From 34c7a25fa03503be34f67f3c8bb64da802d342d1 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Wed, 13 Dec 2023 20:10:26 +0000
Subject: [PATCH 01/18] Deactivate CI

---
 .github/dependabot.yml           | 20 --------------------
 .github/workflows/build_docs.yml |  8 ++++----
 .github/workflows/release.yml    |  8 ++++----
 .github/workflows/testing.yml    | 18 ++++++++++--------
 4 files changed, 18 insertions(+), 36 deletions(-)
 delete mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
deleted file mode 100644
index 57fa59b4..00000000
--- a/.github/dependabot.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-# To get started with Dependabot version updates, you'll need to specify which
-# package ecosystems to update and where the package manifests are located.
-# Please see the documentation for all configuration options:
-# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
-
-version: 2
-updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
-    schedule:
-      interval: "daily"
-    reviewers:
-      - "jGaboardi"
-
-  - package-ecosystem: "pip"
-    directory: "/"
-    schedule:
-      interval: "daily"
-    reviewers:
-      - "jGaboardi"
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 4d42cf22..0adc82df 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -2,10 +2,10 @@
  name: Build Docs
  
  on:
-   push:
-     # Sequence of patterns matched against refs/tags
-     tags:
-       - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+  #  push:
+  #    # Sequence of patterns matched against refs/tags
+  #    tags:
+  #      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
    workflow_dispatch:
      inputs:
        version:
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index b5418e6a..f46c6165 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,10 +1,10 @@
 name: Release Package
 
 on:
-  push:
-    # Sequence of patterns matched against refs/tags
-    tags:
-      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+  # push:
+  #   # Sequence of patterns matched against refs/tags
+  #   tags:
+  #     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
   workflow_dispatch:
     inputs:
       version:
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8a7cf603..94c1931e 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -1,14 +1,16 @@
 name: Continuous Integration
 
 on:
-  push:
-    branches:
-      - "*"
-  pull_request:
-    branches:
-      - "*"
-  schedule:
-    - cron: "59 21 * * *"
+  # push:
+  #   branches:
+  #     - "*"
+  # pull_request:
+  #   branches:
+  #     - "*"
+  # schedule:
+  #   - cron: "59 21 * * *"
+  workflow_dispatch:
+      
 
 jobs:
   testing:

From 2a85d9e56b7e2c0d0ab96f1e8ea7a4cfcf730460 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Wed, 13 Dec 2023 20:58:41 +0000
Subject: [PATCH 02/18] Add _fisher_jenks_means_without_numpy and Monkey patch
 code.

---
 README.md                  |  18 +++++
 mapclassify/classifiers.py | 136 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 152 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9f73d132..41b660f5 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,21 @@
+# mapclassif-Iron:  _fisher_jenks_means for IronPython, and other environments without numpy.
+
+*Warning!* Installing the main branch of this fork normally with pip, will not produce a working library.
+An ImportError will be raised on import.  Unless your Python finds numpy, pandas and SciKitlearn, in which 
+case you are most likely running CPython or Jupyter anyway, and therefore you have no need of this fork and
+should use mapclassify instead.
+
+This project is included as a dependency in another project (sDNA_GH) by static linking the code 
+(copy and pasting) from a branch that has everything that won't work without 
+numpy, pandas and SciKitlearn etc. removed.
+
+Only the function, _fisher_jenks_means has been adapted (back to something similar to 
+Daniel J Lewis's original snippet).  
+
+No other functionality from mapclassify has been changed, and none has been added.
+
+Parent project's README.md:
+
 # mapclassify: Classification Schemes for Choropleth Maps
 
 [![Continuous Integration](https://github.com/pysal/mapclassify/actions/workflows/testing.yml/badge.svg)](https://github.com/pysal/mapclassify/actions/workflows/testing.yml)
diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 27d5188d..638926e7 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -1,14 +1,17 @@
 """
 A module of classification schemes for choropleth mapping.
 """
+import sys
 import copy
 import functools
 import warnings
 
-import numpy as np
 import scipy.stats as stats
 from sklearn.cluster import KMeans
 
+
+
+
 __author__ = "Sergio J. Rey"
 
 __all__ = [
@@ -60,6 +63,58 @@
 
 FMT = "{:.2f}"
 
+
+
+
+
+
+class MockNumpy(object):
+    
+    def __init__(self, int_type = None, float_type = None):
+        if int_type is None or float_type is None:
+            try:
+                if sys.implementation.name != 'ironpython':
+                    raise ImportError
+                import System
+            except ImportError:
+                class System:
+                    Int16 = int
+                    Single = float
+        
+        self.int32 = int_type or System.Int16
+        self.float32 = float_type or System.Single
+    
+    @classmethod
+    def zeros(self, dims, dtype = System.Int16):
+
+        if len(dims) == 1:
+            zero = dtype(0)
+            return [zero for __ in range(dims[0])]
+            
+        return [cls.zeros(dims[1:], dtype) for __ in range(dims[0])] 
+        
+    int32 = System.Int16
+    float32 = System.Single
+    inf = System.Single('inf')
+    
+    @staticmethod
+    def delete(arr, index):
+        return arr[:index] + arr[index+1:]
+
+
+try:
+    if sys.implementation.name != 'cpython':
+        raise ImportError
+    import numpy as np  
+    HAS_NUMPY = True
+except ImportError:
+    HAS_NUMPY = False
+
+    default_mock_numpy = MockNumpy()
+
+
+
+
 try:
     from numba import njit
 
@@ -581,7 +636,7 @@ def natural_breaks(values, k=5, init=10):
 
 
 @njit("f8[:](f8[:], u2)")
-def _fisher_jenks_means(values, classes=5):
+def _fisher_jenks_means_numpy(values, classes=5):
     """
     Jenks Optimal (Natural Breaks) algorithm implemented in Python.
 
