Merge pull request numenta#34 from htm-community/numenta_update

Numenta update

.circleci/config.yml

@@ -0,0 +1,142 @@
+version: 2
+jobs:
+  build-and-test:
+    macos:
+      xcode: '9.0.1'
+    working_directory: ~/numenta/nupic.core
+    parallelism: 1
+    environment:
+      XCODE_SCHEME: nupic
+      XCODE_WORKSPACE: nupic
+      ARCHFLAGS: -arch x86_64
+      PYTHONPATH: ~/Library/Python/2.7/lib/python/site-packages
+      PYBIN: ~/Library/Python/2.7/bin
+    steps:
+      # Machine Setup
+      - run:
+          name: Make sure to use OS X in CircleCI Web UI
+          command: |
+            if [[ "$OSTYPE" != "darwin"* ]]; then
+              echo "Must set option to use OS X in CircleCI Web UI" && exit 1;
+            fi
+      - run: sudo systemsetup -settimezone 'GMT'
+      - run:
+          name: Restoring system python
+          command: |
+            brew uninstall python
+            curl https://bootstrap.pypa.io/get-pip.py | python - --user
+            echo 'export PATH=$HOME/Library/Python/2.7/bin:$PATH' >> $BASH_ENV 
+      - run:
+          name: Installing cmake 
+          command: brew install cmake
+
+      - checkout
+
+      # Dependencies
+      # Restore the dependency cache
+      - restore_cache:
+          keys:
+          # This branch if available
+          - v1-dep-{{ .Branch }}-
+          # Default branch if not
+          - v1-dep-master-
+          # Any branch if there are none on the default branch - this should be 
+          # unnecessary if you have your default branch configured correctly
+          - v1-dep-
+
+      - run:
+          name: Installing dependencies
+          command: |
+            pip install --user --upgrade --verbose pip setuptools setuptools-scm
+            pip install --no-cache-dir --user -r bindings/py/requirements.txt  --verbose || exit
+
+      # Save dependency cache
+      - save_cache:
+          key: v1-dep-{{ .Branch }}-{{ epoch }}
+          paths:
+          # This is a broad list of cache paths to include many possible 
+          # development environments.
+          - vendor/bundle
+          - ~/virtualenvs
+          - ~/.m2
+          - ~/.ivy2
+          - ~/.bundle
+          - ~/.go_workspace
+          - ~/.gradle
+          - ~/.cache/bower
+
+      # Build 
+      - run:
+          name: Compiling
+          environment:
+            VERBOSE: 1
+          command: |
+            mkdir -p build/scripts
+            cd build/scripts
+            cmake ../.. -DCMAKE_BUILD_TYPE=Release -DNTA_COV_ENABLED=ON -DCMAKE_INSTALL_PREFIX=../release -DPY_EXTENSIONS_DIR=../../bindings/py/src/nupic/bindings
+            make | grep -v -F '\\-\\- Installing:'
+            make install 2>&1 | grep -v -F 'Installing:'
+      - run:
+          name: Build distribution
+          command: |
+            python setup.py bdist_wheel
+            mkdir -p dist/include/nupic
+            mv bindings/py/dist/*.whl dist/
+            cp bindings/py/requirements.txt dist/
+            cp build/release/include/nupic/Version.hpp dist/include/nupic/
+      
+      # Test
+      - run:
+          name: Running python tests
+          command: |
+            mkdir -p tests/py
+            pip install --user --no-index --find-links=$CIRCLE_WORKING_DIRECTORY/dist/ nupic.bindings
+            py.test --junitxml tests/py/junit-test-results.xml bindings/py/tests
+      - run:
+          name: Running C++ Tests
+          command: |
+            mkdir -p tests/cpp
+            pushd build/release/bin
+            ./cpp_region_test
+            ./py_region_test
+            ./helloregion
+            ./hello_sp_tp
+            ./prototest
+            ./unit_tests --gtest_output=xml:$CIRCLE_WORKING_DIRECTORY/tests/cpp/unit_tests_report.xml
+
+      - store_test_results:
+          path: tests
+
+      - store_artifacts:
+          path: dist/*.whl
+
+      - persist_to_workspace:
+          root: dist
+          paths:
+          - nupic.bindings*.whl
+          - requirements.txt
+          - include/nupic
+
+  deploy-s3:
+    machine: true
+    steps:
+      - attach_workspace:
+          at: dist
+      - run:
+          name: Deploying to S3
+          command: |
+            pip install awscli --upgrade --user
+            tar -zcv -f nupic_core-${CIRCLE_SHA1}-darwin64.tar.gz dist
+            aws s3 cp nupic_core-${CIRCLE_SHA1}-darwin64.tar.gz s3://artifacts.numenta.org/numenta/nupic.core/circle/
+
+workflows:
+  version: 2
+  build-test-deploy:
+    jobs:
+      - build-and-test
+      - deploy-s3:
+          requires: 
+            - build-and-test
+          filters:
+            branches:
+              only: master

