Added coverage report in generated ci files

.gitignore

@@ -36,6 +36,7 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+*.pytest_cache/
 
 # PyInstaller
 #################################################################################  Usually these files are written by a python script from a template

.gitlab-ci.yml

@@ -8,6 +8,7 @@ services:
 stages:
   - build
   - test
+  - coverage
   - cleanup
 
 build:
@@ -18,19 +19,49 @@ build:
     - docker build --pull -t "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME" .
     - docker push "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME"
 
+coverage:
+  stage: coverage
+  image: registry-gitlab.pasteur.fr/bis-aria/ariaec:master
+  script:
+    - pytest --cov=aria
+  coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
+  artifacts:
+    paths:
+      - htmlcov/
+
+
+coverage:
+    stage: coverage
+    script:
+        - nosetests -c .noserc -q --cover-html-dir=build --cover-html
+        - coverage report -m
+    coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
+    artifacts:
+        paths:
+            - build
+
 pages:
   image: registry-gitlab.pasteur.fr/bis-aria/ariaec:master
+  dependencies:
+    - coverage
   script:
     - cd ${CI_PROJECT_DIR}/docs/
     - make html
     - cd ${CI_PROJECT_DIR}
     - mv ${CI_PROJECT_DIR}/docs/_build/html/ public
+    - mv htmlcov public/
   artifacts:
     paths:
       - public
   only:
     - master
 
+pytest:
+  image: registry-gitlab.pasteur.fr/bis-aria/ariaec:master
+  stage: test
+  script:
+    - pytest -sx --doctest-modules --doctest-ignore-import-errors --cov=aria
+
 # unittest:
 #   image: registry-gitlab.pasteur.fr/bis-aria/ariaec:master
 #   stage: test

Dockerfile

@@ -4,7 +4,7 @@ MAINTAINER Fabrice Allain <fabrice.allain@pasteur.fr>
 RUN yum install -y epel-release
 RUN yum install -y python2-pip python-devel gcc make
 
-RUN pip install --upgrade pip ; pip install --upgrade setuptools; pip install sphinx; pip install numpy; pip install matplotlib
+RUN pip install --upgrade pip ; pip install --upgrade setuptools; pip install sphinx; pip install numpy; pip install matplotlib; pip install coverage;
 
 RUN mkdir build-aria
 ADD aria /build-aria/aria

PKG-INFO

-Version: 0.2.3
+Version: 0.0.17

README.rst

+de Novo Ambiguous Restraints for Iterative Assignment
+=====================================================
+
+**A pipeline for automated de novo contact map assignment**
+
+|Pipeline status| |Coverage report|
+
+``ariaec``  is a Python_ library that provides *de novo* structure prediction
+based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
+
+The package add several command line interfaces aside the usual ARIA commands in
+ order to convert data, setup an ARIA project with evolutionary restraints,
+ analyze contact maps or protein structures and generate statistics from a culled
+ list of PDB files. An exhaustive list of the commands is available in the
+ section
+``nbsphinx`` is a Sphinx_ extension that provides a source parser for
+``*.ipynb`` files.
+Custom Sphinx directives are used to show `Jupyter `_ code cells (and of
+course their results) in both HTML and LaTeX output.
+Un-evaluated notebooks -- i.e. notebooks without stored output cells -- will be
+automatically executed during the Sphinx build process.
+
+Quick Start:
+------------
+    #. Be sure to check if ``pip`` (>= 9.0), ``setuptools`` (>= 18.0), ``numpy``
+(>= 1.11) and ``matplotlib`` are actually instaled in your personnal python
+installation or virtual environment.
+
+    #. Download the ``zip`` or ``tar`` version at https://gitlab.pasteur.fr/bis-aria/ariaec
+
+    #. Edit your ``index.rst`` and add the names of your ``*.ipynb`` files
+       to the ``toctree``.
+
+    #. Run Sphinx!
+
+Online documentation (and example of use):
+    http://nbsphinx.readthedocs.io/
+
+Source code repository (and issue tracker):
+    https://github.com/spatialaudio/nbsphinx/
+
+License:
+--------
+.. MIT -- see the file ``LICENSE`` for details.
+
+.. Hyperlinks
+.. _ARIA: http://aria.pasteur.fr
+.. _Python: https://www.python.org
+.. _Sphinx: http://sphinx-doc.org/
+.. _Jupyter Notebook: http://jupyter.org/

