Assure that gaussfamily likelihoods have methods called in the right order

.github/workflows/ci.yml

@@ -97,7 +97,7 @@ jobs:
           pylint --rcfile firecrown/models/pylintrc firecrown/models
       - name: Running pytest
         shell: bash -l {0}
-        run: python -m pytest -vv
+        run: python -m pytest -vv --runslow
       - name: Running example - cosmosis - cosmic-shear
         shell: bash -l {0}
         run: |

docs/conf.py

@@ -19,11 +19,11 @@
 # -- Project information -----------------------------------------------------
 
 project = "firecrown"
-copyright = "2022, LSST DESC Firecrown Contributors"
+copyright = "2022--2024, LSST DESC Firecrown Contributors"
 author = "LSST DESC Firecrown Contributors"
 
 # The full version, including alpha/beta/rc tags
-release = "1.1"
+release = "1.6.1a0"
 
 
 # -- General configuration ---------------------------------------------------

docs/developer_installation.rst

@@ -150,7 +150,7 @@ Please also file an issue in the GitHub issue tracker describing the failure.
     # Update the pip-installed products.
     # The --no-deps flag is critical to avoid accidentally installing new packages
     # with pip (rather than with conda).
-    python -m pip install --upgrade --no-deps autoclasstoc cobaya
+    python -m pip install --upgrade --no-deps autoclasstoc cobaya pygobject-stubs
     # Rebuild the CSL
     cd ${CSL_DIR}
     # Optionally, you may want to update to the newest version of the CSL

firecrown/likelihood/gauss_family/gauss_family.py

@@ -8,6 +8,7 @@
 """
 
 from __future__ import annotations
+from enum import Enum
 from typing import List, Optional, Tuple, Sequence
 from typing import final
 import warnings
@@ -18,24 +19,46 @@
 
 import sacc
 
+from ...parameters import ParamsMap
 from ..likelihood import Likelihood
 from ...modeling_tools import ModelingTools
 from ...updatable import UpdatableCollection
 from .statistic.statistic import Statistic, GuardedStatistic
 
 
+class State(Enum):
+    """The states used in GaussFamily."""
+
+    INITIALIZED = 1
+    READY = 2
+    UPDATED = 3
+
+
 class GaussFamily(Likelihood):
     """GaussFamily is an abstract class. It is the base class for all likelihoods
     based on a chi-squared calculation. It provides an implementation of
     Likelihood.compute_chisq. Derived classes must implement the abstract method
     compute_loglike, which is inherited from Likelihood.
+
+    GaussFamily (and all classes that inherit from it) must abide by the the
+    following rules regarding the order of calling of methods.
+
+      1. after a new object is created, :meth:`read` must be called before any
+         other method in the interfaqce.
+      2. after :meth:`read` has been called it is legal to call
+         :meth:`get_data_vector`, or to call :meth:`update`.
+      3. after :meth:`update` is called it is then legal to call
+         :meth:`calculate_loglike` or :meth:`get_data_vector`, or to reset
+         the object (returning to the pre-update state) by calling
+         :meth:`reset`.
     """
 
     def __init__(
         self,
         statistics: Sequence[Statistic],
     ):
         super().__init__()
+        self.state: State = State.INITIALIZED
         if len(statistics) == 0:
             raise ValueError("GaussFamily requires at least one statistic")
         self.statistics: UpdatableCollection = UpdatableCollection(
@@ -45,9 +68,28 @@ def __init__(
         self.cholesky: Optional[npt.NDArray[np.float64]] = None
         self.inv_cov: Optional[npt.NDArray[np.float64]] = None
 
+    def _update(self, _: ParamsMap) -> None:
+        """Handle the state resetting required by :class:`GaussFamily`
+        likelihoods. Any derived class that needs to implement :meth:`_update`
+        for its own reasons must be sure to do what this does: check the state
+        at the start of the method, and change the state at the end of the
+        method."""
+        assert self.state == State.READY, "read() must be called before update()"
+        self.state = State.UPDATED
+
+    def _reset(self) -> None:
+        """Handle the state resetting required by :class:`GaussFamily`
+        likelihoods. Any derived class that needs to implement :meth:`reset`
+        for its own reasons must be sure to do what this does: check the state
+        at the start of the method, and change the state at the end of the
+        method."""
+        assert self.state == State.UPDATED, "update() must be called before reset()"
+        self.state = State.READY
+
     def read(self, sacc_data: sacc.Sacc) -> None:
         """Read the covariance matrix for this likelihood from the SACC file."""
 
