Apply the v1.16.1 fixes to master

dependencies-validated.yaml

@@ -5,10 +5,10 @@
 # firecrown-deps-validated metapackage.
 #
 # The digest records which environment.yml the lockfiles were solved
-# from, so that pins left behind by a manifest edit are detected.
-environment-sha256: "8ada10463b470da5f4f2d7d49d676498d471c635cd770c1a7037b927387edcf8"
+# from as historical metadata; --check verifies constraints from locks.
+environment-sha256: "52bad1a39356cd718b23ced5b6cbe6a2174801a7ab5109885c91a87b2c62bd6d"
 constraints:
-  astropy: ">=8.0.1,<8.1"
+  astropy: ">=8.0.2,<8.1"
   camb: ">=1.6.5,<1.7"
   charset-normalizer: ">=3.5.1,<3.6"
   clmm: ">=1.16.10,<1.17"
@@ -23,20 +23,20 @@ constraints:
   idna: ">=3.20,<3.21"
   lsstdesc-crow: ">=1.0.12,<1.1"
   matplotlib-base: ">=3.11.2,<3.12"
-  more-itertools: ">=11.1.0,<11.2"
-  numcosmo: ">=0.27.0,<0.28"
+  more-itertools: ">=11.2.1,<11.3"
+  numcosmo: ">=0.28.0,<0.29"
   numpy: ">=2.3.5,<2.4"
-  pip: ">=26.2.1,<26.3"
+  pip: ">=26.2.2,<26.3"
   portalocker: ">=3.2.0,<3.3"
   pybobyqa: ">=1.5.0,<1.6"
   pyccl: ">=3.3.6,<3.4"
-  pydantic: ">=2.13.5,<2.14"
+  pydantic: ">=2.14.1,<2.15"
   pyyaml: ">=6.0.3,<6.1"
   rich: ">=15.0.0,<15.1"
   sacc: ">=2.4,<2.5"
   scipy: ">=1.18.1,<1.19"
   tabulate: ">=0.10.0,<0.11"
-  typer: ">=0.27.2,<0.28"
+  typer: ">=0.27.3,<0.28"
   types-pyyaml: ">=6.0.12.20260906,<6.1"
   typing_extensions: ">=4.16.0,<4.17"
   urllib3: ">=2.8.0,<2.9"

dependencies.yaml

@@ -58,7 +58,8 @@ runtime:
     conda: false
     note: cobaya connector; not packaged on conda-forge
   - name: cosmosis
-    version: ">=3.0"
+    version: ">=3.0,<3.26"
+    note: 3.26 .mod files need gfortran 15; camb <2.0 holds compilers at 14
   - name: cosmosis-build-standard-library
     pip: false
     import: false
@@ -71,7 +72,7 @@ runtime:
     import: matplotlib
     note: firecrown sacc view
   - name: numcosmo
-    version: ">=0.27"
+    version: ">=0.28,<1.0"
     pip: numcosmo_py
     import: numcosmo_py
   - name: numpy
@@ -121,6 +122,8 @@ devenv:
   - name: pandas
     note: tutorials
   - name: plotnine
+  - name: pygobject-stubs
+    version: "<2.18"
   - name: pylint
   - name: pytest
   - name: pytest-cov

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - charset-normalizer
   - clmm # part of the DESC stack; needed indirectly through lsstdesc-crow
   - compilers # two-phase cosmosis-standard-library installation
-  - cosmosis >=3.0
+  - cosmosis >=3.0,<3.26 # 3.26 .mod files need gfortran 15; camb <2.0 holds compilers at 14
   - cosmosis-build-standard-library
   - coverage
   - cython
@@ -33,7 +33,7 @@ dependencies:
   - matplotlib-base # firecrown sacc view
   - more-itertools
   - mypy
-  - numcosmo >=0.27
+  - numcosmo >=0.28,<1.0
   - numpy >=2.0,<2.4
   - pandas # tutorials
   - pip >=20.1 # installs cobaya, which conda-forge does not package
@@ -46,6 +46,7 @@ dependencies:
   - pybobyqa
   - pyccl >=2.8.0
   - pydantic
+  - pygobject-stubs <2.18
   - pylint
   - pytest
   - pytest-cov

firecrown/app/analysis/_numcosmo.py

@@ -441,14 +441,14 @@ def _setup_cosmology(
 
     assert mapping is not None
 
+    prim = Nc.HIPrimPowerLaw.new()  # pylint: disable=no-value-for-parameter
+    reion = Nc.HIReionCamb.new()  # pylint: disable=no-value-for-parameter
     cosmo = Nc.HICosmoDECpl(
-        massnu_length=options.cosmo_spec.get_num_massive_neutrinos()
+        massnu_length=options.cosmo_spec.get_num_massive_neutrinos(),
+        prim=prim,
+        reion=reion,
     )
     cosmo.omega_x2omega_k()
-    prim = Nc.HIPrimPowerLaw.new()  # pylint: disable=no-value-for-parameter
-    reion = Nc.HIReionCamb.new()  # pylint: disable=no-value-for-parameter
-    cosmo.add_submodel(prim)
-    cosmo.add_submodel(reion)
     mset.set(cosmo)
 