aria.shub

@@ -4,7 +4,7 @@ FROM: centos:centos7
 %labels
 	maintainer Fabrice Allain <fabrice.allain@pasteur.fr>
 	package.name ariaec
-	package.version 0.2.3
+	package.version 0.1.0
 	package.homepage https://gitlab.pasteur.fr/bis-aria/ariaec
 
 %post

aria/core/JobManager.py

@@ -42,27 +42,6 @@ import subprocess
 import pkg_resources as pkgr
 
 
-def check_output(*popenargs, **kwargs):
-    r"""Run command with arguments and return its output as a byte string.
-
-    Backported from Python 2.7 as it's implemented as pure python on stdlib.
-
-    >>> check_output(['/usr/bin/python', '--version'])
-    Python 2.6.2
-    """
-    process = subprocess.Popen(stdout=subprocess.PIPE, *popenargs, **kwargs)
-    output, unused_err = process.communicate()
-    retcode = process.poll()
-    if retcode:
-        cmd = kwargs.get("args")
-        if cmd is None:
-            cmd = popenargs[0]
-        error = subprocess.CalledProcessError(retcode, cmd)
-        error.output = output
-        raise error
-    return output
-
-
 class PartlyUsedNodesFinder:
     def __init__(self, queue, exclude_list=None):
         if exclude_list is None:
@@ -72,7 +51,7 @@ class PartlyUsedNodesFinder:
 
     def find(self):
         # Retrieve qstat -f result and split in lines
-        qstat_array = check_output(['qstat', '-f']).split('\n')[:-1]
+        qstat_array = subprocess.check_output(['qstat', '-f']).split('\n')[:-1]
         # Filter results for the appropiate queue
         qstat_array = filter(lambda x: self.queue in x, qstat_array)
         # split qstat -f row into columns

aria/core/ccpn2top.py

@@ -41,7 +41,6 @@ from .Topology import Topology, BaseResidueSettings, BaseResidue, \
 
 # TODO [FALLAIN] works with py3 ?
 from ccp.general.Io import getChemComp
-
 from memops.api import Implementation
 
 # TODO [FALLAIN] lines below not used if installation done with setuptools

aria/core/legacy/AminoAcid.py

@@ -18,7 +18,7 @@ def AminoAcid(input):
             the 3-letter-code as element 1 and the name as element 2.
             all returned 1- and 3-letter codes are uppercase, the name
             is lowercase.
-    if the input is not a common amino acid, the elements 0 and 1 will be
+    if the input is not a common amino acid, the elements 0 and 1 will be empty
 
     Parameters
     ----------

aria/core/legacy/test/test_AminoAcid.py

@@ -5,14 +5,19 @@ Created on 9/16/16
 @author: fallain
 """
 import pytest
+from aria.core.legacy.AminoAcid import AminoAcid
 
-from core.legacy.AminoAcid import AminoAcid
 
-
-@pytest.fixture()
-def amino_acid_2l3l():
-    return ((),())
+@pytest.fixture(scope="module", params=[
+    'A', 'ALA', 'R', 'ARG', 'N', 'ASN', 'D', 'ASP', 'C', 'CYS', 'Q', 'GLN', 'E',
+    'GLU', 'G', 'GLY', 'H', 'HIS', 'I', 'ILE', 'L', 'LEU', 'K', 'LYS', 'M',
+    'MET', 'F', 'PHE', 'P', 'PRO', 'S', 'SER', 'T', 'THR', 'W', 'TRP', 'Y',
+    'TYR', 'V', 'VAL'])
+def amino_acid_2l3l(request):
+    yield request.param
 
 
 def test_convert_amino_acid(amino_acid_2l3l):
-    pass
\ No newline at end of file
+    aa = AminoAcid(amino_acid_2l3l)
+    assert len(aa) == 3
+    assert aa[0]

aria/core/scientific/FortranFormat.py

@@ -21,36 +21,27 @@
 #
 
 """
-Fortran-style formatted input/output
+    Fortran-style formatted input/output
 
-This module provides two classes that aid in reading and writing
-Fortran-formatted text files.
+    This module provides two classes that aid in reading and writing
+    Fortran-formatted text files.
 