@@ -637,6 +692,83 @@ def _fisher_jenks_means(values, classes=5):
     return np.delete(kclass, 0)
 
 
+def _fisher_jenks_means_without_numpy(
+    values,
+    classes=5,
+    np = default_mock_numpy
+    ):
+    """
+    As for _fisher_jenks_means_numpy above, to keep the code as far as possible
+    exactly the same, except with np passable in as a dependency, and with
+    matrix[i, j] replaced with matrix[i][j] for speed.
+
+
+    Jenks Optimal (Natural Breaks) algorithm implemented in Python.
+
+    Notes
+    -----
+
+    The original Python code comes from here:
+    http://danieljlewis.org/2010/06/07/jenks-natural-breaks-algorithm-in-python/
+    and is based on a JAVA and Fortran code available here:
+    https://stat.ethz.ch/pipermail/r-sig-geo/2006-March/000811.html
+
+
+
+    """
+    values.sort()
+    n_data = len(values)
+    mat1 = np.zeros((n_data + 1, classes + 1), dtype=np.int32)
+    mat2 = np.zeros((n_data + 1, classes + 1), dtype=np.float32)
+    
+    # System.Array.Fill not suppported on Multi-dimensional arrays
+    for j in range(1, classes + 1):
+        mat1[1][j] = 1
+        for i in range(2, n_data+1):
+            mat2[i][j] = np.inf
+    v = 0
+    for _l in range(2, len(values) + 1):
+        s1 = 0
+        s2 = 0
+        w = 0
+        for m in range(1, _l + 1):
+            i3 = _l - m + 1
+            val = values[i3 - 1]
+            s2 += val * val
+            s1 += val
+            w += 1
+            v = s2 - (s1 * s1) / np.float32(w)
+            i4 = i3 - 1
+            if i4 != 0:
+                for j in range(2, classes + 1):
+                    if mat2[_l][j] >= (v + mat2[i4][j - 1]):
+                        mat1[_l][j] = i3
+                        mat2[_l][j] = v + mat2[i4][j - 1]
+
+        mat1[_l][1] = 1
+        mat2[_l][1] = v
+
+#    for row in mat1:
+#        print(row)
+    k = len(values)
+
+    kclass = np.zeros((classes + 1,), dtype=type(values[0]))
+    kclass[classes] = values[len(values) - 1]
+    kclass[0] = values[0]
+    for countNum in range(classes, 1, -1):
+        pivot = mat1[k][countNum]
+        _id = int(pivot - 2)
+        kclass[countNum - 1] = values[_id]
+        k = int(pivot - 1)
+    return np.delete(kclass, 0)
+
+
+if HAS_NUMPY:
+    _fisher_jenks_means = _fisher_jenks_means_numpy
+else:
+    _fisher_jenks_means = _fisher_jenks_means_without_numpy
+
+
 class MapClassifier:
     r"""
     Abstract class for all map classifications :cite:`Slocum_2009`

From 6fac0d217ad6c084e120e768872a7c33dcb785d4 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Wed, 13 Dec 2023 21:07:33 +0000
Subject: [PATCH 03/18] Update README.md

---
 README.md | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 41b660f5..5b863d1e 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,7 @@
 # mapclassif-Iron:  _fisher_jenks_means for IronPython, and other environments without numpy.
 
-*Warning!* Installing the main branch of this fork normally with pip, will not produce a working library.
-An ImportError will be raised on import.  Unless your Python finds numpy, pandas and SciKitlearn, in which 
-case you are most likely running CPython or Jupyter anyway, and therefore you have no need of this fork and
-should use mapclassify instead.
-
-This project is included as a dependency in another project (sDNA_GH) by static linking the code 
-(copy and pasting) from a branch that has everything that won't work without 
-numpy, pandas and SciKitlearn etc. removed.
+This branch does not currently work, but is intended to very soon work with, and provide PRs for mapclassify, and the 
+resulting installation should work when installed by directing pip to this github repository branch
 
 Only the function, _fisher_jenks_means has been adapted (back to something similar to 
 Daniel J Lewis's original snippet).  

From 270d47565dbd2b271038dc5f79eff54350850199 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 00:12:09 +0000
Subject: [PATCH 04/18] Monkey patch in _fisher_jenks_means_without_numpy if no
 Numba (even if Numpy)

---
 mapclassify/classifiers.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 638926e7..269ead09 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -110,7 +110,6 @@ def delete(arr, index):
 except ImportError:
     HAS_NUMPY = False
 
-    default_mock_numpy = MockNumpy()
 
 
 
@@ -132,6 +131,9 @@ def wrapper_decorator(*args, **kwargs):
 
         return decorator_njit
 
+    # Numba requires Numpy    
+    default_mock_numpy = MockNumpy()
+
 
 def _format_intervals(mc, fmt="{:.0f}"):
     """
@@ -763,7 +765,7 @@ def _fisher_jenks_means_without_numpy(
     return np.delete(kclass, 0)
 
 
-if HAS_NUMPY:
+if HAS_NUMBA:
     _fisher_jenks_means = _fisher_jenks_means_numpy
 else:
     _fisher_jenks_means = _fisher_jenks_means_without_numpy

From 51a79fba4cc4a810b06ed2000d1f0b6bebc5393b Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 10:26:36 +0000
Subject: [PATCH 05/18] Only use CPython types.

---
 mapclassify/classifiers.py | 24 +++++++-----------------
 1 file changed, 7 insertions(+), 17 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 269ead09..d810a289 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -71,21 +71,14 @@
 class MockNumpy(object):
     
     def __init__(self, int_type = None, float_type = None):
-        if int_type is None or float_type is None:
-            try:
-                if sys.implementation.name != 'ironpython':
-                    raise ImportError
-                import System
-            except ImportError:
-                class System:
-                    Int16 = int
-                    Single = float
-        
-        self.int32 = int_type or System.Int16
-        self.float32 = float_type or System.Single
+
+        self.int32 = int_type or int
+        self.float32 = float_type or float
+
+        self.inf = self.float32('inf')
     
     @classmethod
-    def zeros(self, dims, dtype = System.Int16):
+    def zeros(self, dims, dtype = int):
 
         if len(dims) == 1:
             zero = dtype(0)
@@ -93,10 +86,7 @@ def zeros(self, dims, dtype = System.Int16):
             
         return [cls.zeros(dims[1:], dtype) for __ in range(dims[0])] 
         
-    int32 = System.Int16
-    float32 = System.Single
-    inf = System.Single('inf')
-    
+
     @staticmethod
     def delete(arr, index):
         return arr[:index] + arr[index+1:]

From 8c44ba0edf126b9122306009e9d96012739a87db Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 10:43:24 +0000
Subject: [PATCH 06/18] FisherJenks now accepts _fisher_jenks_means as an
 injected dependency.  Remove unused HAS_NUMPY check

---
 mapclassify/classifiers.py | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index d810a289..293d9db8 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -8,7 +8,7 @@
 
 import scipy.stats as stats
 from sklearn.cluster import KMeans
-
+import numpy as np  
 
 
 
@@ -92,13 +92,6 @@ def delete(arr, index):
         return arr[:index] + arr[index+1:]
 
 
-try:
-    if sys.implementation.name != 'cpython':
-        raise ImportError
-    import numpy as np  
-    HAS_NUMPY = True
-except ImportError:
-    HAS_NUMPY = False
 
 
 
@@ -2084,14 +2077,20 @@ class FisherJenks(MapClassifier):
 
     """
 
