Renamed to pyrivet, made tests pass

pr-check.sh

@@ -18,9 +18,9 @@
 
 set -ev
 
-if [ ! -f atlatl/__init__.py ]
+if [ ! -f pyrivet/__init__.py ]
 then
-    echo "Run "$(basename "$0")" from the root of the Atlatl repository"
+    echo "Run "$(basename "$0")" from the root of the pyrivet repository"
     exit 1
 fi
 
@@ -95,7 +95,7 @@ else
 fi
 
 # optional, but highly recommended: create a virtualenv to isolate tests
-venv=$(mktemp -u atlatl_pr_venv_XXXXX) || \
+venv=$(mktemp -u pyrivet_pr_venv_XXXXX) || \
     exit_with_error "mktemp -u error"
 $create_venv $venv || {
     exit_with_error "virtualenv creation failed"
@@ -105,9 +105,9 @@ $activate_venv $venv || {
     exit_with_error "virtualenv activation failed"
 }
 
-# install atlatl in editable mode (required for testing)
+# install pyrivet in editable mode (required for testing)
 pip3 install $ignore_installed -U -e . || \
-    exit_with_error_and_venv "pip3 failed to install atlatl"
+    exit_with_error_and_venv "pip3 failed to install pyrivet"
 
 # install developer dependencies
 pip3 install $ignore_installed -U -r requirements-dev.txt || \

atlatl/matching_distance.py → pyrivet/matching_distance.py

@@ -1,7 +1,7 @@
 import math
 import numpy as np
-from atlatl import rivet, barcode, hera
-from atlatl.rivet import Point, PointCloud
+from pyrivet import rivet, barcode, hera
+from pyrivet.rivet import Point, PointCloud
 
 
 def find_offset(sl, pt):
@@ -120,7 +120,7 @@ def matching_distance(module1, module2, grid_size, normalize, fixed_bounds=None)
     # the line, and also the normalization, which changes both the effective
     # weight and the effective bottleneck distance.
 
-    slope = lines[:, 0]
+    slope = np.array(lines)[:, 0]
     w = calculate_weight(slope, normalize, delta_x, delta_y)
 
     # moreover, normalization changes the length of a line segment along the line (slope,offset),
@@ -159,6 +159,7 @@ def generate_lines(grid_size, upper_left, lower_right):
             for j in range(grid_size):
                 offset = LR_offset + j * (UL_offset - LR_offset) / (grid_size - 1)
                 lines.append((slope, float(offset)))
+    assert lines
     return lines
 
 
@@ -189,7 +190,7 @@ def calculate_weight(slopes, normalize=False, delta_x=None, delta_y=None):
         mn = m * delta_x / delta_y
 
         # so the associated weight in the normalized case is given by
-        q = max(mn, 1 / mn)
+        q = np.max(np.vstack([mn, 1 / mn]), axis=0)
         w = 1 / np.sqrt(1 + q ** 2)
 
         # of course, this code can be made more compact, but hopefully this

atlatl/rank.py → pyrivet/rank.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from atlatl import rivet, matching_distance
+from pyrivet import rivet, matching_distance
 
 
 def find_parameters(slopes, offsets, points):

run-checks.sh

@@ -17,5 +17,5 @@
 set -ev
 set -o pipefail
 
-flake8 --config setup.cfg atlatl
+flake8 --config setup.cfg pyrivet
 rst-lint *.rst | { grep -v "is clean.$" || true; }

run-tests.sh

@@ -16,9 +16,9 @@
 
 set -ev
 
-pip freeze | grep -qi /atlatl || {
-    echo "You must install atlatl in editable mode using \"pip install -e\""`
-        `" before calling "$(basename "$0")
+pip freeze | grep -qi pyrivet || {
+    echo "You must install pyrivet in editable mode using \"pip install -e\"
+     before calling "$(basename "$0")
     exit 1
 }
 

setup.py

@@ -97,7 +97,7 @@ def finalize_options(self):
 
 
 setup(
-    name='atlatl',
+    name='pyrivet',
     use_scm_version=True,
     setup_requires=[
         # 'cython',
@@ -120,7 +120,7 @@ def finalize_options(self):
     ],
     author='Princeton Neuroscience Institute and Intel Corporation',
     author_email='bryn.keller@intel.com',
-    url='https://github.com/IntelPNI/atlatl',
+    url='https://github.com/IntelPNI/pyrivet',
     description='Algebraic Topology Loves All These Libraries',
     license='Apache 2',
     keywords='topology, algebraic topology, topological data analysis',

tests/atlatl/test_dimension.py → tests/pyrivet/test_dimension.py

@@ -5,9 +5,9 @@
 
 import sys
 
-from atlatl import rivet, hera, barcode, matching_distance
+from pyrivet import rivet, hera, barcode, matching_distance
 import numpy as np
-from atlatl.dimension_distance import SplitMat, Dimension, DimensionQueryResult
+from pyrivet.dimension_distance import SplitMat, Dimension, DimensionQueryResult
 
 
 def test_splitmat():

tests/atlatl/test_matching.py → tests/pyrivet/test_matching.py

@@ -6,7 +6,7 @@
 
 import sys
 
-from atlatl import rivet, hera, barcode, matching_distance, rank
+from pyrivet import rivet, hera, barcode, matching_distance, rank
 
 inf = float('inf')
 

tests/atlatl/test_pointclouds.py → tests/pyrivet/test_pointclouds.py

@@ -1,5 +1,5 @@
 # Borrowed from https://github.com/IntelPNI/brainiak-extras
-from atlatl import rivet, hera, barcode
+from pyrivet import rivet, hera, barcode
 
 inf = float('inf')
 

tests/atlatl/test_rank_norm.py → tests/pyrivet/test_rank_norm.py

@@ -1,4 +1,4 @@
-from atlatl import rivet, rank
+from pyrivet import rivet, rank
 import math
 
 prism_3 = rivet.Bifiltration("x_label", "y_label", [