+        assert self.state == State.INITIALIZED, "read() must only be called once"
         if sacc_data.covariance is None:
             msg = (
                 f"The {type(self).__name__} likelihood requires a covariance, "
@@ -71,20 +113,26 @@ def read(self, sacc_data: sacc.Sacc) -> None:
         self.cholesky = scipy.linalg.cholesky(self.cov, lower=True)
         self.inv_cov = np.linalg.inv(cov)
 
+        self.state = State.READY
+
     @final
     def get_cov(self) -> npt.NDArray[np.float64]:
         """Gets the current covariance matrix."""
+        assert self._is_ready(), "read() must be called before get_cov()"
         assert self.cov is not None
+        # We do not change the state.
         return self.cov
 
     @final
     def get_data_vector(self) -> npt.NDArray[np.float64]:
         """Get the data vector from all statistics and concatenate in the right
         order."""
+        assert self._is_ready(), "read() must be called before get_data_vector()"
 
         data_vector_list: List[npt.NDArray[np.float64]] = [
             stat.get_data_vector() for stat in self.statistics
         ]
+        # We do not change the state.
         return np.concatenate(data_vector_list)
 
     @final
@@ -93,18 +141,22 @@ def compute_theory_vector(self, tools: ModelingTools) -> npt.NDArray[np.float64]
 
         :param tools: Current ModelingTools object
         """
+        assert (
+            self.state == State.UPDATED
+        ), "update() must be called before compute_theory_vector()"
 
         theory_vector_list: List[npt.NDArray[np.float64]] = [
             stat.compute_theory_vector(tools) for stat in self.statistics
         ]
+        # We do not change the state
         return np.concatenate(theory_vector_list)
 
     @final
     def compute(
         self, tools: ModelingTools
     ) -> Tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
         """Calculate and return both the data and theory vectors."""
-
+        assert self.state == State.UPDATED, "update() must be called before compute()"
         warnings.simplefilter("always", DeprecationWarning)
         warnings.warn(
             "The use of the `compute` method on Statistic is deprecated."
@@ -113,11 +165,15 @@ def compute(
             category=DeprecationWarning,
         )
 
+        # We do not change the state.
         return self.get_data_vector(), self.compute_theory_vector(tools)
 
     @final
     def compute_chisq(self, tools: ModelingTools) -> float:
         """Calculate and return the chi-squared for the given cosmology."""
+        assert (
+            self.state == State.UPDATED
+        ), "update() must be called before compute_chisq()"
         theory_vector: npt.NDArray[np.float64]
         data_vector: npt.NDArray[np.float64]
         residuals: npt.NDArray[np.float64]
@@ -136,4 +192,9 @@ def compute_chisq(self, tools: ModelingTools) -> float:
         x = scipy.linalg.solve_triangular(self.cholesky, residuals, lower=True)
         chisq = np.dot(x, x)
 
+        # We do not change the state.
         return chisq
+
+    def _is_ready(self) -> bool:
+        """Return True if the state is either READY or UPDATED."""
+        return self.state in (State.READY, State.UPDATED)

firecrown/likelihood/gauss_family/statistic/statistic.py

@@ -4,7 +4,7 @@
 ================================
 
 The Statistic class describing objects that implement methods to compute the
-data and theory vectors for a GaussianFamily subclass.
+data and theory vectors for a :class:`GaussFamily` subclass.
 
 """
 

tests/likelihood/gauss_family/test_student_t.py

@@ -29,6 +29,12 @@ def test_require_nonempty_statistics():
         _ = StudentT(statistics=[])
 
 
+def test_update_fails_before_read(trivial_stats, trivial_params_student_t):
+    likelihood = StudentT(statistics=trivial_stats)
+    with pytest.raises(AssertionError):
+        likelihood.update(trivial_params_student_t)
+
+
 def test_get_cov_fails_before_read(trivial_stats):
     likelihood = StudentT(statistics=trivial_stats)
     with pytest.raises(AssertionError):