-    def __init__(self, y, k=K):
+    def __init__(self, y, k=K, _fisher_jenks_means = None):
         if not HAS_NUMBA:
             warnings.warn(
                 "Numba not installed. Using slow pure python version.",
                 UserWarning,
                 stacklevel=3,
             )
+            _fisher_jenks_means = _fisher_jenks_means or _fisher_jenks_means_without_numpy
+        else:
+            
+            _fisher_jenks_means = _fisher_jenks_means or _fisher_jenks_means_numpy
 
+        self._fisher_jenks_means = _fisher_jenks_means
+        
         nu = len(np.unique(y))
         if nu < k:
             raise ValueError(
@@ -2101,9 +2100,11 @@ def __init__(self, y, k=K):
         MapClassifier.__init__(self, y)
         self.name = "FisherJenks"
 
+
+
     def _set_bins(self):
         x = np.sort(self.y).astype("f8")
-        self.bins = _fisher_jenks_means(x, classes=self.k)
+        self.bins = self._fisher_jenks_means(x, classes=self.k)
 
 
 class FisherJenksSampled(MapClassifier):

From b125267d18b0263da811ebb8b10c8794595eea12 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 12:57:05 +0000
Subject: [PATCH 07/18] Add test

---
 README.md                               |  5 +-
 mapclassify/_classify_API.py            |  1 +
 mapclassify/classifiers.py              | 25 ++++-----
 mapclassify/tests/time_fisher_jenkss.py | 67 +++++++++++++++++++++++++
 4 files changed, 81 insertions(+), 17 deletions(-)
 create mode 100644 mapclassify/tests/time_fisher_jenkss.py

diff --git a/README.md b/README.md
index 5b863d1e..1b98bc1e 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,8 @@
 # mapclassif-Iron:  _fisher_jenks_means for IronPython, and other environments without numpy.
 
-This branch does not currently work, but is intended to very soon work with, and provide PRs for mapclassify, and the 
-resulting installation should work when installed by directing pip to this github repository branch
+This branch does not currently work, but is intended to very soon work with, when installed by 
+directing pip to this github repository branch.  This branch is primarily for convenient
+PRs for mapclassify.  
 
 Only the function, _fisher_jenks_means has been adapted (back to something similar to 
 Daniel J Lewis's original snippet).  
diff --git a/mapclassify/_classify_API.py b/mapclassify/_classify_API.py
index c0c0fa8b..7f1c0a7d 100644
--- a/mapclassify/_classify_API.py
+++ b/mapclassify/_classify_API.py
@@ -24,6 +24,7 @@
     "boxplot": BoxPlot,
     "equalinterval": EqualInterval,
     "fisherjenks": FisherJenks,
+    "fisherjenks_nonumpy": FisherJenks,
     "fisherjenkssampled": FisherJenksSampled,
     "headtailbreaks": HeadTailBreaks,
     "jenkscaspall": JenksCaspall,
diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 293d9db8..02215dab 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -84,7 +84,7 @@ def zeros(self, dims, dtype = int):
             zero = dtype(0)
             return [zero for __ in range(dims[0])]
             
-        return [cls.zeros(dims[1:], dtype) for __ in range(dims[0])] 
+        return [self.zeros(dims[1:], dtype) for __ in range(dims[0])] 
         
 
     @staticmethod
@@ -621,7 +621,7 @@ def natural_breaks(values, k=5, init=10):
 
 
 @njit("f8[:](f8[:], u2)")
-def _fisher_jenks_means_numpy(values, classes=5):
+def _fisher_jenks_means(values, classes=5):
     """
     Jenks Optimal (Natural Breaks) algorithm implemented in Python.
 
@@ -677,13 +677,13 @@ def _fisher_jenks_means_numpy(values, classes=5):
     return np.delete(kclass, 0)
 
 
-def _fisher_jenks_means_without_numpy(
+def _fjm_without_numpy(
     values,
     classes=5,
     np = default_mock_numpy
     ):
     """
-    As for _fisher_jenks_means_numpy above, to keep the code as far as possible
+    As for _fisher_jenks_means above, to keep the code as far as possible
     exactly the same, except with np passable in as a dependency, and with
     matrix[i, j] replaced with matrix[i][j] for speed.
 
@@ -748,10 +748,6 @@ def _fisher_jenks_means_without_numpy(
     return np.delete(kclass, 0)
 
 
-if HAS_NUMBA:
-    _fisher_jenks_means = _fisher_jenks_means_numpy
-else:
-    _fisher_jenks_means = _fisher_jenks_means_without_numpy
 
 
 class MapClassifier:
@@ -2077,19 +2073,18 @@ class FisherJenks(MapClassifier):
 
     """
 
-    def __init__(self, y, k=K, _fisher_jenks_means = None):
+    def __init__(self, y, k=K):
         if not HAS_NUMBA:
             warnings.warn(
                 "Numba not installed. Using slow pure python version.",
                 UserWarning,
                 stacklevel=3,
             )
-            _fisher_jenks_means = _fisher_jenks_means or _fisher_jenks_means_without_numpy
-        else:
-            
-            _fisher_jenks_means = _fisher_jenks_means or _fisher_jenks_means_numpy
+ 
+
+        self._fjm = _fisher_jenks_means if HAS_NUMBA else _fjm_without_numpy
 
-        self._fisher_jenks_means = _fisher_jenks_means
+         
         
         nu = len(np.unique(y))
         if nu < k:
@@ -2104,7 +2099,7 @@ def __init__(self, y, k=K, _fisher_jenks_means = None):
 
     def _set_bins(self):
         x = np.sort(self.y).astype("f8")
-        self.bins = self._fisher_jenks_means(x, classes=self.k)
+        self.bins = self._fjm(x, classes=self.k)
 
 
 class FisherJenksSampled(MapClassifier):
diff --git a/mapclassify/tests/time_fisher_jenkss.py b/mapclassify/tests/time_fisher_jenkss.py
new file mode 100644
index 00000000..7dc155c2
--- /dev/null
+++ b/mapclassify/tests/time_fisher_jenkss.py
@@ -0,0 +1,67 @@
+import random
+import timeit
+import functools
+
+import matplotlib.pyplot as plt
+
+import mapclassify
+
+try:
+    import numba
+    raise Exception(
+        f"""This test is to compare execution times of two alternatives 
+        to the Numba-optimised function (both of which we already 
+        know are far slower).  
+        
+        Please run {__file__} again in a venv, 
+        in which Numba is not installed. """
+        )
+except ImportError:
+    pass
+
+number_tests = 1
+
+
+   
+def test_fisher_jenks(N):
+
+    data = [random.randint(1, 1000) for __ in range(N)]
+
+    mapclassify.classify(y = data, scheme = 'fisherjenks', k=8)
+
+descriptions = ["without Numpy, proposed less slow Pure Python code",
+                'with Numpy, existing "slow pure python" code',
+               ]
+
+data_sizes = [100, 300, 900, 1400, 2100, 3800, 10000]
+
+
+fig, ax = plt.subplots(figsize=(5, 2.7), layout='constrained')
+
+
+
+
+for HAS_NUMBA, description in zip([False, True], descriptions):
+
+    times = []
+
+    for N in data_sizes:
+        
+        # This hack avoids changing the FisherJenks 
+        # interface, just for this profiling code.
+        mapclassify.classifiers.HAS_NUMBA = HAS_NUMBA
+
+        t = timeit.timeit(functools.partial(test_fisher_jenks, N=N), number=number_tests)
+
+        print(f'Time: {t} seconds, data points: {N} {description}, {number_tests=}')
+
+        times.append(t)
+
+    ax.plot(data_sizes, times, label=description)
+
+ax.set_xlabel('Size of data classified')  # Add an x-label to the axes.
+ax.set_ylabel('Run time')  # Add a y-label to the axes.
+ax.set_title('Comparison of Fisher Jenks implementations. ')  # Add a title to the axes.
+ax.legend()  # Add a legend.
+
+plt.show()
\ No newline at end of file

