Merge branch 'develop' for release-0.21.0a8

VarIr · Sep 12, 2019 · 22c9331 · 22c9331
2 parents a16f9c7 + 6541f9a
commit 22c9331
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Showing 60 changed files with 2,063 additions and 962 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -15,4 +15,7 @@ exclude_lines =
     raise TypeError
     warnings.warn
     only on win32
+    sys.platform == 'win32'
+    except ImportError
+    ModuleNotFoundError
     if __name__ == .__main__.:
diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,7 @@
 new_test_pypi_release.bash
 new_pypi_release.bash
 coverage.html/*
-
+_autosummary/
 .idea/
 venv/
 *__pycache__*

diff --git a/.travis.yml b/.travis.yml
@@ -7,11 +7,20 @@ matrix:
   include:
     - os: linux
       dist: xenial
-      sudo: false
+      sudo: true
+    - os: osx
+      osx_image: xcode10.3  # default is 9.x, which fails
+      sudo: true
     - os: osx
-      # osx_image: xcode10.2
+      osx_image: xcode11
       sudo: true
 
+#addons:
+#  homebrew:
+#    packages:
+#    - cmake
+#    - gcc@9
+
 env:
   global:
   - CACHE_DIR="$HOME/virtualenv"
@@ -22,21 +31,29 @@ before_install:
   - travis/install-conda.sh
   - export PATH="$MINICONDA_DIR/bin:$PATH"
   - hash -r
-  - travis/install-pip.sh
+  - conda install -y numpy                                  # install optimized numpy first
+  - conda install -y llvm libgcc || true                    # Try to fix build errors on MacOS
+  - pip install pybind11                                    # so that nmslib can build
+  - travis/install-pip.sh                                   # install all the other requirements
+  - travis/install-build-puffinn.sh  # install from cache or build first
+  - travis/install-build-ngtpy.sh                           # build and install NGT (others might be added)
 
 install:
-  - python setup.py build
-  - python setup.py install
+  - python3 setup.py build
+  - python3 setup.py install
 
 before_script:
   - flake8 --exit-zero .
 
 script:
-  - python setup.py test
-  - pytest --cov=skhubness
+  - pytest skhubness --cov=skhubness
 
 after_success:
-  - codecov
+  # Only on linux, all libraries are supported, thus tested
+  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then codecov; fi
+
+before_cache:
+  - brew cleanup || true
 
 cache:
   - pip
@@ -46,6 +63,7 @@ cache:
       - "$HOME/.cache/pip"
       - "$HOME/virtualenv"
       - "$HOME/miniconda"
+      - "$HOME/Library/Caches/Homebrew"
 
 branches:
   only:

diff --git a/README.md b/README.md
@@ -53,7 +53,18 @@ pip install scikit-hubness
 Dependencies are installed automatically, if necessary.
 `scikit-hubness` requires `numpy`, `scipy` and `scikit-learn`.
 Approximate nearest neighbor search and approximate hubness reduction
-additionally requires `nmslib` and/or `falconn`.
+additionally requires at least one of the following packges:
+* [`nmslib`](https://github.com/nmslib/nmslib)
+    for hierachical navigable small-world graphs ('hnsw')
+* [`ngtpy`](https://github.com/yahoojapan/NGT/)
+    for nearest neighbor graphs ('onng')
+* [`puffinn`](https://github.com/puffinn/puffinn)
+    for locality-sensitive hashing ('lsh')
+* [`falconn`](https://github.com/FALCONN-LIB/FALCONN)
+    for alternative LSH ('falconn_lsh') , or
+* [`annoy`](https://github.com/spotify/annoy)
+    for random projection forests ('rptree').
+
 Some modules require `tqdm` or `joblib`. All these packages are available
 from open repositories, such as [PyPI](https://pypi.org).
 
@@ -65,6 +76,12 @@ http://scikit-hubness.readthedocs.io/en/latest/user_guide/installation.html).
 Documentation is available online: 
 http://scikit-hubness.readthedocs.io/en/latest/index.html
 
+
+## What's new
+
+See the [changelog](docs/changelog.md) to find what's new in the latest package version.
+
+
 ## Quickstart
 
 Users of `scikit-hubness` may want to 

diff --git a/docs/_autosummary/skhubness.analysis.Hubness.rst b/docs/_autosummary/skhubness.analysis.Hubness.rst
diff --git a/docs/_autosummary/skhubness.neighbors.BallTree.rst b/docs/_autosummary/skhubness.neighbors.BallTree.rst
diff --git a/docs/_autosummary/skhubness.neighbors.DistanceMetric.rst b/docs/_autosummary/skhubness.neighbors.DistanceMetric.rst
diff --git a/docs/_autosummary/skhubness.neighbors.HNSW.rst b/docs/_autosummary/skhubness.neighbors.HNSW.rst
diff --git a/docs/_autosummary/skhubness.neighbors.KDTree.rst b/docs/_autosummary/skhubness.neighbors.KDTree.rst
diff --git a/docs/_autosummary/skhubness.neighbors.KNeighborsClassifier.rst b/docs/_autosummary/skhubness.neighbors.KNeighborsClassifier.rst
diff --git a/docs/_autosummary/skhubness.neighbors.KNeighborsRegressor.rst b/docs/_autosummary/skhubness.neighbors.KNeighborsRegressor.rst
diff --git a/docs/_autosummary/skhubness.neighbors.KernelDensity.rst b/docs/_autosummary/skhubness.neighbors.KernelDensity.rst