diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 52e024a4478c103b413275d5487ff16e48892fcc..a1d727dce9c2d87992e2110aa716f8113b5028e0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,16 +1,13 @@
# run the test suite
-
tests:
image: registry.gitlab.lis-lab.fr:5005/skmad-suite/madarrays/ubuntu:18.04
tags:
- docker
script:
- - pip3 install . --no-deps
+ - pip3 install --no-deps .
- pytest-3
-
# generate the documentation
-
pages:
image: registry.gitlab.lis-lab.fr:5005/skmad-suite/madarrays/ubuntu:18.04
tags:
@@ -18,7 +15,7 @@ pages:
only:
- master
script:
- - pip3 install . --no-deps
+ - pip3 install --no-deps .
- python3 setup.py build_sphinx
- cp -r build/sphinx/html public
artifacts:
diff --git a/doc/conf.py b/doc/conf.py
index db08bb74a0b8b04aa235481c086f27abc40efd80..a1699d94d99a71e677a0263e5e04b9a54f86d0f1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -25,7 +25,6 @@ extensions = ['sphinx.ext.autodoc',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
- 'sphinx_paramlinks',
'numpydoc',
'nbsphinx',
'IPython.sphinxext.ipython_console_highlighting',
@@ -48,7 +47,7 @@ master_doc = 'index'
# General information about the project.
project = 'madarrays'
-author = 'V. Emiya and R. Hamon'
+author = 'V. Emiya, R. Hamon, F. Jaillet'
copyright = '2017-{}, {}'.format(date.today().year, author)
# The version info for the project you're documenting, acts as replacement for
@@ -217,7 +216,7 @@ latex_elements = {
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'madarray.tex', 'madarray Documentation',
- 'V. Emiya, R. Hamon.', 'manual'),
+ 'V. Emiya, R. Hamon., F. Jaillet', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
diff --git a/docker/Dockerfile_ubuntu_18.04 b/docker/Dockerfile_ubuntu_18.04
index dedc3fb2b7d6dae814944e8a9e82516e5942f33e..faab03fcf5b0476f7634bff4265fefa6b38f500d 100644
--- a/docker/Dockerfile_ubuntu_18.04
+++ b/docker/Dockerfile_ubuntu_18.04
@@ -4,7 +4,7 @@ WORKDIR /
ENV DEBIAN_FRONTEND noninteractive
# In the following "apt-get install ..." command, cmake, make, g++,
# libfftw3-dev, and liblapack-dev are not needed for madarrays but are added
-# to be able to install ltfatpy via pip
+# to be able to install ltfatpy in the container via pip
RUN apt-get update && \
apt-get upgrade -y && \
apt-get install -y --no-install-recommends \
@@ -25,7 +25,6 @@ RUN apt-get update && \
python3-pytest \
python3-pytest-cov \
python3-sphinx \
- python3-sphinx-paramlinks \
python3-numpydoc \
python3-nbsphinx \
jupyter-client \
diff --git a/madarrays/mad_array.py b/madarrays/mad_array.py
index c18200cf58b53bb1401065aa571189efcc026234..d501dd24a72867852c5ec53004252acf0c463508 100644
--- a/madarrays/mad_array.py
+++ b/madarrays/mad_array.py
@@ -116,8 +116,8 @@ class MadArray(np.ndarray):
whose entries are equal to True if the corresponding data entry is
masked, or False otherwise.
- This is the default mode and the mode selected when specifying
- :paramref:`mask` during creation.
+ This is the default mode and the mode selected when specifying ``mask``
+ during creation.
* Complex entries can have only the magnitude or phase component masked, or
both. The resulting mask has integers entries, equal to:
@@ -129,13 +129,12 @@ class MadArray(np.ndarray):
* *3* if the magnitude and the phase are masked (unknown magnitude and
phase).
- This mode is selected when specifying :paramref:`mask_magnitude` and/or
- :paramref:`mask_phase` during creation.
+ This mode is selected when specifying ``mask_magnitude`` and/or
+ ``mask_phase`` during creation.
Entries are converted to a complex type.
- If entries are complex values and :paramref:`mask` is given during
- creation, both the magnitude and phase are masked and the boolean mask
- mode is used.
+ If entries are complex values and ``mask`` is given during creation, both
+ the magnitude and phase are masked and the boolean mask mode is used.
.. _indexing_madarray:
@@ -145,35 +144,34 @@ class MadArray(np.ndarray):
* a :class:`MadArray` object with shape corresponding to the indices is
returned, with both the data matrix and the mask properly indexed. This
is the default mode;
- * a :class:`MadArray` object with unchanged shape is returned,
- where non-indexed entries are set as masked. This mode is selected by
- setting the parameter :paramref:`masked_indexing` to True.
+ * a :class:`MadArray` object with unchanged shape is returned, where
+ non-indexed entries are set as masked. This mode is selected by setting
+ the parameter ``masked_indexing`` to True.
.. _numpy_behaviour_madarray:
**Numpy behaviour**: it is possible to use standard operations (+, -, /,
//, \*, T) between two :class:`MadArray` objects, likewise operations
- between numpy
- arrays. The resulting object has a mask consisting of the union of the
- operands. It is also possible to use pickle operations to jointly store the
- data and the mask.
+ between numpy arrays. The resulting object has a mask consisting of the
+ union of the operands. It is also possible to use pickle operations to
+ jointly store the data and the mask.
