Merge pull request #175 from alexdb27/master

Fix few bugs and bump to v1.4.0
pierrepo · Jan 27, 2021 · 1aea178 · 1aea178
2 parents ba12909 + 10877bd
commit 1aea178
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diff --git a/.zenodo.json b/.zenodo.json
@@ -1,13 +1,13 @@
 {
-    "title": "PBxplore (v1.3.8): A program to explore protein structures with Protein Blocks",
+    "title": "PBxplore (v1.4.0): A program to explore protein structures with Protein Blocks",
     "creators": [{
         "name": "Barnoud, Jonathan",
         "orcid": "0000-0003-0343-7796"
-    }, 
+    },
     {
         "name": "Santuz, Hubert",
         "orcid": "0000-0001-6149-9480"
-    }, 
+    },
     {
         "name": "de Brevern, Alexandre G.",
         "orcid": "0000-0001-7112-5626"

diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,10 @@
 **Dev**
+
+**1.4.0**
+- Drop support for python2
+- Fix weblogo dependancy (package changed name)
+- Fix pytest
+
 **1.3.8**
 - Add and update version number in zenodo config file
 - Update authors affiliations in README
@@ -66,6 +72,3 @@
 - PBxplore is installable via pypi
 - api documentation
 - PBXplore is installable with setup.py
-
-
-
diff --git a/README.rst b/README.rst
@@ -1,7 +1,7 @@
 PBxplore
 ========
 
-.. image:: https://img.shields.io/badge/Python-2.7%203.4%203.5%203.6-brightgreen.svg
+.. image:: https://img.shields.io/badge/Python-3.6%203.8-brightgreen.svg
     :alt: Python version
     :target: https://pypi.python.org/pypi/pbxplore
 
@@ -44,7 +44,7 @@ Requirements
 
 PBxplore requires:
 
-* Python 2.7 or Python 3.x (>= 3.4)
+* Python 3.x (>= 3.6)
 * Python modules: `NumPy <http://numpy.scipy.org/>`_, `Matplotlib <http://matplotlib.org/>`_, `MDAnalysis <https://code.google.com/p/mdanalysis/>`_ (version >= 0.11).
 
 Optionally, PBxplore can use:
@@ -90,10 +90,10 @@ Contact & Support
 
 PBxplore is a research software and has been developped by:
 
-* Pierre Poulain, "Mitochondria, Metals and Oxidative Stress" group, Institut Jacques Monod, UMR 7592, Univ. Paris Diderot, CNRS, Sorbonne Paris Cité, France.
+* Pierre Poulain, "Mitochondria, Metals and Oxidative Stress" group, Institut Jacques Monod, UMR 7592, Univ. Paris, CNRS, France.
 * Jonathan Barnoud, University of Groningen, Groningen, The Netherlands.
 * Hubert Santuz, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France.
-* Alexandre G. de Brevern, DSIMB, INSERM, U 1134, INTS, Paris, France.
+* Alexandre G. de Brevern & Gabriel Cretin, DSIMB, INSERM, UMR_S 1134, INTS, Univ Paris, Paris, France.
 
 If you want to report a bug, request a feature,
 use the `GitHub issue system <https://github.com/pierrepo/PBxplore/issues>`_.

diff --git a/devtools/bumpversion.cfg b/devtools/bumpversion.cfg
@@ -1,9 +1,9 @@
 [bumpversion]
 commit = True
 tag = True
-current_version = 1.3.8
+current_version = 1.4.0
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
-serialize = 
+serialize =
 	{major}.{minor}.{patch}
 
 [bumpversion:file:setup.py]
@@ -18,4 +18,3 @@ serialize =
 search = **Dev**
 replace = **Dev**
 	**{new_version}**
-
diff --git a/devtools/conda/pbxplore/meta.yaml b/devtools/conda/pbxplore/meta.yaml
@@ -1,10 +1,10 @@
 package:
   name: pbxplore
-  version: "1.3.8"
+  version: "1.4.0"
 
 source:
   git_url: https://github.com/pierrepo/PBxplore.git
-  git_rev: v1.3.8
+  git_rev: v1.4.0
 
 build:
   entry_points:

