[0] * u.Unit("cm"), 584.335 * u.Unit("Angstrom"), ) diff --git a/tardis/model/base.py b/tardis/model/base.py index fba93a7efbd..5d0d0dd152a 100644 --- a/tardis/model/base.py +++ b/tardis/model/base.py @@ -593,7 +593,7 @@ def from_config(cls, config, atom_data=None): # v boundaries. no_of_shells = len(velocity) - 1 - if temperature: + if temperature is not None: t_radiative = temperature elif config.plasma.initial_t_rad > 0 * u.K: t_radiative = ( diff --git a/tardis/montecarlo/montecarlo_numba/base.py b/tardis/montecarlo/montecarlo_numba/base.py index ada2389f1b5..028a91ff775 100644 --- a/tardis/montecarlo/montecarlo_numba/base.py +++ b/tardis/montecarlo/montecarlo_numba/base.py @@ -1,8 +1,5 @@ from numba import prange, njit, objmode -from numba.np.ufunc.parallel import ( - _get_thread_id as get_thread_id, - get_num_threads, -) +from numba.np.ufunc.parallel import get_thread_id, get_num_threads import numpy as np diff --git a/tardis/montecarlo/montecarlo_numba/formal_integral.py b/tardis/montecarlo/montecarlo_numba/formal_integral.py index 6e2db7bbdde..fbb443e79a1 100644 --- a/tardis/montecarlo/montecarlo_numba/formal_integral.py +++ b/tardis/montecarlo/montecarlo_numba/formal_integral.py @@ -454,7 +454,7 @@ def make_source_function(self): upper_level_index = self.atomic_data.lines.index.droplevel( "level_number_lower" ) - e_dot_lu = pd.DataFrame(Edotlu, index=upper_level_index) + e_dot_lu = pd.DataFrame(Edotlu.values, index=upper_level_index) e_dot_u = e_dot_lu.groupby(level=[0, 1, 2]).sum() e_dot_u_src_idx = macro_ref.loc[e_dot_u.index].references_idx.values diff --git a/tardis/montecarlo/tests/test_spectrum.py b/tardis/montecarlo/tests/test_spectrum.py index 418317f822c..7f31fbcfa2e 100644 --- a/tardis/montecarlo/tests/test_spectrum.py +++ b/tardis/montecarlo/tests/test_spectrum.py @@ -38,7 +38,7 @@ def spectrum(request): request.param["lum"], ) distance = request.param["distance"] - if distance: + if distance is not None: data.distance = distance return data @@ -67,7 +67,7 @@ def test_luminosity_density_lambda(spectrum): def test_flux_nu(spectrum): - if getattr(spectrum, "distance", None): + if getattr(spectrum, "distance", None) is not None: with pytest.warns(DeprecationWarning): test_helper.assert_quantity_allclose( @@ -82,7 +82,7 @@ def test_flux_nu(spectrum): def test_flux_lambda(spectrum): - if getattr(spectrum, "distance", None): + if getattr(spectrum, "distance", None) is not None: with pytest.warns(DeprecationWarning): test_helper.assert_quantity_allclose( diff --git a/tardis/plasma/properties/ion_population.py b/tardis/plasma/properties/ion_population.py index caf4eb81ee4..c70bd06965a 100644 --- a/tardis/plasma/properties/ion_population.py +++ b/tardis/plasma/properties/ion_population.py @@ -53,7 +53,6 @@ class PhiSahaLTE(ProcessingPlasmaProperty): @staticmethod def calculate(g_electron, beta_rad, partition_function, ionization_data): - phis = np.empty( ( partition_function.shape[0] @@ -70,9 +69,9 @@ def calculate(g_electron, beta_rad, partition_function, ionization_data): current_phis = current_block[1:] / current_block[:-1] phis[start_id - i : end_id - i - 1] = current_phis - broadcast_ionization_energy = ionization_data[ + broadcast_ionization_energy = ionization_data.reindex( partition_function.index - ].dropna() + ).dropna() phi_index = broadcast_ionization_energy.index broadcast_ionization_energy = broadcast_ionization_energy.values diff --git a/tardis/plasma/standard_plasmas.py b/tardis/plasma/standard_plasmas.py index 4961d0c6dd6..01e40fde22e 100644 --- a/tardis/plasma/standard_plasmas.py +++ b/tardis/plasma/standard_plasmas.py @@ -278,7 +278,7 @@ def assemble_plasma(config, model, atom_data=None): else: plasma_modules += helium_lte_properties - if model._electron_densities: + if model._electron_densities is not None: electron_densities = pd.Series(model._electron_densities.cgs.value) if config.plasma.helium_treatment == "numerical-nlte": property_kwargs[IonNumberDensityHeNLTE] = dict( diff --git a/tardis/plasma/tests/test_complete_plasmas.py b/tardis/plasma/tests/test_complete_plasmas.py index 5e1e9dbfa24..4320f0d8284 100644 --- a/tardis/plasma/tests/test_complete_plasmas.py +++ b/tardis/plasma/tests/test_complete_plasmas.py @@ -2,8 +2,10 @@ import warnings import pandas as pd +import pandas.testing as pdt import pytest -from pandas.util import testing as pdt + +import numpy as np from numpy.testing import assert_almost_equal from tardis.io.configuration.config_reader import Configuration from tardis.simulation import Simulation @@ -169,13 +171,21 @@ def plasma(self, request, chianti_he_db_fpath, config, tardis_ref_data): def test_plasma_properties(self, plasma, tardis_ref_data, config, attr): if hasattr(plasma, attr): actual = getattr(plasma, attr) + if hasattr(actual, "unit"): + actual = actual.value if actual.ndim == 1: actual = pd.Series(actual) else: actual = pd.DataFrame(actual) key = os.path.join(config.plasma.save_path, "plasma", attr) expected = tardis_ref_data[key] - pdt.assert_almost_equal(actual, expected) + if type(actual) == pd.DataFrame: + pdt.assert_frame_equal(actual, expected) + elif type(actual) == pd.Series: + pdt.assert_series_equal(actual, expected) + else: + raise TypeError(f"Unexpected type {type(actual)}") + # we used this before - assert_almost_equal(actual.values, expected.values) else: warnings.warn(f'Property "{attr}" not found') @@ -183,7 +193,7 @@ def test_levels(self, plasma, tardis_ref_data, config): actual = pd.DataFrame(plasma.levels) key = os.path.join(config.plasma.save_path, "plasma", "levels") expected = tardis_ref_data[key] - pdt.assert_almost_equal(actual, expected) + pdt.assert_frame_equal(actual, expected) @pytest.mark.parametrize("attr", scalars_properties) def test_scalars_properties(self, plasma, tardis_ref_data, config, attr): @@ -192,7 +202,7 @@ def test_scalars_properties(self, plasma, tardis_ref_data, config, attr): actual = actual.cgs.value key = os.path.join(config.plasma.save_path, "plasma", "scalars") expected = tardis_ref_data[key][attr] - pdt.assert_almost_equal(actual, expected) + assert_almost_equal(actual, expected) def test_helium_treatment(self, plasma, tardis_ref_data, config): actual = plasma.helium_treatment diff --git a/tardis/plasma/tests/test_hdf_plasma.py b/tardis/plasma/tests/test_hdf_plasma.py index 028ab4f40d1..00edec980d2 100644 --- a/tardis/plasma/tests/test_hdf_plasma.py +++ b/tardis/plasma/tests/test_hdf_plasma.py @@ -1,8 +1,9 @@ import os import pandas as pd import pytest -import pandas.util.testing as pdt + from numpy.testing import assert_almost_equal +import pandas.testing as pdt from tardis.plasma.properties import property_collections ### @@ -68,7 +69,7 @@ def test_hdf_levels(hdf_file_path, simulation_verysimple): actual = actual.cgs.value path = os.path.join("plasma", "levels") expected = pd.read_hdf(hdf_file_path, path) - pdt.assert_almost_equal(pd.DataFrame(actual), expected) + pdt.assert_frame_equal(pd.DataFrame(actual), expected) scalars_list = ["time_explosion", "link_t_rad_t_electron"] diff --git a/tardis/simulation/tests/test_simulation.py b/tardis/simulation/tests/test_simulation.py index 3c0039f31ec..e44519281f8 100644 --- a/tardis/simulation/tests/test_simulation.py +++ b/tardis/simulation/tests/test_simulation.py @@ -8,10 +8,11 @@ from tardis.io.configuration.config_reader import Configuration from tardis.simulation import Simulation from tardis import run_tardis +import pandas.testing as pdt import numpy as np import pandas as pd -import pandas.util.testing as pdt + import astropy.units as u import tardis @@ -88,10 +89,12 @@ def test_plasma_estimates(simulation_one_loop, refdata, name): actual = getattr(simulation_one_loop.transport, name) except AttributeError: actual = getattr(simulation_one_loop.model, name) - + if name in ["t_radiative", "output_nu", "output_energy"]: + # removing the quantitiness of the data + actual = actual.value actual = pd.Series(actual) - pdt.assert_almost_equal(actual, refdata(name)) + pdt.assert_series_equal(actual, refdata(name), rtol=1e-5, atol=1e-8) @pytest.mark.parametrize( @@ -111,7 +114,12 @@ def test_plasma_state_iterations(simulation_one_loop, refdata, name): except Exception: actual = pd.DataFrame(actual) - pdt.assert_almost_equal(actual, refdata(name)) + if type(actual) == pd.DataFrame: + pdt.assert_frame_equal(actual, refdata(name), rtol=1e-5, atol=1e-8) + elif type(actual) == pd.Series: + pdt.assert_series_equal(actual, refdata(name)) + else: + raise ValueError(f"Unknown type of actual {type(actual)}") @pytest.fixture(scope="module") diff --git a/tardis/tests/test_tardis_full_formal_integral.py b/tardis/tests/test_tardis_full_formal_integral.py index e8fb5d07132..62a4abb0a21 100644 --- a/tardis/tests/test_tardis_full_formal_integral.py +++ b/tardis/tests/test_tardis_full_formal_integral.py @@ -90,11 +90,6 @@ def test_spectrum_integrated(self, transport, refdata): refdata("spectrum_integrated/luminosity"), "erg /s" ) - print( - "actual, desired: ", - luminosity, - transport.spectrum_integrated.luminosity, - ) assert_quantity_allclose( transport.spectrum_integrated.luminosity, luminosity ) diff --git a/tardis/visualization/tools/sdec_plot.py b/tardis/visualization/tools/sdec_plot.py index a9ba221609b..bcd3195c11b 100644 --- a/tardis/visualization/tools/sdec_plot.py +++ b/tardis/visualization/tools/sdec_plot.py @@ -596,7 +596,7 @@ def _calculate_plotting_data( self.plot_frequency = self.data[packets_mode].spectrum_frequency # Filter their plottable range based on packet_wvl_range specified - if packet_wvl_range: + if packet_wvl_range is not None: packet_nu_range = packet_wvl_range.to("Hz", u.spectral()) # Index of value just before the 1st value that is > packet_nu_range[1] @@ -1224,7 +1224,7 @@ def generate_plot_mpl( # Set legends and labels self.ax.legend(fontsize=12) self.ax.set_xlabel(r"Wavelength $[\mathrm{\AA}]$", fontsize=12) - if distance: # Set y-axis label for flux + if distance is not None: # Set y-axis label for flux self.ax.set_ylabel( r"$F_{\lambda}$ [erg $\mathrm{s^{-1}}$ $\mathrm{cm^{-2}}$ $\mathrm{\AA^{-1}}$]", fontsize=12, @@ -1632,7 +1632,7 @@ def generate_plot_ply( # Set label and other layout options xlabel = pu.axis_label_in_latex("Wavelength", u.AA) - if distance: # Set y-axis label for flux + if distance is not None: # Set y-axis label for flux ylabel = pu.axis_label_in_latex( "F_{\\lambda}", u.Unit("erg/(s cm**2 AA)"), only_text=False ) diff --git a/tardis/visualization/tools/tests/test_sdec_plot.py b/tardis/visualization/tools/tests/test_sdec_plot.py index 5e62044d7c0..975d5aa03fb 100644 --- a/tardis/visualization/tools/tests/test_sdec_plot.py +++ b/tardis/visualization/tools/tests/test_sdec_plot.py @@ -408,12 +408,14 @@ def test_generate_plot_mpl( species_list : list of str """ subgroup_name = make_valid_name("mpl" + request.node.callspec.id) + if distance is None: + observed_spectrum = None fig = plotter.generate_plot_mpl( packets_mode=packets_mode, packet_wvl_range=packet_wvl_range, distance=distance, show_modeled_spectrum=show_modeled_spectrum, - observed_spectrum=observed_spectrum if distance else None, + observed_spectrum=observed_spectrum, nelements=nelements, species_list=species_list, ) @@ -549,12 +551,16 @@ def test_generate_plot_ply( species_list : list of str """ subgroup_name = make_valid_name("ply" + request.node.callspec.id) + if distance is not None: + observed_spectrum = observed_spectrum + else: + observed_spectrum = None fig = plotter.generate_plot_ply( packets_mode=packets_mode, packet_wvl_range=packet_wvl_range, distance=distance, show_modeled_spectrum=show_modeled_spectrum, - observed_spectrum=observed_spectrum if distance else None, + observed_spectrum=observed_spectrum, nelements=nelements, species_list=species_list, ) diff --git a/tardis/visualization/widgets/line_info.py b/tardis/visualization/widgets/line_info.py index 8b0c209e11d..c21993a5fec 100644 --- a/tardis/visualization/widgets/line_info.py +++ b/tardis/visualization/widgets/line_info.py @@ -328,7 +328,7 @@ class variable :code:`GROUP_MODES` (default value is for ( line_id, count, - ) in grouped_line_interactions.size().iteritems(): + ) in grouped_line_interactions.size().items(): current_line_in = self.lines_data.loc[line_id[0]] current_line_out = self.lines_data.loc[line_id[1]] last_line_interaction_string.append( @@ -350,7 +350,7 @@ class variable :code:`GROUP_MODES` (default value is for ( line_id, count, - ) in grouped_line_interactions.size().iteritems(): + ) in grouped_line_interactions.size().items(): current_line_in = self.lines_data.loc[line_id] last_line_interaction_string.append( f"exc. {int(current_line_in.level_number_lower):02d}-" @@ -368,7 +368,7 @@ class variable :code:`GROUP_MODES` (default value is for ( line_id, count, - ) in grouped_line_interactions.size().iteritems(): + ) in grouped_line_interactions.size().items(): current_line_out = self.lines_data.loc[line_id] last_line_interaction_string.append( f"de-exc. {int(current_line_out.level_number_upper):02d}-" diff --git a/tardis/visualization/widgets/tests/test_shell_info.py b/tardis/visualization/widgets/tests/test_shell_info.py index 91b9b41cfe7..8d6af014617 100644 --- a/tardis/visualization/widgets/tests/test_shell_info.py +++ b/tardis/visualization/widgets/tests/test_shell_info.py @@ -43,11 +43,12 @@ def test_shells_data(self, base_shell_info, simulation_verysimple): 2, ) assert np.allclose( - shells_data.iloc[:, 0].map(np.float), + shells_data.iloc[:, 0].map(np.float64), simulation_verysimple.model.t_radiative.value, ) assert np.allclose( - shells_data.iloc[:, 1].map(np.float), simulation_verysimple.model.w + shells_data.iloc[:, 1].map(np.float64), + simulation_verysimple.model.w, ) @pytest.mark.parametrize("shell_num", [1, 20]) @@ -60,7 +61,7 @@ def test_element_count_data( 2, ) assert np.allclose( - element_count_data.iloc[:, -1].map(np.float), + element_count_data.iloc[:, -1].map(np.float64), simulation_verysimple.plasma.abundance[shell_num - 1], ) @@ -81,7 +82,7 @@ def test_ion_count_data( ) assert ion_count_data.shape == (len(sim_ion_number_density), 2) assert np.allclose( - ion_count_data.iloc[:, -1].map(np.float), + ion_count_data.iloc[:, -1].map(np.float64), sim_ion_number_density / sim_element_number_density, ) @@ -111,7 +112,7 @@ def test_level_count_data( ) assert level_count_data.shape == (len(sim_level_number_density), 1) assert np.allclose( - level_count_data.iloc[:, 0].map(np.float), + level_count_data.iloc[:, 0].map(np.float64), sim_level_number_density / sim_ion_number_density, ) diff --git a/tardis_env3.yml b/tardis_env3.yml index 24c7e8d1432..efa0e7b399e 100644 --- a/tardis_env3.yml +++ b/tardis_env3.yml @@ -8,17 +8,17 @@ dependencies: # WARNING: any change to this section must be applied to the conda-forge # package recipe at https://github.com/conda-forge/tardis-sn-feedstock - - python =3.8 + - python - setuptools - - setuptools_scm <7 + - setuptools_scm - pip - - numpy =1.19 - - scipy =1.5 - - pandas =1.0 - - astropy =5.0 - - numba =0.53 + - numpy + - scipy + - pandas + - astropy + - numba - numexpr - - radioactivedecay >=0.4.12 + - radioactivedecay # Plasma - networkx @@ -27,7 +27,7 @@ dependencies: # I/O - pyyaml - jsonschema - - hdf5 =1.12 + - hdf5 - h5py - pytables - requests @@ -47,7 +47,7 @@ dependencies: - lxml # Documentation - - sphinx <=7.1 + - sphinx - sphinx-astropy - sphinx_bootstrap_theme - sphinx-jsonschema