From e73d83012d11fc1f8441692a288a20551280a204 Mon Sep 17 00:00:00 2001
From: Matt Bartos <mdbartos@umich.edu>
Date: Mon, 25 Mar 2019 23:38:42 -0400
Subject: [PATCH] Fix error with coveralls build (#51)

* Update dev from master (#47)

* Working version of insert_point

* Fix bug with query and insertpoint

* Cleanup disp and codisp functions

* Reorder methods

* Insertpoint operational, add docstrings

* Small fix

* Remove old files

* Allow empty tree; handle duplicates in insert_point and forget_point

* Account for duplicates in tree construction

* Add ability to print tree

* Update docstrings and minor fixes

* Docstring fix

* Minor fixes

* Bugfix for forget_point

* Add image

* Update readme

* Update README.md

* Type check for point

* Update README.md

* Update README.md

* Store bounding boxes

* Minor changes

* Fix bbox bug, add unit tests

* Add support for CI

* Remove Python 3.7

* Update README.md

* Fix duplicate precision bug

* Fix duplicates issue?

* Use new indexing strategy with forget_point

* Update n bug

* Return 0 for codisp if leaf is root

* Add efficient shingle

* Add sine wave image

* Update README.md

* Minor cleanup

* sklearn test

* Add classification notebook

* Updated gitignore

* Edit classification notebook

* taxi data test

* removed swamp

* taxi data 200 tree run

* IF test

* Add OC-SVM example with sine wave

* Add OC-SVM example with taxi data

* Add IF example with sine wave

* Minor changes

* Minor updates

* Delete old sine_ocsvm_test notebook

* Delete old taxi_ocsvm_test notebook

* Delete old sine_if notebook

* Add IF example with sine wave

* Add OC-SVM example with sine wave

* Add OC-SVM example with taxi data

* Delete old taxi_ocsvm notebook

* Add OC-SVM example with taxi data

* sine wave comaprasion

* table1 notebook

* rrcf notebook

* renamed rrcf

* taxi data if

* Fix shingle bug; clean up classification example

* Set theme jekyll-theme-minimal

* Add index labels

* Update batch image

* Update README.md

* Update README.md

* Update README.md

* Create _config.yml

* Create default.html

* Create index.md

* Update index.md

* Create nav.html

* Create nav.yml

* Create tree-construction.html

* Rename tree-construction.html to tree-construction.md

* Create insert-and-delete.md

* Create anomaly-scoring.md

* Create batch.md

* Create streaming.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update insert-and-delete.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update insert-and-delete.md

* Update anomaly-scoring.md

* Create related-work.md

* Update nav.yml

* Update related-work.md

* Create random-cut-tree.md

* Update nav.yml

* Create modifying-rctree.md

* Update nav.yml

* Update random-cut-tree.md

* Update random-cut-tree.md

* Update random-cut-tree.md

* Update random-cut-tree.md

* Update modifying-rctree.md

* Update random-cut-tree.md

* Create scoring-rctree.md

* Update nav.yml

* Update scoring-rctree.md

* Update README.md

* Update README.md

* Update index.md

* Update index.md

* Update index.md

* Create paper.md

* Create paper.bib

* Add files via upload

* Update paper.md

* Update README.md

* Delete figure_1.png

* Add files via upload

* Update paper.md

* Add files via upload

* Create taxi.md

* Update nav.yml

* Update batch.md

* Update streaming.md

* Update streaming.md

* Update streaming.md

* Update streaming.md

* Update taxi.md

* Update related-work.md

* Update related-work.md

* Update related-work.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update anomaly-scoring.md

* Update related-work.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update taxi.md

* Update README.md

* Update batch.md

* Update streaming.md

* Updates to authors

* Update paper

* updated abhi orcid

* Create rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update nav.yml

* Update rctree-api.md

* Update rctree-api.md

* Update docstrings

* Update rctree-api.md

* Update rctree-api.md

* Update anomaly-scoring.md

* Update random-cut-tree.md

* Update rctree-api.md

* Update related-work.md

* Update rctree-api.md

* Update setup.py

* Update __init__.py

* Update paper.md

* Update paper.md

* JOSS review updates (#48)

