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Sheshuk/fix model notebooks #402

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2bcc90a
Adding expand_dims, so Container would work with sdqueezed data arrays
Sheshuk Jul 4, 2025
effde21
Updated plot method
Sheshuk Jul 3, 2025
fc243c7
Skip integration over scalar dimension
Sheshuk Jul 4, 2025
3c9fdca
Updated the notebooks to use Flux.plot
Sheshuk Jul 4, 2025
9deea4d
Adding nbtest to run notebooks as tests separtely from doc building
Sheshuk Jul 7, 2025
b17bd24
Fix typo
Sheshuk Jul 7, 2025
78fa753
Allow errors in the notebooks, when building docs
Sheshuk Jul 7, 2025
238049a
Remove seaborn style
Sheshuk Jul 7, 2025
6b512eb
Fix Fornax: store additional parameters as attributes instead of pass…
Sheshuk Jul 9, 2025
c148c65
Fix Fornax_2021
Sheshuk Jul 9, 2025
3f03a48
Fix fornax_2022
Sheshuk Jul 9, 2025
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3 changes: 3 additions & 0 deletions .github/workflows/integration.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,9 @@ jobs:
run: |
python -m unittest python/snewpy/test/simplerate_integrationtest.py
pytest -m 'snowglobes'
- name: Run notebooks test
run: |
pytest --nbval-lax doc/source/nb
- uses: r-lib/actions/setup-pandoc@v2

- name: Build HTML docs
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1 change: 1 addition & 0 deletions doc/source/conf.py
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Expand Up @@ -79,6 +79,7 @@
# directories to ignore when looking for source files.
exclude_patterns = ['nb/dev']

nbsphinx_allow_errors = True
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I’d like to be very strict here, because any errors that slip through will make it to the published documentation.

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It is still strict: I've added the pytest --nbval step, so we're still having the notebooks checked, but it provides more information: instead of just failing on the first failed notebook during the documentation build, it will run each of them as test and give the output.

# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
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21 changes: 8 additions & 13 deletions doc/source/nb/ccsn/Bollig_2016.ipynb
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Expand Up @@ -141,28 +141,23 @@
"\n",
"for i, spec in enumerate([ispec, ospec_nmo]):\n",
" ax = axes[i]\n",
" for flavor in Flavor:\n",
" ax.plot(E, spec[flavor],\n",
" label=flavor.to_tex(),\n",
" color='C0' if flavor.is_electron else 'C1',\n",
" ls='-' if flavor.is_neutrino else ':', lw=2,\n",
" alpha=0.7)\n",
"\n",
" ax.set(xlabel=r'$E$ [{}]'.format(E.unit),\n",
" title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" plt.sca(ax)\n",
" spec.plot('energy')\n",
" \n",
" ax.set(title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" ax.grid()\n",
" ax.legend(loc='upper right', ncol=2, fontsize=16)\n",
"\n",
"ax = axes[0]\n",
"ax.set(ylabel=r'flux [erg$^{-1}$ s$^{-1}$]')\n",
"ax.set(ylabel=r'flux, MeV')\n",
"\n",
"fig.tight_layout();"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "snewpy",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -176,9 +171,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.2"
"version": "3.13.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
21 changes: 6 additions & 15 deletions doc/source/nb/ccsn/Fischer_2020.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -121,24 +121,15 @@
"\n",
"for i, spec in enumerate([ispec, ospec_nmo]):\n",
" ax = axes[i]\n",
" for flavor in Flavor:\n",
" if flavor.is_electron == True:\n",
" color='C0'\n",
" else:\n",
" color='C1'\n",
" ax.plot(E, spec[flavor],\n",
" label=flavor.to_tex(),\n",
" color=color,\n",
" ls='-' if flavor.is_neutrino else ':', lw=2,\n",
" alpha=0.7)\n",
"\n",
" ax.set(xlabel=r'$E$ [{}]'.format(E.unit),\n",
" title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" plt.sca(ax)\n",
" spec.plot('energy')\n",
" \n",
" ax.set(title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" ax.grid()\n",
" ax.legend(loc='upper right', ncol=2, fontsize=16)\n",
"\n",
"ax = axes[0]\n",
"ax.set(ylabel=r'flux [erg$^{-1}$ s$^{-1}$]')\n",
"ax.set(ylabel=r'flux, MeV')\n",
"\n",
"fig.tight_layout();"
]
Expand All @@ -160,7 +151,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.3"
"version": "3.13.5"
},
"vscode": {
"interpreter": {
Expand Down
27 changes: 14 additions & 13 deletions doc/source/nb/ccsn/Fornax_2021.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@
"\n",
"for i, ax in enumerate(axes.flatten()):\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][i], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,i].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('$t$ = {:g}'.format(times[i]), fontsize=16)\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand Down Expand Up @@ -164,11 +164,12 @@
"\n",
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"spectra = model.get_initial_spectra(times, E, interpolation='nearest')\n",
"model.interpolation='nearest'\n",
"spectra = model.get_initial_spectra(times, E)\n",
"\n",
"for i, ax in enumerate(axes.flatten()):\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][i], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,i].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('$t$ = {:g}'.format(times[i]), fontsize=16)\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand Down Expand Up @@ -227,13 +228,13 @@
" ax.legend(ncol=3, fontsize=12, title=r'$\\bar{\\nu}_e$');\n",
" \n",
" ax = axes[2]\n",
" flavor = Flavor.NU_X\n",
" flavor = Flavor.NU_MU\n",
" ax.plot(model.time, model.luminosity[flavor], lw=2, color=colors2[i], ls=linestyles[i%4],\n",
" label='${0.value:g}$ {0.unit:latex}'.format(model.progenitor_mass))\n",
" ax.set(xlabel='time [s]',\n",
" ylabel=r'$L_{\\nu_X}(t)$ [erg s$^{-1}$]')\n",
" ylabel=r'$L_{\\nu_\\mu}(t)$ [erg s$^{-1}$]')\n",
" ax.grid(ls=':', which='both')\n",
" ax.legend(ncol=3, fontsize=12, title=r'$\\nu_X$');"
" ax.legend(ncol=3, fontsize=12, title=r'$\\nu_\\mu$');"
]
},
{
Expand Down Expand Up @@ -265,11 +266,11 @@
"fig, axes = plt.subplots(2,4, figsize=(16,6), sharex=True, sharey=True, tight_layout=True)\n",
"\n",
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"model.interpolation='linear'\n",
"for model, ax in zip(models.values(), axes.flatten()):\n",
" spectra = model.get_initial_spectra(t, E)\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][0], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,0].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('${0.value:g}$ {0.unit:latex}'.format(model.progenitor_mass))\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand Down Expand Up @@ -300,11 +301,11 @@
"fig, axes = plt.subplots(2,4, figsize=(16,6), sharex=True, sharey=True, tight_layout=True)\n",
"\n",
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"model.interpolation='nearest'\n",
"for model, ax in zip(models.values(), axes.flatten()):\n",
" spectra = model.get_initial_spectra(t, E, interpolation='nearest')\n",
" spectra = model.get_initial_spectra(t, E)\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][0], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,0].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('${0.value:g}$ {0.unit:latex}'.format(model.progenitor_mass))\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand All @@ -317,7 +318,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.9.5 ('snews')",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -331,7 +332,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.3"
"version": "3.13.5"
},
"vscode": {
"interpreter": {
Expand Down
29 changes: 15 additions & 14 deletions doc/source/nb/ccsn/Fornax_2022.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -151,12 +151,12 @@
"fig, axes = plt.subplots(5,4, figsize=(15,12), sharex=True, sharey=True, tight_layout=True)\n",