.clang-format

@@ -1,66 +1,5 @@
 ---
-Language:        Cpp
-# BasedOnStyle:  LLVM
-AccessModifierOffset: -2
-AlignAfterOpenBracket: true
-AlignEscapedNewlinesLeft: false
-AlignOperands:   true
-AlignTrailingComments: true
-AlignConsecutiveAssignments: false
-AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortBlocksOnASingleLine: false
-AllowShortCaseLabelsOnASingleLine: false
-AllowShortIfStatementsOnASingleLine: false
-AllowShortLoopsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AlwaysBreakAfterDefinitionReturnType: false
-AlwaysBreakTemplateDeclarations: false
-AlwaysBreakBeforeMultilineStrings: false
-BreakBeforeBinaryOperators: None
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
-BinPackParameters: true
-BinPackArguments: true
-ColumnLimit:     80
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
-ConstructorInitializerIndentWidth: 4
-DerivePointerAlignment: false
-ExperimentalAutoDetectBinPacking: false
-IndentCaseLabels: false
-IndentWrappedFunctionNames: false
-IndentFunctionDeclarationAfterType: false
-MaxEmptyLinesToKeep: 1
-KeepEmptyLinesAtTheStartOfBlocks: true
-NamespaceIndentation: None
-ObjCBlockIndentWidth: 2
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
-PenaltyBreakBeforeFirstCallParameter: 19
-PenaltyBreakComment: 300
-PenaltyBreakString: 1000
-PenaltyBreakFirstLessLess: 120
-PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60
-PointerAlignment: Right
-SpacesBeforeTrailingComments: 1
-Cpp11BracedListStyle: true
-Standard:        Cpp11
-IndentWidth:     2
-TabWidth:        8
-UseTab:          Never
-BreakBeforeBraces: Attach
-SpacesInParentheses: false
-SpacesInSquareBrackets: false
-SpacesInAngles:  false
-SpaceInEmptyParentheses: false
-SpacesInCStyleCastParentheses: false
-SpaceAfterCStyleCast: false
-SpacesInContainerLiterals: true
-SpaceBeforeAssignmentOperators: true
-ContinuationIndentWidth: 4
-CommentPragmas:  '^ IWYU pragma:'
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-SpaceBeforeParens: ControlStatements
-DisableFormat:   false
+Language: Cpp
+BasedOnStyle: LLVM
+DisableFormat: false
 ...
-

.gitignore

@@ -6,12 +6,20 @@
 *.DS_Store
 *.swp
 *.pyc
+*.pkl
+
+# Coverage files 
+.coverage
+htmlcov/
 
 # IDE project files
 /nbproject/
+.vscode
+.ycm_extra_conf.py
 
 # Build files
 build/
+junit-test-results.xml
 
 # /
 /.gdb_history
@@ -20,6 +28,8 @@ build/
 html/
 
 # SWIG
-bindings/py/nupic/bindings/*.cxx
-bindings/py/nupic/bindings/*.py
-bindings/py/nupic/bindings/*.so
+bindings/py/src/nupic/bindings/*.cxx
+bindings/py/src/nupic/bindings/*.py
+bindings/py/src/nupic/bindings/*.so
+bindings/py/src/nupic/*.so
+bindings/py/src/nupic.bindings.egg-info

