From e6cedb370cd630632d13a8e1cb61901cb1c598f5 Mon Sep 17 00:00:00 2001
From: James Gaboardi <jgaboardi@gmail.com>
Date: Tue, 24 Oct 2023 11:28:33 -0400
Subject: [PATCH] final migration

---
 giddy/ergodic.py |  2 +-
 giddy/markov.py  | 16 ++++++++--------
 pyproject.toml   | 34 ++++++++++++----------------------
 3 files changed, 21 insertions(+), 31 deletions(-)

diff --git a/giddy/ergodic.py b/giddy/ergodic.py
index b7c3dc7..d1a3858 100644
--- a/giddy/ergodic.py
+++ b/giddy/ergodic.py
@@ -299,7 +299,7 @@ def mfpt(P, fill_empty_classes=False):
     ValueError: Input transition probability matrix has 1 rows full of 0s. \
 Please set fill_empty_classes=True to set diagonal elements for these \
 rows to be 1 to make sure the matrix is stochastic.
-    """  
+    """
 
     P = np.asarray(P)
     rows0 = (P.sum(axis=1) == 0).sum()
diff --git a/giddy/markov.py b/giddy/markov.py
index ca46f0b..5b1d5a8 100644
--- a/giddy/markov.py
+++ b/giddy/markov.py
@@ -1910,18 +1910,18 @@ def summary(self, file_name=None, title="Markov Homogeneity Test"):
                 c = []
                 fmt = "r" * (k + 1)
                 s = "\\begin{tabular}{|%s|}\\hline\n" % fmt
-                s += "\\multicolumn{%s}{|c|}{%s}" % (ks, title)  # noqa UP031
+                s += "\\multicolumn{%s}{|c|}{%s}" % (ks, title)
                 c.append(s)
                 s = "Number of classes: %d" % int(self.k)
-                c.append("\\hline\\multicolumn{%s}{|l|}{%s}" % (ks, s))  # noqa UP031
+                c.append("\\hline\\multicolumn{%s}{|l|}{%s}" % (ks, s))
                 s = "Number of transitions: %d" % int(self.t_total)
-                c.append("\\multicolumn{%s}{|l|}{%s}" % (ks, s))  # noqa UP031
+                c.append("\\multicolumn{%s}{|l|}{%s}" % (ks, s))
                 s = "Number of regimes: %d" % int(self.m)
-                c.append("\\multicolumn{%s}{|l|}{%s}" % (ks, s))  # noqa UP031
+                c.append("\\multicolumn{%s}{|l|}{%s}" % (ks, s))
                 s = "Regime names: "
                 s += ", ".join(regime_names)
-                c.append("\\multicolumn{%s}{|l|}{%s}" % (ks, s))  # noqa UP031
-                s = "\\hline\\multicolumn{2}{|l}{%s}" % ("Test")  # noqa UP031
+                c.append("\\multicolumn{%s}{|l|}{%s}" % (ks, s))
+                s = "\\hline\\multicolumn{2}{|l}{%s}" % ("Test")
                 s += "&\\multicolumn{2}{r}{LR}&\\multicolumn{2}{r|}{Q}"
                 c.append(s)
                 s = "Stat."
@@ -1929,11 +1929,11 @@ def summary(self, file_name=None, title="Markov Homogeneity Test"):
                 s += "&\\multicolumn{2}{r}{%.3f}" % self.LR
                 s += "&\\multicolumn{2}{r|}{%.3f}" % self.Q
                 c.append(s)
-                s = "\\multicolumn{2}{|l}{%s}" % ("DOF")  # noqa UP031
+                s = "\\multicolumn{2}{|l}{%s}" % ("DOF")
                 s += "&\\multicolumn{2}{r}{%d}" % int(self.dof)
                 s += "&\\multicolumn{2}{r|}{%d}" % int(self.dof)
                 c.append(s)
-                s = "\\multicolumn{2}{|l}{%s}" % ("p-value")  # noqa UP031
+                s = "\\multicolumn{2}{|l}{%s}" % ("p-value")
                 s += "&\\multicolumn{2}{r}{%.3f}" % self.LR_p_value
                 s += "&\\multicolumn{2}{r|}{%.3f}" % self.Q_p_value
                 c.append(s)
diff --git a/pyproject.toml b/pyproject.toml
index 528edb7..0c126a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -79,39 +79,29 @@ select = ["E", "F", "W", "I", "UP", "N", "B", "A", "C4", "SIM", "ARG"]
 target-version = "py39"
 exclude = ["giddy/tests/*", "docs/*"]
 [tool.ruff.per-file-ignores]
-"__init__.py" = ["F401"] # imported but unused
-"giddy/directional.py" = [
-    "ARG002",  # Unused method argument
-    "N803",  # Argument name should be lowercase
-    "N806",  # Variable in function should be lowercase
+"__init__.py" = [
+    "F401"      # imported but unused
 ]
-"giddy/ergodic.py" = [
-    "N803",  # Argument name should be lowercase
-    "N806",  # Variable in function should be lowercase
+"giddy/{directional,ergodic,markov,rank,sequence,util}.py" = [
+    "ARG002",   # Unused method argument
+    "N801",     # Class name should use CapWords convention
+    "N802",     # Function name should be lowercase
+    "N803",     # Argument name should be lowercase
+    "N806",     # Variable in function should be lowercase
 ]
 "giddy/markov.py" = [
-    "B006",  # Do not use mutable data structures for argument defaults
-    "N801",  # Class name should use CapWords convention
-    "N802",  # Function name should be lowercase
-    "N803",
-    "N806",
+    "B006",     # Do not use mutable data structures for argument defaults
+    "UP031",    # Use format specifiers instead of percent format
 ]
-"giddy/rank.py" = [
-    "ARG002",
-    "N801",
-    "N803",
-    "N806",
+"giddy/{ergodic,markov,sequence}.py" = [
+    "E501",     # Line too long
 ]
-"giddy/sequence.py" = ["N806"]
-"giddy/util.py" = ["N803"]
 
 [tool.coverage.run]
 source = ["./giddy"]
 
 [tool.coverage.report]
 exclude_lines = [
-    "if self.debug:",
-    "pragma: no cover",
     "raise NotImplementedError",
     "except ModuleNotFoundError:",
     "except ImportError",