Merge pull request #469 from achilleas-k/feat/dimension-links

Dimension links

.travis.yml

@@ -22,6 +22,10 @@ matrix:
       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
@@ -56,25 +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/python@3.8/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${pymajor} --version
@@ -83,7 +90,11 @@ install:
   - python${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

nixio/block.py

@@ -337,11 +337,10 @@ def create_data_frame(self, name="", type_="", col_dict=None,
             else:  # if col_names is None
                 if data is not None and type(data[0]) == np.void:
                     col_dtype = data[0].dtype
-                    for i, dt in enumerate(col_dtype.fields.values()):
-                        cn = list(col_dtype.fields.keys())
-                        raw_dt = col_dtype.fields.values()
-                        raw_dt = list(raw_dt)
-                        raw_dt_list = [ele[0] for ele in raw_dt]
+                    cn = list(col_dtype.fields.keys())
+                    raw_dt = col_dtype.fields.values()
+                    raw_dt = list(raw_dt)
+                    raw_dt_list = [ele[0] for ele in raw_dt]
                     col_dict = OrderedDict(zip(cn, raw_dt_list))
                     if len(col_dtype.fields.values()) != len(col_dict):
                         raise exceptions.DuplicateColumnName

nixio/data_array.py

@@ -16,12 +16,11 @@
 from .source_link_container import SourceLinkContainer
 from .datatype import DataType
 from .dimensions import (Dimension, SampledDimension, RangeDimension,
-                         SetDimension, DataFrameDimension,
-                         DimensionType, DimensionContainer)
+                         SetDimension, DimensionType, DimensionContainer)
 from . import util
 from .compression import Compression
 
-from .exceptions import InvalidUnit, IncompatibleDimensions
+from .exceptions import IncompatibleDimensions
 from .section import Section
 
 
@@ -118,7 +117,7 @@ def append_sampled_dimension(self, sampling_interval, label=None,
             self.force_updated_at()
         return smpldim
 
-    def append_range_dimension(self, ticks, label=None, unit=None):
+    def append_range_dimension(self, ticks=None, label=None, unit=None):
         """
         Append a new RangeDimension to the list of existing dimension
         descriptors.
@@ -138,61 +137,6 @@ def append_range_dimension(self, ticks, label=None, unit=None):
             self.force_updated_at()
         return rdim
 
-    def append_data_frame_dimension(self, data_frame, column_idx=None):
-        """
-        Append a new DataFrameDimension to the list of existing dimension
-        descriptors.
-
-        :param data_frame: The referenced DataFrame
-        :type data_frame: nix.DataFrame
-
-        :param column_idx: Index of the referenced column of the DataFrame.
-                           The default column determines the default label,
-                           ticks, and unit of this Dimension.
-        :type column_idx: int or None
-
-        :returns: Thew newly created DataFrameDimension.
-        :rtype: DataFrameDimension
-        """
-        index = len(self.dimensions) + 1
-        dfdim = DataFrameDimension.create_new(self, index,
-                                              data_frame, column_idx)
-        if self.file.auto_update_timestamps:
-            self.force_updated_at()
-        return dfdim
-
-    def append_alias_range_dimension(self):
-        """
-        Append a new RangeDimension that uses the data stored in this
-        DataArray as ticks. This works only(!) if the DataArray is 1-D and
-        the stored data is numeric. A ValueError will be raised otherwise.
-
-        :returns: The created dimension descriptor.
-        :rtype: RangeDimension
-
-        """
-        if (len(self.data_extent) > 1 or
-                not DataType.is_numeric_dtype(self.dtype)):
-            raise ValueError("AliasRangeDimensions only allowed for 1D "
-                             "numeric DataArrays.")
-        if self._dimension_count() > 0:
-            raise ValueError("Cannot append additional alias dimension. "
-                             "There must only be one!")
-        # check if existing unit is SI
-        if self.unit:
-            u = self.unit
-            if not (util.units.is_si(u) or util.units.is_compound(u)):
-                raise InvalidUnit(
-                    "AliasRangeDimensions are only allowed when SI or "
-                    "composites of SI units are used. "
-                    "Current SI unit is {}".format(u),
-                    "DataArray.append_alias_range_dimension"
-                )
-        aliasdim = RangeDimension.create_new_alias(self, 1)
-        if self.file.auto_update_timestamps:
-            self.force_updated_at()
-        return aliasdim
-
     def delete_dimensions(self):
         """
         Delete all the dimension descriptors for this DataArray.
@@ -311,15 +255,6 @@ def unit(self, u):
         if u == "":
             u = None
         util.check_attr_type(u, str)
-        if (self._dimension_count() == 1 and
-                self.dimensions[0].dimension_type == DimensionType.Range and
-                self.dimensions[0].is_alias and u is not None):
-            if not (util.units.is_si(u) or util.units.is_compound(u)):
-                raise InvalidUnit(
-                    "[{}]: Non-SI units are not allowed if the DataArray "
-                    "has an AliasRangeDimension.".format(u),
-                    "DataArray.unit"
-                )
         self._h5group.set_attr("unit", u)
         if self.file.auto_update_timestamps:
             self.force_updated_at()

nixio/data_frame.py

@@ -185,7 +185,7 @@ def write_rows(self, rows, index):
             self._write_data(rows, sl=index)
         else:
             cr_list = []
-            for i, cr in enumerate(rows):
+            for cr in rows:
                 cr_list.append(tuple(cr))
             self._write_data(cr_list, sl=index)