Prepare classes in sacc supportpy for move to sacc (#282)

* Adjust pyccl calls to match pyccl 2.8.0 release
* Adjust names and add documentation
* Adjust examples and notebooks for name changes
* Apply black
* Attempted fix for CCL 2.8.0 upgrade

examples/cluster_number_counts/demo_sacc_for_clusters.ipynb

@@ -264,16 +264,16 @@
     "s_count.add_tracer(\"cluster_survey\", survey_name, area)\n",
     "\n",
     "for i, z_bin in enumerate(zip(z_edges[:-1], z_edges[1:])):\n",
-    "    z_lower, z_upper = z_bin\n",
+    "    lower, upper = z_bin\n",
     "    bin_z_label = f\"bin_z_{i}\"\n",
-    "    s_count.add_tracer(\"bin_z\", bin_z_label, z_lower, z_upper)\n",
+    "    s_count.add_tracer(\"bin_z\", bin_z_label, lower, upper)\n",
     "    bin_z_labels.append(bin_z_label)\n",
     "\n",
     "for i, richness_bin in enumerate(zip(richness_edges[:-1], richness_edges[1:])):\n",
-    "    richness_lower, richness_upper = richness_bin\n",
+    "    lower, upper = richness_bin\n",
     "    bin_richness_label = f\"bin_rich_{i}\"\n",
     "    s_count.add_tracer(\n",
-    "        \"bin_richness\", bin_richness_label, richness_lower, richness_upper\n",
+    "        \"bin_richness\", bin_richness_label, lower, upper\n",
     "    )\n",
     "    bin_richness_labels.append(bin_richness_label)\n",
     "\n",
@@ -404,16 +404,16 @@
     "s_count2.add_tracer(\"cluster_survey\", survey_name, area)\n",
     "\n",
     "for i, z_bin in enumerate(zip(z_edges[:-1], z_edges[1:])):\n",
-    "    z_lower, z_upper = z_bin\n",
+    "    lower, upper = z_bin\n",
     "    bin_z_label = f\"bin_z_{i}\"\n",
-    "    s_count2.add_tracer(\"bin_z\", bin_z_label, z_lower, z_upper)\n",
+    "    s_count2.add_tracer(\"bin_z\", bin_z_label, lower, upper)\n",
     "    bin_z_labels.append(bin_z_label)\n",
     "\n",
     "for i, richness_bin in enumerate(zip(richness_edges[:-1], richness_edges[1:])):\n",
-    "    richness_lower, richness_upper = richness_bin\n",
+    "    lower, upper = richness_bin\n",
     "    bin_richness_label = f\"bin_rich_{i}\"\n",
     "    s_count2.add_tracer(\n",
-    "        \"bin_richness\", bin_richness_label, richness_lower, richness_upper\n",
+    "        \"bin_richness\", bin_richness_label, lower, upper\n",
     "    )\n",
     "    bin_richness_labels.append(bin_richness_label)\n",
     "\n",
@@ -560,7 +560,7 @@
    "source": [
     "DS0 = [s_count2.get_data_points(data_type='cluster_shear', tracers=('NC_mock_redshift_richness', 'bin_z_1', 'bin_rich_0', f'bin_radius_{i}'))[0].value for i in np.arange(len(radius_edges)-1)]\n",
     "DS2 = [s_count2.get_data_points(data_type='cluster_shear', tracers=('NC_mock_redshift_richness', 'bin_z_1', 'bin_rich_2', f'bin_radius_{i}'))[0].value for i in np.arange(len(radius_edges)-1)]\n",
-    "r_arr = [s_count2.get_tracer(f'bin_radius_{i}').r_center for i in np.arange(len(radius_edges)-1)]"
+    "r_arr = [s_count2.get_tracer(f'bin_radius_{i}').center for i in np.arange(len(radius_edges)-1)]"
    ]
   },
   {

