From 9091c3f9e4648111a7b36e0c5fdf1a7202d200b3 Mon Sep 17 00:00:00 2001
From: Jennifer A Clark <jennifer.a.clark13@gmail.com>
Date: Mon, 30 Sep 2024 19:25:35 -0400
Subject: [PATCH] Issue docstring harmonic (#541)

* Remove tracking of project settings

* Fix docstring for HarmonicOscillator

* black

* Fix bar ParameterError
---
 .gitignore                                 |  3 +++
 .vscode/settings.json                      |  5 -----
 pymbar/other_estimators.py                 |  2 +-
 pymbar/testsystems/harmonic_oscillators.py | 10 ++++++----
 4 files changed, 10 insertions(+), 10 deletions(-)
 delete mode 100644 .vscode/settings.json

diff --git a/.gitignore b/.gitignore
index 6b353eff..cb5a29e5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -118,6 +118,9 @@ venv.bak/
 .spyderproject
 .spyproject
 
+# VSCode project settings
+.vscode/
+
 # Rope project settings
 .ropeproject
 
diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index 36fe635c..00000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "python.linting.enabled": true,
-    "python.linting.pylintEnabled": true,
-    "python.pythonPath": "/home/jaime/.conda/envs/pymbar/bin/python"
-}
\ No newline at end of file
diff --git a/pymbar/other_estimators.py b/pymbar/other_estimators.py
index d9539df0..1796823f 100644
--- a/pymbar/other_estimators.py
+++ b/pymbar/other_estimators.py
@@ -242,7 +242,7 @@ def bar(
         DeltaF_initial = DeltaF
 
     if method not in ["self-consistent-iteration", "false-position", "bisection"]:
-        raise ParameterError("method {:d} is not defined for bar".format(method))
+        raise ParameterError("method {} is not defined for bar".format(method))
 
     if uncertainty_method not in ["BAR", "MBAR"]:
         raise ParameterError(
diff --git a/pymbar/testsystems/harmonic_oscillators.py b/pymbar/testsystems/harmonic_oscillators.py
index 32ac4cd6..7a1862bf 100644
--- a/pymbar/testsystems/harmonic_oscillators.py
+++ b/pymbar/testsystems/harmonic_oscillators.py
@@ -10,7 +10,7 @@ class HarmonicOscillatorsTestCase(object):
     Generate energy samples with default parameters.
 
     >>> testcase = HarmonicOscillatorsTestCase()
-    >>> x_kn, u_kln, N_k, s_n = testcase.sample()
+    >>> x_n, u_kn, N_k, s_n = testcase.sample()
 
     Retrieve analytical properties.
 
@@ -22,12 +22,12 @@ class HarmonicOscillatorsTestCase(object):
 
     Generate energy samples with default parameters in one line.
 
-    >>> x_kn, u_kln, N_k, s_n = HarmonicOscillatorsTestCase().sample()
+    >>> x_n, u_kn, N_k, s_n = HarmonicOscillatorsTestCase().sample()
 
     Generate energy samples with specified parameters.
 
     >>> testcase = HarmonicOscillatorsTestCase(O_k=[0, 1, 2, 3, 4], K_k=[1, 2, 4, 8, 16])
-    >>> x_kn, u_kln, N_k, s_n = testcase.sample(N_k=[10, 20, 30, 40, 50])
+    >>> x_n, u_kn, N_k, s_n = testcase.sample(N_k=[10, 20, 30, 40, 50])
 
     Test sampling in different output modes.
 
@@ -131,9 +131,11 @@ def sample(self, N_k=(10, 20, 30, 40, 50), mode="u_kn", seed=None):
         s_n : np.ndarray, shape=(n_samples), dtype='int'
             s_n is the state of origin of x_n
 
+        if mode == 'u_kln':
+
         x_kn : np.ndarray, shape=(n_states, n_samples), dtype=float
             1D harmonic oscillator positions
-        u_kln : np.ndarray, shape=(n_states, n_states, n_samples), dytpe=float, only if mode='u_kln'
+        u_kln : np.ndarray, shape=(n_states, n_states, n_samples), dytpe=float
            u_kln[k,l,n] is reduced potential of sample n from state k evaluated at state l.
         N_k : np.ndarray, shape=(n_states), dtype=int32
            N_k[k] is the number of samples generated from state k