* Working version of insert_point

* Fix bug with query and insertpoint

* Cleanup disp and codisp functions

* Reorder methods

* Insertpoint operational, add docstrings

* Small fix

* Remove old files

* Allow empty tree; handle duplicates in insert_point and forget_point

* Account for duplicates in tree construction

* Add ability to print tree

* Update docstrings and minor fixes

* Docstring fix

* Minor fixes

* Bugfix for forget_point

* Add image

* Update readme

* Update README.md

* Type check for point

* Update README.md

* Update README.md

* Store bounding boxes

* Minor changes

* Fix bbox bug, add unit tests

* Add support for CI

* Remove Python 3.7

* Update README.md

* Fix duplicate precision bug

* Fix duplicates issue?

* Use new indexing strategy with forget_point

* Update n bug

* Return 0 for codisp if leaf is root

* Add efficient shingle

* Add sine wave image

* Update README.md

* Minor cleanup

* sklearn test

* Add classification notebook

* Updated gitignore

* Edit classification notebook

* taxi data test

* removed swamp

* taxi data 200 tree run

* IF test

* Add OC-SVM example with sine wave

* Add OC-SVM example with taxi data

* Add IF example with sine wave

* Minor changes

* Minor updates

* Delete old sine_ocsvm_test notebook

* Delete old taxi_ocsvm_test notebook

* Delete old sine_if notebook

* Add IF example with sine wave

* Add OC-SVM example with sine wave

* Add OC-SVM example with taxi data

* Delete old taxi_ocsvm notebook

* Add OC-SVM example with taxi data

* sine wave comaprasion

* table1 notebook

* rrcf notebook

* renamed rrcf

* taxi data if

* Fix shingle bug; clean up classification example

* Set theme jekyll-theme-minimal

* Add index labels

* Update batch image

* Update README.md

* Update README.md

* Update README.md

* Create _config.yml

* Create default.html

* Create index.md

* Update index.md

* Create nav.html

* Create nav.yml

* Create tree-construction.html

* Rename tree-construction.html to tree-construction.md

* Create insert-and-delete.md

* Create anomaly-scoring.md

* Create batch.md

* Create streaming.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update insert-and-delete.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update insert-and-delete.md

* Update anomaly-scoring.md

* Create related-work.md

* Update nav.yml

* Update related-work.md

* Create random-cut-tree.md

* Update nav.yml

* Create modifying-rctree.md

* Update nav.yml

* Update random-cut-tree.md

* Update random-cut-tree.md

* Update random-cut-tree.md

* Update random-cut-tree.md

* Update modifying-rctree.md

* Update random-cut-tree.md

* Create scoring-rctree.md

* Update nav.yml

* Update scoring-rctree.md

* Update README.md

* Update README.md

* Update index.md

* Update index.md

* Update index.md

* Create paper.md

* Create paper.bib

* Add files via upload

* Update paper.md

* Update README.md

* Delete figure_1.png

* Add files via upload

* Update paper.md

* Add files via upload

* Create taxi.md

* Update nav.yml

* Update batch.md

* Update streaming.md

* Update streaming.md

* Update streaming.md

* Update streaming.md

* Update taxi.md

* Update related-work.md

* Update related-work.md

* Update related-work.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update anomaly-scoring.md

* Update related-work.md

* Update tree-construction.md

* Update insert-and-delete.md

* Update taxi.md

* Update README.md

* Update batch.md

* Update streaming.md

* Updates to authors

* Update paper

* updated abhi orcid

* Create rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update rctree-api.md

* Update nav.yml

* Update rctree-api.md

* Update rctree-api.md

* Update docstrings

* Update rctree-api.md

* Update rctree-api.md

* Update anomaly-scoring.md

* Update random-cut-tree.md

* Update rctree-api.md

* Update related-work.md

* Update rctree-api.md

* Update setup.py

* Update __init__.py

* Update paper.md

* Update paper.md

* Update README.md

* Update paper.bib

* Update paper.md

* Update paper.md

* JOSS review suggested changes

* Add license badge

* Move installation instructions; list dependencies

* Add coveralls support

* Add classification and comparison to docs

* Move notebook material into documentation

* Add example data

* Update data locations in docs

* Fix error with coveralls build

* Add coveralls badge

* Add init for pytest

* Increase test coverage
---
 .travis.yml       |  2 +-
 README.md         |  2 +-
 test/__init__.py  |  0
 test/test_rrcf.py | 57 +++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 test/__init__.py

