Preparation for 0.5.0 release - versions and dependencies bump (require python 3.11 and astropy 7.0)

Author: grzegorzbor

.github/workflows/test.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v3

.zenodo.json

@@ -79,5 +79,5 @@
     ],
     "title": "agnpy",
     "upload_type": "software",
-    "version": "0.4.0"
+    "version": "0.5.0"
 }

agnpy/fit/data.py

@@ -130,8 +130,7 @@ def load_gammapy_flux_points(sed_path, E_min, E_max, systematics_dict=None):
         dataset = FluxPointsDataset(data=data, name=name)
 
         # set the minimum energy to be used for the fit
-        mask = (dataset.data.energy_ref >= E_min) * (dataset.data.energy_ref <= E_max)
-        dataset.mask_fit = mask
+        dataset.mask_fit = dataset.data.geom.energy_mask(energy_min=E_min, energy_max=E_max)
 
         datasets.append(dataset)
 

agnpy/fit/gammapy_wrapper.py

@@ -134,7 +134,7 @@ def __init__(self, n_e, ssa=False):
         self._emission_region_pars_names = list(emission_region_pars.keys())
 
         # group the model parameters, add the norm at the bottom of the list
-        norm = Parameter("norm", 1, min=0.1, max=10, is_norm=True, frozen=True)
+        norm = Parameter("norm", 1, min=0.1, max=10, frozen=True)
         self.default_parameters = Parameters(
             [*spectral_pars.values(), *emission_region_pars.values(), norm]
         )
@@ -163,7 +163,7 @@ def evaluate(self, energy, **kwargs):
         NOTE: All the model parameters will be passed as kwargs by
         SpectralModel.evaluate()."""
 
-        nu = energy.to("Hz", equivalencies=u.spectral())
+        nu = energy.reshape([energy.shape[0]]).to("Hz", equivalencies=u.spectral())
 
         args = _sort_spectral_parameters(self._spectral_pars_names, self._n_e, **kwargs)
         z, d_L, delta_D, B, R_b = _sort_emission_region_parameters("ssc", **kwargs)
@@ -180,15 +180,8 @@ def evaluate(self, energy, **kwargs):
         )
         sed = sed_synch + sed_ssc
 
-        # to avoid the problem pointed out in
-        # https://github.com/cosimoNigro/agnpy/issues/117
-        # we can do here something like
-        # sed = sed.reshape(energy.shape)
-        # this is done in Gammapy's `NaimaSpectralModel`
-        # https://github.com/gammapy/gammapy/blob/master/gammapy/modeling/models/spectral.py#L2119
-
         # gammapy requires a differential flux in input
-        return (sed / energy**2).to("1 / (cm2 eV s)")
+        return (sed.reshape(energy.shape) / energy**2).to("1 / (cm2 eV s)")
 
 
 class ExternalComptonSpectralModel(SpectralModel):
@@ -234,7 +227,7 @@ def __init__(self, n_e, targets, ssa=False):
         self._targets_pars_names = list(targets_pars.keys())
 
         # group the model parameters, add the norm at the bottom of the list
-        norm = Parameter("norm", 1, min=0.1, max=10, is_norm=True, frozen=True)
+        norm = Parameter("norm", 1, min=0.1, max=10, frozen=True)
         self.default_parameters = Parameters(
             [
                 *spectral_pars.values(),
@@ -295,8 +288,7 @@ def evaluate(self, energy, **kwargs):
         """Evaluate the SED model.
         NOTE: All the model parameters will be passed as kwargs by
         SpectralModel.evaluate()."""
-
-        nu = energy.to("Hz", equivalencies=u.spectral())
+        nu = energy.reshape([energy.shape[0]]).to("Hz", equivalencies=u.spectral())
 
         args = _sort_spectral_parameters(self._spectral_pars_names, self._n_e, **kwargs)
         z, d_L, delta_D, B, R_b, mu_s, r = _sort_emission_region_parameters(
@@ -365,9 +357,4 @@ def evaluate(self, energy, **kwargs):
             )
             sed += sed_bb_dt
 