examples/cluster_number_counts/generate_rich_mean_mass_sacc_data.py

@@ -164,17 +164,15 @@ def generate_sacc_file():
     s_count.add_tracer("cluster_survey", survey_name, area)
 
     for i, z_bin in enumerate(zip(z_edges[:-1], z_edges[1:])):
-        z_lower, z_upper = z_bin
+        lower, upper = z_bin
         bin_z_label = f"bin_z_{i}"
-        s_count.add_tracer("bin_z", bin_z_label, z_lower, z_upper)
+        s_count.add_tracer("bin_z", bin_z_label, lower, upper)
         bin_z_labels.append(bin_z_label)
 
     for i, richness_bin in enumerate(zip(richness_edges[:-1], richness_edges[1:])):
-        richness_lower, richness_upper = richness_bin
+        lower, upper = richness_bin
         bin_richness_label = f"rich_{i}"
-        s_count.add_tracer(
-            "bin_richness", bin_richness_label, richness_lower, richness_upper
-        )
+        s_count.add_tracer("bin_richness", bin_richness_label, lower, upper)
         bin_richness_labels.append(bin_richness_label)
 
     #  pylint: disable-next=no-member

firecrown/connector/cobaya/ccl.py

@@ -35,7 +35,7 @@ def initialize(self):
 
         self.a_bg = np.linspace(0.1, 1.0, 50)
         self.z_bg = 1.0 / self.a_bg - 1.0
-        self.z_Pk = np.arange(0.2, 6.0, 1)
+        self.z_Pk = np.arange(0.0, 6.0, 1)
         self.Pk_kmax = 1.0
 
     def get_param(self, p: str) -> None:

firecrown/models/cluster_mass_rich_proxy.py

@@ -115,7 +115,7 @@ def gen_bin_from_tracer(self, tracer: sacc.BaseTracer) -> ClusterMassArgument:
             raise ValueError("Tracer must be a BinRichnessTracer")
 
         return ClusterMassRichBinArgument(
-            self, self.logMl, self.logMu, tracer.richness_lower, tracer.richness_upper
+            self, self.logMl, self.logMu, tracer.lower, tracer.upper
         )
 
 

firecrown/models/cluster_redshift_spec.py

@@ -50,8 +50,8 @@ def gen_bins_by_array(self, z_bins: np.ndarray) -> List[ClusterRedshiftArgument]
         # itertools.pairwise is only available in Python 3.10
         # using zip instead
         return [
-            ClusterRedshiftSpecArgument(z_lower, z_upper)
-            for z_lower, z_upper in zip(z_bins[:-1], z_bins[1:])
+            ClusterRedshiftSpecArgument(lower, upper)
+            for lower, upper in zip(z_bins[:-1], z_bins[1:])
         ]
 
     def point_arg(self, z: float) -> ClusterRedshiftArgument:
@@ -65,7 +65,7 @@ def gen_bin_from_tracer(self, tracer: sacc.BaseTracer) -> ClusterRedshiftArgumen
         if not isinstance(tracer, sacc_support.BinZTracer):
             raise ValueError("Tracer must be a BinZTracer")
 
-        return ClusterRedshiftSpecArgument(tracer.z_lower, tracer.z_upper)
+        return ClusterRedshiftSpecArgument(tracer.lower, tracer.upper)
 
 
 class ClusterRedshiftSpecArgument(ClusterRedshiftArgument):

firecrown/sacc_support.py

@@ -18,17 +18,17 @@
 class BinZTracer(BaseTracer, tracer_type="bin_z"):  # type: ignore
     """A tracer for a single redshift bin."""
 
-    def __init__(self, name: str, z_lower: float, z_upper: float, **kwargs):
+    def __init__(self, name: str, lower: float, upper: float, **kwargs):
         """
         Create a tracer corresponding to a single redshift bin.
 
