Provide a mechanism for collecting needed citations

src/tdastro/base_models.py

@@ -1,3 +1,6 @@
+from tdastro.common_citations import numpy_citation
+
+
 class PhysicalModel:
     """A physical model of a source of flux.
 
@@ -110,6 +113,39 @@ def evaluate(self, times, wavelengths, **kwargs):
             flux_density = effect.apply(flux_density, wavelengths, self, **kwargs)
         return flux_density
 
+    def _get_citation(self):
+        """Get the citation for this specific model.
+
+        Returns
+        -------
+        citations : `set`
+            A set of strings containing citations needed for this model.
+        """
+        return set()
+
+    def get_citations(self):
+        """Get the citations for this model, its host, and its effects.
+
+        Returns
+        -------
+        citations : `set`
+            A set of citation strings.
+        """
+        # Numpy is a base citation for all models.
+        citations = set([numpy_citation])
+
+        # Add model specific citations.
+        citations = citations.union(self._get_citation())
+
+        # Add any host specific citations.
+        if self.host is not None:
+            citations = citations.union(self.host.get_citations())
+
+        # Add citations for each effect.
+        for effect in self.effects:
+            citations = citations.union(effect.get_citations())
+        return citations
+
 
 class EffectModel:
     """A physical or systematic effect to apply to an observation."""
@@ -149,3 +185,13 @@ def apply(self, flux_density, wavelengths=None, physical_model=None, **kwargs):
             A length T x N matrix of flux densities after the effect is applied.
         """
         raise NotImplementedError()
+
+    def get_citations(self):
+        """Get the citation for this specific effect.
+
+        Returns
+        -------
+        citations : `set`
+            A set of strings with at most one element.
+        """
+        return set()

src/tdastro/common_citations.py

@@ -0,0 +1,84 @@
+numpy_citation = """@Article{         harris2020array,
+ title         = {Array programming with {NumPy}},
+ author        = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
+                 van der Walt and Ralf Gommers and Pauli Virtanen and David
+                 Cournapeau and Eric Wieser and Julian Taylor and Sebastian
+                 Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
+                 and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
+                 Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
+                 R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
+                 G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
+                 Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
+                 Travis E. Oliphant},
+ year          = {2020},
+ month         = sep,
+ journal       = {Nature},
+ volume        = {585},
+ number        = {7825},
+ pages         = {357--362},
+ doi           = {10.1038/s41586-020-2649-2},
+ publisher     = {Springer Science and Business Media {LLC}},
+ url           = {https://doi.org/10.1038/s41586-020-2649-2}
+}
+"""
+
+scipy_citation = """@ARTICLE{2020SciPy-NMeth,
+  author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
+            Haberland, Matt and Reddy, Tyler and Cournapeau, David and
+            Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
+            Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
+            Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
+            Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
+            Kern, Robert and Larson, Eric and Carey, C J and
+            Polat, {\\.I}lhan and Feng, Yu and Moore, Eric W. and
+            {VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
+            Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
+            Harris, Charles R. and Archibald, Anne M. and
+            Ribeiro, Ant{\\^o}nio H. and Pedregosa, Fabian and
+            {van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
+  title   = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
+            Computing in Python}},
+  journal = {Nature Methods},
+  year    = {2020},
+  volume  = {17},
+  pages   = {261--272},
+  adsurl  = {https://rdcu.be/b08Wh},
+  doi     = {10.1038/s41592-019-0686-2},
+}
+"""
+
+sncosmo_citation = """@software{barbary_2024_10684802,
+  author       = {Barbary, Kyle and
+                  Bailey, Stephen and
+                  Barentsen, Geert and
+                  Barclay, Tom and
+                  Biswas, Rahul and
+                  Boone, Kyle and
+                  Craig, Matt and
+                  Feindt, Ulrich and
+                  Friesen, Brian and
+                  Goldstein, Danny and
+                  Jha, Saurabh W. and
+                  Jones, David O. and
+                  Mondon, Florian and
+                  Papadogiannakis, Seméli and
+                  Perrefort, Daniel and
+                  Pierel, Justin and
+                  Rodney, Steve and
+                  Rose, Benjamin and
+                  Saunders, Clare and
+                  Sipőcz, Brigitta and
+                  Sofiatti, Caroline and
+                  Thomas, Rollin C. and
+                  van Santen, Jakob and
+                  Vincenzi, Maria and
+                  Wang, David and
+                  Wood-Vasey, Michael},
+  title        = {SNCosmo},
+  month        = feb,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v2.10.4},
+  doi          = {10.5281/zenodo.10684802},
+  url          = {https://doi.org/10.5281/zenodo.10684802}
+}"""

src/tdastro/sources/spline_model.py

@@ -8,6 +8,7 @@
 from scipy.interpolate import RectBivariateSpline
 
 from tdastro.base_models import PhysicalModel
+from tdastro.common_citations import scipy_citation, sncosmo_citation
 
 
 class SplineModel(PhysicalModel):
@@ -88,3 +89,13 @@ def _evaluate(self, times, wavelengths, **kwargs):
             A length T x N matrix of SED values.
         """
         return self.amplitude * self._spline(times, wavelengths, grid=True)
+
+    def _get_citation(self):
+        """Get the citation for this specific model.
+
+        Returns
+        -------
+        citations : `set`
+            A set of strings containing citations needed for this model.
+        """
+        return set([scipy_citation, sncosmo_citation])

tests/tdastro/sources/test_spline_source.py

@@ -1,4 +1,5 @@
 import numpy as np
+from tdastro.common_citations import numpy_citation, scipy_citation, sncosmo_citation
 from tdastro.sources.spline_model import SplineModel
 
 
@@ -40,3 +41,17 @@ def test_spline_model_interesting() -> None:
         [[1.0, 3.0, 5.0, 1.0], [3.0, 5.25, 7.5, 3.0], [5.0, 7.5, 10.0, 5.0], [1.0, 3.0, 5.0, 3.0]]
     )
     np.testing.assert_array_almost_equal(values, expected)
+
+
+def test_static_source_citations() -> None:
+    """Test that we get the citation string for a SplineModel."""
+    times = np.linspace(1.0, 5.0, 20)
+    wavelengths = np.linspace(100.0, 500.0, 25)
+    fluxes = np.full((len(times), len(wavelengths)), 1.0)
+    model = SplineModel(times, wavelengths, fluxes)
+
+    citations = model.get_citations()
+    assert len(citations) == 3
+    assert numpy_citation in citations
+    assert scipy_citation in citations
+    assert sncosmo_citation in citations

tests/tdastro/sources/test_static_source.py

@@ -1,4 +1,5 @@
 import numpy as np
+from tdastro.common_citations import numpy_citation
 from tdastro.sources.static_source import StaticSource
 
 
@@ -27,3 +28,11 @@ def test_static_source_host() -> None:
     assert model.ra == 1.0
     assert model.dec == 2.0
     assert model.distance == 3.0
+
+
+def test_static_source_citations() -> None:
+    """Test that we get the citation string for numpy."""
+    model = StaticSource(brightness=10.0)
+    citations = model.get_citations()
+    assert len(citations) == 1
+    assert numpy_citation in citations