Parameters
----------
data : array_like
Multidimensional array. See :ref:`Type of Entry<type_entry_madarray>`.
mask : boolean array_like, optional
- Mask for boolean masking mode. See
- :ref:`Masking<masking_madarray>`.
+ Mask for boolean masking mode.
+ See :ref:`Masking<masking_madarray>`.
mask_magnitude : boolean array_like or None, optional
- Magnitude mask for masking with complex data. See
- :ref:`Masking<masking_madarray>`.
+ Magnitude mask for masking with complex data.
+ See :ref:`Masking<masking_madarray>`.
mask_phase : boolean or array_like or None, optional
- Phase mask for masking with complex data. See
- :ref:`Masking<masking_madarray>`.
+ Phase mask for masking with complex data.
+ See :ref:`Masking<masking_madarray>`.
masked_indexing : bool or None, optional
- Indicate how the indexing is performed. If None, set to False. See
- :ref:`Indexing<indexing_madarray>`.
+ Indicate how the indexing is performed. If None, set to False.
+ See :ref:`Indexing<indexing_madarray>`.
Warnings
--------
@@ -189,7 +187,7 @@ class MadArray(np.ndarray):
Notes
-----
This class implements an alternative masked array different from
- :class:`np.ma.MaskedArray`. The reason of this choice is that it is only
+ :class:`numpy.ma.MaskedArray`. The reason of this choice is that it is only
used as a container of a ndarray and a mask. No masked operations are
needed.
"""
@@ -385,8 +383,7 @@ class MadArray(np.ndarray):
"""Number of missing data (double or tuple).
Number of masked coefficients if dtype is int or float. Number of
- masked coefficients in phase and magnitude masks if dtype is
- complex.
+ masked coefficients in phase and magnitude masks if dtype is complex.
"""
if self._complex_masking:
return (np.sum(self.get_unknown_mask('magnitude')),
@@ -399,8 +396,7 @@ class MadArray(np.ndarray):
"""Ratio of missing data (double or tuple).
Ratio of masked coefficients if dtype is int or float. Ratio of
- masked coefficients in phase and magnitude masks if dtype is
- complex.
+ masked coefficients in phase and magnitude masks if dtype is complex.
"""
if self._complex_masking:
return (np.average(self.get_unknown_mask('magnitude')),
@@ -415,16 +411,16 @@ class MadArray(np.ndarray):
def to_np_array(self, fill_value=None):
"""Return a numpy array.
- If :paramref:`fill_value` is not None, masked elements are replaced
- according to the type of entries:
+ If ``fill_value`` is not None, masked elements are replaced according
+ to the type of entries:
- * :paramref:`fill_value` if the type of entries is *int* or *float*;
+ * ``fill_value`` if the type of entries is *int* or *float*;
* If the type is *complex*, missing entries are replaced either by:
* a complex number with the known magnitude value without the phase
information if only the phase is masked;
* a complex number of magnitude 1 with the known phase if only the
magnitude is masked;
- * by :paramref:`fill_value` if both magnitude and phase are masked.
+ * by ``fill_value`` if both magnitude and phase are masked.
Parameters
----------
diff --git a/madarrays/waveform.py b/madarrays/waveform.py
index 3bed1d6f3ec9f73682410998c80017ec0fc8dfd5..854baf05d0586b58a36d5e297c7bd6b9139b56a2 100644
--- a/madarrays/waveform.py
+++ b/madarrays/waveform.py
@@ -136,11 +136,11 @@ class Waveform(MadArray):
[N, 2]-shape array for a stereo signal
fs : int or float, optional
Sampling frequency of the original signal, in Hz. If float, truncated.
- If None and :paramref:`data` is a Waveform, use `data.fs`, otherwise it
+ If None and ``data`` is a Waveform, use ``data.fs``, otherwise it
is set to 1.
mask : nd-array, optional
Boolean mask with True values for missing samples. Its shape must be
- the same as :paramref:`data`.
+ the same as ``data``.
indexing :
See :class:`MadArray`.
"""
diff --git a/requirements/doc.txt b/requirements/doc.txt
index 88f5dc8239412107b6242808b0dde514e2935324..97d1e46a0562693529e73ddaa62b935627b886bb 100644
--- a/requirements/doc.txt
+++ b/requirements/doc.txt
@@ -4,4 +4,3 @@ sphinx
nbsphinx
numpydoc
jupyter
-sphinx-paramlinks
diff --git a/setup.py b/setup.py
index 8cc0ef42600e71b75cab7aebfd551b555524eca2..4f604613cb0076f493e99bb6d9938acdb59473f3 100644
--- a/setup.py
+++ b/setup.py
@@ -73,7 +73,7 @@ CLASSIFIERS = [
PYTHON_REQUIRES = '>=3.5'
EXTRAS_REQUIRE = {
'dev': ['coverage', 'pytest', 'pytest-cov', 'pytest-randomly', 'ipython'],
- 'doc': ['sphinx', 'nbsphinx', 'numpydoc', 'sphinx-paramlinks']}
+ 'doc': ['sphinx', 'nbsphinx', 'numpydoc']}
PROJECT_URLS = {'Bug Reports': URL + '/issues',
'Source': URL}
KEYWORDS = 'audio, data structures, missing data'