Merge branch 'master' into v1.5

* master: (129 commits)
  [travis] Extra build without compat tests
  Code quality: Remove unnecessary for loop
  Code quality: Remove all unused imports and variables
  TestLinkDimension: Property change tests
  DimensionLink: Write through label and unit
  TestLinkDimension: Remove unnecessary np.app() checks
  Test dimension link index errors
  Index validation for DataArray dimension link
  Index validation for DataFrame dimension link
  Remove AliasRangeDimension and DataFrameDimension
  TestLinkDimension: DataFrame for Range and Set dimensions
  RangeDimension.label: Read through to linked label
  RangeDimension.unit: Read through to linked unit
  Remove unnecessary SampledDimension redirect
  DimensionLink to DataFrame: Apply index to column
  TestLinkDimension: Self link tests
  TestLinkDimension: SetDimension->DA link tests
  SetDimension.labels: Read through to linked data
  Multidimensional indexing should use a tuple
  TestLinkDimension: RangeDimension->DA link tests
  ...

.travis.yml

@@ -11,15 +11,21 @@ matrix:
   include:
     - python: "2.7"
       os: linux
+      dist: xenial
       env: pymajor=2
     - python: "3.6"
       os: linux
+      dist: xenial
       env: pymajor=3
     - python: "3.7"
       os: linux
       env: pymajor=3 coverage=1
       dist: xenial
       sudo: true
+    - python: "3.7"
+      os: linux
+      env: pymajor=3 nocompat=1
+      dist: xenial
     - language: generic
       os: osx
       env: pymajor=2
@@ -54,23 +60,28 @@ addons:
       - libboost-all-dev
 
 before_install:
-  - nixprefix="/usr/local"
-  - export NIX_INCDIR=${nixprefix}/include/nixio-1.0
-  - export NIX_LIBDIR=${nixprefix}/lib
-  - export PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${nixprefix}/lib/pkgconfig
+  # build nix for compat tests
+  - if [[ -z "${nocompat}" ]]; then
+      nixprefix="/usr/local";
+      export NIX_INCDIR=${nixprefix}/include/nixio-1.0;
+      export NIX_LIBDIR=${nixprefix}/lib;
+      export PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${nixprefix}/lib/pkgconfig;
+      git clone --branch ${NIX_BRANCH} https://github.com/G-Node/nix /tmp/libnix;
+      pushd /tmp/libnix;
+      mkdir build;
+      pushd build;
+      cmake -DCMAKE_INSTALL_PREFIX=${nixprefix} ..;
+      make;
+      sudo make install;
+      popd;
+      popd;
+    fi
+  # For macOS python3
+  - export PATH="/usr/local/opt/[email protected]/bin:$PATH"
   - alias pip2='pip'
   - if [[ "${TRAVIS_OS_NAME}" != "osx" ]]; then pip${pymajor} install --upgrade numpy; fi
   - pip${pymajor} install --upgrade h5py pytest pytest-xdist pytest-cov six;
   - if [[ "${pymajor}" == 2 ]]; then pip${pymajor} install enum34; fi
-  - git clone --branch ${NIX_BRANCH} https://github.com/G-Node/nix /tmp/libnix
-  - pushd /tmp/libnix
-  - mkdir build
-  - pushd build
-  - cmake -DCMAKE_INSTALL_PREFIX=${nixprefix} ..
-  - make
-  - sudo make install
-  - popd
-  - popd
   - which pip${pymajor}
   - which python${pymajor}
   - python${pymajor} --version
@@ -79,7 +90,11 @@ install:
   - python${pymajor} setup.py build
 
 script:
-  - pytest --cov=nixio --nix-compat -nauto;
+  - if [[ "${nocompat}" == 1 ]]; then
+      pytest --cov=nixio -nauto;
+    else
+      pytest --cov=nixio --nix-compat -nauto;
+    fi
 
 after_success:
   - if [[ "${coverage}" == 1 ]]; then

MANIFEST.in

@@ -1,4 +1,3 @@
 include LICENSE README.rst
 recursive-include docs *
-recursive-include scripts *
 include nixio/info.json

README.rst

@@ -51,7 +51,7 @@ Check out the API documentation for further tutorials.
 NIXPY API Documentation
 -----------------------
 
-The API documentation can be found `here <http://g-node.github.io/nixpy/>`_.
+The API documentation can be found `here <https://nixpy.readthedocs.io/>`_.
 
 
 .. _nixio: https://pypi.python.org/pypi/nixio

docs/source/api/modules.rst

@@ -0,0 +1,7 @@
+nixio
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   nixio

docs/source/api/nixio.cmd.rst

@@ -0,0 +1,22 @@
+nixio.cmd package
+=================
+
+Submodules
+----------
+
+nixio.cmd.validate module
+-------------------------
+
+.. automodule:: nixio.cmd.validate
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nixio.cmd
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/nixio.exceptions.rst

@@ -0,0 +1,22 @@
+nixio.exceptions package
+========================
+
+Submodules
+----------
+
+nixio.exceptions.exceptions module
+----------------------------------
+
+.. automodule:: nixio.exceptions.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nixio.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/nixio.hdf5.rst

@@ -0,0 +1,30 @@
+nixio.hdf5 package
+==================
+
+Submodules
+----------
+
+nixio.hdf5.h5dataset module
+---------------------------
+
+.. automodule:: nixio.hdf5.h5dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.hdf5.h5group module
+-------------------------
+
+.. automodule:: nixio.hdf5.h5group
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nixio.hdf5
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/nixio.rst

@@ -0,0 +1,209 @@
+nixio package
+=============
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nixio.cmd
+   nixio.exceptions
+   nixio.hdf5
+   nixio.test
+   nixio.util
+
+Submodules
+----------
+
+nixio.block module
+------------------
+
+.. automodule:: nixio.block
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.compression module
+------------------------
+
+.. automodule:: nixio.compression
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.container module
+----------------------
+
+.. automodule:: nixio.container
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.data\_array module
+------------------------
+
+.. automodule:: nixio.data_array
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.data\_frame module
+------------------------
+
+.. automodule:: nixio.data_frame
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.data\_set module
+----------------------
+
+.. automodule:: nixio.data_set
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.data\_view module
+-----------------------
+
+.. automodule:: nixio.data_view
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.datatype module
+---------------------
+
+.. automodule:: nixio.datatype
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.dimension\_type module
+----------------------------
+
+.. automodule:: nixio.dimension_type
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.dimensions module
+-----------------------
+
+.. automodule:: nixio.dimensions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.entity module
+-------------------
+
+.. automodule:: nixio.entity
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.feature module
+--------------------
+
+.. automodule:: nixio.feature
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.file module
+-----------------
+
+.. automodule:: nixio.file
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.group module
+------------------
+
+.. automodule:: nixio.group
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.info module
+-----------------
+
+.. automodule:: nixio.info
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.link\_type module
+-----------------------
+
+.. automodule:: nixio.link_type
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.multi\_tag module
+-----------------------
+
+.. automodule:: nixio.multi_tag
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.property module
+---------------------
+
+.. automodule:: nixio.property
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.section module
+--------------------
+
+.. automodule:: nixio.section
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.source module
+-------------------
+
+.. automodule:: nixio.source
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.source\_link\_container module
+------------------------------------
+
+.. automodule:: nixio.source_link_container
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.tag module
+----------------
+
+.. automodule:: nixio.tag
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nixio.validator module
+----------------------
+
+.. automodule:: nixio.validator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nixio
+   :members:
+   :undoc-members:
+   :show-inheritance: