From 71ba37bd628ac78306429f9ad32cce8588ca5c21 Mon Sep 17 00:00:00 2001
From: jayh <jayaram.hariharan@utexas.edu>
Date: Sun, 4 Sep 2022 15:31:43 -0400
Subject: [PATCH 1/2] update install instructions

---
 docs/source/gallery/dong2022.ipynb      | 2 +-
 docs/source/gallery/dong2022.rst        | 2 +-
 docs/source/gallery/hariharan2022.ipynb | 2 +-
 docs/source/gallery/hariharan2022.rst   | 2 +-
 docs/source/gallery/knights2020.ipynb   | 2 +-
 docs/source/gallery/knights2020.rst     | 2 +-
 docs/source/gallery/konkol2022.ipynb    | 2 +-
 docs/source/gallery/konkol2022.rst      | 2 +-
 docs/source/gallery/tejedor2022.ipynb   | 2 +-
 docs/source/gallery/tejedor2022.rst     | 2 +-
 docs/source/install/index.rst           | 8 +++++---
 11 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/docs/source/gallery/dong2022.ipynb b/docs/source/gallery/dong2022.ipynb
index 26774fc..91a08d6 100644
--- a/docs/source/gallery/dong2022.ipynb
+++ b/docs/source/gallery/dong2022.ipynb
@@ -46,7 +46,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.1"
+      "version": "3.10.4"
     }
   },
   "nbformat": 4,
diff --git a/docs/source/gallery/dong2022.rst b/docs/source/gallery/dong2022.rst
index c466e82..a7d864f 100644
--- a/docs/source/gallery/dong2022.rst
+++ b/docs/source/gallery/dong2022.rst
@@ -2,7 +2,7 @@
 .. DO NOT EDIT.
 .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
 .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "gallery\dong2022.py"
+.. "gallery/dong2022.py"
 .. LINE NUMBERS ARE GIVEN BELOW.
 
 .. only:: html
diff --git a/docs/source/gallery/hariharan2022.ipynb b/docs/source/gallery/hariharan2022.ipynb
index ba1d725..0e48b09 100644
--- a/docs/source/gallery/hariharan2022.ipynb
+++ b/docs/source/gallery/hariharan2022.ipynb
@@ -46,7 +46,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.1"
+      "version": "3.10.4"
     }
   },
   "nbformat": 4,
diff --git a/docs/source/gallery/hariharan2022.rst b/docs/source/gallery/hariharan2022.rst
index 5dde4b8..833e088 100644
--- a/docs/source/gallery/hariharan2022.rst
+++ b/docs/source/gallery/hariharan2022.rst
@@ -2,7 +2,7 @@
 .. DO NOT EDIT.
 .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
 .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "gallery\hariharan2022.py"
+.. "gallery/hariharan2022.py"
 .. LINE NUMBERS ARE GIVEN BELOW.
 
 .. only:: html
diff --git a/docs/source/gallery/knights2020.ipynb b/docs/source/gallery/knights2020.ipynb
index 0c43be3..4996a01 100644
--- a/docs/source/gallery/knights2020.ipynb
+++ b/docs/source/gallery/knights2020.ipynb
@@ -46,7 +46,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.1"
+      "version": "3.10.4"
     }
   },
   "nbformat": 4,
diff --git a/docs/source/gallery/knights2020.rst b/docs/source/gallery/knights2020.rst
index 28de201..1317d28 100644
--- a/docs/source/gallery/knights2020.rst
+++ b/docs/source/gallery/knights2020.rst
@@ -2,7 +2,7 @@
 .. DO NOT EDIT.
 .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
 .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "gallery\knights2020.py"
+.. "gallery/knights2020.py"
 .. LINE NUMBERS ARE GIVEN BELOW.
 
 .. only:: html
diff --git a/docs/source/gallery/konkol2022.ipynb b/docs/source/gallery/konkol2022.ipynb
index 66ace4a..405b8d6 100644
--- a/docs/source/gallery/konkol2022.ipynb
+++ b/docs/source/gallery/konkol2022.ipynb
@@ -46,7 +46,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.1"
+      "version": "3.10.4"
     }
   },
   "nbformat": 4,
diff --git a/docs/source/gallery/konkol2022.rst b/docs/source/gallery/konkol2022.rst
index 7e6e034..c2b9c58 100644
--- a/docs/source/gallery/konkol2022.rst
+++ b/docs/source/gallery/konkol2022.rst
@@ -2,7 +2,7 @@
 .. DO NOT EDIT.
 .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
 .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "gallery\konkol2022.py"
+.. "gallery/konkol2022.py"
 .. LINE NUMBERS ARE GIVEN BELOW.
 
 .. only:: html
diff --git a/docs/source/gallery/tejedor2022.ipynb b/docs/source/gallery/tejedor2022.ipynb
index 339d0e9..4892fa9 100644
--- a/docs/source/gallery/tejedor2022.ipynb
+++ b/docs/source/gallery/tejedor2022.ipynb
@@ -46,7 +46,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.1"
+      "version": "3.10.4"
     }
   },
   "nbformat": 4,
diff --git a/docs/source/gallery/tejedor2022.rst b/docs/source/gallery/tejedor2022.rst
index c91bced..1b306f4 100644
--- a/docs/source/gallery/tejedor2022.rst
+++ b/docs/source/gallery/tejedor2022.rst
@@ -2,7 +2,7 @@
 .. DO NOT EDIT.
 .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
 .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
-.. "gallery\tejedor2022.py"
+.. "gallery/tejedor2022.py"
 .. LINE NUMBERS ARE GIVEN BELOW.
 