From eba2180403fc8098effe7baf0a86008337acee63 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 15:21:19 +0000
Subject: [PATCH 08/18] Use sorted, not np.sort.astype.  Compare times with and
 without overhead.

---
 mapclassify/classifiers.py              |  15 ++--
 mapclassify/tests/time_fisher_jenkss.py | 101 ++++++++++++++++++------
 2 files changed, 85 insertions(+), 31 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 02215dab..b4e4762d 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -666,7 +666,8 @@ def _fisher_jenks_means(values, classes=5):
 
     k = len(values)
 
-    kclass = np.zeros(classes + 1, dtype=values.dtype)
+    # kclass = np.zeros(classes + 1, dtype=values.dtype)
+    kclass = np.zeros(classes + 1, dtype=int if isinstance(values[0], int) else float)
     kclass[classes] = values[len(values) - 1]
     kclass[0] = values[0]
     for countNum in range(classes, 1, -1):
@@ -2076,13 +2077,11 @@ class FisherJenks(MapClassifier):
     def __init__(self, y, k=K):
         if not HAS_NUMBA:
             warnings.warn(
-                "Numba not installed. Using slow pure python version.",
+                "Numba not installed. Using the new, less slow, pure python version.",
                 UserWarning,
                 stacklevel=3,
             )
- 
-
-        self._fjm = _fisher_jenks_means if HAS_NUMBA else _fjm_without_numpy
+            self._set_bins = self._set_bins_without_numpy 
 
          
         
@@ -2099,7 +2098,11 @@ def __init__(self, y, k=K):
 
     def _set_bins(self):
         x = np.sort(self.y).astype("f8")
-        self.bins = self._fjm(x, classes=self.k)
+        self.bins = _fisher_jenks_means(x, classes=self.k)
+
+    def _set_bins_without_numpy(self):
+        x = sorted(self.y)
+        self.bins = _fjm_without_numpy(x, classes=self.k)
 
 
 class FisherJenksSampled(MapClassifier):
diff --git a/mapclassify/tests/time_fisher_jenkss.py b/mapclassify/tests/time_fisher_jenkss.py
index 7dc155c2..d662a662 100644
--- a/mapclassify/tests/time_fisher_jenkss.py
+++ b/mapclassify/tests/time_fisher_jenkss.py
@@ -2,9 +2,16 @@
 import timeit
 import functools
 
-import matplotlib.pyplot as plt
+try:
+    import matplotlib.pyplot as plt
+    HAS_MATPLOTLIB = True
+except ImportError:
+    HAS_MATPLOTLIB = False
 
 import mapclassify
+import mapclassify.classifiers
+
+import numpy as np
 
 try:
     import numba
@@ -19,49 +26,93 @@
 except ImportError:
     pass
 
+
 number_tests = 1
+k = 8
 
 
    
-def test_fisher_jenks(N):
+def test_fisher_jenks_means(N, HAS_NUMBA):
 
-    data = [random.randint(1, 1000) for __ in range(N)]
+    data = [random.uniform(1.0, 1000.0) for __ in range(N)]
 
-    mapclassify.classify(y = data, scheme = 'fisherjenks', k=8)
+    if HAS_NUMBA:
+        func = mapclassify.classifiers._fisher_jenks_means(np.sort(data).astype("f8"), classes=k)
+    else:
+        func = mapclassify.classifiers._fjm_without_numpy(sorted(data), classes=k)
+   
 
-descriptions = ["without Numpy, proposed less slow Pure Python code",
-                'with Numpy, existing "slow pure python" code',
-               ]
 
-data_sizes = [100, 300, 900, 1400, 2100, 3800, 10000]
+def test_mapclassify_classify_fisherjenks(N, HAS_NUMBA):
 
+    data = [random.uniform(1.0, 1000.0) for __ in range(N)]
 
-fig, ax = plt.subplots(figsize=(5, 2.7), layout='constrained')
 
+    # This hack avoids changing the interface of the 
+    # FisherJenks class, just for this timing code.
+    mapclassify.classifiers.HAS_NUMBA = HAS_NUMBA
 
 
+    mapclassify.classify(y = data, scheme = 'fisherjenks', k=k)
 
-for HAS_NUMBA, description in zip([False, True], descriptions):
 
-    times = []
+    
+
+
+
+data_sizes = [100, 300, 1000, 2800, 8000]
+
+
+
+
+def compare_times(test_runner, descriptions, title):
+
+
+    print(f'{title}\n')
+
+    if HAS_MATPLOTLIB:
+        fig, ax = plt.subplots(figsize=(8.5, 5), layout='constrained')
+
+
+
+
+    for HAS_NUMBA, description in zip([False, True], descriptions):
+
+        times = []
+
+        for N in data_sizes:
+            
+            t = timeit.timeit(functools.partial(test_runner, N=N, HAS_NUMBA = HAS_NUMBA), number=number_tests)
+
+            print(f'Time: {t:.3f} seconds, data points: {N} {description}, {number_tests=}')
+
+            times.append(t)
 
-    for N in data_sizes:
-        
-        # This hack avoids changing the FisherJenks 
-        # interface, just for this profiling code.
-        mapclassify.classifiers.HAS_NUMBA = HAS_NUMBA
 
-        t = timeit.timeit(functools.partial(test_fisher_jenks, N=N), number=number_tests)
+        if HAS_MATPLOTLIB:
+            ax.plot(data_sizes, times, 'o-', label=description)
 
-        print(f'Time: {t} seconds, data points: {N} {description}, {number_tests=}')
 
-        times.append(t)
+    if HAS_MATPLOTLIB:
+        ax.set_xlabel('Number of random data points classified')  
+        ax.set_ylabel('Run time (seconds)')  
+        ax.set_title(title)  
+        ax.legend() 
 