-        # eventual reshaping
-        # we can do here something like
-        # sed = sed.reshape(energy.shape)
-        # see the same comment in the SSC model
-
-        return (sed / energy**2).to("1 / (cm2 eV s)")
+        return (sed.reshape(energy.shape) / energy**2).to("1 / (cm2 eV s)")

agnpy/time_evolution/tests/test_time_evolution.py

@@ -248,7 +248,7 @@ def test_heun_method_compared_to_euler(self):
         print("Average error Euler method", average_error_euler)
         print("Average error Heun  method", average_error_heun)
         assert average_error_heun < average_error_euler
-        assert np.alltrue(errors_heun <= errors_euler)
+        assert np.all(errors_heun <= errors_euler)
 
     def test_heun_method_compared_to_euler_for_automatic_intervals_method(self):
         """ Heun method should give better results than Euler method.
@@ -282,7 +282,7 @@ def test_heun_method_compared_to_euler_for_automatic_intervals_method(self):
         print("Average error Euler method", average_error_euler)
         print("Average error Heun  method", average_error_heun)
         assert average_error_heun < average_error_euler
-        assert np.alltrue(errors_heun <= errors_euler)
+        assert np.all(errors_heun <= errors_euler)
 
     def test_automatic_and_fixed_intervals_approach_with_single_loop(self):
         """ Automatic intervals approach with an "undemanding" threshold should use just one run of calculations, so should give the same result

codemeta.json

@@ -7,9 +7,9 @@
     "dateModified": "2023-02-12",
     "codeRepository": "https://github.com/cosimoNigro/agnpy",
     "issueTracker": "https://github.com/cosimoNigro/agnpy/issues",
-    "downloadUrl": "https://github.com/cosimoNigro/agnpy/releases/tag/v0.4.0",
+    "downloadUrl": "https://github.com/cosimoNigro/agnpy/releases/tag/v0.5.0",
     "name": "agnpy",
-    "version": "0.4.0",
+    "version": "0.5.0",
     "identifier": "10.5281/zenodo.4055175",
     "description": "agnpy is a python package focusing on the computation of the radiative processes of relativistic particles accelerated in the jets of Active Galactic Nuclei (AGN). It includes classes describing the galaxy components responsible for line and thermal emission and calculates the absorption due to gamma-gamma pair production on soft (IR-UV) photon fields.",
     "applicationCategory": "Astronomy",
@@ -18,7 +18,7 @@
     "isPartOf": "https://www.astropy.org/affiliated/",
     "referencePublication": "https://doi.org/10.1051/0004-6361/202142000",
     "readme": "https://agnpy.readthedocs.io/en/latest/",
-    "softwareVersion": "0.4.0",
+    "softwareVersion": "0.5.0",
     "funder": {
         "@type": "Organization",
         "name": "European Union's Horizon 2020 research and innovation programme"

docs/conf.py

@@ -22,7 +22,7 @@
 author = "Cosimo Nigro"
 
 # The full version, including alpha/beta/rc tags
-release = "0.4.0"
+release = "0.5.0"
 
 
 # -- General configuration ---------------------------------------------------

environment.yml

@@ -5,13 +5,13 @@ channels:
   - sherpa
 
 dependencies:
-  - python>=3.9,<3.12
-  - astropy>=5.0,<6.0
-  - numpy>=1.21
+  - python>=3.11,<3.14
+  - astropy>=7.0
+  - numpy>=1.24,<2.3
   - pandas>=1.5
-  - scipy>=1.5,<1.10
-  - pyyaml # needed to read astropy ecsv file
-  - matplotlib>=3.4,<=3.9
+  - scipy>=1.14
+  - pyyaml>=6.0 # needed to read astropy ecsv file
+  - matplotlib>=3.9.1
   - sherpa
   - pre-commit
-  - gammapy<1.2
+  - gammapy>=1.3

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="agnpy",
-    version="0.4.0",
+    version="0.5.0",
     author="Cosimo Nigro",
     author_email="cosimonigro2@gmail.com.com",
     description="Modelling jetted Active Galactic Nuclei radiative processes with python",
@@ -20,6 +20,6 @@
         "License :: OSI Approved :: BSD License",
         "Operating System :: OS Independent",
     ],
-    install_requires=["astropy>=5.0,<6.0", "numpy>=1.21", "pandas>=1.5", "scipy>=1.5,<1.10", "pyyaml", "matplotlib>=3.4,<=3.9", "sherpa", "pre-commit", "gammapy<1.2"],
-    python_requires=">=3.9,<3.12",
+    install_requires=["astropy>=7.0", "numpy>=1.24,<2.3", "pandas>=1.5", "scipy>=1.14", "pyyaml>=6.0", "matplotlib>=3.9.1", "sherpa", "pre-commit", "gammapy>=1.3"],
+    python_requires=">=3.11,<3.14",
 )