From 28062121a1d1e50742550bb8ce69e83ce5d7ba37 Mon Sep 17 00:00:00 2001
From: paxtonfitzpatrick <Paxton.C.Fitzpatrick@Dartmouth.edu>
Date: Thu, 3 Jun 2021 11:21:21 -0400
Subject: [PATCH 1/6] fix double parentheses

---
 quail/analysis/recmat.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/quail/analysis/recmat.py b/quail/analysis/recmat.py
index d5a0fe8..bb3cf77 100644
--- a/quail/analysis/recmat.py
+++ b/quail/analysis/recmat.py
@@ -51,7 +51,7 @@ def recall_matrix(egg, match='exact', distance='euclidean', features=None):
         return _recmat_smooth(egg.pres, egg.rec, features, distance, match)
 
 def _recmat_exact(presented, recalled, features):
-    lists = presented.index.to_numpy()()
+    lists = presented.index.to_numpy()
     cols = max(presented.shape[1], recalled.shape[1])
     result = np.empty((presented.shape[0], cols))*np.nan
     for li, l in enumerate(lists):
@@ -59,8 +59,8 @@ def _recmat_exact(presented, recalled, features):
         r_list = recalled.loc[l]
         for i, feature in enumerate(features):
             get_feature = lambda x: np.array(x[feature]) if not np.array(pd.isnull(x['item'])).any() else np.nan
-            p = np.vstack(p_list.apply(get_feature).to_numpy()())
-            r = r_list.dropna().apply(get_feature).to_numpy()()
+            p = np.vstack(p_list.apply(get_feature).to_numpy())
+            r = r_list.dropna().apply(get_feature).to_numpy()
             r = np.vstack(list(filter(lambda x: x is not np.nan, r)))
             try:
                 m = [np.where((p==x).all(axis=1))[0] for x in r]
@@ -90,15 +90,15 @@ def _recmat_smooth(presented, recalled, features, distance, match):
     return recmat
 
 def _similarity_smooth(presented, recalled, features, distance):
-    lists = presented.index.to_numpy()()
+    lists = presented.index.to_numpy()
     res = np.empty((len(lists), len(features), recalled.iloc[0].shape[0], presented.iloc[0].shape[0]))*np.nan
     for li, l in enumerate(lists):
         p_list = presented.loc[l]
         r_list = recalled.loc[l]
         for i, feature in enumerate(features):
             get_feature = lambda x: np.array(x[feature]) if np.array(pd.notna(x['item'])).any() else np.nan
-            p = np.vstack(p_list.apply(get_feature).to_numpy()())
-            r = r_list.dropna().apply(get_feature).to_numpy()()
+            p = np.vstack(p_list.apply(get_feature).to_numpy())
+            r = r_list.dropna().apply(get_feature).to_numpy()
             r = np.vstack(list(filter(lambda x: x is not np.nan, r)))
             tmp = 1 - cdist(r, p, distance)
             res[li, i, :tmp.shape[0], :] =  tmp

From caab6c1643befb0142b963b851f7685f896bd05f Mon Sep 17 00:00:00 2001
From: paxtonfitzpatrick <Paxton.C.Fitzpatrick@Dartmouth.edu>
Date: Thu, 3 Jun 2021 11:57:35 -0400
Subject: [PATCH 2/6] bumped pandas requirement to min version with .to_numpy()

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index ecfe191..3516a25 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,7 @@ numpy>=1.10.4
 scipy>=0.17.1
 matplotlib>=1.5.1
 seaborn>=0.9.0
-pandas>=0.18.1
+pandas>=0.24.0
 future
 six
 deepdish

From fdefd10f79d435f31020d3747c83a24ddaae4cf9 Mon Sep 17 00:00:00 2001
From: paxtonfitzpatrick <Paxton.C.Fitzpatrick@Dartmouth.edu>
Date: Thu, 3 Jun 2021 12:00:32 -0400
Subject: [PATCH 3/6] remove tests for python 3.5, add 3.7 & 3.8

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 22e9f83..cfebb25 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,8 +4,9 @@ services:
 - xvfb
 python:
 - '2.7'
-- '3.5'
 - '3.6'
+- '3.7'
+- '3.8'
 before_script:
 - export DISPLAY=:99.0
 - sleep 3

From e811a7943089e20074e813aa07ed7289d0725560 Mon Sep 17 00:00:00 2001
From: paxtonfitzpatrick <Paxton.C.Fitzpatrick@Dartmouth.edu>
Date: Thu, 3 Jun 2021 12:09:06 -0400
Subject: [PATCH 4/6] drop support for python 2.7, add 3.9

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index cfebb25..e67c21d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,10 +3,10 @@ sudo: false
 services:
 - xvfb
 python:
-- '2.7'
 - '3.6'
 - '3.7'
 - '3.8'
+- '3.9'
 before_script:
 - export DISPLAY=:99.0
 - sleep 3

From 90bdd37c218e01f7656de0a9f5c1855138782140 Mon Sep 17 00:00:00 2001
From: paxtonfitzpatrick <Paxton.C.Fitzpatrick@Dartmouth.edu>
Date: Thu, 3 Jun 2021 12:57:38 -0400
Subject: [PATCH 5/6] bump version

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

diff --git a/setup.py b/setup.py
index 6d7fd9b..c5d356e 100755
--- a/setup.py
+++ b/setup.py
@@ -27,7 +27,7 @@
 
 setup(
     name='quail',
-    version='0.2.0',
+    version='0.2.1',
     description=DESCRIPTION,
     long_description=LONG_DESCRIPTION,
     author='Contextual Dynamics Lab',

From 4d6041b497adea63b17f31270c0663038a7f50cf Mon Sep 17 00:00:00 2001
From: paxtonfitzpatrick <Paxton.C.Fitzpatrick@Dartmouth.edu>
Date: Thu, 3 Jun 2021 13:00:45 -0400
Subject: [PATCH 6/6] update python version requirement in readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e6918d9..0e6ff8b 100644
--- a/README.md
+++ b/README.md
@@ -58,7 +58,7 @@ This will work on clean systems, but if you encounter issues you may need to run
 
 <h2>Requirements</h2>
 
-+ python 2.7, 3.4+
++ python>=3.6
 + pandas>=0.18.0
 + seaborn>=0.7.1
 + matplotlib>=1.5.1