From 90191e5f6a58d7281b3e587113f3aa380c4be2e7 Mon Sep 17 00:00:00 2001
From: rccreswell <56924958+rccreswell@users.noreply.github.com>
Date: Fri, 21 Oct 2022 08:47:32 -0500
Subject: [PATCH 1/5] set visibility on add_data

---
 seirmo/plots/_figures.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/seirmo/plots/_figures.py b/seirmo/plots/_figures.py
index 05769de..d46a115 100644
--- a/seirmo/plots/_figures.py
+++ b/seirmo/plots/_figures.py
@@ -48,7 +48,8 @@ def add_data(
             go.Bar(
                 x=data[time_key],
                 y=data[inc_key],
-                name='cases'
+                name='cases',
+                visible='legendonly'
             )
         )
 

From cac6d695e36a171b4b4e6d74c3b0ee91a991c83a Mon Sep 17 00:00:00 2001
From: rcw5890 <richard.creswell@hertford.ox.ac.uk>
Date: Mon, 31 Oct 2022 09:00:08 +0000
Subject: [PATCH 2/5] fix lines in figures

---
 seirmo/plots/_figures.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/seirmo/plots/_figures.py b/seirmo/plots/_figures.py
index d46a115..f4b5f61 100644
--- a/seirmo/plots/_figures.py
+++ b/seirmo/plots/_figures.py
@@ -49,7 +49,6 @@ def add_data(
                 x=data[time_key],
                 y=data[inc_key],
                 name='cases',
-                visible='legendonly'
             )
         )
 
@@ -111,8 +110,8 @@ def _update_axis_labels(self, x_label, y_label):
         # does not match the old one if it already exist;
         if (old_y_label is not None) and (old_y_label != y_label):
             warnings.warn(
-                '''The incidence key does not match the previous incidence label.
-                   The y label was set to the new incidence key,
+                '''The incidence key does not match the previous incidence
+                   label. The y label was set to the new incidence key,
                    but may no longer be appropriate for
                    the previously set data.''')
 
@@ -200,8 +199,8 @@ def _update_axis_labels(self, x_label, y_label):
         # does not match the old one if it already exist;
         if (old_y_label is not None) and (old_y_label != y_label):
             warnings.warn(
-                '''The incidence key does not match the previous incidence label.
-                   The y label was set to the new incidence key,
+                '''The incidence key does not match the previous incidence
+                   label. The y label was set to the new incidence key,
                    but may no longer be appropriate for
                    the previously set data.''')
 

From 02613ef0ea8a296a8be229a18a3d5de41cbd1d86 Mon Sep 17 00:00:00 2001
From: rcw5890 <richard.creswell@hertford.ox.ac.uk>
Date: Mon, 31 Oct 2022 09:06:56 +0000
Subject: [PATCH 3/5] fix test plotter

---
 seirmo/tests/test_plotters.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/seirmo/tests/test_plotters.py b/seirmo/tests/test_plotters.py
index 4f5a49b..366ff9e 100644
--- a/seirmo/tests/test_plotters.py
+++ b/seirmo/tests/test_plotters.py
@@ -184,7 +184,7 @@ def test_deletion_function(self):
         figure.begin(1, 1)
         fig_num = figure[0].number
         self.assertTrue(matplotlib.pyplot.fignum_exists(fig_num))
-        del(figure)
+        del figure
         self.assertFalse(matplotlib.pyplot.fignum_exists(fig_num))
 
     @mock.patch("seirmo.plots._plot_from_numpy.plt")

From 570c2e183df2844d4f59e21b0d7d233a5e1e0b3b Mon Sep 17 00:00:00 2001
From: rcw5890 <richard.creswell@hertford.ox.ac.uk>
Date: Mon, 31 Oct 2022 09:49:34 +0000
Subject: [PATCH 4/5] remove pints

---
 setup.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/setup.py b/setup.py
index 15a59fe..bf7a763 100644
--- a/setup.py
+++ b/setup.py
@@ -68,14 +68,10 @@ def get_readme():
         'numpy',
         'pandas',
         'parameterized',
-        'pints @ git+git://github.com/pints-team/pints.git#egg=pints-latest', 
+        'pints @ git+git://github.com/pints-team/pints.git#egg=pints-latest',
         'plotly',
         'scipy',
     ],
-    dependency_links=[
-     "git+git://github.com/pints-team/pints.git#egg=pints-latest",
-    ],
-
     extras_require={
         'docs': [
             # Sphinx for doc generation. Version 1.7.3 has a bug:
@@ -86,4 +82,4 @@ def get_readme():
             'flake8>=3',
         ],
     },
-)
\ No newline at end of file
+)

From cc97339dba9304aea64eabf9305c358e4214a8b7 Mon Sep 17 00:00:00 2001
From: rcw5890 <richard.creswell@hertford.ox.ac.uk>
Date: Mon, 31 Oct 2022 09:49:49 +0000
Subject: [PATCH 5/5] remove pints requires github

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bf7a763..721b9cf 100644
--- a/setup.py
+++ b/setup.py
@@ -68,7 +68,7 @@ def get_readme():
         'numpy',
         'pandas',
         'parameterized',
-        'pints @ git+git://github.com/pints-team/pints.git#egg=pints-latest',
+        'pints',
         'plotly',
         'scipy',
     ],