MOVED

.github/workflows/publish.yml

@@ -0,0 +1,35 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+

.gitignore

@@ -11,3 +11,9 @@ temp.*
 *.swp
 doc/_build
 MANIFEST
+
+# Files generated by protobuf.
+distributions/io/schema_pb2.py
+include/distributions/io/schema.pb.cc
+include/distributions/io/schema.pb.h
+src/io/schema.pb.cc

.travis.yml

@@ -5,11 +5,10 @@ virtualenv:
   system_site_packages: true
 before_install:
   - pip uninstall numpy -y || echo 'numpy not installed'
-  - sudo add-apt-repository -y ppa:cython-dev/master-ppa
   - sudo apt-get update -qq
-  - sudo apt-get install -qq cython python-numpy python-scipy
-  - sudo apt-get install libprotobuf-dev libeigen3-dev
-  - pip install cpplint
+  - sudo apt-get install -qq cython python-numpy python-pil python-scipy
+  - sudo apt-get install libprotobuf-dev libeigen3-dev protobuf-compiler
+  - pip install cpplint pyflakes
 env:
   - FLAVOR=_cc
   - FLAVOR=_cc DISTRIBUTIONS_USE_PROTOBUF=1

CMakeLists.txt

@@ -42,7 +42,8 @@ if(DEFINED EXTRA_LIBRARY_PATH)
 endif()
 
 find_package(Eigen3 REQUIRED)
-include_directories(${EIGEN3_INCLUDE_DIRS})
+get_filename_component(PARENT_DIR ${EIGEN3_INCLUDE_DIR} PATH)
+include_directories(${PARENT_DIR})
 
 find_package(Yeppp)
 if(YEPPP_FOUND)

Makefile

@@ -1,5 +1,5 @@
 uname:=$(shell uname -s)
-cpu_count=$(shell python -c 'import multiprocessing as m; print m.cpu_count()')
+cpu_count=$(shell python -c 'import multiprocessing as m; print(m.cpu_count())')
 
 
 ld_library_path=
@@ -16,14 +16,18 @@ endif
 cmake_args=
 nose_env:=NOSE_PROCESSES=$(cpu_count) NOSE_PROCESS_TIMEOUT=240
 ifdef VIRTUAL_ENV
-	cmake_args=-DCMAKE_INSTALL_PREFIX=$(VIRTUAL_ENV)
-	library_path=$(LIBRARY_PATH):$(VIRTUAL_ENV)/lib/
-	nose_env+=$(ld_library_path)=$($(ld_library_path)):$(VIRTUAL_ENV)/lib/
+	root_path=$(VIRTUAL_ENV)
 else
-	cmake_args=-DCMAKE_INSTALL_PREFIX=../..
-	library_path=$(LIBRARY_PATH):`pwd`/lib/
-	nose_env+=$(ld_library_path)=$($(ld_library_path)):`pwd`/lib/
+	ifdef CONDA_ROOT
+		root_path=$(CONDA_ROOT)
+	else
+		root_path='../..'
+	endif
 endif
+cmake_args=-DCMAKE_INSTALL_PREFIX=$(root_path)
+library_path=$(LIBRARY_PATH):$(root_path)/lib/
+nose_env+=$(ld_library_path)=$($(ld_library_path)):$(root_path)/lib/
+
 ifdef CMAKE_INSTALL_PREFIX
 	cmake_args=-DCMAKE_INSTALL_PREFIX=$(CMAKE_INSTALL_PREFIX)
 endif
@@ -32,12 +36,12 @@ all: test
 
 headers:=$(shell find include | grep '\.hpp' | grep -v protobuf | sort -d)
 src/test_headers.cc: $(headers)
-	echo $(headers) \
-	  | sed 's/include\/\(\S*\)\s*/#include <\1>\n/g' \
+	find include | grep '\.hpp' | grep -v protobuf | sort -d \
+	  | sed 's/include\/\(.*\)/#include <\1>/g' \
 	  > src/test_headers.cc
-	echo 'int main () { return 0; }' >> src/test_headers.cc
+	@echo '\nint main () { return 0; }' >> src/test_headers.cc
 
-prepare_cc: src/test_headers.cc FORCE
+prepare_cc: src/test_headers.cc protobuf FORCE
 	mkdir -p lib
 
 build/python: prepare_cc FORCE
@@ -73,7 +77,7 @@ dev_cy: deps_cy FORCE
 	LIBRARY_PATH=$(library_path) pip install -e .
 
 install_cy: deps_cy FORCE
-	LIBRARY_PATH=$(library_path) pip install .
+	LIBRARY_PATH=$(library_path) pip install --upgrade .
 
