Merge pull request #66 from TUW-GEO/develop

Release v0.3.4

.travis.yml

@@ -13,6 +13,7 @@ python:
   - "2.7"
   - "3.3"
   - "3.4"
+  - "3.5"
 install:
   # You may want to periodically update this, although the conda update
   # conda line below will keep everything up-to-date.  We do this

CHANGES.md

@@ -1,3 +1,9 @@
+# v0.3.4, 2015-10-23
+
+* fix #63 by moving data preparation before period checks
+* fix bug in exponential and boxcar filter. Problem was that nan values were not
+  ignored correctly
+
 # v0.3.3, 2015-08-26
 
 * add option to temporal resampling to exclude window boundaries

appveyor.yml

@@ -6,39 +6,55 @@ environment:
     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\appveyor\\run_with_compiler.cmd"
 
   matrix:
-    - PYTHON: "C:\\Python27"
+    - PYTHON: "C:\\Python27_32"
       PYTHON_VERSION: "2.7.8"
       PYTHON_ARCH: "32"
+      MINICONDA_VERSION: ""
 
-    - PYTHON: "C:\\Python27-x64"
+    - PYTHON: "C:\\Python27_64"
       PYTHON_VERSION: "2.7.8"
       PYTHON_ARCH: "64"
+      MINICONDA_VERSION: ""
 
-    - PYTHON: "C:\\Python33"
-      PYTHON_VERSION: "3.3.5"
+    - PYTHON: "C:\\Python33_32"
+      PYTHON_VERSION: "3.3"
       PYTHON_ARCH: "32"
+      MINICONDA_VERSION: "3"
 
-    - PYTHON: "C:\\Python33-x64"
-      PYTHON_VERSION: "3.3.5"
+    - PYTHON: "C:\\Python33_64"
+      PYTHON_VERSION: "3.3"
       PYTHON_ARCH: "64"
+      MINICONDA_VERSION: "3"
 
-    - PYTHON: "C:\\Python34"
+    - PYTHON: "C:\\Python34_32"
       PYTHON_VERSION: "3.4.1"
       PYTHON_ARCH: "32"
+      MINICONDA_VERSION: "3"
 
-    - PYTHON: "C:\\Python34-x64"
+    - PYTHON: "C:\\Python34_64"
       PYTHON_VERSION: "3.4.1"
       PYTHON_ARCH: "64"
+      MINICONDA_VERSION: "3"
+
+    - PYTHON: "C:\\Python35_32"
+      PYTHON_VERSION: "3.5"
+      PYTHON_ARCH: "32"
+      MINICONDA_VERSION: "3"
+
+    - PYTHON: "C:\\Python35_64"
+      PYTHON_VERSION: "3.5"
+      PYTHON_ARCH: "64"
+      MINICONDA_VERSION: "3"
 
 install:
+  - "git submodule update --init --recursive"
   - ECHO "Filesystem root:"
   - ps: "ls \"C:/\""
 
   - ECHO "Installed SDKs:"
   - ps: "ls \"C:/Program Files/Microsoft SDKs/Windows\""
 
-  # Install Python (from the official .msi of http://python.org) and pip when
-  # not already installed.
+  # install miniconda with the powershell script install.ps1
   - "powershell ./appveyor/install.ps1"
 
   # Prepend newly installed Python to the PATH of this build (this cannot be
@@ -54,14 +70,19 @@ install:
   # compiled extensions and are not provided as pre-built wheel packages,
   # pip will build them from source using the MSVC compiler matching the
   # target Python version and architecture
-  - "%CMD_IN_ENV% pip install cython"
-  - "%CMD_IN_ENV% pip install -i https://pypi.binstar.org/carlkl/simple numpy"
+  - "conda update --yes conda"
+  - "conda create -q --yes -n test python=%PYTHON_VERSION% numpy scipy pandas statsmodels netCDF4  cython pytest pip matplotlib pyproj"
+  - "activate test"
+  - "pip install pygeogrids"
+  - "pip install pyresample"
+  - "python --version"
+  - "where python"
 
 build: false  # Not a C# project, build stuff at the test step instead.
 
 test_script:
   # Build the compiled extension and run the project tests
-  - "echo Skipped"
+  - "%CMD_IN_ENV% python setup.py test"
 
 after_test:
   # If tests are successful, create a whl package for the project.

appveyor/install.ps1

@@ -1,16 +1,15 @@
-# Sample script to install Python and pip under Windows
-# Authors: Olivier Grisel and Kyle Kastner
-# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+# Sample script to install anaconda under windows
+# Authors: Stuart Mumford
+# Borrwed from: Olivier Grisel and Kyle Kastner
+# License: BSD 3 clause
 
-$BASE_URL = "https://www.python.org/ftp/python/"
-$GET_PIP_URL = "https://bootstrap.pypa.io/get-pip.py"
-$GET_PIP_PATH = "C:\get-pip.py"
+$MINICONDA_URL = "http://repo.continuum.io/miniconda/"
 
