From a66de571a729c4cc6becb1d57864aa3d6545be0b Mon Sep 17 00:00:00 2001
From: Bryn Keller <xoltar@xoltar.org>
Date: Tue, 19 Jun 2018 17:32:40 -0700
Subject: [PATCH] Renamed to pyrivet, made tests pass

---
 pr-check.sh                                   | 10 +++++-----
 {atlatl => pyrivet}/Codensity_Estimate.py     |  0
 {atlatl => pyrivet}/Coeccentricity.py         |  0
 {atlatl => pyrivet}/__init__.py               |  0
 {atlatl => pyrivet}/barcode.py                |  0
 {atlatl => pyrivet}/dimension_distance.py     |  0
 {atlatl => pyrivet}/hera.py                   |  0
 {atlatl => pyrivet}/matching_distance.py      |  9 +++++----
 {atlatl => pyrivet}/rank.py                   |  2 +-
 {atlatl => pyrivet}/rivet.py                  |  0
 run-checks.sh                                 |  2 +-
 run-tests.sh                                  |  6 +++---
 setup.py                                      |  4 ++--
 tests/{atlatl => pyrivet}/test_dimension.py   |  4 ++--
 tests/{atlatl => pyrivet}/test_matching.py    |  2 +-
 tests/{atlatl => pyrivet}/test_pointclouds.py |  2 +-
 tests/{atlatl => pyrivet}/test_rank_norm.py   |  2 +-
 17 files changed, 22 insertions(+), 21 deletions(-)
 rename {atlatl => pyrivet}/Codensity_Estimate.py (100%)
 rename {atlatl => pyrivet}/Coeccentricity.py (100%)
 rename {atlatl => pyrivet}/__init__.py (100%)
 rename {atlatl => pyrivet}/barcode.py (100%)
 rename {atlatl => pyrivet}/dimension_distance.py (100%)
 rename {atlatl => pyrivet}/hera.py (100%)
 rename {atlatl => pyrivet}/matching_distance.py (97%)
 rename {atlatl => pyrivet}/rank.py (99%)
 rename {atlatl => pyrivet}/rivet.py (100%)
 rename tests/{atlatl => pyrivet}/test_dimension.py (92%)
 rename tests/{atlatl => pyrivet}/test_matching.py (98%)
 rename tests/{atlatl => pyrivet}/test_pointclouds.py (95%)
 rename tests/{atlatl => pyrivet}/test_rank_norm.py (98%)

diff --git a/pr-check.sh b/pr-check.sh
index 01f5764..c7949da 100755
--- a/pr-check.sh
+++ b/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 || \
diff --git a/atlatl/Codensity_Estimate.py b/pyrivet/Codensity_Estimate.py
similarity index 100%
rename from atlatl/Codensity_Estimate.py
rename to pyrivet/Codensity_Estimate.py
diff --git a/atlatl/Coeccentricity.py b/pyrivet/Coeccentricity.py
similarity index 100%
rename from atlatl/Coeccentricity.py
rename to pyrivet/Coeccentricity.py
diff --git a/atlatl/__init__.py b/pyrivet/__init__.py
similarity index 100%
rename from atlatl/__init__.py
rename to pyrivet/__init__.py
diff --git a/atlatl/barcode.py b/pyrivet/barcode.py
similarity index 100%
rename from atlatl/barcode.py
rename to pyrivet/barcode.py
diff --git a/atlatl/dimension_distance.py b/pyrivet/dimension_distance.py
similarity index 100%
rename from atlatl/dimension_distance.py
rename to pyrivet/dimension_distance.py
diff --git a/atlatl/hera.py b/pyrivet/hera.py
similarity index 100%
rename from atlatl/hera.py
rename to pyrivet/hera.py
diff --git a/atlatl/matching_distance.py b/pyrivet/matching_distance.py
similarity index 97%
rename from atlatl/matching_distance.py
rename to pyrivet/matching_distance.py
index df15fd1..ae90d98 100644
--- a/atlatl/matching_distance.py
+++ b/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
diff --git a/atlatl/rank.py b/pyrivet/rank.py
similarity index 99%
rename from atlatl/rank.py
rename to pyrivet/rank.py
index 818173e..ecc51c7 100644
--- a/atlatl/rank.py
+++ b/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):
diff --git a/atlatl/rivet.py b/pyrivet/rivet.py
similarity index 100%
rename from atlatl/rivet.py
rename to pyrivet/rivet.py
diff --git a/run-checks.sh b/run-checks.sh
index 8ed2cf6..d58e5c8 100755
--- a/run-checks.sh
+++ b/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; }
diff --git a/run-tests.sh b/run-tests.sh
index e36c061..be65df0 100755
--- a/run-tests.sh
+++ b/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
 }
 
diff --git a/setup.py b/setup.py
index c91d74c..0da2056 100644
--- a/setup.py
+++ b/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',
diff --git a/tests/atlatl/test_dimension.py b/tests/pyrivet/test_dimension.py
similarity index 92%
rename from tests/atlatl/test_dimension.py
rename to tests/pyrivet/test_dimension.py
index 53539d9..fd17c65 100644
--- a/tests/atlatl/test_dimension.py
+++ b/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():
diff --git a/tests/atlatl/test_matching.py b/tests/pyrivet/test_matching.py
similarity index 98%
rename from tests/atlatl/test_matching.py
rename to tests/pyrivet/test_matching.py
index 25c38eb..1ae9bf2 100644
--- a/tests/atlatl/test_matching.py
+++ b/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')
 
diff --git a/tests/atlatl/test_pointclouds.py b/tests/pyrivet/test_pointclouds.py
similarity index 95%
rename from tests/atlatl/test_pointclouds.py
rename to tests/pyrivet/test_pointclouds.py
index 5943fad..565320e 100644
--- a/tests/atlatl/test_pointclouds.py
+++ b/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')
 
diff --git a/tests/atlatl/test_rank_norm.py b/tests/pyrivet/test_rank_norm.py
similarity index 98%
rename from tests/atlatl/test_rank_norm.py
rename to tests/pyrivet/test_rank_norm.py
index 4adcf62..073d56f 100644
--- a/tests/atlatl/test_rank_norm.py
+++ b/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", [