Releasing v2.2

CITATION

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+To reference iced in publication, please cite the following:
+
+@Article{servant:hicpro,
+   Author="Servant, N.  and Varoquaux, N.  and Lajoie, B. R.  and Viara, E.
+   and Chen, C. J.  and Vert, J. P.  and Heard, E.  and Dekker, J.  and
+   Barillot, E. ",
+   Title="{{H}i{C}-{P}ro: an optimized and flexible pipeline for {H}i-{C} data processing}",
+   Journal="Genome Biol.",
+   Year="2015",
+   Volume="16",
+   Pages="259"
+  }

MANIFEST.in

@@ -1 +1,2 @@
 recursive-include iced *.c *.h *.py
+recursive-include *.matrix *.bed

README.rst

@@ -1,15 +1,10 @@
 .. -*- mode: rst -*-
 
-|Travis|_ |AppVeyor|_ |Coveralls|_
+|Travis|_ |Coveralls|_
 
 .. |Travis| image:: https://api.travis-ci.org/hiclib/iced.png?branch=master
 .. _Travis: https://travis-ci.org/hiclib/iced
 
-.. |AppVeyor| image::
-   https://ci.appveyor.com/api/projects/status/github/hiclib/iced?branch=master&svg=true
-.. _AppVeyor:
-   https://ci.appveyor.com/project/sklearn-ci/scikit-learn/history
-
 .. |Coveralls| image::
    https://coveralls.io/repos/hiclib/iced/badge.svg?branch=master&service=github
 .. _Coveralls: https://coveralls.io/r/hiclib/iced

appveyor.yml

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+# AppVeyor.com is a Continuous Integration service to build and run tests under
+# Windows
+# https://ci.appveyor.com/project/iced-ci/iced
+
+environment:
+  global:
+    # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
+    # /E:ON and /V:ON options are not enabled in the batch script interpreter
+    # See: http://stackoverflow.com/a/13751649/163740
+    CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\build_tools\\appveyor\\run_with_env.cmd"
+    WHEELHOUSE_UPLOADER_USERNAME: iced-appveyor
+    WHEELHOUSE_UPLOADER_SECRET:
+      secure: BQm8KfEj6v2Y+dQxb2syQvTFxDnHXvaNktkLcYSq7jfbTOO6eH9n09tfQzFUVcWZ
+
+    # Make sure we don't download large datasets when running the test on
+    # continuous integration platform
+    iced_SKIP_NETWORK_TESTS: 1
+
+  matrix:
+    - PYTHON: "C:\\Python27"
+      PYTHON_VERSION: "2.7.8"
+      PYTHON_ARCH: "32"
+
+    - PYTHON: "C:\\Python27-x64"
+      PYTHON_VERSION: "2.7.8"
+      PYTHON_ARCH: "64"
+
+    - PYTHON: "C:\\Python35"
+      PYTHON_VERSION: "3.5.0"
+      PYTHON_ARCH: "32"
+
+    - PYTHON: "C:\\Python35-x64"
+      PYTHON_VERSION: "3.5.0"
+      PYTHON_ARCH: "64"
+
+
+
+install:
+  # Install Python (from the official .msi of http://python.org) and pip when
+  # not already installed.
+  - "powershell ./build_tools/appveyor/install.ps1"
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+  - "python -m pip install -U pip"
+
+  # Check that we have the expected version and architecture for Python
+  - "python --version"
+  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+  - "pip --version"
+
+  # Install the build and runtime dependencies of the project.
+  - "%CMD_IN_ENV% pip install --timeout=60 --trusted-host 28daf2247a33ed269873-7b1aad3fab3cc330e1fd9d109892382a.r6.cf2.rackcdn.com -r build_tools/appveyor/requirements.txt"
+  - "%CMD_IN_ENV% python setup.py bdist_wheel bdist_wininst -b doc/logos/scikit-learn-logo.bmp"
+  - ps: "ls dist"
+
+  # Install the generated wheel package to test it
+  - "pip install --pre --no-index --find-links dist/ scikit-learn"
+
+# Not a .NET project, we build scikit-learn in the install step instead
+build: false
+
+test_script:
+  # Change to a non-source folder to make sure we run the tests on the
+  # installed library.
+  - "mkdir empty_folder"
+  - "cd empty_folder"
+
+  - "python -c \"import nose; nose.main()\" --with-timer --timer-top-n 20 -s -v iced"
+
+  # Move back to the project folder
+  - "cd .."
+
+artifacts:
+  # Archive the generated wheel package in the ci.appveyor.com build report.
+  - path: dist\*
+
+on_success:
+  # Upload the generated wheel package to Rackspace
+  # On Windows, Apache Libcloud cannot find a standard CA cert bundle so we
+  # disable the ssl checks.
+  - "python -m wheelhouse_uploader upload --no-ssl-check --local-folder=dist iced-windows-wheels"
+
+notifications:
+  - provider: Webhook
+    url: https://webhooks.gitter.im/e/0dc8e57cd38105aeb1b4
+    on_build_success: false
+    on_build_failure: True
+
+cache:
+  # Use the appveyor cache to avoid re-downloading large archives such
+  # the MKL numpy and scipy wheels mirrored on a rackspace cloud
+  # container, speed up the appveyor jobs and reduce bandwidth
+  # usage on our rackspace account.
+  - '%APPDATA%\pip\Cache'