-
-function DownloadPython ($python_version, $platform_suffix) {
+function DownloadMiniconda ($miniconda_version, $platform_suffix) {
     $webclient = New-Object System.Net.WebClient
-    $filename = "python-" + $python_version + $platform_suffix + ".msi"
-    $url = $BASE_URL + $python_version + "/" + $filename
+    $filename = "Miniconda" + $miniconda_version + "-latest" + "-Windows-" + $platform_suffix + ".exe"
+
+    $url = $MINICONDA_URL + $filename
 
     $basedir = $pwd.Path + "\"
     $filepath = $basedir + $filename
@@ -19,9 +18,9 @@ function DownloadPython ($python_version, $platform_suffix) {
         return $filepath
     }
 
-    # Download and retry up to 5 times in case of network transient errors.
+    # Download and retry up to 3 times in case of network transient errors.
     Write-Host "Downloading" $filename "from" $url
-    $retry_attempts = 3
+    $retry_attempts = 2
     for($i=0; $i -lt $retry_attempts; $i++){
         try {
             $webclient.DownloadFile($url, $filepath)
@@ -31,55 +30,42 @@ function DownloadPython ($python_version, $platform_suffix) {
             Start-Sleep 1
         }
    }
-   Write-Host "File saved at" $filepath
+   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 InstallPython ($python_version, $architecture, $python_home) {
-    Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
+function InstallMiniconda ($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 "32") {
-        $platform_suffix = ""
+        $platform_suffix = "x86"
     } else {
-        $platform_suffix = ".amd64"
+        $platform_suffix = "x86_64"
     }
-    $filepath = DownloadPython $python_version $platform_suffix
+    $filepath = DownloadMiniconda $miniconda_version $platform_suffix
     Write-Host "Installing" $filepath "to" $python_home
-    $args = "/qn /i $filepath TARGETDIR=$python_home"
-    Write-Host "msiexec.exe" $args
-    Start-Process -FilePath "msiexec.exe" -ArgumentList $args -Wait -Passthru
-    Write-Host "Python $python_version ($architecture) installation complete"
-    return $true
-}
-
-
-function InstallPip ($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 $GET_PIP_PATH
-        Start-Process -FilePath "$python_path" -ArgumentList "$GET_PIP_PATH" -Wait -Passthru
+    $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 "pip already installed."
+        Write-Host "Failed to install Python in $python_home"
+        Exit 1
     }
 }
 
-function InstallPackage ($python_home, $pkg) {
-    $pip_path = $python_home + "/Scripts/pip.exe"
-    & $pip_path install $pkg
-}
-
 function main () {
-    InstallPython $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
-    InstallPip $env:PYTHON
-    InstallPackage $env:PYTHON wheel
+    InstallMiniconda $env:MINICONDA_VERSION $env:PYTHON_ARCH $env:PYTHON
 }
 
 main

docs/Triple collocation.rst

@@ -325,4 +325,4 @@ References
 .. [Gruber_2015] Gruber, A., Su, C., Zwieback, S., Crow, W., Dorigo, W., Wagner, W.
        (2015). Recent advances in (soil moisture) triple collocation analysis.
        International Journal of Applied Earth Observation and Geoinformation,
-       in review
+       in press. 10.1016/j.jag.2015.09.002

pytesmo/time_series/filtering.py

@@ -15,7 +15,7 @@
 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 # ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 # WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL VIENNA UNIVERSITY OF TECHNOLOGY, 
+# DISCLAIMED. IN NO EVENT SHALL VIENNA UNIVERSITY OF TECHNOLOGY,
 # DEPARTMENT OF GEODESY AND GEOINFORMATION BE LIABLE FOR ANY
 # DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 # (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
@@ -36,17 +36,18 @@
 from pytesmo.timedate.julian import julday
 from pytesmo.time_series.filters import boxcar_filter
 
+
 def moving_average(Ser,
                    window_size=1):
     '''
     Applies a moving average (box) filter on an input time series
-    
+
     Parameters
     ----------
     Ser : pandas.Series (index must be a DateTimeIndex or julian date)
-    
+
     window_size : float, optional
-        The size of the moving_average window [days] that will be applied on the 
+        The size of the moving_average window [days] that will be applied on the
         input Series
         Default: 1
 
@@ -57,15 +58,16 @@ def moving_average(Ser,
     '''
     # if index is datetimeindex then convert it to julian date
     if type(Ser.index) == pd.DatetimeIndex:
-        
+
         jd_index = julday(Ser.index.month, Ser.index.day, Ser.index.year,
-                      Ser.index.hour, Ser.index.minute, Ser.index.second)
-        
+                          Ser.index.hour, Ser.index.minute, Ser.index.second)
+
     else:
         jd_index = Ser.index.values
-
-    filtered = boxcar_filter(np.squeeze(Ser.values.astype(np.double)), jd_index.astype(np.double), window=window_size)
 
-    result = pd.Series(filtered, index=Ser.index)   
-
+    filtered = boxcar_filter(np.squeeze(
+        Ser.values.astype(np.double)), jd_index.astype(np.double), window=window_size)
+
+    result = pd.Series(filtered, index=Ser.index)
+
     return result