Continuous integration and documentation (#2)

* Initial commit for the baseline package

This package includes the code that was used in the publication of :
L. P. René de Cotret and B. J. Siwick, A general method for
baseline-removal in ultrafast electron powder diffraction data using the
dual-tree complex wavelet transform, Struct. Dyn. 4 (2016)

* Initial documentation for the baseline package

* Removed links to PyUp and saythanks

* Added installation of NumPy before setup.py can be run on Appveyor

* Revert "Added installation of NumPy before setup.py can be run on Appveyor"

This reverts commit dd4ab54.

* FIX: appveyor builds failing fue to numpy not being

* Removed TOX dependency in Appveyor CI

* FIX: Install numpy & friends from conda on appveyor CI

* FIX: remove optional installation of conda

* FIX: typo in appveyor.yml

* FIX: Escape characters

* FIX: Yet another typo

* f

* Installation of skimage through conda

* UTF-8 encoding

* appveyor.yml typo

* build_sphinx command

* Not installign the right python version

* f

* 23rd time's the charm

* Refactoring of the baseline package

Iterative baseline functions are pretty similar, and they now share a
common implementation for the 1D case.

* Documentation setup based on SHAMPOO

* DOC: updated documentation to reflect the pywavelets dependency

* Sphinx RTD theme added

* Appveyor testing via unittest

* FIX: appveyor.yml typo

* FIX: Python 3.5 install from Miniconda3s

* FIX: Appveyor.yml typo

* CI overhaul

- Removed travis CI
- switched Appveyor testing to a modified version of Astropy's
CI-Helpers

* FIX: appveyor os not found

* FIX: code climate and readme

.appveyor/install-miniconda.ps1

@@ -0,0 +1,183 @@
+# Sample script to install anaconda under windows
+# Authors: Stuart Mumford
+# Borrowed from: Olivier Grisel and Kyle Kastner
+# License: BSD 3 clause
+
+$MINICONDA_URL = "https://repo.continuum.io/miniconda/"
+
+$env:ASTROPY_LTS_VERSION = "1.0"
+$env:LATEST_ASTROPY_STABLE = "1.3"
+$env:LATEST_NUMPY_STABLE = "1.12"
+
+# We pin the version for conda as it's not the most stable package from
+# release to release. Add note here if version is pinned due to a bug upstream.
+if (! $env:CONDA_VERSION) {
+   $env:CONDA_VERSION = "4.3.6"
+}
+
+function DownloadMiniconda ($version, $platform_suffix) {
+    $webclient = New-Object System.Net.WebClient
+    $filename = "Miniconda3-" + $version + "-Windows-" + $platform_suffix + ".exe"
+
+    $url = $MINICONDA_URL + $filename
+
+    $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 $filepath
+}
+
+function InstallMiniconda ($miniconda_version, $architecture, $python_home) {
+    Write-Host "Installing miniconda" $miniconda_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 "x86") {
+        $platform_suffix = "x86"
+    } else {
+        $platform_suffix = "x86_64"
+    }
+    $filepath = DownloadMiniconda $miniconda_version $platform_suffix
+    Write-Host "Installing" $filepath "to" $python_home
+    $args = "/InstallationType=AllUsers /S /AddToPath=1 /RegisterPython=1 /D=" + $python_home
+    Write-Host $filepath $args
+    Start-Process -FilePath $filepath -ArgumentList $args -Wait -Passthru
+    #Start-Sleep -s 15
+    if (Test-Path $python_home) {
+        Write-Host "Miniconda $miniconda_version ($architecture) installation complete"
+    } else {
+        Write-Host "Failed to install Python in $python_home"
+        Exit 1
+    }
+}
+
+# Install miniconda, if no version is given use the latest
+if (! $env:MINICONDA_VERSION) {
+   $env:MINICONDA_VERSION="latest"
+}
+
+InstallMiniconda $env:MINICONDA_VERSION $env:PLATFORM $env:PYTHON
+
+# Set environment variables
+$env:PATH = "${env:PYTHON};${env:PYTHON}\Scripts;" + $env:PATH
+
+# Conda config
+conda config --set always_yes true
+conda config --add channels defaults
+
+if ($env:CONDA_CHANNELS) {
+   $CONDA_CHANNELS=$env:CONDA_CHANNELS.split(" ")
+   foreach ($CONDA_CHANNEL in $CONDA_CHANNELS) {
+           conda config --add channels $CONDA_CHANNEL
+   }
+   Remove-Variable CONDA_CHANNELS
+   rm env:CONDA_CHANNELS
+}
+
+# Install the build and runtime dependencies of the project.
+conda install -q conda=$env:CONDA_VERSION
+
+if (! $env:CONDA_CHANNEL_PRIORITY) {
+   $CONDA_CHANNEL_PRIORITY="false"
+} else {
+   $CONDA_CHANNEL_PRIORITY=$env:CONDA_CHANNEL_PRIORITY.ToLower()
+}
+
+# We need to add this after the update, otherwise the ``channel_priority``
+# key may not yet exists
+conda config  --set channel_priority $CONDA_CHANNEL_PRIORITY
+
+# Create a conda environment using the astropy bonus packages
+conda create -q -n test python=$env:PYTHON_VERSION
+activate test
+
+# Set environment variables for environment (activate test doesn't seem to do the trick)
+$env:PATH = "${env:PYTHON}\envs\test;${env:PYTHON}\envs\test\Scripts;${env:PYTHON}\envs\test\Library\bin;" + $env:PATH
+
+# Check that we have the expected version of Python
+python --version
+
+# CORE DEPENDENCIES: PIP
+# Could install other core dependencies here, e.g. pytest
+#conda install -q -n test pip pytest
+conda install -q -n test pip
+
+# Check whether a specific version of Numpy is required
+if ($env:NUMPY_VERSION) {
+    if($env:NUMPY_VERSION -match "stable") {
+        $NUMPY_OPTION = "numpy=" + $env:LATEST_NUMPY_STABLE
+    } elseif($env:NUMPY_VERSION -match "dev") {
+        $NUMPY_OPTION = "Cython pip".Split(" ")
+    } else {
+        $NUMPY_OPTION = "numpy=" + $env:NUMPY_VERSION
+    }
+    conda install -n test -q $NUMPY_OPTION
+} else {
+    $NUMPY_OPTION = ""
+}
+
+# Install the specified versions of numpy and other dependencies
+if ($env:CONDA_DEPENDENCIES) {
+    $CONDA_DEPENDENCIES = $env:CONDA_DEPENDENCIES.split(" ")
+} else {
+    $CONDA_DEPENDENCIES = ""
+}
+
+# Check whether the installation is successful, if not abort the build
+$output = cmd /c conda install -n test -q $NUMPY_OPTION $CONDA_DEPENDENCIES 2>&1
+
+echo $output
+if ($output | select-string UnsatisfiableError, PackageNotFoundError) {
+   echo "Installing dependencies with conda was unsuccessful, using pip instead"
+   $output = cmd /c pip install $CONDA_DEPENDENCIES 2>&1
+   echo $output
+   if ($output | select-string UnsatisfiableError, PackageNotFoundError) {
+      $host.SetShouldExit(1)
+   }
+}
+
+# Check whether the developer version of Numpy is required and if yes install it
+if ($env:NUMPY_VERSION -match "dev") {
+   Invoke-Expression "${env:CMD_IN_ENV} pip install git+https://github.com/numpy/numpy.git#egg=numpy --upgrade --no-deps"
+}
+
+# We finally install the dependencies listed in PIP_DEPENDENCIES. 
+
+if ($env:PIP_FLAGS) {
+    $PIP_FLAGS = $env:PIP_FLAGS.split(" ")
+} else {
+    $PIP_FLAGS = ""
+}
+
+if ($env:PIP_DEPENDENCIES) {
+    $PIP_DEPENDENCIES = $env:PIP_DEPENDENCIES.split(" ")
+} else {
+    $PIP_DEPENDENCIES = ""
+}
+
+if ($env:PIP_DEPENDENCIES) {
+    pip install $PIP_DEPENDENCIES $PIP_FLAGS
+}