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -15,8 +15,8 @@
 import sys
 import os
 
-AUTHORS = [u'Jonathan Barnoud', u'Hubert Santuz',
-           u'Alexandre G. de Brevern', u'Pierre Poulain']
+AUTHORS = ['Jonathan Barnoud', 'Hubert Santuz',
+           'Alexandre G. de Brevern', 'Pierre Poulain']
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -52,8 +52,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'PBxplore'
-copyright = u'2017, Jonathan Barnoud, Hubert Santuz, Alexandre G. de Brevern, and Pierre Poulain'
+project = 'PBxplore'
+copyright = '2017, Jonathan Barnoud, Hubert Santuz, Alexandre G. de Brevern, and Pierre Poulain'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -209,7 +209,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('ind', 'PBxploreAPI.tex', u'PBxplore API Documentation',
+  ('ind', 'PBxploreAPI.tex', 'PBxplore API Documentation',
    ' '.join(AUTHORS), 'manual'),
 ]
 
@@ -239,7 +239,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('ind', 'pbxploreapi', u'PBxplore API Documentation',
+    ('ind', 'pbxploreapi', 'PBxplore API Documentation',
      AUTHORS, 1)
 ]
 
@@ -253,7 +253,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('ind', 'PBxploreAPI', u'PBxplore API Documentation',
+  ('ind', 'PBxploreAPI', 'PBxplore API Documentation',
    ' '.join(AUTHORS), 'PBxploreAPI', 'One line description of project.',
    'Miscellaneous'),
 ]

diff --git a/doc/source/installation.rst b/doc/source/installation.rst
@@ -7,7 +7,7 @@ we try in this document to provide few guidelines regarding PBxplore setup.
 Supported Platforms
 -------------------
 
-Currently, `PBxplore` run with Python 2.7, 3.4, 3.5 and 3.6 on Linux and Mac OS X.
+Currently, `PBxplore` run with Python >=3.6 on Linux and Mac OS X.
 
 
 Dependencies
@@ -50,7 +50,7 @@ If none of the dependencies were previously installed, the installation process
     The former command will install the PBxplore command-line scripts in:
 
     - ``$HOME/.local/bin`` on Linux.
-    - ``~/Library/Python/X.Y/bin`` on Mac OSX, where ``X.Y`` stands for the Python version (for instance ``2.7`` for Python 2.7 and ``3.5`` for Python 3.5).
+    - ``~/Library/Python/X.Y/bin`` on Mac OSX, where ``X.Y`` stands for the Python version (for instance ``3.8`` for Python 3.8).
 
     Do not forget to update your ``$PATH`` environment variable to make all PBxplore tools accessible. As an example, with the Bash shell, this gives:
 

diff --git a/pbxplore/PB.py b/pbxplore/PB.py
@@ -31,7 +31,7 @@
 .. autoexception:: InvalidBlockError
 """
 
-from __future__ import print_function, absolute_import
+
 
 # Standard modules
 import os

diff --git a/pbxplore/__init__.py b/pbxplore/__init__.py
@@ -15,7 +15,7 @@
    See :func:`pbxplore.assignment.assign`
 """
 
-__version__ = "1.3.8"
+__version__ = "1.4.0"
 
 from .structure.loader import *
 from .assignment import assign
@@ -40,7 +40,7 @@ def test():
 
     #Get informations about system
     tests.system_info()
-    print("pytest version {}".format(pytest.__version__))
+    print(("pytest version {}".format(pytest.__version__)))
 