     _set_standard_params(options, mset, cosmo, prim, reion, priors)

firecrown/app/examples/_cluster_data.py

@@ -119,11 +119,9 @@ class StackedProfiles:
 
 def _numcosmo_cosmology() -> Nc.HICosmoDEXcdm:
     """Create the fiducial NumCosmo cosmology normalized to sigma8."""
-    cosmo = Nc.HICosmoDEXcdm()
     reion = Nc.HIReionCamb.new()  # pylint: disable=no-value-for-parameter
     prim = Nc.HIPrimPowerLaw.new()  # pylint: disable=no-value-for-parameter
-    cosmo.add_submodel(reion)
-    cosmo.add_submodel(prim)
+    cosmo = Nc.HICosmoDEXcdm(prim=prim, reion=reion)
 
     psml = Nc.PowspecMLTransfer.new(
         Nc.TransferFuncEH.new()  # pylint: disable=no-value-for-parameter

firecrown/likelihood/_binned_cluster.py

@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+from abc import ABC
+
 import numpy as np
 from crow.properties import ClusterProperty
 from crow.recipes.binned_parent import (
@@ -20,7 +22,7 @@
 from firecrown.models.cluster import ClusterData, SaccBin
 
 
-class BinnedCluster(Statistic):
+class BinnedCluster(Statistic, ABC):
     """A statistic representing clusters in a z, mass bin."""
 
     def __init__(

firecrown/likelihood/_gaussfamily.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import warnings
+from abc import ABC
 from collections.abc import Callable, Sequence
 from enum import Enum
 from functools import wraps
@@ -113,7 +114,7 @@ def wrapper_repeat(*args: P.args, **kwargs: P.kwargs) -> T:
     return decorator_enforce_states
 
 
-class GaussFamily(Likelihood):
+class GaussFamily(Likelihood, ABC):
     """GaussFamily is the base class for likelihoods based on a chi-squared calculation.
 
     It provides an implementation of Likelihood.compute_chisq. Derived classes must

firecrown/likelihood/_student_t.py

@@ -4,6 +4,7 @@
 from typing import cast
 
 import numpy as np
+import numpy.typing as npt
 
 from firecrown.likelihood._gaussfamily import GaussFamily
 from firecrown.likelihood_base import Statistic
@@ -43,3 +44,12 @@ def compute_loglike(self, tools: ModelingTools) -> float:
         """
         chi2 = self.compute_chisq(tools)
         return -0.5 * self.nu * np.log(1.0 + chi2 / (self.nu - 1.0))
+
+    def make_realization_vector(self) -> npt.NDArray[np.float64]:
+        """Create a new realization of the model.
+
+        Realizations are not available for the Student-t likelihood.
+
+        :raises NotImplementedError: always.
+        """
+        raise NotImplementedError("StudentT does not support realizations.")

firecrown/likelihood_base.py

@@ -14,7 +14,7 @@
 from __future__ import annotations
 
 import warnings
-from abc import abstractmethod
+from abc import ABC, abstractmethod
 from collections.abc import Mapping, Sequence
 from dataclasses import dataclass, replace
 from typing import Annotated, Generic, Literal, TypeVar, cast, final
@@ -1107,9 +1107,11 @@ def apply(
         return replace(tracer_arg, field=self.field)
 
 
-class SourceGalaxy(Source, Generic[_SourceGalaxyArgsT]):
+class SourceGalaxy(Source, Generic[_SourceGalaxyArgsT], ABC):
     """Source class for galaxy based sources."""
 
+    tracer_args: _SourceGalaxyArgsT
+
     def __init__(
         self,
         *,
@@ -1129,7 +1131,6 @@ def __init__(
         self.systematics: UpdatableCollection[
             SourceGalaxySystematic[_SourceGalaxyArgsT]
         ] = UpdatableCollection(systematics)
-        self.tracer_args: _SourceGalaxyArgsT
 
     def read_systematics(self, sacc_data: sacc.Sacc) -> None:
         """Read the systematics for this source from the SACC file.

firecrown/models/two_point/_theory.py

@@ -129,6 +129,6 @@ def get_tracers_and_scales(
     def generate_ells_for_interpolation(self) -> npt.NDArray[np.int64]:
         """Generate ells for interpolation."""
         assert self.ells is not None
-        min_ell = int(self.ells[0])
-        max_ell = int(self.ells[-1])
+        min_ell = int(np.min(self.ells))
+        max_ell = int(np.max(self.ells))
         return self.interp_ells_gen.generate(min_ell, max_ell)

pyproject.toml

@@ -14,12 +14,12 @@ dependencies = [
     "astropy",
     "camb<2.0",
     "cobaya",
-    "cosmosis>=3.0",
+    "cosmosis>=3.0,<3.26",
     "fitsio",
     "isitgr",
     "lsstdesc-crow",
     "matplotlib",
-    "numcosmo_py>=0.27",
+    "numcosmo_py>=0.28,<1.0",
     "numpy>=2.0,<2.4",
     "pyccl>=2.8.0",
     "pydantic",

tests/app/analysis/test_numcosmo_parameters.py

@@ -85,9 +85,8 @@ def test_set_amplitude_a_s_no_prior(
         )
 
         # Create minimal NumCosmo objects with proper hierarchy
-        cosmo = Nc.HICosmoDECpl.new()  # pylint: disable=no-value-for-parameter
         prim = Nc.HIPrimPowerLaw.new()  # pylint: disable=no-value-for-parameter
-        cosmo.add_submodel(prim)
+        cosmo = Nc.HICosmoDECpl(prim=prim)
         mset = Ncm.MSet.new_array([cosmo])
 
         priors: list[Ncm.Prior] = []

tests/connector/numcosmo/conftest.py

@@ -10,28 +10,26 @@
 @pytest.fixture(name="numcosmo_cosmo_xcdm")
 def fixture_numcosmo_cosmo_xcdm():
     """Create a NumCosmo cosmology instance of XCDM."""
-    cosmo = Nc.HICosmoDEXcdm(massnu_length=1)
+    prim = Nc.HIPrimPowerLaw.new()
+    prim.param_set_by_name(  # pylint: disable=no-member
+        "ln10e10ASA", math.log(1.0e10 * 2.0e-09)
+    )
+    prim.param_set_by_name("n_SA", 0.971)  # pylint: disable=no-member
+    reion = Nc.HIReionCamb.new()
+    bbn = Nc.BBNParametrized.new()
+    bbn.param_set_by_name("Yp", 0.2454)  # pylint: disable=no-member
+
+    cosmo = Nc.HICosmoDEXcdm(massnu_length=1, prim=prim, reion=reion, bbn=bbn)
     cosmo.omega_x2omega_k()
     cosmo.param_set_by_name("H0", 68.2)
     cosmo.param_set_by_name("Omegak", 0.0)
     cosmo.param_set_by_name("Omegab", 0.022558514 / 0.682**2)
     cosmo.param_set_by_name("Omegac", 0.118374058 / 0.682**2)
     cosmo.param_set_by_name("massnu_0", 0.06)
     cosmo.param_set_by_name("ENnu", 2.0328)
-    cosmo.param_set_by_name("Yp", 0.2454)
     cosmo.param_set_by_name("w", -1.0)
 
-    prim = Nc.HIPrimPowerLaw.new()
-    prim.param_set_by_name(  # pylint: disable=no-member
-        "ln10e10ASA", math.log(1.0e10 * 2.0e-09)
-    )
-    prim.param_set_by_name("n_SA", 0.971)  # pylint: disable=no-member
-
-    reion = Nc.HIReionCamb.new()
-    reion.set_z_from_tau(cosmo, 0.0561)  # pylint: disable=no-member
-
-    cosmo.add_submodel(prim)
-    cosmo.add_submodel(reion)
+    reion.set_z_from_tau(0.0561)  # pylint: disable=no-member
 
     p_ml = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
     p_mnl = Nc.PowspecMNLHaloFit.new(p_ml, 3.0, 1.0e-5)
@@ -44,27 +42,25 @@ def fixture_numcosmo_cosmo_xcdm():
 @pytest.fixture(name="numcosmo_cosmo_xcdm_no_nu")
 def fixture_numcosmo_cosmo_xcdm_no_nu():
     """Create a NumCosmo cosmology instance of XCDM without neutrinos."""
-    cosmo = Nc.HICosmoDEXcdm()
+    prim = Nc.HIPrimPowerLaw.new()
+    prim.param_set_by_name(  # pylint: disable=no-member
+        "ln10e10ASA", math.log(1.0e10 * 2.0e-09)
+    )
+    prim.param_set_by_name("n_SA", 0.971)  # pylint: disable=no-member
+    reion = Nc.HIReionCamb.new()
+    bbn = Nc.BBNParametrized.new()
+    bbn.param_set_by_name("Yp", 0.2454)  # pylint: disable=no-member
+
+    cosmo = Nc.HICosmoDEXcdm(prim=prim, reion=reion, bbn=bbn)
     cosmo.omega_x2omega_k()
     cosmo.param_set_by_name("H0", 68.2)
     cosmo.param_set_by_name("Omegak", 0.0)
     cosmo.param_set_by_name("Omegab", 0.022558514 / 0.682**2)
     cosmo.param_set_by_name("Omegac", 0.118374058 / 0.682**2)
     cosmo.param_set_by_name("ENnu", 3.046)
-    cosmo.param_set_by_name("Yp", 0.2454)
     cosmo.param_set_by_name("w", -1.0)
 
-    prim = Nc.HIPrimPowerLaw.new()
-    prim.param_set_by_name(  # pylint: disable=no-member
-        "ln10e10ASA", math.log(1.0e10 * 2.0e-09)
-    )
-    prim.param_set_by_name("n_SA", 0.971)  # pylint: disable=no-member
-
-    reion = Nc.HIReionCamb.new()
-    reion.set_z_from_tau(cosmo, 0.0561)  # pylint: disable=no-member
-
-    cosmo.add_submodel(prim)
-    cosmo.add_submodel(reion)
+    reion.set_z_from_tau(0.0561)  # pylint: disable=no-member
 
     p_ml = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
     p_mnl = Nc.PowspecMNLHaloFit.new(p_ml, 3.0, 1.0e-5)
@@ -79,28 +75,26 @@ def fixture_numcosmo_cosmo_cpl():
     """Create a NumCosmo cosmology instance using CPL parametrization for the dark
     energy equation of state."""
 
-    cosmo = Nc.HICosmoDECpl()
+    prim = Nc.HIPrimPowerLaw.new()
+    prim.param_set_by_name(  # pylint: disable=no-member
+        "ln10e10ASA", math.log(1.0e10 * 2.0e-09)
+    )
+    prim.param_set_by_name("n_SA", 0.971)  # pylint: disable=no-member
+    reion = Nc.HIReionCamb.new()
+    bbn = Nc.BBNParametrized.new()
+    bbn.param_set_by_name("Yp", 0.2454)  # pylint: disable=no-member
+
+    cosmo = Nc.HICosmoDECpl(prim=prim, reion=reion, bbn=bbn)
     cosmo.omega_x2omega_k()
     cosmo.param_set_by_name("H0", 68.2)
     cosmo.param_set_by_name("Omegak", 0.0)
     cosmo.param_set_by_name("Omegab", 0.022558514 / 0.682**2)
     cosmo.param_set_by_name("Omegac", 0.118374058 / 0.682**2)
     cosmo.param_set_by_name("ENnu", 3.046)
-    cosmo.param_set_by_name("Yp", 0.2454)
     cosmo.param_set_by_name("w0", -1.0)
     cosmo.param_set_by_name("w1", 0.1)
 
-    prim = Nc.HIPrimPowerLaw.new()
-    prim.param_set_by_name(  # pylint: disable=no-member
-        "ln10e10ASA", math.log(1.0e10 * 2.0e-09)
-    )
-    prim.param_set_by_name("n_SA", 0.971)  # pylint: disable=no-member
-
-    reion = Nc.HIReionCamb.new()
-    reion.set_z_from_tau(cosmo, 0.0561)  # pylint: disable=no-member
-
-    cosmo.add_submodel(prim)
-    cosmo.add_submodel(reion)
+    reion.set_z_from_tau(0.0561)  # pylint: disable=no-member
 
     p_ml = Nc.PowspecMLTransfer.new(Nc.TransferFuncEH.new())
     p_mnl = Nc.PowspecMNLHaloFit.new(p_ml, 3.0, 1.0e-5)

tests/connector/numcosmo/test_numcosmo_connector.py

@@ -455,9 +455,7 @@ def test_numcosmo_data_pure_ccl_mode():
     model.params_set_default_ftype()
 
     # Create a basic cosmology model as well
-    cosmo = Nc.HICosmoDEXcdm()
-    cosmo.add_submodel(Nc.HIPrimPowerLaw.new())
-    cosmo.add_submodel(Nc.HIReionCamb.new())
+    cosmo = Nc.HICosmoDEXcdm(prim=Nc.HIPrimPowerLaw.new(), reion=Nc.HIReionCamb.new())
 
     mset = Ncm.MSet()
     mset.set(cosmo)
@@ -569,9 +567,7 @@ def test_numcosmo_gauss_cov_pure_ccl_mode():
     model.params_set_default_ftype()
 
     # Create a basic cosmology model as well
-    cosmo = Nc.HICosmoDEXcdm()
-    cosmo.add_submodel(Nc.HIPrimPowerLaw.new())
-    cosmo.add_submodel(Nc.HIReionCamb.new())
+    cosmo = Nc.HICosmoDEXcdm(prim=Nc.HIPrimPowerLaw.new(), reion=Nc.HIReionCamb.new())
 
     mset = Ncm.MSet()
     mset.set(cosmo)