-    ax.plot(data_sizes, times, label=description)
+        plt.show()
 
-ax.set_xlabel('Size of data classified')  # Add an x-label to the axes.
-ax.set_ylabel('Run time')  # Add a y-label to the axes.
-ax.set_title('Comparison of Fisher Jenks implementations. ')  # Add a title to the axes.
-ax.legend()  # Add a legend.
+compare_times(
+    test_fisher_jenks_means,
+    title="Run times of the proposed function vs the original (excluding MapClassifier overhead)",
+    descriptions = [" _fjm_without_numpy",
+                    " _fisher_jenks_means",
+                   ]
+    )
 
-plt.show()
\ No newline at end of file
+compare_times(
+    test_mapclassify_classify_fisherjenks,
+    title="Run times for end user, of the proposed code vs the original (inc MapClassifier overhead)",
+    descriptions = ["without Numpy, much less slow, pure python code",
+                    'with Numpy, existing "slow pure python" code',
+                   ],
+    )
\ No newline at end of file

From 583ae81010d7aca4da3a22c66fa1d7dc664ca17a Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 16:07:55 +0000
Subject: [PATCH 09/18] Adjust typing in docstring.  Correct function name.

---
 mapclassify/classifiers.py              | 10 +++++-----
 mapclassify/tests/time_fisher_jenkss.py |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index b4e4762d..5cddf341 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -678,7 +678,7 @@ def _fisher_jenks_means(values, classes=5):
     return np.delete(kclass, 0)
 
 
-def _fjm_without_numpy(
+def _fisher_jenks_means_without_numpy(
     values,
     classes=5,
     np = default_mock_numpy
@@ -2040,7 +2040,7 @@ class FisherJenks(MapClassifier):
     Parameters
     ----------
 
-    y : numpy.array
+    y : collections.abc.Iterable[numbers.Real]
         :math:`(n,1)`, values to classify.
     k : int (default 5)
         The number of classes required.
@@ -2050,7 +2050,7 @@ class FisherJenks(MapClassifier):
 
     yb : numpy.array
         :math:`(n,1)`, bin IDs for observations.
-    bins : numpy.array
+    bins : collections.abc.Sequence[numbers.Real]
         :math:`(k,1)`, the upper bounds of each class.
     k : int
         The number of classes.
@@ -2077,7 +2077,7 @@ class FisherJenks(MapClassifier):
     def __init__(self, y, k=K):
         if not HAS_NUMBA:
             warnings.warn(
-                "Numba not installed. Using the new, less slow, pure python version.",
+                "Numba not installed. Using a less slow, pure python version.",
                 UserWarning,
                 stacklevel=3,
             )
@@ -2102,7 +2102,7 @@ def _set_bins(self):
 
     def _set_bins_without_numpy(self):
         x = sorted(self.y)
-        self.bins = _fjm_without_numpy(x, classes=self.k)
+        self.bins = _fisher_jenks_means_without_numpy(x, classes=self.k)
 
 
 class FisherJenksSampled(MapClassifier):
diff --git a/mapclassify/tests/time_fisher_jenkss.py b/mapclassify/tests/time_fisher_jenkss.py
index d662a662..15ece69b 100644
--- a/mapclassify/tests/time_fisher_jenkss.py
+++ b/mapclassify/tests/time_fisher_jenkss.py
@@ -39,7 +39,7 @@ def test_fisher_jenks_means(N, HAS_NUMBA):
     if HAS_NUMBA:
         func = mapclassify.classifiers._fisher_jenks_means(np.sort(data).astype("f8"), classes=k)
     else:
-        func = mapclassify.classifiers._fjm_without_numpy(sorted(data), classes=k)
+        func = mapclassify.classifiers._fisher_jenks_means_without_numpy(sorted(data), classes=k)
    
 
 

From 1c79a9de095a15dde39cf3a709ecdfdbe54d951a Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 16:51:59 +0000
Subject: [PATCH 10/18] Revert "Deactivate CI"

This reverts commit 34c7a25fa03503be34f67f3c8bb64da802d342d1.
---
 .github/dependabot.yml           | 20 ++++++++++++++++++++
 .github/workflows/build_docs.yml |  8 ++++----
 .github/workflows/release.yml    |  8 ++++----
 .github/workflows/testing.yml    | 18 ++++++++----------
 4 files changed, 36 insertions(+), 18 deletions(-)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..57fa59b4
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,20 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    reviewers:
+      - "jGaboardi"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    reviewers:
+      - "jGaboardi"
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 0adc82df..4d42cf22 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -2,10 +2,10 @@
  name: Build Docs
  
  on:
-  #  push:
-  #    # Sequence of patterns matched against refs/tags
-  #    tags:
-  #      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+   push:
+     # Sequence of patterns matched against refs/tags
+     tags:
+       - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
    workflow_dispatch:
      inputs:
        version:
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f46c6165..b5418e6a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,10 +1,10 @@
 name: Release Package
 
 on:
-  # push:
-  #   # Sequence of patterns matched against refs/tags
-  #   tags:
-  #     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
   workflow_dispatch:
     inputs:
       version:
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 94c1931e..8a7cf603 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -1,16 +1,14 @@
 name: Continuous Integration
 
 on:
-  # push:
-  #   branches:
-  #     - "*"
-  # pull_request:
-  #   branches:
-  #     - "*"
-  # schedule:
-  #   - cron: "59 21 * * *"
-  workflow_dispatch:
-      
+  push:
+    branches:
+      - "*"
+  pull_request:
+    branches:
+      - "*"
+  schedule:
+    - cron: "59 21 * * *"
 
 jobs:
   testing:

From 81501db7e12a03f088764dd3cbf6cc798cf105c0 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 16:56:37 +0000
Subject: [PATCH 11/18] Revert README.md to original

---
 README.md | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/README.md b/README.md
index 1b98bc1e..9f73d132 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,3 @@
-# mapclassif-Iron:  _fisher_jenks_means for IronPython, and other environments without numpy.
-
-This branch does not currently work, but is intended to very soon work with, when installed by 
-directing pip to this github repository branch.  This branch is primarily for convenient
-PRs for mapclassify.  
-
-Only the function, _fisher_jenks_means has been adapted (back to something similar to 
-Daniel J Lewis's original snippet).  
-
-No other functionality from mapclassify has been changed, and none has been added.
-
-Parent project's README.md:
-
 # mapclassify: Classification Schemes for Choropleth Maps
 
 [![Continuous Integration](https://github.com/pysal/mapclassify/actions/workflows/testing.yml/badge.svg)](https://github.com/pysal/mapclassify/actions/workflows/testing.yml)