-Examples::
+    :Example:
 
-  Input::
 
-    >>>s = '   59999'
-    >>>format = FortranFormat('2I4')
-    >>>line = FortranLine(s, format)
-    >>>print(line[0])
-    >>>print(line[1])
+    >>> s = '   59999'
+    >>> format = FortranFormat('2I4')
+    >>> line = FortranLine(s, format)
+    >>> print(line[0])
+    5
+    >>> print(line[1])
+    9999
 
-  prints::
+    >>> format = FortranFormat('2D15.5')
+    >>> line = FortranLine([3.1415926, 2.71828], format)
+    >>> print(str(line))
+        3.14159D+00    2.71828D+00
 
-    >>>5
-    >>>9999
-
-
-  Output::
-
-    >>>format = FortranFormat('2D15.5')
-    >>>line = FortranLine([3.1415926, 2.71828], format)
-    >>>print(str(line))
-
-  prints::
-
-    '3.14159D+00    2.71828D+00'
 """
 
 import string

aria/core/scientific/PDB.py

@@ -6,50 +6,55 @@
 # 
 
 """
-Parsing and writing of Protein Data Bank (PDB) files
-
-This module provides classes that represent PDB (Protein Data Bank)
-files and configurations contained in PDB files. It provides access to
-PDB files on two levels: low-level (line by line) and high-level
-(chains, residues, and atoms).
-
-Caution: The PDB file format has been heavily abused, and it is
-probably impossible to write code that can deal with all variants
-correctly. This modules tries to read the widest possible range of PDB
-files, but gives priority to a correct interpretation of the PDB
-format as defined by the Brookhaven National Laboratory.
-
-A special problem are atom names. The PDB file format specifies that
-the first two letters contain the right-justified chemical element
-name. A later modification allowed the initial space in hydrogen names
-to be replaced by a digit. Many programs ignore all this and treat the
-name as an arbitrary left-justified four-character name. This makes it
-difficult to extract the chemical element accurately; most programs
-write the '"CA"' for C_alpha in such a way that it actually stands for
-a calcium atom. For this reason a special element field has been added
-later, but only few files use it. In the absence of an element field,
-the code in this module attempts to guess the element using all information
-available.
-
-The low-level routines in this module do not try to deal with the atom
-name problem; they return and expect four-character atom names
-including spaces in the correct positions. The high-level routines use
-atom names without leading or trailing spaces, but provide and use the
-element field whenever possible. For output, they use the element
-field to place the atom name correctly, and for input, they construct
-the element field content from the atom name if no explicit element
-field is found in the file.
-
-Except where indicated, numerical values use the same units and
-conventions as specified in the PDB format description.
-
-Example::
-
-  >>>conf = Structure('example.pdb')
-  >>>print(conf)
-  >>>for residue in conf.residues:
-  >>>    for atom in residue:
-  >>>        print(atom)
+    Parsing and writing of Protein Data Bank (PDB) files
+
+    This module provides classes that represent PDB (Protein Data Bank)
+    files and configurations contained in PDB files. It provides access to
+    PDB files on two levels: low-level (line by line) and high-level
+    (chains, residues, and atoms).
+
+    Caution: The PDB file format has been heavily abused, and it is
+    probably impossible to write code that can deal with all variants
+    correctly. This modules tries to read the widest possible range of PDB
+    files, but gives priority to a correct interpretation of the PDB
+    format as defined by the Brookhaven National Laboratory.
+
+    A special problem are atom names. The PDB file format specifies that
+    the first two letters contain the right-justified chemical element
+    name. A later modification allowed the initial space in hydrogen names
+    to be replaced by a digit. Many programs ignore all this and treat the
+    name as an arbitrary left-justified four-character name. This makes it
+    difficult to extract the chemical element accurately; most programs
+    write the '"CA"' for C_alpha in such a way that it actually stands for
+    a calcium atom. For this reason a special element field has been added
+    later, but only few files use it. In the absence of an element field,
+    the code in this module attempts to guess the element using all information
+    available.
+
+    The low-level routines in this module do not try to deal with the atom
+    name problem; they return and expect four-character atom names
+    including spaces in the correct positions. The high-level routines use
+    atom names without leading or trailing spaces, but provide and use the
+    element field whenever possible. For output, they use the element
+    field to place the atom name correctly, and for input, they construct
+    the element field content from the atom name if no explicit element
+    field is found in the file.
+
+    Except where indicated, numerical values use the same units and
+    conventions as specified in the PDB format description.
+
+    :Example:
+
+    >>> conf = Structure('examples/werner/result/hrdc_10_water.pdb')
+    >>> print(conf)
+    Structure('examples/werner/result/hrdc_10_water.pdb'):
+      Peptide chain of length 91
+    <BLANKLINE>
+    >>> for residue in conf.residues:
+    ...     for atom in residue:
+    ...         pass
+    >>> print(atom)
+    Atom OT2 at [7.831 6.168 6.392]
 
