From c19f8f3d188033d38fd5d558e5afc9b8f264f7a3 Mon Sep 17 00:00:00 2001
From: Jason McEwen <jason.mcewen@gmail.com>
Date: Thu, 20 Mar 2025 17:48:56 +0000
Subject: [PATCH 1/3] Add old plot_realisations that works with legacy examples

This is taken from commit dd38bcd6a2d09ed15dc8d2c4cd403001c6b71e04,
before commit 4aef1b2a157da77d9f377e295bdf5446ebdfab13 broke this for
legacy examples.
---
 examples/plot_realisations_old.py | 72 +++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 examples/plot_realisations_old.py

diff --git a/examples/plot_realisations_old.py b/examples/plot_realisations_old.py
new file mode 100644
index 00000000..d237fdee
--- /dev/null
+++ b/examples/plot_realisations_old.py
@@ -0,0 +1,72 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import argparse
+import os
+import ex_utils
+
+savefigs = True
+
+# Parse arguments.
+parser = argparse.ArgumentParser(
+    "Create violin plot of inverse evidences" + "from many realisations"
+)
+parser.add_argument(
+    "filename_realisations",
+    metavar="filename_realisations",
+    type=str,
+    help="Name of file containing realisations",
+)
+parser.add_argument(
+    "filename_analytic",
+    metavar="filename_analytic",
+    type=str,
+    help="Name of file containing analytic inverse variance",
+)
+args = parser.parse_args()
+
+# Load data.
+evidence_inv_summary = np.loadtxt(args.filename_realisations)
+evidence_inv_realisations = evidence_inv_summary[:, 0]
+evidence_inv_var_realisations = evidence_inv_summary[:, 1]
+evidence_inv_var_var_realisations = evidence_inv_summary[:, 2]
+
+evidence_inv_analytic = np.loadtxt(args.filename_analytic)
+
+# Plot inverse evidence.
+plt.rcParams.update({"font.size": 20})
+ax = ex_utils.plot_realisations(
+    mc_estimates=evidence_inv_realisations,
+    std_estimated=np.sqrt(np.mean(evidence_inv_var_realisations)),
+    analytic_val=evidence_inv_analytic,
+    analytic_text=r"Truth",
+)
+plt.ticklabel_format(style="sci", axis="y", scilimits=(0, 0))
+ax.set_ylabel(r"Inverse evidence ($\rho$)")
+# ax.set_ylim([0.0, 0.01])
+
+filename_base = os.path.basename(args.filename_realisations)
+filename_base_noext = os.path.splitext(filename_base)[0]
+if savefigs:
+    plt.savefig(
+        "./examples/plots/" + filename_base_noext + "_evidence_inv.png",
+        bbox_inches="tight",
+    )
+
+# Plot variance of inverse evidence.
+ax = ex_utils.plot_realisations(
+    mc_estimates=evidence_inv_var_realisations,
+    std_estimated=np.sqrt(np.mean(evidence_inv_var_var_realisations)),
+)
+plt.ticklabel_format(style="sci", axis="y", scilimits=(0, 0))
+ax.set_ylabel(r"Inverse evidence variance ($\sigma^2$)")
+# ax.set_ylim([-0.1, 1])
+
+if savefigs:
+    plt.savefig(
+        "./examples/plots/" + filename_base_noext + "_evidence_inv_var.png",
+        bbox_inches="tight",
+    )
+
+plt.show(block=False)
+
+input("\nPress Enter to continue...")

From 9fb4b10cfeec1dc6947813def3a1b9c0dd58e941 Mon Sep 17 00:00:00 2001
From: Jason McEwen <jason.mcewen@gmail.com>
Date: Thu, 20 Mar 2025 17:51:21 +0000
Subject: [PATCH 2/3] Fix bug in cross_validation

This broke when removing non-log evidence values (PR290), which were
previously used for logging only.  Updated to work with log values only.
---
 harmonic/utils.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/harmonic/utils.py b/harmonic/utils.py
index b3528285..6bc98c56 100644
--- a/harmonic/utils.py
+++ b/harmonic/utils.py
@@ -334,20 +334,22 @@ def cross_validation(
                 )
             )
             hm.logs.debug_log(
-                "cross_validation: evidence_inv = {}".format(ev.evidence_inv)
+                "cross_validation: ln_evidence_inv = {}".format(ev.ln_evidence_inv)
             )
             hm.logs.debug_log(
-                "cross_validation: evidence_inv_var = {}".format(ev.evidence_inv_var)
+                "cross_validation: ln_evidence_inv_var = {}".format(
+                    ev.ln_evidence_inv_var
+                )
             )
             hm.logs.debug_log(
                 "cross_validation:"
-                + " evidence_inv_var**0.5/evidence_inv = {}".format(
-                    ev.evidence_inv_var**0.5 / ev.evidence_inv
+                + " np.exp(ev.ln_evidence_inv_var)**0.5 / np.exp(ev.ln_evidence_inv) = {}".format(
+                    np.exp(ev.ln_evidence_inv_var) ** 0.5 / np.exp(ev.ln_evidence_inv)
                 )
             )
             hm.logs.debug_log(
-                "cross_validation: evidence_inv_var_var = {}".format(
-                    ev.evidence_inv_var_var
+                "cross_validation: ln_evidence_inv_var_var = {}".format(
+                    ev.ln_evidence_inv_var_var
                 )
             )
 

From a53d226c0825bce9387149ad68872b2ec46996e5 Mon Sep 17 00:00:00 2001
From: Jason McEwen <jason.mcewen@gmail.com>
Date: Thu, 20 Mar 2025 17:54:42 +0000
Subject: [PATCH 3/3] Pin version of dm-tree to 0.1.8

Since no mac wheels for latest version 0.1.9.
---
 requirements/requirements-core.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/requirements/requirements-core.txt b/requirements/requirements-core.txt
index 8a8ceb9a..10874ad0 100644
--- a/requirements/requirements-core.txt
+++ b/requirements/requirements-core.txt
@@ -1,4 +1,5 @@
 numpy <= 1.26.4
+dm-tree==0.1.8 # No mac wheels for latest version 0.1.9 (as of 20/03/2025)
 setuptools==68.0.0
 wheel==0.41.0
 cython>=0.29.30
@@ -15,4 +16,4 @@ flax
 #chex==0.1.6
 distrax
 cloudpickle
-getdist
\ No newline at end of file
+getdist