Merge branch 'main' into cevns-fixes

.github/workflows/integration.yml

@@ -23,9 +23,9 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -38,3 +38,14 @@ jobs:
         run: |
           python -m unittest python/snewpy/test/simplerate_integrationtest.py
           pytest -m 'snowglobes'
+      - name: Run Jupyter notebooks
+        run: |
+          pip install nbclient ipykernel
+          jupyter kernelspec list
+          cd doc/nb/
+          jupyter execute ccsn/*.ipynb
+          jupyter execute presn/*.ipynb
+          jupyter execute AnalyticFluence.ipynb FlavorTransformation.ipynb
+          # Download necessary progenitor file, before executing the notebook
+          python -c 'from snewpy.models.ccsn import Zha_2021; from astropy import units as u; _ = Zha_2021(progenitor_mass=17*u.solMass)'
+          jupyter execute SNOwGLoBES_usage.ipynb

.github/workflows/publish.yml

@@ -13,31 +13,35 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
+
+    - name: Check and get Version Number
+      id: get_version
+      run: |
+        pip install .
+        PYTHON_VERSION=`python -c 'import snewpy; print(snewpy.__version__)'`
+        echo "PYTHON_VERSION=${PYTHON_VERSION}"
+        GIT_VERSION=${GITHUB_REF/refs\/tags\/v/}
+        echo "GIT_VERSION=${GIT_VERSION}"
+        if [ $PYTHON_VERSION != $GIT_VERSION ]; then exit 1; fi
+        echo "VERSION=${PYTHON_VERSION}" >> $GITHUB_OUTPUT
+
     - name: Build and publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_JM }}
       run: |
-        python -c 'import python.snewpy; python.snewpy._get_model_urls()'
-        cat python/snewpy/_model_urls.py
-        pip install .
-        python -c 'import snewpy; snewpy.get_models(models="Bollig_2016")'
-        rm -r SNEWPY_models/
         python setup.py sdist bdist_wheel
         twine upload dist/*
 
-    - name: Get Version Number
-      id: get_version
-      run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//}
     - name: Create Draft Release
       # Go to https://github.com/SNEWS2/snewpy/releases to edit this draft release and publish it
       # Once it is published, the release automatically is pushed to Zenodo: https://doi.org/10.5281/zenodo.4498940

.github/workflows/tests.yml

@@ -24,21 +24,25 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # Set up the Python environment and dependencies
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
       - name: Install SNEWPY
         run: |
-          pip install ".[dev]"
+          pip install ".[dev,docs]"
       
-      # Run the unit tests
-      - name: Test with pytest
+      - name: Run unit tests with pytest
         run: |
           pytest -m 'not snowglobes'
+
+      - name: Build HTML docs
+        run: |
+          cd doc/
+          make html

.gitignore

@@ -9,13 +9,15 @@ dist/
 # default directory for downloaded model files
 SNEWPY_models/
 
-# snewpy.snowglobes output files
+## SNEWPY output files
+# snewpy.snowglobes intermediate results
 *_SNOprocessed.tar.gz
 *.npy
 *.npz
-
 # used for integration tests in test_snowglobes.py
 fluence_Bollig_2016_s*
+# plots generated by FlavorTransformation.ipynb
+doc/nb/*_adiabaticmsw*.pdf
 
 # editor-specific
 .ipynb_checkpoints/

README.md

@@ -1,6 +1,6 @@
 # SNEWPY: Supernova Neutrino Early Warning Models for Python
 
-<img src="/doc/source/snewpy-logo.png" alt="snewpy logo: The word 'snewpy' in a monospace font, with an explosion emoji inside the letter 'p'." style="width: 300px; max-width: 100%;" />
+<img src="https://github.com/SNEWS2/snewpy/blob/v1.4/doc/source/snewpy-logo.png?raw=true" alt="snewpy logo: The word 'snewpy' in a monospace font, with an explosion emoji inside the letter 'p'." style="width: 300px; max-width: 100%;" />
 
 [![DOI](https://zenodo.org/badge/221705586.svg)](https://zenodo.org/badge/latestdoi/221705586)
 [![PyPI](https://img.shields.io/pypi/v/snewpy)](https://pypi.org/project/snewpy/)
@@ -53,9 +53,9 @@ flux = bollig.get_flux(distance=10*u.kpc, transformation=msw_nmo)
 
 You can also calculate the observed event rate in all neutrino detectors supported by SNOwGLoBES, use the included SN models and flavor transformations in event generators like sntools, and much more.
 
-Example scripts which show how SNEWPY can be used are available in the
-`python/snewpy/scripts/` subfolder as well as notebooks in `doc/nb/`.
-Most downloadable models also include a Jupyter notebook with simple usage examples.
+Jupyter notebooks showcasing the downloadable supernova models available through SNEWPY and much of its functionality are available in the `doc/nb/` subfolder.
+Additional example scripts are in the
+`python/snewpy/scripts/` subfolder.
 
 Papers describing SNEWPY and the underlying physics are published in the Astrophysical Journal ([DOI:10.3847/1538-4357/ac350f](https://dx.doi.org/10.3847/1538-4357/ac350f), [arXiv:2109.08188](https://arxiv.org/abs/2109.08188)) and the Journal of Open Source Software ([DOI:10.21105/joss.03772](https://dx.doi.org/10.21105/joss.03772)).
 

doc/Makefile

@@ -15,7 +15,7 @@ endif
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+ALLSPHINXOPTS   = -W --keep-going -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 

doc/nb/AnalyticFluence.ipynb

@@ -25,23 +25,17 @@
     "import matplotlib as mpl\n",
     "import numpy as np\n",
     "\n",
-    "from snewpy import snowglobes\n",
+    "from snewpy import snowglobes, model_path\n",
     "from snewpy.neutrino import Flavor\n",
-    "from snewpy.models import Analytic3Species\n",
+    "from snewpy.models.ccsn import Analytic3Species\n",
     "\n",
     "mpl.rc('font', size=14)\n",
     "\n",
     "SNOwGLoBES_path = None  # change to SNOwGLoBES directory if using a custom detector configuration\n",
-    "SNEWPY_models_base = \"/path/to/snewpy/models/\"  # change to local directory where models are located\n",
-    "\n",
-    "model_folder = f\"{SNEWPY_models_base}/AnalyticFluence/\"\n",
-    "try:\n",
-    "    os.mkdir(model_folder)\n",
-    "except OSError as e:\n",
-    "    print(model_folder)\n",
-    "    print(f\"Folder {model_folder} already exists or path is wrong\")\n",
-    "else:\n",
-    "    print(f\"Created folder {model_folder}\")\n"
+    "\n",
+    "model_folder = f\"{model_path}/AnalyticFluence/\"\n",
+    "os.makedirs(model_folder, exist_ok=True)\n",
+    "print(f\"Using folder `{model_folder}`.\")"
    ]
   },
   {
@@ -97,7 +91,7 @@
     "    print(\"incorrect second moment method: rms or pinch\")\n",
     "\n",
     "filename = \"AnalyticFluence_demo.dat\"\n",
-    "table.write(model_folder+\"/\"+filename,format='ascii',overwrite=True)"
+    "table.write(model_folder + filename, format='ascii', overwrite=True)"
    ]
   },
   {
@@ -115,7 +109,7 @@
    "source": [
     "%matplotlib inline\n",
     "filename = \"AnalyticFluence_demo.dat\"\n",
-    "model = Analytic3Species(model_folder+\"/\"+filename)\n",
+    "model = Analytic3Species(model_folder + filename)\n",
     "flavors = [Flavor.NU_E,Flavor.NU_E_BAR,Flavor.NU_X]\n",
     "\n",
     "fig,axes = plt.subplots(1,3,figsize=(16,3))\n",

doc/nb/FlavorTransformation.ipynb

@@ -244,9 +244,11 @@
    "outputs": [],
    "source": [
     "fig = plot_total_flux(model, AdiabaticMSW(), AdiabaticMSW(mh=MassHierarchy.INVERTED) )\n",
-    "fig.savefig('flux_adiabaticmsw.pdf')\n",
+    "fig.show()\n",
+    "# fig.savefig('flux_adiabaticmsw.pdf')\n",
     "fig = plot_spectra(model, AdiabaticMSW(), AdiabaticMSW(mh=MassHierarchy.INVERTED), 100*u.ms)\n",
-    "fig.savefig('spectra_adiabaticmsw.pdf')"
+    "fig.show()\n",
+    "# fig.savefig('spectra_adiabaticmsw.pdf')"
    ]
   },
   {
@@ -264,9 +266,11 @@
     "xf_imo = AdiabaticMSWes(angles_imo)\n",
     "\n",
     "fig = plot_total_flux(model, xf_nmo, xf_imo)\n",
-    "fig.savefig('flux_adiabaticmswes.pdf')\n",
+    "fig.show()\n",
+    "# fig.savefig('flux_adiabaticmswes.pdf')\n",
     "fig = plot_spectra(model, xf_nmo, xf_imo, 100*u.ms)\n",
-    "fig.savefig('spectra_adiabaticmswes.pdf')"
+    "fig.show()\n",
+    "# fig.savefig('spectra_adiabaticmswes.pdf')"
    ]
   }
  ],
@@ -286,7 +290,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.12.3"
   },
   "vscode": {
    "interpreter": {