From f68bd5e90df80bdc9885097179935473b8adbe70 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 16:59:34 +0000
Subject: [PATCH 12/18] Remove unused entry and unused import

---
 mapclassify/_classify_API.py | 1 -
 mapclassify/classifiers.py   | 1 -
 2 files changed, 2 deletions(-)

diff --git a/mapclassify/_classify_API.py b/mapclassify/_classify_API.py
index 7f1c0a7d..c0c0fa8b 100644
--- a/mapclassify/_classify_API.py
+++ b/mapclassify/_classify_API.py
@@ -24,7 +24,6 @@
     "boxplot": BoxPlot,
     "equalinterval": EqualInterval,
     "fisherjenks": FisherJenks,
-    "fisherjenks_nonumpy": FisherJenks,
     "fisherjenkssampled": FisherJenksSampled,
     "headtailbreaks": HeadTailBreaks,
     "jenkscaspall": JenksCaspall,
diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 5cddf341..4521ba8e 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -1,7 +1,6 @@
 """
 A module of classification schemes for choropleth mapping.
 """
-import sys
 import copy
 import functools
 import warnings

From 9784bfd185a3cf442f14a1d6188f22325ebcdf74 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 17:09:25 +0000
Subject: [PATCH 13/18] Tweak to reduce number of changes in PR

---
 mapclassify/classifiers.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 4521ba8e..fae1766c 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -5,9 +5,9 @@
 import functools
 import warnings
 
+import numpy as np  
 import scipy.stats as stats
 from sklearn.cluster import KMeans
-import numpy as np  
 
 
 
@@ -113,7 +113,8 @@ def wrapper_decorator(*args, **kwargs):
 
         return decorator_njit
 
-    # Numba requires Numpy    
+    # Numba requires Numpy.  This is still used when 
+    # Numpy is present, but Numba isn't.
     default_mock_numpy = MockNumpy()
 
 
@@ -665,8 +666,7 @@ def _fisher_jenks_means(values, classes=5):
 
     k = len(values)
 
-    # kclass = np.zeros(classes + 1, dtype=values.dtype)
-    kclass = np.zeros(classes + 1, dtype=int if isinstance(values[0], int) else float)
+    kclass = np.zeros(classes + 1, dtype=values.dtype)
     kclass[classes] = values[len(values) - 1]
     kclass[0] = values[0]
     for countNum in range(classes, 1, -1):
@@ -706,7 +706,6 @@ def _fisher_jenks_means_without_numpy(
     mat1 = np.zeros((n_data + 1, classes + 1), dtype=np.int32)
     mat2 = np.zeros((n_data + 1, classes + 1), dtype=np.float32)
     
-    # System.Array.Fill not suppported on Multi-dimensional arrays
     for j in range(1, classes + 1):
         mat1[1][j] = 1
         for i in range(2, n_data+1):
@@ -733,8 +732,6 @@ def _fisher_jenks_means_without_numpy(
         mat1[_l][1] = 1
         mat2[_l][1] = v
 
-#    for row in mat1:
-#        print(row)
     k = len(values)
 
     kclass = np.zeros((classes + 1,), dtype=type(values[0]))

From 49a06a9a6350ea5a639c394c170b0924cc15d782 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 17:11:31 +0000
Subject: [PATCH 14/18] Remove whitespace

---
 mapclassify/classifiers.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index fae1766c..cc0ec5f5 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -5,12 +5,10 @@
 import functools
 import warnings
 
-import numpy as np  
+import numpy as np
 import scipy.stats as stats
 from sklearn.cluster import KMeans
 
-
-
 __author__ = "Sergio J. Rey"
 
 __all__ = [

From dbb3b8d83fc36c3a3b3a238b2db2addab34752d8 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 17:37:40 +0000
Subject: [PATCH 15/18] Fix error when numba present.  Add timing test that
 starts from np arrays

---
 mapclassify/classifiers.py              |  9 ++++-----
 mapclassify/tests/time_fisher_jenkss.py | 22 +++++++++++++++-------
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index cc0ec5f5..fabbeabf 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -111,10 +111,6 @@ def wrapper_decorator(*args, **kwargs):
 
         return decorator_njit
 
-    # Numba requires Numpy.  This is still used when 
-    # Numpy is present, but Numba isn't.
-    default_mock_numpy = MockNumpy()
-
 
 def _format_intervals(mc, fmt="{:.0f}"):
     """
@@ -678,7 +674,7 @@ def _fisher_jenks_means(values, classes=5):
 def _fisher_jenks_means_without_numpy(
     values,
     classes=5,
-    np = default_mock_numpy
+    np = None
     ):
     """
     As for _fisher_jenks_means above, to keep the code as far as possible
@@ -699,6 +695,9 @@ def _fisher_jenks_means_without_numpy(
 
 
     """
+    if np is None:
+        np = MockNumpy()
+
     values.sort()
     n_data = len(values)
     mat1 = np.zeros((n_data + 1, classes + 1), dtype=np.int32)
diff --git a/mapclassify/tests/time_fisher_jenkss.py b/mapclassify/tests/time_fisher_jenkss.py
index 15ece69b..41729841 100644
--- a/mapclassify/tests/time_fisher_jenkss.py
+++ b/mapclassify/tests/time_fisher_jenkss.py
@@ -40,6 +40,14 @@ def test_fisher_jenks_means(N, HAS_NUMBA):
         func = mapclassify.classifiers._fisher_jenks_means(np.sort(data).astype("f8"), classes=k)
     else:
         func = mapclassify.classifiers._fisher_jenks_means_without_numpy(sorted(data), classes=k)
+
+
+    # data = np.sort([random.uniform(1.0, 1000.0) for __ in range(N)]).astype("f8")
+
+    # if HAS_NUMBA:
+    #     func = mapclassify.classifiers._fisher_jenks_means(data, classes=k)
+    # else:
+    #     func = mapclassify.classifiers._fisher_jenks_means_without_numpy(data, classes=k)
    
 
 
@@ -109,10 +117,10 @@ def compare_times(test_runner, descriptions, title):
                    ]
     )
 
-compare_times(
-    test_mapclassify_classify_fisherjenks,
-    title="Run times for end user, of the proposed code vs the original (inc MapClassifier overhead)",
-    descriptions = ["without Numpy, much less slow, pure python code",
-                    'with Numpy, existing "slow pure python" code',
-                   ],
-    )
\ No newline at end of file
+# compare_times(
+#     test_mapclassify_classify_fisherjenks,
+#     title="Run times for end user, of the proposed code vs the original (inc MapClassifier overhead)",
+#     descriptions = ["without Numpy, much less slow, pure python code",
+#                     'with Numpy, existing "slow pure python" code',
+#                    ],
+#     )
\ No newline at end of file