"\n",
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"model.interpolation='linear'\n",
"spectra = model.get_initial_spectra(times, E)\n",
"\n",
"for i, ax in enumerate(axes.flatten()):\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][i], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,i].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('$t$ = {:g}'.format(times[i]), fontsize=16)\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand Down Expand Up @@ -186,12 +186,12 @@
"fig, axes = plt.subplots(5,4, figsize=(15,12), sharex=True, sharey=True, tight_layout=True)\n",
"\n",
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"spectra = model.get_initial_spectra(times, E, interpolation='nearest')\n",
"model.interpolation='nearest'\n",
"spectra = model.get_initial_spectra(times, E)\n",
"\n",
"for i, ax in enumerate(axes.flatten()):\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][i], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,i].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('$t$ = {:g}'.format(times[i]), fontsize=16)\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand Down Expand Up @@ -250,13 +250,13 @@
" ax.legend(ncol=3, fontsize=12, title=r'$\\bar{\\nu}_e$');\n",
" \n",
" ax = axes[2]\n",
" flavor = Flavor.NU_X\n",
" flavor = Flavor.NU_MU\n",
" ax.plot(model.time, model.luminosity[flavor], lw=2, color=colors2[i], ls=linestyles[i%4],\n",
" label='${0.value:g}$ {0.unit:latex}{1}'.format(model.progenitor_mass, ' (BH)' if 'bh' in model.progenitor else ''))\n",
" label='${0.value:g}$ {0.unit:latex}'.format(model.progenitor_mass))\n",
" ax.set(xlabel='time [s]',\n",
" ylabel=r'$L_{\\nu_X}(t)$ [erg s$^{-1}$]')\n",
" ylabel=r'$L_{\\nu_\\mu}(t)$ [erg s$^{-1}$]')\n",
" ax.grid(ls=':', which='both')\n",
" ax.legend(ncol=3, fontsize=12, title=r'$\\nu_X$');"
" ax.legend(ncol=3, fontsize=12, title=r'$\\nu_\\mu$');"
]
},
{
Expand Down Expand Up @@ -284,9 +284,10 @@
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"for model, ax in zip(models.values(), axes.flatten()):\n",
" model.interpolation='linear'\n",
" spectra = model.get_initial_spectra(t, E)\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][0], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,0].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('${0.value:g}$ {0.unit:latex}{1}'.format(model.progenitor_mass, ' (BH)' if 'bh' in model.progenitor else ''))\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand Down Expand Up @@ -317,11 +318,11 @@
"fig, axes = plt.subplots(2,3, figsize=(12,6), sharex=True, sharey=True, tight_layout=True)\n",
"\n",
"linestyles = ['-', '--', '-.', ':']\n",
"\n",
"for model, ax in zip(models.values(), axes.flatten()):\n",
" spectra = model.get_initial_spectra(t, E, interpolation='nearest')\n",
" model.interpolation='nearest'\n",
" spectra = model.get_initial_spectra(t, E)\n",
" for line, flavor in zip(linestyles, Flavor):\n",
" ax.plot(E, spectra[flavor][0], lw=3, ls=line, label=flavor.to_tex())\n",
" ax.plot(E, spectra[flavor,0].array.squeeze(), lw=3, ls=line, label=flavor.to_tex())\n",
" ax.set(xlim=(0,100))\n",
" ax.set_title('${0.value:g}$ {0.unit:latex}{1}'.format(model.progenitor_mass, ' (BH)' if 'bh' in model.progenitor else ''))\n",
" ax.legend(loc='upper right', ncol=2, fontsize=12)\n",
Expand All @@ -348,7 +349,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.3"
"version": "3.13.5"
}
},
"nbformat": 4,
Expand Down
21 changes: 8 additions & 13 deletions doc/source/nb/ccsn/Kuroda_2020.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -152,28 +152,23 @@
"\n",
"for i, spec in enumerate([ispec, ospec_nmo]):\n",
" ax = axes[i]\n",
" for flavor in Flavor:\n",
" ax.plot(E, spec[flavor],\n",
" label=flavor.to_tex(),\n",
" color='C0' if flavor.is_electron else 'C1',\n",
" ls='-' if flavor.is_neutrino else ':', lw=2,\n",
" alpha=0.7)\n",
"\n",
" ax.set(xlabel=r'$E$ [{}]'.format(E.unit),\n",
" title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" plt.sca(ax)\n",
" spec.plot('energy')\n",
" \n",
" ax.set(title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" ax.grid()\n",
" ax.legend(loc='upper right', ncol=2, fontsize=16)\n",
"\n",
"ax = axes[0]\n",
"ax.set(ylabel=r'flux [erg$^{-1}$ s$^{-1}$]')\n",
"ax.set(ylabel=r'flux, MeV')\n",
"\n",
"fig.tight_layout();"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3.9.5 ('snews')",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -187,7 +182,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.5"
"version": "3.13.5"
},
"vscode": {
"interpreter": {
Expand All @@ -196,5 +191,5 @@
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
19 changes: 8 additions & 11 deletions doc/source/nb/ccsn/Nakazato_2013.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -165,20 +165,17 @@
"\n",
"for i, spec in enumerate([ispec, ospec_nmo]):\n",
" ax = axes[i]\n",
" for flavor in Flavor:\n",
" ax.plot(E, spec[flavor],\n",
" label=flavor.to_tex(),\n",
" color='C0' if flavor.is_electron else 'C1',\n",
" ls='-' if flavor.is_neutrino else ':', lw=2,\n",
" alpha=0.7)\n",
"\n",
" ax.set(xlabel=r'$E$ [{}]'.format(E.unit),\n",
" title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" plt.sca(ax)\n",
" spec.plot('energy')\n",
" \n",
" ax.set(title='Initial Spectra: $t = ${:.1f}'.format(t) if i==0 else 'Oscillated Spectra: $t = ${:.1f}'.format(t))\n",
" ax.grid()\n",
" ax.legend(loc='upper right', ncol=2, fontsize=16)\n",
"\n",
"ax = axes[0]\n",
"ax.set(ylabel=r'flux [erg$^{-1}$ s$^{-1}$]');"
"ax.set(ylabel=r'flux, MeV')\n",
"\n",
"fig.tight_layout();"
]
}
],
Expand All @@ -198,7 +195,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
"version": "3.13.5"
},
"vscode": {
"interpreter": {
Expand Down
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