build_tools/appveyor/install.ps1

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+# Sample script to install Python and pip under Windows
+# Authors: Olivier Grisel, Jonathan Helmus, Kyle Kastner, and Alex Willmer
+# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+
+$MINICONDA_URL = "http://repo.continuum.io/miniconda/"
+$BASE_URL = "https://www.python.org/ftp/python/"
+$GET_PIP_URL = "https://bootstrap.pypa.io/get-pip.py"
+$GET_PIP_PATH = "C:\get-pip.py"
+
+$PYTHON_PRERELEASE_REGEX = @"
+(?x)
+(?<major>\d+)
+\.
+(?<minor>\d+)
+\.
+(?<micro>\d+)
+(?<prerelease>[a-z]{1,2}\d+)
+"@
+
+
+function Download ($filename, $url) {
+    $webclient = New-Object System.Net.WebClient
+
+    $basedir = $pwd.Path + "\"
+    $filepath = $basedir + $filename
+    if (Test-Path $filename) {
+        Write-Host "Reusing" $filepath
+        return $filepath
+    }
+
+    # Download and retry up to 3 times in case of network transient errors.
+    Write-Host "Downloading" $filename "from" $url
+    $retry_attempts = 2
+    for ($i = 0; $i -lt $retry_attempts; $i++) {
+        try {
+            $webclient.DownloadFile($url, $filepath)
+            break
+        }
+        Catch [Exception]{
+            Start-Sleep 1
+        }
+    }
+    if (Test-Path $filepath) {
+        Write-Host "File saved at" $filepath
+    } else {
+        # Retry once to get the error message if any at the last try
+        $webclient.DownloadFile($url, $filepath)
+    }
+    return $filepath
+}
+
+
+function ParsePythonVersion ($python_version) {
+    if ($python_version -match $PYTHON_PRERELEASE_REGEX) {
+        return ([int]$matches.major, [int]$matches.minor, [int]$matches.micro,
+                $matches.prerelease)
+    }
+    $version_obj = [version]$python_version
+    return ($version_obj.major, $version_obj.minor, $version_obj.build, "")
+}
+
+
+function DownloadPython ($python_version, $platform_suffix) {
+    $major, $minor, $micro, $prerelease = ParsePythonVersion $python_version
+
+    if (($major -le 2 -and $micro -eq 0) `
+        -or ($major -eq 3 -and $minor -le 2 -and $micro -eq 0) `
+        ) {
+        $dir = "$major.$minor"
+        $python_version = "$major.$minor$prerelease"
+    } else {
+        $dir = "$major.$minor.$micro"
+    }
+
+    if ($prerelease) {
+        if (($major -le 2) `
+            -or ($major -eq 3 -and $minor -eq 1) `
+            -or ($major -eq 3 -and $minor -eq 2) `
+            -or ($major -eq 3 -and $minor -eq 3) `
+            ) {
+            $dir = "$dir/prev"
+        }
+    }
+
+    if (($major -le 2) -or ($major -le 3 -and $minor -le 4)) {
+        $ext = "msi"
+        if ($platform_suffix) {
+            $platform_suffix = ".$platform_suffix"
+        }
+    } else {
+        $ext = "exe"
+        if ($platform_suffix) {
+            $platform_suffix = "-$platform_suffix"
+        }
+    }
+
+    $filename = "python-$python_version$platform_suffix.$ext"
+    $url = "$BASE_URL$dir/$filename"
+    $filepath = Download $filename $url
+    return $filepath
+}
+
+
+function InstallPython ($python_version, $architecture, $python_home) {
+    Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
+    if (Test-Path $python_home) {
+        Write-Host $python_home "already exists, skipping."
+        return $false
+    }
+    if ($architecture -eq "32") {
+        $platform_suffix = ""
+    } else {
+        $platform_suffix = "amd64"
+    }
+    $installer_path = DownloadPython $python_version $platform_suffix
+    $installer_ext = [System.IO.Path]::GetExtension($installer_path)
+    Write-Host "Installing $installer_path to $python_home"
+    $install_log = $python_home + ".log"
+    if ($installer_ext -eq '.msi') {
+        InstallPythonMSI $installer_path $python_home $install_log
+    } else {
+        InstallPythonEXE $installer_path $python_home $install_log
+    }
+    if (Test-Path $python_home) {
+        Write-Host "Python $python_version ($architecture) installation complete"
+    } else {
+        Write-Host "Failed to install Python in $python_home"