From 0b4885468118edd4e215319123ebe22aa679fb32 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 19:38:27 +0000
Subject: [PATCH 16/18] Set bins to be a numpy array

---
 mapclassify/classifiers.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index fabbeabf..5a83a2fe 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -698,7 +698,6 @@ def _fisher_jenks_means_without_numpy(
     if np is None:
         np = MockNumpy()
 
-    values.sort()
     n_data = len(values)
     mat1 = np.zeros((n_data + 1, classes + 1), dtype=np.int32)
     mat2 = np.zeros((n_data + 1, classes + 1), dtype=np.float32)
@@ -744,6 +743,7 @@ def _fisher_jenks_means_without_numpy(
 
 
 
+
 class MapClassifier:
     r"""
     Abstract class for all map classifications :cite:`Slocum_2009`
@@ -2069,12 +2069,12 @@ class FisherJenks(MapClassifier):
 
     def __init__(self, y, k=K):
         if not HAS_NUMBA:
+            self._set_bins = self._set_bins_without_numpy 
             warnings.warn(
                 "Numba not installed. Using a less slow, pure python version.",
                 UserWarning,
                 stacklevel=3,
             )
-            self._set_bins = self._set_bins_without_numpy 
 
          
         
@@ -2095,7 +2095,7 @@ def _set_bins(self):
 
     def _set_bins_without_numpy(self):
         x = sorted(self.y)
-        self.bins = _fisher_jenks_means_without_numpy(x, classes=self.k)
+        self.bins = np.asarray(_fisher_jenks_means_without_numpy(x, classes=self.k))
 
 
 class FisherJenksSampled(MapClassifier):
@@ -2135,14 +2135,20 @@ class FisherJenksSampled(MapClassifier):
 
     """
 
+    ids = None
+
     def __init__(self, y, k=K, pct=0.10, truncate=True):
+        print(f'Got: {k=}, {pct=}, {truncate=}')
         self.k = k
         n = y.size
 
         if (pct * n > 1000) and truncate:
             pct = 1000.0 / n
+        # if FisherJenksSampled.ids is None:
+            # FisherJenksSampled.ids = np.random.randint(0, n, int(n * pct))
         ids = np.random.randint(0, n, int(n * pct))
         y = np.asarray(y)
+        # yr = y[FisherJenksSampled.ids]
         yr = y[ids]
         yr[-1] = max(y)  # make sure we have the upper bound
         yr[0] = min(y)  # make sure we have the min

From 921646207b43d050fcada25fceb026336fae2770 Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Thu, 14 Dec 2023 20:59:46 +0000
Subject: [PATCH 17/18] Change exception if numba present to a UserWarning

---
 mapclassify/tests/time_fisher_jenkss.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/mapclassify/tests/time_fisher_jenkss.py b/mapclassify/tests/time_fisher_jenkss.py
index 41729841..3c26ae3e 100644
--- a/mapclassify/tests/time_fisher_jenkss.py
+++ b/mapclassify/tests/time_fisher_jenkss.py
@@ -1,6 +1,8 @@
 import random
 import timeit
 import functools
+import warnings
+
 
 try:
     import matplotlib.pyplot as plt
@@ -15,14 +17,17 @@
 
 try:
     import numba
-    raise Exception(
-        f"""This test is to compare execution times of two alternatives 
+
+    warnings.warn(
+       f"""This test is to compare execution times of two alternatives 
         to the Numba-optimised function (both of which we already 
         know are far slower).  
         
         Please run {__file__} again in a venv, 
-        in which Numba is not installed. """
-        )
+        in which Numba is not installed. """,
+        UserWarning,
+        stacklevel=3,
+        ) 
 except ImportError:
     pass
 

From 268c1d5a2195ee3ae79d3a538a6b409cffcb231d Mon Sep 17 00:00:00 2001
From: JamesParrott <80779630+JamesParrott@users.noreply.github.com>
Date: Fri, 15 Dec 2023 10:41:56 +0000
Subject: [PATCH 18/18] Make zeros an instance method and MockNumpy a Python 3
 style class

---
 mapclassify/classifiers.py              | 51 +++++------------
 mapclassify/tests/time_fisher_jenkss.py | 74 +++++++++++--------------
 2 files changed, 45 insertions(+), 80 deletions(-)

diff --git a/mapclassify/classifiers.py b/mapclassify/classifiers.py
index 5a83a2fe..7eca9af2 100644
--- a/mapclassify/classifiers.py
+++ b/mapclassify/classifiers.py
@@ -61,37 +61,23 @@
 FMT = "{:.2f}"
 
 
-
-
-
-
-class MockNumpy(object):
-    
-    def __init__(self, int_type = None, float_type = None):
-
+class MockNumpy:
+    def __init__(self, int_type=None, float_type=None):
         self.int32 = int_type or int
         self.float32 = float_type or float
 
-        self.inf = self.float32('inf')
-    
-    @classmethod
-    def zeros(self, dims, dtype = int):
+        self.inf = self.float32("inf")
 
+    def zeros(self, dims, dtype=int):
         if len(dims) == 1:
             zero = dtype(0)
             return [zero for __ in range(dims[0])]
-            
-        return [self.zeros(dims[1:], dtype) for __ in range(dims[0])] 
-        
+
+        return [self.zeros(dims[1:], dtype) for __ in range(dims[0])]
 
     @staticmethod
     def delete(arr, index):
-        return arr[:index] + arr[index+1:]
-
-
-
-
-
+        return arr[:index] + arr[index + 1 :]
 
 
 try:
@@ -671,11 +657,7 @@ def _fisher_jenks_means(values, classes=5):
     return np.delete(kclass, 0)
 
 
-def _fisher_jenks_means_without_numpy(
-    values,
-    classes=5,
-    np = None
-    ):
+def _fisher_jenks_means_without_numpy(values, classes=5, np=None):
     """
     As for _fisher_jenks_means above, to keep the code as far as possible
     exactly the same, except with np passable in as a dependency, and with
@@ -701,10 +683,10 @@ def _fisher_jenks_means_without_numpy(
     n_data = len(values)
     mat1 = np.zeros((n_data + 1, classes + 1), dtype=np.int32)
     mat2 = np.zeros((n_data + 1, classes + 1), dtype=np.float32)
-    
+
     for j in range(1, classes + 1):
         mat1[1][j] = 1
-        for i in range(2, n_data+1):
+        for i in range(2, n_data + 1):
             mat2[i][j] = np.inf
     v = 0
     for _l in range(2, len(values) + 1):
@@ -741,9 +723,6 @@ def _fisher_jenks_means_without_numpy(
     return np.delete(kclass, 0)
 
