Merge in master

.travis.yml

@@ -5,54 +5,44 @@ matrix:
   include:
     # "Legacy" environments: oldest supported versions, without and with numba
     - python: "2.7"
-      env: DEPS="numpy=1.8.2 scipy=0.12.0 matplotlib=1.3 pillow==2.1 pandas=0.13.0 scikit-image=0.9 pyyaml pytables" BUILD_DOCS=false
+      env: DEPS="numpy=1.8.2 scipy=0.12.0 matplotlib=1.3 pillow=2.1 pandas=0.13.0 scikit-image=0.9 pytables scikit-learn=0.14.1 pyyaml" BUILD_DOCS=false SKIP_SLOW=true
     - python: "2.7"
-      env: DEPS="numpy=1.8.2 scipy=0.13.3 matplotlib=1.3 pillow==2.5.1 pandas=0.13.0 scikit-image=0.9 pyyaml numba=0.13.4 pytables" BUILD_DOCS=false
-    # "Recommended" environments: More recent versions, for Py2 and Py3.
+      env: DEPS="numpy=1.8.2 scipy=0.12.0 matplotlib=1.3 pillow=2.1 pandas=0.13.0 scikit-image=0.9 numba=0.13.4 pytables scikit-learn=0.14.1 pyyaml" BUILD_DOCS=false SKIP_SLOW=true
+    # "Typical" environments: package versions from 2016
     - python: "2.7"
-      env: DEPS="libgfortran=1.0 numpy=1.9 scipy=0.16 matplotlib=1.4 pillow==2.9 pandas=0.16 scikit-image=0.11 pyyaml numba=0.20 pytables pyfftw" BUILD_DOCS=false
-    - python: "3.4"
-      env: DEPS="libgfortran=1.0 numpy=1.9 scipy=0.16 matplotlib=1.4 pillow==3.0 pandas=0.16 scikit-image=0.11 pyyaml numba=0.20 pytables pyfftw" BUILD_DOCS=true
+      env: DEPS="numpy=1.10 scipy=0.17 matplotlib=1.5 pillow=3.1 pandas=0.18.1 scikit-image=0.12 pytables numba=0.23.1 scikit-learn=0.17.1 pyyaml" BUILD_DOCS=false SKIP_SLOW=true
     - python: "3.5"
-      env: DEPS="numpy scipy matplotlib pillow pandas!=0.18.0 scikit-image pyyaml pytables numba"  BUILD_DOCS=false
+      env: DEPS="numpy=1.10 scipy=0.17 matplotlib=1.5 pillow=3.1 pandas=0.18.1 scikit-image=0.12 pytables numba=0.23.1 scikit-learn=0.17.1 pyyaml" BUILD_DOCS=true SKIP_SLOW=true
+    # Environments with most recent versions, on python 2.7 and python 3.6
+    - python: "2.7"
+      env: DEPS="numpy scipy matplotlib pillow pandas scikit-image pyyaml pytables numba scikit-learn" BUILD_DOCS=false SKIP_SLOW=true
     - python: "3.6"
-      env: DEPS="numpy scipy matplotlib pillow pandas!=0.18.0 scikit-image pyyaml pytables numba"  BUILD_DOCS=false
+      env: DEPS="numpy scipy matplotlib pillow pandas scikit-image pyyaml pytables numba scikit-learn"  BUILD_DOCS=false SKIP_SLOW=false
 
 
 install:
-  # See:
-  # https://groups.google.com/a/continuum.io/forum/#!topic/conda/RSFENqovnro
-  # - conda update --yes --no-deps conda
-  # OK, this used to *fix* the build, but now it *breaks* the build.
-  # If you're reading this, good luck out there. I'm not sure what to tell you.
   - conda update --yes conda
-  # Append the conda-forge channel, instead of adding it. See:
-  # https://github.com/conda-forge/conda-forge.github.io/issues/232)
-  - conda config --append channels conda-forge
-  - conda create -n testenv --yes $DEPS pip nose setuptools python=$TRAVIS_PYTHON_VERSION
+  - conda create -n testenv --yes $DEPS nose python=$TRAVIS_PYTHON_VERSION
   - source activate testenv
-  - |
-      if [ $BUILD_DOCS == true ]; then
-        conda install -n testenv --yes ipython=5.1.0 sphinx=1.4.8 numpydoc=0.6.0 nbconvert=4.2.0
-        pip install sphinx_bootstrap_theme==0.4.12
-      fi
+
   # for debugging...
   - echo $PATH
   - which python
   - conda info
   - conda list
-  - python setup.py install
 