+        Get-Content -Path $install_log
+        Exit 1
+    }
+}
+
+
+function InstallPythonEXE ($exepath, $python_home, $install_log) {
+    $install_args = "/quiet InstallAllUsers=1 TargetDir=$python_home"
+    RunCommand $exepath $install_args
+}
+
+
+function InstallPythonMSI ($msipath, $python_home, $install_log) {
+    $install_args = "/qn /log $install_log /i $msipath TARGETDIR=$python_home"
+    $uninstall_args = "/qn /x $msipath"
+    RunCommand "msiexec.exe" $install_args
+    if (-not(Test-Path $python_home)) {
+        Write-Host "Python seems to be installed else-where, reinstalling."
+        RunCommand "msiexec.exe" $uninstall_args
+        RunCommand "msiexec.exe" $install_args
+    }
+}
+
+function RunCommand ($command, $command_args) {
+    Write-Host $command $command_args
+    Start-Process -FilePath $command -ArgumentList $command_args -Wait -Passthru
+}
+
+
+function InstallPip ($python_home) {
+    $pip_path = $python_home + "\Scripts\pip.exe"
+    $python_path = $python_home + "\python.exe"
+    if (-not(Test-Path $pip_path)) {
+        Write-Host "Installing pip..."
+        $webclient = New-Object System.Net.WebClient
+        $webclient.DownloadFile($GET_PIP_URL, $GET_PIP_PATH)
+        Write-Host "Executing:" $python_path $GET_PIP_PATH
+        & $python_path $GET_PIP_PATH
+    } else {
+        Write-Host "pip already installed."
+    }
+}
+
+
+function DownloadMiniconda ($python_version, $platform_suffix) {
+    if ($python_version -eq "3.4") {
+        $filename = "Miniconda3-3.5.5-Windows-" + $platform_suffix + ".exe"
+    } else {
+        $filename = "Miniconda-3.5.5-Windows-" + $platform_suffix + ".exe"
+    }
+    $url = $MINICONDA_URL + $filename
+    $filepath = Download $filename $url
+    return $filepath
+}
+
+
+function InstallMiniconda ($python_version, $architecture, $python_home) {
+    Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
+    if (Test-Path $python_home) {
+        Write-Host $python_home "already exists, skipping."
+        return $false
+    }
+    if ($architecture -eq "32") {
+        $platform_suffix = "x86"
+    } else {
+        $platform_suffix = "x86_64"
+    }
+    $filepath = DownloadMiniconda $python_version $platform_suffix
+    Write-Host "Installing" $filepath "to" $python_home
+    $install_log = $python_home + ".log"
+    $args = "/S /D=$python_home"
+    Write-Host $filepath $args
+    Start-Process -FilePath $filepath -ArgumentList $args -Wait -Passthru
+    if (Test-Path $python_home) {
+        Write-Host "Python $python_version ($architecture) installation complete"
+    } else {
+        Write-Host "Failed to install Python in $python_home"
+        Get-Content -Path $install_log
+        Exit 1
+    }
+}
+
+
+function InstallMinicondaPip ($python_home) {
+    $pip_path = $python_home + "\Scripts\pip.exe"
+    $conda_path = $python_home + "\Scripts\conda.exe"
+    if (-not(Test-Path $pip_path)) {
+        Write-Host "Installing pip..."
+        $args = "install --yes pip"
+        Write-Host $conda_path $args
+        Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
+    } else {
+        Write-Host "pip already installed."
+    }
+}
+
+function main () {
+    InstallPython $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
+    InstallPip $env:PYTHON
+}
+
+main

build_tools/appveyor/requirements.txt

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+# Fetch numpy and scipy wheels from the sklearn rackspace wheelhouse.
+# Those wheels were collected from http://www.lfd.uci.edu/~gohlke/pythonlibs/
+# This is a temporary solution. As soon as numpy and scipy provide official
+# wheel for windows we ca delete this --find-links line.
+--find-links http://28daf2247a33ed269873-7b1aad3fab3cc330e1fd9d109892382a.r6.cf2.rackcdn.com/
+
+# fix the versions of numpy to force the use of numpy and scipy to use the whl
+# of the rackspace folder instead of trying to install from more recent
+# source tarball published on PyPI
+numpy==1.9.3
+scipy==0.16.0
+sklearn==0.15.0
+nose
+wheel
+wheelhouse_uploader