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Revision to installation instructions and scipy importing #84

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Sep 6, 2022
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Revision to installation instructions and scipy importing #84

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71ba37b
update install instructions
elbeejay Sep 4, 2022
91549f7
scipy deprecation
elbeejay Sep 4, 2022
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2 changes: 1 addition & 1 deletion docs/source/gallery/dong2022.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.1"
"version": "3.10.4"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/source/gallery/dong2022.rst
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.. 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
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2 changes: 1 addition & 1 deletion docs/source/gallery/hariharan2022.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.1"
"version": "3.10.4"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/source/gallery/hariharan2022.rst
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.. 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
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2 changes: 1 addition & 1 deletion docs/source/gallery/knights2020.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.1"
"version": "3.10.4"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/source/gallery/knights2020.rst
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.. 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
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2 changes: 1 addition & 1 deletion docs/source/gallery/konkol2022.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.1"
"version": "3.10.4"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/source/gallery/konkol2022.rst
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.. 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
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2 changes: 1 addition & 1 deletion docs/source/gallery/tejedor2022.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.1"
"version": "3.10.4"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/source/gallery/tejedor2022.rst
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.. 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
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8 changes: 5 additions & 3 deletions docs/source/install/index.rst
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Expand Up @@ -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:
::
Expand All @@ -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
------------------------
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2 changes: 1 addition & 1 deletion rivgraph/classes.py
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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
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2 changes: 1 addition & 1 deletion rivgraph/deltas/delta_directionality.py
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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

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2 changes: 1 addition & 1 deletion rivgraph/im_utils.py
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion rivgraph/mask_utils.py
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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
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4 changes: 2 additions & 2 deletions rivgraph/rivers/river_utils.py
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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
Expand Down Expand Up @@ -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):
"""
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