 install: install_cc install_cy FORCE
 
@@ -90,7 +94,7 @@ test_cc_examples: install_cc_examples FORCE
 CPP_SOURCES:=$(shell find include src examples benchmarks | grep -v 'vendor\|\.pb\.'  | grep -v 'src/test_headers.cc' | grep '\.\(cc\|hpp\)$$')
 
 lint_cc: FORCE
-	cpplint --filter=-build/include_order,-readability/streams,-readability/function,-runtime/arrays $(CPP_SOURCES)
+	cpplint --filter=-build/include_order,-readability/streams,-readability/function,-runtime/arrays,-runtime/reference,-runtime/explicit,-readability/alt_tokens,-build/c++11 $(CPP_SOURCES)
 
 test_cc: install_cc lint_cc FORCE
 	cd build && ctest
@@ -101,7 +105,7 @@ PY_SOURCES=setup.py update_license.py distributions derivations examples/mixture
 
 test_cy: dev_cy FORCE
 	pyflakes $(PY_SOURCES)
-	pep8 --repeat --ignore=E265 --exclude=*_pb2.py,vendor $(PY_SOURCES)
+	pep8 --repeat --ignore=E265,E402,W503 --exclude=*_pb2.py,vendor $(PY_SOURCES)
 	$(nose_env) nosetests -v distributions derivations examples
 	@echo '----------------'
 	@echo 'PASSED CY TESTS'

README.md

@@ -1,9 +1,9 @@
-[![Build Status](https://travis-ci.org/forcedotcom/distributions.svg?branch=master)](https://travis-ci.org/forcedotcom/distributions)
-[![Code Quality](http://img.shields.io/scrutinizer/g/forcedotcom/distributions.svg)](https://scrutinizer-ci.com/g/forcedotcom/distributions/code-structure/master/hot-spots)
-[![Latest Version](https://badge.fury.io/py/distributions.svg)](https://pypi.python.org/pypi/distributions)
-
 # Distributions
 
+[![Build Status](https://travis-ci.org/posterior/distributions.svg?branch=master)](https://travis-ci.org/posterior/distributions)
+[![Latest Version](https://badge.fury.io/py/distributions.svg)](https://pypi.python.org/pypi/distributions)
+[![DOI](https://zenodo.org/badge/29212688.svg)](https://zenodo.org/badge/latestdoi/29212688)
+
 Distributions provides low-level primitives for
 collapsed Gibbs sampling in Python and C++ including:
 

conda/distributions/build.sh

@@ -5,7 +5,7 @@ fi
 echo "Conda build env"
 printenv
 echo "protoc: `which protoc`"
-git clone https://github.com/forcedotcom/distributions.git
+git clone https://github.com/posterior/distributions.git
 cd distributions && git checkout tags/2.0.26
 make protobuf
 mkdir build && cd build

conda/distributions/meta.yaml

@@ -26,4 +26,4 @@ test:
     - distributions.lp.models.bb
 
 about:
-  home: https://github.com/forcedotcom/distributions
+  home: https://github.com/posterior/distributions

conda/libprotobuf/schema.proto

@@ -1,3 +1,30 @@
+// Copyright (c) 2014, Salesforce.com, Inc.  All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+//
+// - Redistributions of source code must retain the above copyright
+//   notice, this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+//   notice, this list of conditions and the following disclaimer in the
+//   documentation and/or other materials provided with the distribution.
+// - Neither the name of Salesforce.com nor the names of its contributors
+//   may be used to endorse or promote products derived from this
+//   software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+// FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE
+// COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+// OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+// TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+// USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 message HelloWorld {
   required string message = 1;
 }

conda/libprotobuf/test.cc

@@ -1,3 +1,30 @@
+// Copyright (c) 2014, Salesforce.com, Inc.  All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+//
+// - Redistributions of source code must retain the above copyright
+//   notice, this list of conditions and the following disclaimer.
+// - Redistributions in binary form must reproduce the above copyright
+//   notice, this list of conditions and the following disclaimer in the
+//   documentation and/or other materials provided with the distribution.
+// - Neither the name of Salesforce.com nor the names of its contributors
+//   may be used to endorse or promote products derived from this
+//   software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+// FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE
+// COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+// OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+// TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+// USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 #include "schema.pb.h"
 #include <cassert>
 int

derivations/betabinomial.py

@@ -47,7 +47,7 @@ def simtwo(alpha, beta, n, ITERS):
     thetas = np.random.beta(alpha, beta, size=ITERS)
     for i in range(ITERS):
         if i % 1000000 == 0:
-            print i
+          print(i)
 
         counts[i] = np.random.binomial(n, thetas[i], size=2)
     return counts
@@ -126,7 +126,7 @@ def test_post_pred_equal_likelihood():
     for alpha in [5.0]:
         for beta in [5.0]:
             for ks in [[9, 1], [1, 9]]:
-                print "-" * 60
+                print("-" * 60)
                 hps.alpha = alpha
                 hps.beta = beta
 
@@ -139,12 +139,12 @@ def test_post_pred_equal_likelihood():
 
                 total_score = compute_total_likelihood(hps, ss)
                 res = two_d_hist(alpha, beta, hps.N, 10000000)
-                print res
-                print res.shape
+                print(res)
+                print(res.shape)
                 emp_score = res[ks[0], ks[1]]
                 d1 = abs(pred_score - emp_score)
                 d2 = abs(emp_score - total_score)
                 d3 = abs(total_score - pred_score)
-                print "alpha=", alpha, "beta=", beta, "ks =", ks
-                print pred_score, total_score, emp_score
-                print "error=", d1 + d2 + d3
+                print("alpha=", alpha, "beta=", beta, "ks =", ks)
+                print(pred_score, total_score, emp_score)
+                print("error=", d1 + d2 + d3)