         :param name: The name of the tracer
-        :param z_lower: The lower bound of the redshift bin
-        :param z_upper: The upper bound of the redshift bin
+        :param lower: The lower bound of the redshift bin
+        :param upper: The upper bound of the redshift bin
         """
         super().__init__(name, **kwargs)
-        self.z_lower = z_lower
-        self.z_upper = z_upper
+        self.lower = lower
+        self.upper = upper
 
     def __eq__(self, other) -> bool:
         """Test for equality.  If :python:`other` is not a
@@ -39,8 +39,8 @@ def __eq__(self, other) -> bool:
             return False
         return (
             self.name == other.name
-            and self.z_lower == other.z_lower
-            and self.z_upper == other.z_upper
+            and self.lower == other.lower
+            and self.upper == other.upper
         )
 
     @classmethod
@@ -54,13 +54,13 @@ def to_tables(cls, instance_list):
         :return: List with a single astropy table
         """
 
-        names = ["name", "quantity", "z_lower", "z_upper"]
+        names = ["name", "quantity", "lower", "upper"]
 
         cols = [
             [obj.name for obj in instance_list],
             [obj.quantity for obj in instance_list],
-            [obj.z_lower for obj in instance_list],
-            [obj.z_upper for obj in instance_list],
+            [obj.lower for obj in instance_list],
+            [obj.upper for obj in instance_list],
         ]
 
         table = Table(data=cols, names=names)
@@ -85,11 +85,9 @@ def from_tables(cls, table_list):
             for row in table:
                 name = row["name"]
                 quantity = row["quantity"]
-                z_lower = row["z_lower"]
-                z_upper = row["z_upper"]
-                tracers[name] = cls(
-                    name, quantity=quantity, z_lower=z_lower, z_upper=z_upper
-                )
+                lower = row["lower"]
+                upper = row["upper"]
+                tracers[name] = cls(name, quantity=quantity, lower=lower, upper=upper)
         return tracers
 
 
@@ -105,23 +103,21 @@ def __eq__(self, other) -> bool:
             return False
         return (
             self.name == other.name
-            and self.richness_lower == other.richness_lower
-            and self.richness_upper == other.richness_upper
+            and self.lower == other.lower
+            and self.upper == other.upper
         )
 
-    def __init__(
-        self, name: str, richness_lower: float, richness_upper: float, **kwargs
-    ):
+    def __init__(self, name: str, lower: float, upper: float, **kwargs):
         """
         Create a tracer corresponding to a single richness bin.
 
         :param name: The name of the tracer
-        :param richness_lower: The lower bound of the redshift bin
-        :param richness_upper: The upper bound of the redshift bin
+        :param lower: The lower bound of the redshift bin
+        :param upper: The upper bound of the redshift bin
         """
         super().__init__(name, **kwargs)
-        self.richness_lower = richness_lower
-        self.richness_upper = richness_upper
+        self.lower = lower
+        self.upper = upper
 
     @classmethod
     def to_tables(cls, instance_list):
@@ -133,13 +129,13 @@ def to_tables(cls, instance_list):
         :param instance_list: List of tracer instances
         :return: List with a single astropy table
         """
-        names = ["name", "quantity", "richness_lower", "richness_upper"]
+        names = ["name", "quantity", "lower", "upper"]
 
         cols = [
             [obj.name for obj in instance_list],
             [obj.quantity for obj in instance_list],
-            [obj.richness_lower for obj in instance_list],
-            [obj.richness_upper for obj in instance_list],
+            [obj.lower for obj in instance_list],
+            [obj.upper for obj in instance_list],
         ]
 
         table = Table(data=cols, names=names)
@@ -164,13 +160,13 @@ def from_tables(cls, table_list):
             for row in table:
                 name = row["name"]
                 quantity = row["quantity"]
-                richness_lower = row["richness_lower"]
-                richness_upper = row["richness_upper"]
+                lower = row["lower"]
+                upper = row["upper"]
                 tracers[name] = cls(
                     name,
                     quantity=quantity,
-                    richness_lower=richness_lower,
-                    richness_upper=richness_upper,
+                    lower=lower,
+                    upper=upper,
                 )
         return tracers
 