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.5.5-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.5.5-Linux-x86_64.sh -O miniconda.sh; fi
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b -p /home/travis/mc
   - export PATH=/home/travis/mc/bin:$PATH
 
 script:
-  - nosetests --nologcapture -a '!slow'
+  - if [ $SKIP_SLOW == true ]; then nosetests --nologcapture -a '!slow'; else nosetests --nologcapture; fi
   - |
     if [ $BUILD_DOCS == true ]; then
+      conda config --append channels conda-forge
+      conda install --yes ipython=5.1.0 sphinx=1.4.8 numpydoc=0.6.0 nbconvert=4.2.0 sphinx_bootstrap_theme=0.4
       cd $TRAVIS_BUILD_DIR/..
       git clone https://github.com/soft-matter/trackpy-examples.git
       cd trackpy/doc

README.md

@@ -1,13 +1,13 @@
 trackpy
 =======
 
-[![build status](https://travis-ci.org/soft-matter/trackpy.png?branch=master)](https://travis-ci.org/soft-matter/trackpy) [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.60550.svg)](http://dx.doi.org/10.5281/zenodo.60550)
+[![build status](https://travis-ci.org/soft-matter/trackpy.png?branch=master)](https://travis-ci.org/soft-matter/trackpy) [![Build status](https://ci.appveyor.com/api/projects/status/bc5umcboh3elm8oh?svg=true)](https://ci.appveyor.com/project/caspervdw/trackpy) [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.1213240.svg)](http://dx.doi.org/10.5281/zenodo.1213240)
 
 What is it?
 -----------
 
 **trackpy** is a Python package for particle tracking in 2D, 3D, and higher dimensions.
-**[Read the walkthrough](http://soft-matter.github.io/trackpy/dev/tutorial/walkthrough.html)** to skim or study an example project from start to finish.
+[**Read the walkthrough**](http://soft-matter.github.io/trackpy/dev/tutorial/walkthrough.html) to skim or study an example project from start to finish.
 
 Documentation
 -------------
@@ -16,7 +16,7 @@ Documentation
 
 - an introduction
 - tutorials on the basics, 3D tracking, and much, much more
-- easy installation instructions
+- easy [installation instructions](http://soft-matter.github.io/trackpy/dev/installation.html)
 - the reference guide
 
 If you use trackpy for published research, please

appveyor.yml

@@ -0,0 +1,34 @@
+environment:
+
+  matrix:
+
+    - PYTHON: "C:\\Miniconda"
+      PYTHON_VERSION: "2.7"
+      DEPS: "numpy=1.8.2 scipy=0.14.0 matplotlib=1.3 pillow=2.1 pandas=0.13.0 scikit-image=0.9 numba=0.13.4 pytables scikit-learn=0.14.1 pyyaml"
+
+    - PYTHON: "C:\\Miniconda36-x64"
+      PYTHON_VERSION: "3.6"
+      DEPS: "numpy scipy matplotlib pillow pandas scikit-image pyyaml pytables numba scikit-learn"
+
+init:
+  - "ECHO %PYTHON% %PYTHON_VERSION%"
+
+install:
+  # Prepend to the PATH of this build
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%CONDA_ROOT%\\Library\\bin;%PATH%"
+
+  # Install dependencies
+  - conda update --yes conda
+  - conda create -n testenv --yes %DEPS% nose python=%PYTHON_VERSION%
+  - activate testenv
+
+  # for debugging...
+  - "ECHO %PATH%"
+  - python --version
+  - conda info
+  - conda list
+
+build: false
+
+test_script:
+  - nosetests --nologcapture -A "not slow"

doc/api.rst

@@ -17,7 +17,7 @@ Convenience functions for feature finding, refinement, and linking are readily a
 
     locate
     batch
-    link_df
+    link
 
 For more control on your tracking "pipeline", the following core functions are provided:
 
@@ -44,14 +44,20 @@ Linking
 .. autosummary::
     :toctree: generated/
 
-    link_df
+    link
+    link_iter
     link_df_iter
 
 
-:func:`~trackpy.linking.link_df` and :func:`~trackpy.linking.link_df_iter` run
-the same underlying code, but :func:`~trackpy.linking.link_df_iter` streams
-through large data sets one frame at a time. See the tutorial on large data
-sets for more.
+:func:`~trackpy.linking.link` and :func:`~trackpy.linking.link_df_iter` run
+the same underlying code. :func:`~trackpy.linking.link` operates on a single
+DataFrame containing data for an entire movie.
+:func:`~trackpy.linking.link_df_iter` streams through larger data sets,
+in the form of one DataFrame for each video frame.
+:func:`~trackpy.linking.link_iter` streams through a series of numpy
+ndarrays.
+
+See the tutorial on large data sets for more.
 