 
-
-
-
 class MapClassifier:
     r"""
     Abstract class for all map classifications :cite:`Slocum_2009`
@@ -2069,15 +2048,13 @@ class FisherJenks(MapClassifier):
 
     def __init__(self, y, k=K):
         if not HAS_NUMBA:
-            self._set_bins = self._set_bins_without_numpy 
+            self._set_bins = self._set_bins_without_numpy
             warnings.warn(
                 "Numba not installed. Using a less slow, pure python version.",
                 UserWarning,
                 stacklevel=3,
             )
 
-         
-        
         nu = len(np.unique(y))
         if nu < k:
             raise ValueError(
@@ -2087,8 +2064,6 @@ def __init__(self, y, k=K):
         MapClassifier.__init__(self, y)
         self.name = "FisherJenks"
 
-
-
     def _set_bins(self):
         x = np.sort(self.y).astype("f8")
         self.bins = _fisher_jenks_means(x, classes=self.k)
@@ -2138,14 +2113,14 @@ class FisherJenksSampled(MapClassifier):
     ids = None
 
     def __init__(self, y, k=K, pct=0.10, truncate=True):
-        print(f'Got: {k=}, {pct=}, {truncate=}')
+        print(f"Got: {k=}, {pct=}, {truncate=}")
         self.k = k
         n = y.size
 
         if (pct * n > 1000) and truncate:
             pct = 1000.0 / n
         # if FisherJenksSampled.ids is None:
-            # FisherJenksSampled.ids = np.random.randint(0, n, int(n * pct))
+        # FisherJenksSampled.ids = np.random.randint(0, n, int(n * pct))
         ids = np.random.randint(0, n, int(n * pct))
         y = np.asarray(y)
         # yr = y[FisherJenksSampled.ids]
diff --git a/mapclassify/tests/time_fisher_jenkss.py b/mapclassify/tests/time_fisher_jenkss.py
index 3c26ae3e..7d5d26c9 100644
--- a/mapclassify/tests/time_fisher_jenkss.py
+++ b/mapclassify/tests/time_fisher_jenkss.py
@@ -6,6 +6,7 @@
 
 try:
     import matplotlib.pyplot as plt
+
     HAS_MATPLOTLIB = True
 except ImportError:
     HAS_MATPLOTLIB = False
@@ -19,7 +20,7 @@
     import numba
 
     warnings.warn(
-       f"""This test is to compare execution times of two alternatives 
+        f"""This test is to compare execution times of two alternatives 
         to the Numba-optimised function (both of which we already 
         know are far slower).  
         
@@ -27,7 +28,7 @@
         in which Numba is not installed. """,
         UserWarning,
         stacklevel=3,
-        ) 
+    )
 except ImportError:
     pass
 
@@ -36,16 +37,17 @@
 k = 8
 
 
-   
 def test_fisher_jenks_means(N, HAS_NUMBA):
-
     data = [random.uniform(1.0, 1000.0) for __ in range(N)]
 
     if HAS_NUMBA:
-        func = mapclassify.classifiers._fisher_jenks_means(np.sort(data).astype("f8"), classes=k)
+        func = mapclassify.classifiers._fisher_jenks_means(
+            np.sort(data).astype("f8"), classes=k
+        )
     else:
-        func = mapclassify.classifiers._fisher_jenks_means_without_numpy(sorted(data), classes=k)
-
+        func = mapclassify.classifiers._fisher_jenks_means_without_numpy(
+            sorted(data), classes=k
+        )
 
     # data = np.sort([random.uniform(1.0, 1000.0) for __ in range(N)]).astype("f8")
 
@@ -53,74 +55,62 @@ def test_fisher_jenks_means(N, HAS_NUMBA):
     #     func = mapclassify.classifiers._fisher_jenks_means(data, classes=k)
     # else:
     #     func = mapclassify.classifiers._fisher_jenks_means_without_numpy(data, classes=k)
-   
 
 
 def test_mapclassify_classify_fisherjenks(N, HAS_NUMBA):
-
     data = [random.uniform(1.0, 1000.0) for __ in range(N)]
 
-
-    # This hack avoids changing the interface of the 
+    # This hack avoids changing the interface of the
     # FisherJenks class, just for this timing code.
     mapclassify.classifiers.HAS_NUMBA = HAS_NUMBA
 
-
-    mapclassify.classify(y = data, scheme = 'fisherjenks', k=k)
-
-
-    
-
+    mapclassify.classify(y=data, scheme="fisherjenks", k=k)
 
 
 data_sizes = [100, 300, 1000, 2800, 8000]
 
 
-
-
 def compare_times(test_runner, descriptions, title):
-
-
-    print(f'{title}\n')
+    print(f"{title}\n")
 
     if HAS_MATPLOTLIB:
-        fig, ax = plt.subplots(figsize=(8.5, 5), layout='constrained')
-
-
-
+        fig, ax = plt.subplots(figsize=(8.5, 5), layout="constrained")
 
     for HAS_NUMBA, description in zip([False, True], descriptions):
-
         times = []
 
         for N in data_sizes:
-            
-            t = timeit.timeit(functools.partial(test_runner, N=N, HAS_NUMBA = HAS_NUMBA), number=number_tests)
+            t = timeit.timeit(
+                functools.partial(test_runner, N=N, HAS_NUMBA=HAS_NUMBA),
+                number=number_tests,
+            )
 
-            print(f'Time: {t:.3f} seconds, data points: {N} {description}, {number_tests=}')
+            print(
+                f"Time: {t:.3f} seconds, data points: {N} {description}, {number_tests=}"
+            )
 
             times.append(t)
 
-
         if HAS_MATPLOTLIB:
-            ax.plot(data_sizes, times, 'o-', label=description)
-
+            ax.plot(data_sizes, times, "o-", label=description)
 
     if HAS_MATPLOTLIB:
-        ax.set_xlabel('Number of random data points classified')  
-        ax.set_ylabel('Run time (seconds)')  
-        ax.set_title(title)  
-        ax.legend() 
+        ax.set_xlabel("Number of random data points classified")
+        ax.set_ylabel("Run time (seconds)")
+        ax.set_title(title)
+        ax.legend()
 
         plt.show()
 
+
 compare_times(
     test_fisher_jenks_means,
     title="Run times of the proposed function vs the original (excluding MapClassifier overhead)",
-    descriptions = [" _fjm_without_numpy",
-                    " _fisher_jenks_means",
-                   ]
-    )
+    descriptions=[
+        " _fjm_without_numpy",
+        " _fisher_jenks_means",
+    ],
+)
 
 # compare_times(
 #     test_mapclassify_classify_fisherjenks,
@@ -128,4 +118,4 @@ def compare_times(test_runner, descriptions, title):
 #     descriptions = ["without Numpy, much less slow, pure python code",
 #                     'with Numpy, existing "slow pure python" code',
 #                    ],
-#     )
\ No newline at end of file
+#     )