CHANGELOG.md

@@ -1,5 +1,47 @@
 # Changelog
 
+## 1.0.6
+
+* This release was because of a deployment problem with 1.0.5 and issues with pypi.
+
+## 1.0.5
+
+* 58754cf7 NUP-2519: Upgrade pycapnp to 0.6.3
+* 64fb803e DEVOPS-383: Move deploy to S3 job to circleci workflow
+* 16dbf534 DEVOPS-383: Migrate CircleCI builds from 1.0 to 2.0
+* ec14f2f5 pip install --use-wheel" was deprecated. See https://pip.pypa.io/en/stable/news/#deprecations-and-removals
+* c2d31a95 ignore YCM configuration
+* f7b86e0f "pip install --use-wheel" was deprecated. See https://pip.pypa.io/en/stable/news/#deprecations-and-removals
+* 42df6caa NUP-2504: fix clang link optimization issue on private template function
+* f5bc76b6 NUP-2504: Add unit test to softmax overflow
+* 203493ed NUP-2506: Add missing state fields to serialization
+* 5f1ddcbb NUP-2514: fix traversal limit
+* 7e33ca44 NUP-2506: Add missing operator '==' to classes used in tests
+* e5e48c8e fix accumulate
+* b3513853 add softmax function
+* 0032fbf5 Fix softmax overflow
+
+
+## 1.0.4
+
+* 860459cf NUP-2506: Add operator '==' to classes used in tests
+* ac43320f NUP-2505: Remove win32 build from CI
+* 6a580c06 Fix not include ClassifierResult.hpp error
+* de567a4e NUP-2495: Update clang-format instructions
+* 2f027a7b NUP-2475: Add sparse link validation
+* 3071b8a5 DEVOPS-353: Update "setSparseOutput" documentation
+* 7ae0d64f NUP-2495: Check style using clang-format
+* 8a1d5eeb NUP-2475: Make sure Network API links use the same dtype at both ends
+* 4e800a64 DEVOPS-353: Fix tests to run with nupic.core directly instead of nupic
+* 9ae6155d DEVOPS-353: Implement sparse links
+* de88baaa DEVOPS-353: Add 'isSparse' attribute to input/output
+* 1e486fde DEVOPS-353: Allow element count to be smaller than buffer size
+* c9377d52 Fix cmake version and project name
+* f069c310 Add missing include required for NTA_ASSERT
+* a6c186ae reformat code using clang-format
+* 70d43da1 NUP-2492: Add constructor vs initialize test regarding Issue #1386
+* dabd7f87 NUP-2491: Validate global inhibition parameters
+
 ## 1.0.3
 
 * https://github.com/numenta/nupic.core/issues/1380 Added stronger type checking for SP compute input.

CMakeLists.txt

@@ -20,12 +20,14 @@
 # -----------------------------------------------------------------------------
 
 cmake_minimum_required(VERSION 3.3)
-project(nupic_core_main CXX)
+project(nupic_core CXX)
 
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}")
 
 set(CMAKE_VERBOSE_MAKEFILE OFF)
 
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
 get_filename_component(REPOSITORY_DIR ${PROJECT_SOURCE_DIR} ABSOLUTE)
 
 if( POLICY CMP0046 )

Dockerfile

@@ -34,6 +34,6 @@ RUN pip install \
         --cache-dir /usr/local/src/nupic.core/pip-cache \
         --build /usr/local/src/nupic.core/pip-build \
         --no-clean \
-        pycapnp==0.5.8 \
+        pycapnp==0.6.3 \
         -r bindings/py/requirements.txt && \
     python setup.py bdist bdist_dumb bdist_wheel sdist

VERSION

@@ -1 +1 @@
-1.0.4.dev0
+1.0.7.dev0

appveyor.yml

@@ -25,7 +25,7 @@ init:
   - git config --global core.autocrlf input
 
 clone_folder: c:\projects\nupic-core
-clone_depth: 50
+clone_depth: 1
 
 # Can't have a shallow clone because the CMake process will be
 # calling into git to write the current SHA into the binaries.
@@ -51,12 +51,12 @@ environment:
       wheel_name_suffix: "win_amd64"
 
     # Win32-gcc
-    - PYTHON_VERSION: "2.7.9"
-      PYTHON_ARCH: "32"
-      PYTHONHOME: "C:\\Python27"
-      NC_CMAKE_GENERATOR: "MinGW Makefiles"
-      external_static_subdir: "windows32-gcc"
-      wheel_name_suffix: "win32"
+#    - PYTHON_VERSION: "2.7.9"
+#      PYTHON_ARCH: "32"
+#      PYTHONHOME: "C:\\Python27"
+#      NC_CMAKE_GENERATOR: "MinGW Makefiles"
+#      external_static_subdir: "windows32-gcc"
+#      wheel_name_suffix: "win32"
 
 #    # Win64-Visual Studio
 #    - PYTHON_VERSION: "2.7.9"

bindings/py/requirements.txt

@@ -3,4 +3,4 @@ numpy==1.12.1
 pytest==3.0.7
 pytest-cov==2.5.0
 pytest-xdist==1.16.0
-pycapnp==0.5.12
+pycapnp==0.6.3

bindings/py/setup.py

@@ -223,7 +223,7 @@ def generateExtensions():
         "nupic.bindings": ["*.so", "*.pyd"],
         "nupic.bindings.tools": ["*.capnp"],
     },
-    extras_require = {"capnp": ["pycapnp==0.5.8"]},
+    extras_require = {"capnp": ["pycapnp==0.6.3"]},
     zip_safe=False,
     cmdclass={
       "clean": CleanCommand,