fix type error in queue.hpp, improve distributability and documentation

.github/workflows/wheels.yml

@@ -0,0 +1,66 @@
+name: CI
+
+# Run manually 
+on: workflow_dispatch
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-10.15]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Get deps (macOS)
+        if: matrix.os == 'macos-10.15'
+        run: |
+          brew install boost
+          brew install gmp
+          brew install tbb
+          brew install wiredtiger
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        # to supply options, put them in 'env', like:
+        env:
+          CIBW_ARCHS_LINUX: x86_64
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_24
+          CIBW_SKIP: "*-musllinux_x86_64"
+          CIBW_BEFORE_ALL_LINUX: >
+            apt-get update -y &&
+            apt-get install -y libboost-all-dev &&
+            apt-get install -y libgmp-dev &&
+            apt-get install -y libgmp10 &&
+            apt-get install -y ocl-icd-opencl-dev &&
+            apt-get install -y libtbb-dev &&
+            apt-get install -y wiredtiger
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Build sdist
+        run: python setup.py sdist
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz

.gitignore

@@ -20,4 +20,6 @@ m4
 libtool
 .deps
 gosdt
-gosdt_test
+gosdt_test
+*.DS_Store
+wheelhouse/*

Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.16.1 from Makefile.am.
+# Makefile.in generated by automake 1.16.5 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2018 Free Software Foundation, Inc.
+# Copyright (C) 1994-2021 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -264,15 +264,12 @@ am__define_uniq_tagged_files = \
   unique=`for i in $$list; do \
     if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
   done | $(am__uniquify_input)`
-ETAGS = etags
-CTAGS = ctags
-CSCOPE = cscope
 AM_RECURSIVE_TARGETS = cscope
 am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/build/compile \
 	$(top_srcdir)/build/config.guess \
 	$(top_srcdir)/build/config.sub $(top_srcdir)/build/depcomp \
 	$(top_srcdir)/build/install-sh $(top_srcdir)/build/missing \
-	build/compile build/config.guess build/config.sub \
+	README.md build/compile build/config.guess build/config.sub \
 	build/depcomp build/install-sh build/missing
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
@@ -287,6 +284,8 @@ am__post_remove_distdir = $(am__remove_distdir)
 DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
 DIST_TARGETS = dist-gzip
+# Exists only to be overridden by the user if desired.
+AM_DISTCHECK_DVI_TARGET = dvi
 distuninstallcheck_listfiles = find . -type f -print
 am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
   | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
@@ -307,6 +306,8 @@ CL_CFLAGS = @CL_CFLAGS@
 CL_LIBS = @CL_LIBS@
 CPP = @CPP@
 CPPFLAGS = @CPPFLAGS@
+CSCOPE = @CSCOPE@
+CTAGS = @CTAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
@@ -319,6 +320,7 @@ ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
+ETAGS = @ETAGS@
 EXEEXT = @EXEEXT@
 GREP = @GREP@
 HAVE_CXX11 = @HAVE_CXX11@
@@ -395,6 +397,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -1248,7 +1251,6 @@ cscopelist-am: $(am__tagged_files)
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
 	-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
-
 distdir: $(BUILT_SOURCES)
 	$(MAKE) $(AM_MAKEFLAGS) distdir-am
 
@@ -1307,6 +1309,10 @@ dist-xz: distdir
 	tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
 	$(am__post_remove_distdir)
 
+dist-zstd: distdir
+	tardir=$(distdir) && $(am__tar) | zstd -c $${ZSTD_CLEVEL-$${ZSTD_OPT--19}} >$(distdir).tar.zst
+	$(am__post_remove_distdir)
+
 dist-tarZ: distdir
 	@echo WARNING: "Support for distribution archives compressed with" \
 		       "legacy program 'compress' is deprecated." >&2
@@ -1349,6 +1355,8 @@ distcheck: dist
 	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
+	*.tar.zst*) \
+	  zstd -dc $(distdir).tar.zst | $(am__untar) ;;\
 	esac
 	chmod -R a-w $(distdir)
 	chmod u+w $(distdir)
@@ -1364,7 +1372,7 @@ distcheck: dist
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
 	    --srcdir=../.. --prefix="$$dc_install_base" \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
-	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+	  && $(MAKE) $(AM_MAKEFLAGS) $(AM_DISTCHECK_DVI_TARGET) \
 	  && $(MAKE) $(AM_MAKEFLAGS) check \
 	  && $(MAKE) $(AM_MAKEFLAGS) install \
 	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
@@ -1596,17 +1604,18 @@ uninstall-am: uninstall-binPROGRAMS
 	check-am clean clean-binPROGRAMS clean-cscope clean-generic \
 	cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
 	dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
-	distcheck distclean distclean-compile distclean-generic \
-	distclean-tags distcleancheck distdir distuninstallcheck dvi \
-	dvi-am html html-am info info-am install install-am \
-	install-binPROGRAMS install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am install-html \
-	install-html-am install-info install-info-am install-man \
-	install-pdf install-pdf-am install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	maintainer-clean maintainer-clean-generic mostlyclean \
-	mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
-	tags tags-am uninstall uninstall-am uninstall-binPROGRAMS
+	dist-zstd distcheck distclean distclean-compile \
+	distclean-generic distclean-tags distcleancheck distdir \
+	distuninstallcheck dvi dvi-am html html-am info info-am \
+	install install-am install-binPROGRAMS install-data \
+	install-data-am install-dvi install-dvi-am install-exec \
+	install-exec-am install-html install-html-am install-info \
+	install-info-am install-man install-pdf install-pdf-am \
+	install-ps install-ps-am install-strip installcheck \
+	installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic pdf pdf-am ps ps-am tags tags-am uninstall \
+	uninstall-am uninstall-binPROGRAMS
 
 .PRECIOUS: Makefile
 

README.md

@@ -21,7 +21,7 @@ Currently supported as a Python extension.
 ## Installing Dependencies
 Refer to [**Dependency Installation**](/doc/dependencies.md##Installation)
 
-## As a Stand-Alone Command Line Program
+## Stand-Alone Command Line Program
 ### Installation
 ```
 ./autobuild --install
@@ -38,15 +38,19 @@ For examples of dataset files, refer to `experiments/datasets/compas/binned.csv`
 For an example configuration file, refer to `experiments/configurations/compas.json`.
 For documentation on the configuration file, refer to [**Dependency Installation**](/doc/configuration.md)
 
-## As a Python Library with C++ Extensions
-### Build and Installation
+## Python-wrapped C++ Extension
+### Installation
+#### x86 Linux or macOS
+```
+pip install gosdt-deprecated
+```
+#### Other platforms
 ```
 ./autobuild --install-python
 ```
 _If you have multiple Python installations, please make sure to build and install using the same Python installation as the one intended for interacting with this library._
 
-
-### Importing the C++ Extension
+### C++ extension example usage
 ```python
 import gosdt
 
@@ -56,7 +60,6 @@ with open ("data.csv", "r") as data_file:
 with open ("config.json", "r") as config_file:
     config = config_file.read()
 
-
 print("Config:", config)
 print("Data:", data)
 
@@ -69,7 +72,9 @@ print("Iterations: ", gosdt.iterations())
 print("Graph Size: ", gosdt.size())
 ```
 
-### Importing Extension with local Python Wrapper
+### With local Python wrapper
+This module is local and not packaged; the following example assumes the user is working in the directory `GeneralizedOptimalSparseDecisionTrees/python`.
+
 ```python
 import pandas as pd
 import numpy as np
@@ -96,6 +101,36 @@ print("Training Accuracy: {}".format(training_accuracy))
 print(model.tree)
 ```
 
+## Scikit-learn-style Python module
+This option is currently only supported on x86-running Linux or macOS platforms. 
+
+### Installation
+```
+pip install imodels
+```
+_[imodels](https://github.com/csinva/imodels) is an interpretable machine learning package containing gosdt among many others ._
+
+### Usage
+```python
+import pandas as pd
+import numpy as np
+from imodels import GOSDTClassifier
+
+dataframe = pd.DataFrame(pd.read_csv("experiments/datasets/monk_2/data.csv"))
+
+X = dataframe[dataframe.columns[:-1]]
+y = dataframe[dataframe.columns[-1:]]
+
+model = GOSDT(regularization=0.1, time_limit=3600, verbose=True)
+model.fit(X, y)
+print("Execution Time: {}".format(model.time))
+
+prediction = model.predict(X)
+training_accuracy = model.score(X, y)
+print("Training Accuracy: {}".format(training_accuracy))
+print(model.tree)
+```
+
 ---
 
 # Development
@@ -148,6 +183,9 @@ Refer to [**Dependency Installation**](/doc/dependencies.md##Installation)
    ```
  For a full list of build options, run `./autobuild --help`
 
+### Building wheels for distribution (C++ extension)
+Invoking `.github/workflows/wheels.yml` via Github Actions will output wheels for x86 Linux and macOS platforms using [cibuildwheel](https://github.com/pypa/cibuildwheel), as well as the source distribution.
+
 ---
 
 # Configuration

license.md

@@ -0,0 +1,19 @@
+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

python/requirements.txt

@@ -0,0 +1,6 @@
+gmpy2
+matplotlib
+numpy
+pandas
+sklearn
+sortedcontainers