 @undocumented: atom_format
 @undocumented: anisou_format

docs/conf.py

@@ -37,7 +37,8 @@ extensions = [
     'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon'
+    'sphinx.ext.napoleon',
+    'sphinx.ext.nbsphinx'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -53,20 +54,22 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'ARIA'
-copyright = u'2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin,' \
-            u' Wolfgang Rieping, and Michael Nilges'
+project = u'ARIAEC'
+import time
 author = u'Benjamin Bardiaux, Michael Habeck, Therese Malliavin, ' \
          u'Wolfgang Rieping, and Michael Nilges'
+copyright = u'{}, {}'.format(
+    time.strftime("%Y"), author)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'2'
+import setup
+version = setup.get_version()
 # The full version, including alpha/beta/rc tags.
-release = u'4'
+release = setup.get_version()
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -78,7 +81,7 @@ language = None
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

docs/contents.rst

-.. _contents:
-
-Sphinx documentation contents
-=============================
-
-.. toctree::
-   :maxdepth: 2
-
-   installation
-   tutorial
-   modules
-
-   copyright
-
-
-Indices and tables
-==================
-
-.. only:: builder_html
-
-   * :ref:`genindex`
-   * :ref:`modindex`
-   * :ref:`search`
-   * :ref:`glossary`
-
-.. only:: not builder_html
-
-   * :ref:`modindex`
-   * :ref:`glossary`
\ No newline at end of file

docs/index.rst

@@ -3,13 +3,19 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to ARIAEC's documentation!
-==================================
+
+.. include:: ../README.rst
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+   :maxdepth: 1
+   :caption: Contents
 
+   introduction
+   changelog
+   installation
+   tutorial
+   examples/index
+   api
 
 
 Indices and tables

setup.cfg

@@ -5,3 +5,9 @@
 universal=1
 [egg_info]
 # tag_build = .dev
+[aliases]
+test=pytest
+[tool:pytest]
+log_print=no
+log_cli=no
+log_level=info
\ No newline at end of file

setup.py

@@ -192,8 +192,10 @@ def setup_package():
         setup_requires=[
             # Setuptools 18.0 properly handles Cython extensions.
             'setuptools>=18.0',
-            'cython'
+            'cython',
+            'pytest-runner'
         ],
+        tests_requires=['pytest', 'pytest-cov'],
         # Project uses reStructuredText, so ensure that the docutils get
         # installed or upgraded on the target machine
         install_requires=[
@@ -219,6 +221,7 @@ def setup_package():
             'tqdm',
             'hdbscan',
             'conkit',
+            'nbsphinx',
             # 'scikit-bio'          Doesn't works with python 2.7. Only 3.4 +
         ],
         entry_points={