@@ -187,25 +183,27 @@ def __eq__(self, other) -> bool:
             return False
         return (
             self.name == other.name
-            and self.r_lower == other.r_lower
-            and self.r_center == other.r_center
-            and self.r_upper == other.r_upper
+            and self.lower == other.lower
+            and self.center == other.center
+            and self.upper == other.upper
         )
 
-    def __init__(
-        self, name: str, r_lower: float, r_upper: float, r_center: float, **kwargs
-    ):
+    def __init__(self, name: str, lower: float, upper: float, center: float, **kwargs):
         """
         Create a tracer corresponding to a single radial bin.
 
         :param name: The name of the tracer
-        :param r_lower: The lower bound of the radius bin
-        :param r_upper: The upper bound of the radius bin
+        :param lower: The lower bound of the radius bin
+        :param upper: The upper bound of the radius bin
+        :param center: The value to use if a single point-estimate is needed.
+
+        Note that :python:`center` need not be the midpoint between
+        :python:`lower` and :python:`upper`'.
         """
         super().__init__(name, **kwargs)
-        self.r_lower = r_lower
-        self.r_upper = r_upper
-        self.r_center = r_center
+        self.lower = lower
+        self.upper = upper
+        self.center = center
 
     @classmethod
     def to_tables(cls, instance_list):
@@ -218,14 +216,14 @@ def to_tables(cls, instance_list):
         :return: List with a single astropy table
         """
 
-        names = ["name", "quantity", "r_lower", "r_upper", "r_center"]
+        names = ["name", "quantity", "lower", "upper", "center"]
 
         cols = [
             [obj.name for obj in instance_list],
             [obj.quantity for obj in instance_list],
-            [obj.r_lower for obj in instance_list],
-            [obj.r_upper for obj in instance_list],
-            [obj.r_center for obj in instance_list],
+            [obj.lower for obj in instance_list],
+            [obj.upper for obj in instance_list],
+            [obj.center for obj in instance_list],
         ]
 
         table = Table(data=cols, names=names)
@@ -250,15 +248,15 @@ def from_tables(cls, table_list):
             for row in table:
                 name = row["name"]
                 quantity = row["quantity"]
-                r_lower = row["r_lower"]
-                r_upper = row["r_upper"]
-                r_center = row["r_center"]
+                lower = row["lower"]
+                upper = row["upper"]
+                center = row["center"]
                 tracers[name] = cls(
                     name,
                     quantity=quantity,
-                    r_lower=r_lower,
-                    r_upper=r_upper,
-                    r_center=r_center,
+                    lower=lower,
+                    upper=upper,
+                    center=center,
                 )
         return tracers
 

tests/test_pt_systematics.py

@@ -96,7 +96,7 @@ def test_pt_systematics(weak_lensing_source, number_counts_source, sacc_data):
     mag_bias = 1.0
 
     c_1, c_d, c_2 = pt.translate_IA_norm(
-        ccl_cosmo, z, a1=a_1, a1delta=a_d, a2=a_2, Om_m2_for_c2=False
+        ccl_cosmo, z=z, a1=a_1, a1delta=a_d, a2=a_2, Om_m2_for_c2=False
     )
 
     # Code that creates a Pk2D object:
@@ -267,7 +267,7 @@ def test_pt_mixed_systematics(sacc_data):
     mag_bias = 1.0
 
     c_1, c_d, c_2 = pt.translate_IA_norm(
-        ccl_cosmo, z, a1=a_1, a1delta=a_d, a2=a_2, Om_m2_for_c2=False
+        ccl_cosmo, z=z, a1=a_1, a1delta=a_d, a2=a_2, Om_m2_for_c2=False
     )
 
     # Code that creates a Pk2D object: