Update TARDIS environment after replacing PyNE (#1948)

* first revision of env file

* changes from astropy 4 (deprecated blackbody functions)

* move qt import in gui test

* downgrade pandas

* pin radioactive decay again

* fix changes from astropy 4 (deprecated blackbody functions)

* fix changes from astropy 4 (unit conversion bug)

* fix changes from astropy 4 (unit conversion bug) viz module

* fix changes from astropy 4 (deprecated blackbody functions) opacity calc

* import constants from tardis in opacities

* upgrade black

* remove pickle backport

* use astropy.constants v3 for astropy.units

* remove pinned deps fixed upstream

* pin astropy v5 again

.github/workflows/black-check.yml

@@ -20,7 +20,7 @@ jobs:
           python-version: 3.x
 
       - name: Install Black
-        run: pip install black==21.12b0
+        run: pip install black==22.3
 
       - name: Run Black
         run: black --check tardis

tardis/__init__.py

@@ -15,14 +15,12 @@
 
 # ----------------------------------------------------------------------------
 
-from tardis.base import run_tardis
-from tardis.io.util import yaml_load_config_file as yaml_load
+from astropy import physical_constants, astronomical_constants
 
+physical_constants.set('codata2014')
+astronomical_constants.set('iau2012')
 
 # ----------------------------------------------------------------------------
-# pyne holds Python 3.7 on macOS, but refdata is pickled with protocol 5 (3.8.3)
-
-if sys.version_info < (3, 8, 3):
-    import pickle5
 
-    sys.modules["pickle"] = pickle5
+from tardis.base import run_tardis
+from tardis.io.util import yaml_load_config_file as yaml_load

tardis/analysis/opacities.py

@@ -3,8 +3,8 @@
 import logging
 import numpy as np
 import astropy.units as units
-import astropy.constants as csts
-from astropy.modeling.blackbody import blackbody_nu
+from tardis import constants as const
+from astropy.modeling.models import Blackbody
 
 logger = logging.getLogger(__name__)
 
@@ -320,7 +320,7 @@ def _calc_expansion_opacity(self):
                 tmp
                 * self.nu_bins[i]
                 / (self.nu_bins[i + 1] - self.nu_bins[i])
-                / (csts.c * self.t_exp)
+                / (const.c * self.t_exp)
             )
 
         return kappa_exp.to("1/cm")
@@ -339,7 +339,7 @@ def _calc_thomson_scattering_opacity(self):
         """
 
         try:
-            sigma_T = csts.sigma_T
+            sigma_T = const.sigma_T
         except AttributeError:
             logger.warning("using astropy < 1.1.1: setting sigma_T manually")
             sigma_T = 6.65245873e-29 * units.m ** 2
@@ -373,13 +373,14 @@ def _calc_planck_mean_opacity(self):
         for i in range(self.nshells):
             delta_nu = self.nu_bins[1:] - self.nu_bins[:-1]
             T = self.mdl.plasma.t_rad[i]
+            bb_nu = Blackbody(T)
 
             tmp = (
-                blackbody_nu(self.nu_bins[:-1], T)
+                bb_nu(self.nu_bins[:-1])                
                 * delta_nu
                 * self.kappa_tot[:, 0]
             ).sum()
-            tmp /= (blackbody_nu(self.nu_bins[:-1], T) * delta_nu).sum()
+            tmp /= (bb_nu(self.nu_bins[:-1], T) * delta_nu).sum()
 
             kappa_planck_mean[i] = tmp
 

tardis/gui/tests/test_gui.py

@@ -1,11 +1,11 @@
-from PyQt5 import QtWidgets
 import os
 import pytest
 from tardis.io.config_reader import Configuration
 from tardis.simulation import Simulation
 import astropy.units as u
 
 if "QT_API" in os.environ:
+    from PyQt5 import QtWidgets
     from tardis.gui.widgets import Tardis
     from tardis.gui.datahandler import SimpleTableModel
 

tardis/montecarlo/base.py

@@ -461,7 +461,7 @@ def montecarlo_reabsorbed_luminosity(self):
             np.histogram(
                 self.reabsorbed_packet_nu,
                 weights=self.reabsorbed_packet_luminosity,
-                bins=self.spectrum_frequency.value,
+                bins=self.spectrum_frequency,
             )[0],
             "erg / s",
         )
@@ -472,7 +472,7 @@ def montecarlo_emitted_luminosity(self):
             np.histogram(
                 self.emitted_packet_nu,
                 weights=self.emitted_packet_luminosity,
-                bins=self.spectrum_frequency.value,
+                bins=self.spectrum_frequency,
             )[0],
             "erg / s",
         )

tardis/visualization/tools/sdec_plot.py

@@ -7,7 +7,7 @@
 import numpy as np
 import pandas as pd
 import astropy.units as u
-import astropy.modeling.blackbody as abb
+from astropy.modeling.models import BlackBody
 