 .. only:: html
diff --git a/docs/source/install/index.rst b/docs/source/install/index.rst
index da784cb..57c10b4 100644
--- a/docs/source/install/index.rst
+++ b/docs/source/install/index.rst
@@ -12,7 +12,7 @@ Installation Instructions
 Installation via *conda*
 --------------------------
 
-The latest 'stable' version of *RivGraph* can be installed via `conda`.
+The latest 'stable' version of *RivGraph* can be installed via `conda`; as of this writing we have tested this installation process for Python versions 3.9.x and 3.7.13 (per `issue 83 <https://github.com/VeinsOfTheEarth/RivGraph/issues/83>`_).
 We recommend installing *RivGraph* into a fresh conda environment to minimize the risk of dependency clashes.
 The easiest way to do this is by opening Terminal (Mac/Unix) or Anaconda Prompt (Windows) and typing:
 ::
@@ -27,8 +27,10 @@ If you would rather install *RivGraph* into a pre-existing environment "myenv",
 
 .. warning::
 
- *RivGraph* dependencies may be pinned to specific versions of packages (e.g. geopandas 0.7) that may not mesh with your existing environment.
- Check the `environment file <https://github.com/VeinsOfTheEarth/RivGraph/blob/master/environment.yml>`_ for these cases.
+   *RivGraph* dependencies may be pinned to specific versions of packages that may not mesh with your existing environment.
+   Check the `environment file <https://github.com/VeinsOfTheEarth/RivGraph/blob/master/environment.yml>`_ for these cases.
+   If you are having trouble getting the environment to resolve, or it is taking a very long time, consider using *mamba*
+   as a drop-in replacement for *conda* (see `mamba docs <https://mamba.readthedocs.io/en/latest/>`_).
 
 Installation from source
 ------------------------

From 91549f7df601002022d765d688531a979eacb816 Mon Sep 17 00:00:00 2001
From: jayh <jayaram.hariharan@utexas.edu>
Date: Sun, 4 Sep 2022 15:31:54 -0400
Subject: [PATCH 2/2] scipy deprecation

---
 rivgraph/classes.py                     | 2 +-
 rivgraph/deltas/delta_directionality.py | 2 +-
 rivgraph/im_utils.py                    | 2 +-
 rivgraph/mask_utils.py                  | 2 +-
 rivgraph/rivers/river_utils.py          | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/rivgraph/classes.py b/rivgraph/classes.py
index b8ac831..58ac398 100644
--- a/rivgraph/classes.py
+++ b/rivgraph/classes.py
@@ -15,7 +15,7 @@
 import numpy as np
 import networkx as nx
 from pyproj.crs import CRS
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import distance_transform_edt
 from matplotlib import pyplot as plt
 import geopandas as gpd
 from shapely.geometry import LineString
diff --git a/rivgraph/deltas/delta_directionality.py b/rivgraph/deltas/delta_directionality.py
index 67e153a..e347441 100644
--- a/rivgraph/deltas/delta_directionality.py
+++ b/rivgraph/deltas/delta_directionality.py
@@ -15,7 +15,7 @@
 from scipy.stats import mode, linregress
 from scipy.interpolate import interp1d
 from scipy.spatial import ConvexHull
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import distance_transform_edt
 import rivgraph.io_utils as io
 import rivgraph.directionality as dy
 
diff --git a/rivgraph/im_utils.py b/rivgraph/im_utils.py
index a74f98c..8b2f8f0 100644
--- a/rivgraph/im_utils.py
+++ b/rivgraph/im_utils.py
@@ -892,7 +892,7 @@ def fill_holes(I, maxholesize=0):
     I = np.array(I, dtype=bool)
 
     if maxholesize == 0:
-        I = nd.morphology.binary_fill_holes(I)
+        I = nd.binary_fill_holes(I)
         return I
     else:
         # Fill only holes less than maxholesize
diff --git a/rivgraph/mask_utils.py b/rivgraph/mask_utils.py
index ba67d02..6bb9870 100644
--- a/rivgraph/mask_utils.py
+++ b/rivgraph/mask_utils.py
@@ -14,7 +14,7 @@
 import geopandas as gpd
 import rivgraph.im_utils as iu
 import rivgraph.geo_utils as gu
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import distance_transform_edt
 from shapely.geometry import Polygon
 from shapely.ops import cascaded_union
 from scipy import stats
diff --git a/rivgraph/rivers/river_utils.py b/rivgraph/rivers/river_utils.py
index 129141c..06b3b1d 100644
--- a/rivgraph/rivers/river_utils.py
+++ b/rivgraph/rivers/river_utils.py
@@ -10,7 +10,7 @@
 import numpy as np
 import networkx as nx
 from fastdtw import fastdtw
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import distance_transform_edt
 import shapely
 from shapely.geometry import LineString, Polygon
 from scipy import signal
@@ -641,7 +641,7 @@ def get_transect_indices_along_buffered_lines(cl, mapper):
             pts[i] = idxlist
 
         return pts
-    
+
 
     def get_transect_endpoints_xy(lpts, rpts):
         """