diff --git a/.travis.yml b/.travis.yml
index 14c5169..a3c42c2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,6 +9,6 @@ install:
   - pip install coveralls
 # command to run tests
 script:
-  - pytest --cov=pysheds/
+  - pytest --cov=rrcf/
 after_success:
   - coveralls
diff --git a/README.md b/README.md
index 0a42e14..03d4291 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # rrcf 🌲🌲🌲
-[![Build Status](https://travis-ci.org/kLabUM/rrcf.svg?branch=master)](https://travis-ci.org/kLabUM/rrcf) [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/) ![GitHub](https://img.shields.io/github/license/kLabUM/rrcf.svg)
+[![Build Status](https://travis-ci.org/kLabUM/rrcf.svg?branch=master)](https://travis-ci.org/kLabUM/rrcf) [![Coverage Status](https://coveralls.io/repos/github/kLabUM/rrcf/badge.svg?branch=master)](https://coveralls.io/github/kLabUM/rrcf?branch=master) [![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/) ![GitHub](https://img.shields.io/github/license/kLabUM/rrcf.svg)
 
 Implementation of the *Robust Random Cut Forest Algorithm* for anomaly detection by [Guha et al. (2016)](http://proceedings.mlr.press/v48/guha16.pdf).
 
diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/test/test_rrcf.py b/test/test_rrcf.py
index ffbef6a..6b6cf25 100644
--- a/test/test_rrcf.py
+++ b/test/test_rrcf.py
@@ -5,7 +5,11 @@
 n = 100
 d = 3
 X = np.random.randn(n, d)
+Z = np.copy(X)
+Z[90:, :] = 1
+
 tree = rrcf.RCTree(X)
+duplicate_tree = rrcf.RCTree(Z)
 
 deck = np.arange(n, dtype=int)
 np.random.shuffle(deck)
@@ -23,6 +27,16 @@ def test_batch():
         bbox = tree.get_bbox(branch)
         assert (bbox == branch.b).all()
 
+def test_codisp():
+    for i in range(100):
+        codisp = tree.codisp(i)
+        assert codisp > 0
+
+def test_disp():
+    for i in range(100):
+        disp = tree.disp(i)
+        assert disp > 0
+
 def test_forget_batch():
     # Check stored bounding boxes and leaf counts after forgetting points
     for index in indexes:
@@ -71,3 +85,46 @@ def test_insert_batch():
                 print('Computed:\n', bbox)
                 print('Stored:\n', branch.b)
                 raise
+
+def test_batch_with_duplicates():
+    # Instantiate tree with 10 duplicates
+    leafcount = duplicate_tree._count_leaves(tree.root)
+    assert (leafcount == n)
+    for i in range(90, 100):
+        try:
+            assert duplicate_tree.leaves[i].n == 10
+        except:
+            print(i)
+            print(duplicate_tree.leaves[i].n)
+            raise
+
+def test_insert_duplicate():
+    # Insert duplicate point
+    point = (1., 1., 1.)
+    leaf = duplicate_tree.insert_point(point, index=100)
+    assert leaf.n == 11
+    for i in range(90, 100):
+        try:
+            assert duplicate_tree.leaves[i].n == 11
+        except:
+            print(i)
+            print(duplicate_tree.leaves[i].n)
+            raise
+
+def test_find_duplicate():
+    # Find duplicate point
+    point = (1, 1, 1)
+    duplicate = duplicate_tree.find_duplicate(point)
+    assert duplicate is not None
+
+def test_forget_duplicate():
+    # Forget duplicate point
+    leaf = duplicate_tree.forget_point(100)
+    for i in range(90, 100):
+        assert duplicate_tree.leaves[i].n == 10
+
+def test_shingle():
+    shingle = rrcf.shingle(X, 3)
+    step_0 = next(shingle)
+    step_1 = next(shingle)
+    assert (step_0[1] == step_1[0]).all()