pycall 0.1.0.alpha.20170426 → 0.1.0.alpha.20170502

checksums.yaml

@@ -1,7 +1,7 @@
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data/Rakefile

@@ -1,6 +1,8 @@
 require "bundler/gem_tasks"
 require "rspec/core/rake_task"
 
+Dir[File.expand_path('../tasks/**/*.rake', __FILE__)].each {|f| load f }
+
 RSpec::Core::RakeTask.new(:spec)
 
 task :default => :spec

data/docker/Dockerfile

@@ -0,0 +1,191 @@
+FROM buildpack-deps:xenial
+MAINTAINER Kenta Murata mrkn
+
+###############################################################
+# Ruby based on docker-library/ruby
+###############################################################
+
+# skip installing gem documentation
+RUN mkdir -p /usr/local/etc \
+	&& { \
+		echo 'install: --no-document'; \
+		echo 'update: --no-document'; \
+	} >> /usr/local/etc/gemrc
+
+ENV RUBY_MAJOR 2.4
+ENV RUBY_VERSION 2.4.0
+ENV RUBY_DOWNLOAD_SHA256 3a87fef45cba48b9322236be60c455c13fd4220184ce7287600361319bb63690
+ENV RUBYGEMS_VERSION 2.6.10
+
+# some of ruby's build scripts are written in ruby
+#   we purge system ruby later to make sure our final image uses what we just built
+RUN set -ex \
+	\
+	&& buildDeps=' \
+		bison \
+		libgdbm-dev \
+		ruby \
+	' \
+	&& apt-get update \
+	&& apt-get install -y --no-install-recommends $buildDeps \
+	&& rm -rf /var/lib/apt/lists/* \
+	\
+	&& wget -O ruby.tar.xz "https://cache.ruby-lang.org/pub/ruby/${RUBY_MAJOR%-rc}/ruby-$RUBY_VERSION.tar.xz" \
+	&& echo "$RUBY_DOWNLOAD_SHA256 *ruby.tar.xz" | sha256sum -c - \
+	\
+	&& mkdir -p /usr/src/ruby \
+	&& tar -xJf ruby.tar.xz -C /usr/src/ruby --strip-components=1 \
+	&& rm ruby.tar.xz \
+	\
+	&& cd /usr/src/ruby \
+	\
+# hack in "ENABLE_PATH_CHECK" disabling to suppress:
+#   warning: Insecure world writable dir
+	&& { \
+		echo '#define ENABLE_PATH_CHECK 0'; \
+		echo; \
+		cat file.c; \
+	} > file.c.new \
+	&& mv file.c.new file.c \
+	\
+	&& autoconf \
+	&& ./configure --disable-install-doc --enable-shared \
+	&& make -j"$(nproc)" \
+	&& make install \
+	\
+	&& apt-get purge -y --auto-remove $buildDeps \
+	&& cd / \
+	&& rm -r /usr/src/ruby \
+	\
+	&& gem update --system "$RUBYGEMS_VERSION"
+
+ENV BUNDLER_VERSION 1.14.5
+
+RUN gem install bundler --version "$BUNDLER_VERSION"
+
+# install things globally, for great justice
+# and don't create ".bundle" in all our apps
+ENV GEM_HOME /usr/local/bundle
+ENV BUNDLE_PATH="$GEM_HOME" \
+	BUNDLE_BIN="$GEM_HOME/bin" \
+	BUNDLE_SILENCE_ROOT_WARNING=1 \
+	BUNDLE_APP_CONFIG="$GEM_HOME"
+ENV PATH $BUNDLE_BIN:$PATH
+RUN mkdir -p "$GEM_HOME" "$BUNDLE_BIN" \
+	&& chmod 777 "$GEM_HOME" "$BUNDLE_BIN"
+
+
+###############################################################
+# Python based on docker-library/python
+###############################################################
+
+# ensure local python is preferred over distribution python
+ENV PATH /usr/local/bin:$PATH
+
+# http://bugs.python.org/issue19846
+# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
+ENV LANG C.UTF-8
+
+# runtime dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+		tcl \
+		tk \
+	&& rm -rf /var/lib/apt/lists/*
+
+ENV GPG_KEY 0D96DF4D4110E5C43FBFB17F2D347EA6AA65421D
+ENV PYTHON_VERSION 3.6.0
+
+# if this is called "PIP_VERSION", pip explodes with "ValueError: invalid truth value '<VERSION>'"
+ENV PYTHON_PIP_VERSION 9.0.1
+
+RUN set -ex \
+	&& buildDeps=' \
+		tcl-dev \
+		tk-dev \