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
@@ -868,7 +868,7 @@ def _calculate_emission_luminosities(self, packets_mode, packet_wvl_range):
             self.data[packets_mode].packets_df["nus"][
                 self.packet_nu_range_mask
             ][mask_noint],
-            bins=self.plot_frequency_bins,
+            bins=self.plot_frequency_bins.value,
             weights=weights[mask_noint],
             density=False,
         )
@@ -901,7 +901,7 @@ def _calculate_emission_luminosities(self, packets_mode, packet_wvl_range):
             self.data[packets_mode].packets_df["nus"][
                 self.packet_nu_range_mask
             ][mask_escatter],
-            bins=self.plot_frequency_bins,
+            bins=self.plot_frequency_bins.value,
             weights=weights[mask_escatter],
             density=False,
         )
@@ -938,7 +938,7 @@ def _calculate_emission_luminosities(self, packets_mode, packet_wvl_range):
             # Histogram of specific species
             hist_el = np.histogram(
                 group["nus"],
-                bins=self.plot_frequency_bins,
+                bins=self.plot_frequency_bins.value,
                 weights=group["energies"]
                 / self.lum_to_flux
                 / self.data[packets_mode].time_of_simulation,
@@ -1026,7 +1026,7 @@ def _calculate_absorption_luminosities(
             # Histogram of specific species
             hist_el = np.histogram(
                 group["last_line_interaction_in_nu"],
-                bins=self.plot_frequency_bins,
+                bins=self.plot_frequency_bins.value,
                 weights=group["energies"]
                 / self.lum_to_flux
                 / self.data[packets_mode].time_of_simulation,
@@ -1064,11 +1064,13 @@ def _calculate_photosphere_luminosity(self, packets_mode):
             Luminosity density lambda (or Flux) of photosphere (inner boundary
             of TARDIS simulation)
         """
+        bb_lam = BlackBody(
+            self.data[packets_mode].t_inner,
+            scale=1.0 * u.erg / (u.cm ** 2 * u.AA * u.s * u.sr)
+        )
+
         L_lambda_ph = (
-            abb.blackbody_lambda(
-                self.plot_wavelength,
-                self.data[packets_mode].t_inner,
-            )
+            bb_lam(self.plot_wavelength)
             * 4
             * np.pi ** 2
             * self.data[packets_mode].r_inner[0] ** 2

tardis_env3.yml

@@ -4,14 +4,14 @@ channels:
   - conda-forge
 
 dependencies:
-  - python=3.7
+  - python=3.8
   - setuptools
   - setuptools_scm
   - pip
   - numpy=1.19
   - scipy=1.5
   - pandas=1.0
-  - astropy=3
+  - astropy=5.0
   - numba=0.53
   - numexpr
   - radioactivedecay>=0.4.12
@@ -25,19 +25,17 @@ dependencies:
   - jsonschema=3 # Issue #1807
   - pytables
   - h5py
-  - pickle5 # Issue #1566
   - requests
   - tqdm
 
   # Widgets & Visualization
-  - jupyter
-  - matplotlib
+  - notebook
+  - matplotlib-base
   - ipywidgets
   - plotly
   - qgrid
-  # - pyside2  # (Qt GUI) Issue #1652
 
-  # --- Not required for conda-forge package and Numba integration pipeline ---
+  # --- Not required for conda-forge package ---
 
   # tardis-sn/nuclear dependencies
   - beautifulsoup4
@@ -56,9 +54,8 @@ dependencies:
   - nbconvert
   - nbformat
   - nbsphinx
-  - docutils=0.16 # Issue #1522
   - snakeviz
-  - Jinja2=3.0.3 # github.com/spatialaudio/nbsphinx/issues/641
+  - dot2tex
 
   # Test/Coverage
   - pytest
@@ -68,10 +65,7 @@ dependencies:
   - coverage
 
   # Code quality
-  - black=21.12b0
+  - black=22.3
 
   # Other
   - git-lfs
-
-  - pip:
-      - dot2tex # conda-forge package requires python>=3.8