 Static Analysis
 ---------------
@@ -194,9 +200,9 @@ Utility functions
 .. autosummary::
     :toctree: generated/
 
-    minmass_version_change
+    minmass_v03_change
+    minmass_v04_change
     utils.fit_powerlaw
-    strip_diagnostics
 
 Diagnostic functions
 --------------------

doc/conf.py

@@ -45,9 +45,12 @@
 extlinks = {'issue': ('https://github.com/soft-matter/trackpy/issues/%s',
                       'GH')}
 
+mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.3/MathJax.js'
+
 # Generate the API documentation when building
 autosummary_generate = True
 numpydoc_show_class_members = False
+autodoc_docstring_signature = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

doc/installation.rst

@@ -12,7 +12,7 @@ Installation is simple on Windows, OSX, and Linux, even for Python novices.
 """"""""""""""""""""""""
 
 To get started with Python on any platform, download and install
-`Anaconda <https://store.continuum.io/cshop/anaconda/>`_. It comes with the
+`Anaconda <https://www.anaconda.com/distribution/>`_. It comes with the
 common scientific Python packages built in.
 
 2. Install trackpy
@@ -26,8 +26,11 @@ for Applications > Utilities > Terminal. Type these commands:
 
    conda update conda
    conda install -c conda-forge trackpy
+   conda install -c conda-forge pims
 
-The above installs trackpy and all its requirements.
+The above installs trackpy and all its requirements, plus the recommended
+`PIMS <http://soft-matter.github.io/pims/>`_ package that simplifies image-reading,
+and that is used in the trackpy tutorials.
 
 3. Try it out!
 """"""""""""""
@@ -44,7 +47,7 @@ This will automatically open a browser tab, ready to interpret Python code.
 To get started, check out the links to tutorials at the top of this document.
 
 Updating Your Installation
---------------------------
+""""""""""""""""""""""""""
 
 Before updating to a new version of trackpy, be sure to read the
 :doc:`release notes<whatsnew>` for a list of new features and any changes
@@ -78,6 +81,30 @@ You can easily install a recent build by downloading the source from
 If you plan to edit the code yourself, you should use git and pip as
 explained below.
 
+Using environments
+""""""""""""""""""
+
+Some users often like to separate Python instances into environments, so that
+each project can have its own set of packages. Create a trackpy-dedicated
+environment with the name softmatter as follows:
+
+.. code-block:: bash
+
+    conda create --name softmatter python=3.6 trackpy nb_conda
+
+The `nb_conda` is optional, but we added it to ensure that Jupyter sees this
+environment as well. You can switch to the environment from within Jupyter in
+the Kernels menu. To access the environment on the commandline, type the
+following:
+
+.. code-block:: bash
+
+    source activate softmatter
+
+On Windows systems, leave out the `source`. You can go back to the root conda
+environment by activating `root`.
+
+
 More Information for Experienced Python Users
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -92,7 +119,7 @@ Package for python 2 and python 3 are available for Archlinux on AUR:
 pip
 """
 
-We strongly recommend using conda install trackpy, as described above,
+We strongly recommend using conda to install trackpy, as described above,
 but pip is also supported.
 
 Essential Dependencies:
@@ -106,10 +133,11 @@ Essential Dependencies:
 * `pandas <http://pandas.pydata.org/pandas-docs/stable/overview.html>`__ >=0.13
 * `pyyaml <http://pyyaml.org/>`__
 
-You will also need the image- and video-reader PIMS, which is, like trackpy
-itself, part of the github.com/soft-matter organization. The package is also
-available at conda-forge and PyPI, so installation works the same as
-with trackpy.
+You will also want to install the `pims <http://soft-matter.github.io/pims/>`_
+package that simplifies image-reading, and that is used in the trackpy tutorials.
+The remaining optional dependencies, listed below, are strongly recommended but
+can be challenging to install yourself, hence our recommendation that you
+use `Anaconda <https://www.anaconda.com/distribution/>`_.
 
 Manual installation
 """""""""""""""""""
@@ -156,6 +184,10 @@ started using git.
 Optional Dependencies
 """""""""""""""""""""
 
+These are strongly recommended to make using trackpy more convenient and faster:
+
+* The `PIMS <http://soft-matter.github.io/pims/>`_ package simplifies image-reading,
+      and is used in the trackpy tutorials.
 * `PyTables <http://www.pytables.org/moin>`__ for saving results in an HDF5 file. 
       This is included with Anaconda.
 * `numba <http://numba.pydata.org/>`__ for accelerated feature-finding and linking.