+	' \
+	&& apt-get update && apt-get install -y $buildDeps --no-install-recommends && rm -rf /var/lib/apt/lists/* \
+	\
+	&& wget -O python.tar.xz "https://www.python.org/ftp/python/${PYTHON_VERSION%%[a-z]*}/Python-$PYTHON_VERSION.tar.xz" \
+	&& wget -O python.tar.xz.asc "https://www.python.org/ftp/python/${PYTHON_VERSION%%[a-z]*}/Python-$PYTHON_VERSION.tar.xz.asc" \
+	&& export GNUPGHOME="$(mktemp -d)" \
+	&& gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$GPG_KEY" \
+	&& gpg --batch --verify python.tar.xz.asc python.tar.xz \
+	&& rm -r "$GNUPGHOME" python.tar.xz.asc \
+	&& mkdir -p /usr/src/python \
+	&& tar -xJC /usr/src/python --strip-components=1 -f python.tar.xz \
+	&& rm python.tar.xz \
+	\
+	&& cd /usr/src/python \
+	&& ./configure \
+		--enable-loadable-sqlite-extensions \
+		--enable-shared \
+	&& make -j$(nproc) \
+	&& make install \
+	&& ldconfig \
+	\
+# explicit path to "pip3" to ensure distribution-provided "pip3" cannot interfere
+	&& if [ ! -e /usr/local/bin/pip3 ]; then : \
+		&& wget -O /tmp/get-pip.py 'https://bootstrap.pypa.io/get-pip.py' \
+		&& python3 /tmp/get-pip.py "pip==$PYTHON_PIP_VERSION" \
+		&& rm /tmp/get-pip.py \
+	; fi \
+# we use "--force-reinstall" for the case where the version of pip we're trying to install is the same as the version bundled with Python
+# ("Requirement already up-to-date: pip==8.1.2 in /usr/local/lib/python3.6/site-packages")
+# https://github.com/docker-library/python/pull/143#issuecomment-241032683
+	&& pip3 install --no-cache-dir --upgrade --force-reinstall "pip==$PYTHON_PIP_VERSION" \
+# then we use "pip list" to ensure we don't have more than one pip version installed
+# https://github.com/docker-library/python/pull/100
+	&& [ "$(pip list |tac|tac| awk -F '[ ()]+' '$1 == "pip" { print $2; exit }')" = "$PYTHON_PIP_VERSION" ] \
+	\
+	&& find /usr/local -depth \
+		\( \
+			\( -type d -a -name test -o -name tests \) \
+			-o \
+			\( -type f -a -name '*.pyc' -o -name '*.pyo' \) \
+		\) -exec rm -rf '{}' + \
+	&& apt-get purge -y --auto-remove $buildDeps \
+	&& rm -rf /usr/src/python ~/.cache
+
+# make some useful symlinks that are expected to exist
+RUN cd /usr/local/bin \
+	&& { [ -e easy_install ] || ln -s easy_install-* easy_install; } \
+	&& ln -s idle3 idle \
+	&& ln -s pydoc3 pydoc \
+	&& ln -s python3 python \
+	&& ln -s python3-config python-config
+
+###############################################################
+# pycall
+###############################################################
+
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends libczmq-dev
+
+RUN pip3 install jupyter
+RUN pip3 install numpy
+RUN pip3 install scipy
+RUN pip3 install pandas
+RUN pip3 install matplotlib
+RUN pip3 install seaborn
+RUN pip3 install scikit-learn
+RUN pip3 install gensim
+RUN pip3 install nltk
+RUN pip3 install statsmodels
+RUN pip3 install xray
+
+RUN mkdir -p /app /notebooks/examples /notebooks/local
+WORKDIR /app
+ADD docker/Gemfile /app
+ADD docker/start.sh /app
+
+RUN bundle install
+RUN bundle exec iruby register
+
+# Deploy matplotlib's examples
+RUN mkdir -p /tmp \
+	&& curl -fsSL https://github.com/mrkn/matplotlib.rb/archive/master.tar.gz | tar -xzf - -C /tmp \
+	&& mv /tmp/matplotlib.rb-master/examples /notebooks/examples/matplotlib \
+        && rm -rf /tmp/matplotlib.rb-master
+
+CMD sh /app/start.sh
+EXPOSE 8888

data/docker/Gemfile

@@ -0,0 +1,12 @@
+source 'https://rubygems.org'
+
+# IRuby dependencies
+gem 'pry'
+gem 'pry-doc'
+gem 'awesome_print'
+gem 'cztop', '< 0.3.0'
+gem 'iruby', github: 'sciruby/iruby'
+
+# PyCall related gems
+gem 'pycall', '>= 0.1.0.alpha.20170426'
+gem 'matplotlib', '>= 0.1.0.alpha.20170426'

data/docker/README.md

@@ -0,0 +1,22 @@
+# How to use and build docker image
+
+## Use
+
+Execute the following command.
+
+```
+rake docker:run [port=<PORT>] [attach_local=<DIRECTORY>]
+```
+
+The `port` option is for specifying the port number connecting to iruby notebook.
+
+You can access to a local directory from jupyter notebook in the container by attaching the local directory to `/notebooks/local` in the container using `attach_local` option.  The default value is the current directory, that should be pycall directory.
+
+## Build
+
+You can build your own docker image if you modify pycall.
+Execute the following command to build it.
+
+```
+rake docker:build
+```

data/lib/pycall/dict.rb

@@ -21,6 +21,7 @@ module PyCall
 
     def [](key)
       key = key.to_s if key.is_a? Symbol
+      key = key.__pyobj__ if key.respond_to?(:__pyobj__)
       value = if key.is_a? String
                 LibPython.PyDict_GetItemString(__pyobj__, key).to_ruby
               else
@@ -37,6 +38,7 @@ module PyCall
 
     def []=(key, value)
       key = key.to_s if key.is_a? Symbol
+      key = key.__pyobj__ if key.respond_to?(:__pyobj__)
       value = Conversions.from_ruby(value)
       value = value.__pyobj__ unless value.kind_of? LibPython::PyObjectStruct
       if key.is_a? String
@@ -49,6 +51,7 @@ module PyCall
 
     def delete(key)
       key = key.to_s if key.is_a? Symbol
+      key = key.__pyobj__ if key.respond_to?(:__pyobj__)
       if key.is_a? String
         value = LibPython.PyDict_GetItemString(__pyobj__, key).to_ruby
         LibPython.PyDict_DelItemString(__pyobj__, key)

data/lib/pycall/libpython.rb

@@ -327,7 +327,7 @@ module PyCall
     attach_function :PyDict_SetItem, [PyObjectStruct.by_ref, PyObjectStruct.by_ref, PyObjectStruct.by_ref], :int
     attach_function :PyDict_SetItemString, [PyObjectStruct.by_ref, :string, PyObjectStruct.by_ref], :int
     attach_function :PyDict_DelItem, [PyObjectStruct.by_ref, PyObjectStruct.by_ref], :int
-    attach_function :PyDict_DelItem, [PyObjectStruct.by_ref, :string], :int
+    attach_function :PyDict_DelItemString, [PyObjectStruct.by_ref, :string], :int
     attach_function :PyDict_Size, [PyObjectStruct.by_ref], :ssize_t
     attach_function :PyDict_Keys, [PyObjectStruct.by_ref], PyObjectStruct.by_ref
     attach_function :PyDict_Values, [PyObjectStruct.by_ref], PyObjectStruct.by_ref

data/lib/pycall/version.rb

@@ -1,3 +1,3 @@
 module PyCall
-  VERSION = "0.1.0.alpha.20170426"
+  VERSION = "0.1.0.alpha.20170502"
 end

data/pycall.gemspec

@@ -33,4 +33,5 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "bundler", "~> 1.13"
   spec.add_development_dependency "rake", "~> 10.0"
   spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "launchy"
 end

data/tasks/docker.rake

@@ -0,0 +1,20 @@
+namespace :docker do
+  task :build do
+    Dir.chdir File.expand_path('../..', __FILE__) do
+      system "docker build -f docker/Dockerfile -t rubydata/pycall ."
+    end
+  end
+
+  task :run do
+    require 'securerandom'
+    require 'launchy'
+    token = SecureRandom.hex(48)
+    port = ENV['port'] || '8888'
+    attach_local = File.expand_path(ENV['attach_local'] || Dir.pwd)
+    Thread.start do
+      sleep 3
+      Launchy.open("http://localhost:#{port}/?token=#{token}")
+    end
+    system "docker run -it -e 'JUPYTER_TOKEN=#{token}' -v #{attach_local}:/notebooks/local -p #{port}:8888 --rm --name pycall rubydata/pycall"
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: pycall
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha.20170426
+  version: 0.1.0.alpha.20170502
 platform: ruby
 authors:
 - Kenta Murata
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-04-26 00:00:00.000000000 Z
+date: 2017-05-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -66,6 +66,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: launchy
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: pycall
 email:
 - mrkn@mrkn.jp
@@ -86,6 +100,9 @@ files:
 - bin/rspec
 - bin/setup
 - config/Guardfile
+- docker/Dockerfile
+- docker/Gemfile
+- docker/README.md
 - examples/classifier_comparison.rb
 - examples/hist.rb
 - examples/plot_forest_importances_faces.rb
@@ -111,6 +128,7 @@ files:
 - lib/pycall/utils.rb
 - lib/pycall/version.rb
 - pycall.gemspec
+- tasks/docker.rake
 homepage: https://github.com/mrkn/pycall
 licenses:
 - MIT