     # run pytest
     try:

diff --git a/pbxplore/analysis/compare.py b/pbxplore/analysis/compare.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Third-party module
 import numpy

diff --git a/pbxplore/analysis/count.py b/pbxplore/analysis/count.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 
 # Third-party module

diff --git a/pbxplore/analysis/neq.py b/pbxplore/analysis/neq.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Standard modules
 import math

diff --git a/pbxplore/analysis/utils.py b/pbxplore/analysis/utils.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 
 # Local module

diff --git a/pbxplore/analysis/visualization.py b/pbxplore/analysis/visualization.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Standard modules
 import os
@@ -15,14 +15,14 @@
 import matplotlib.pyplot as plt
 
 try:
-    import weblogolib
+    import weblogo
     # Weblogo compatibility
     # With version < 3.5, the color class is 'ColorGroup'. In version >= 3.5,
     # it is 'SymbolColor'. Here, we change to always have 'ColorGroup'.
     try:
-        ColorGroup = weblogolib.SymbolColor
+        ColorGroup = weblogo.SymbolColor
     except AttributeError:
-        ColorGroup = weblogolib.ColorGroup
+        ColorGroup = weblogo.ColorGroup
 except ImportError:
     IS_WEBLOGO = False
 else:
@@ -221,22 +221,22 @@ def generate_weblogo(fname, count_mat, idx_first_residue=1, residue_min=1, resid
     count = utils._slice_matrix(count_mat, idx_first_residue, residue_min, residue_max)
 
     # Create a custom color scheme for PB
-    colors = weblogolib.ColorScheme([ColorGroup("d", "#1240AB", "strand main"),
+    colors = weblogo.ColorScheme([ColorGroup("d", "#1240AB", "strand main"),
                                      ColorGroup("abcdef", "#1240AB", "strand others"),
                                      ColorGroup("ghij", "#0BD500", "coil"),
                                      ColorGroup("m", "#FD0006", "helix main"),
                                      ColorGroup("klnop", "#FD0006", "helix others")])
 
     # Load data from an occurence matrix
-    data = weblogolib.LogoData.from_counts(PB.NAMES, count)
+    data = weblogo.LogoData.from_counts(PB.NAMES, count)
 
     # Create options
-    options = weblogolib.LogoOptions(fineprint=False, logo_title=title, color_scheme=colors,
-                                     stack_width=weblogolib.std_sizes["large"],
+    options = weblogo.LogoOptions(fineprint=False, logo_title=title, color_scheme=colors,
+                                     stack_width=weblogo.std_sizes["large"],
                                      first_residue=residue_min)
 
     # Generate weblogo
-    logo = weblogolib.LogoFormat(data, options)
+    logo = weblogo.LogoFormat(data, options)
 
     # Retrieve image format
     image_format = os.path.splitext(fname)[1][1:]
@@ -245,7 +245,7 @@ def generate_weblogo(fname, count_mat, idx_first_residue=1, residue_min=1, resid
     try:
         if image_format == 'jpg':
             image_format = 'jpeg'
-        formatter = weblogolib.formatters[image_format]
+        formatter = weblogo.formatters[image_format]
     except KeyError:
         raise ValueError("Invalid format image '{0}'."
                          " Valid ones are : eps, png, pdf, jpg/jpeg, svg".format(image_format))

diff --git a/pbxplore/assignment.py b/pbxplore/assignment.py
@@ -8,7 +8,7 @@
 .. autofunction:: assign
 """
 
-from __future__ import print_function, absolute_import
+
 
 # Third-party module
 import numpy

diff --git a/pbxplore/io/fasta.py b/pbxplore/io/fasta.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Standard modules
 import os

diff --git a/pbxplore/io/write.py b/pbxplore/io/write.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Standard modules
 # import os

diff --git a/pbxplore/scripts/PBassign.py b/pbxplore/scripts/PBassign.py
@@ -8,7 +8,7 @@
 """
 
 # Use print as a function for python 3 compatibility
-from __future__ import print_function
+
 
 # Standard modules
 import os

diff --git a/pbxplore/scripts/PBcount.py b/pbxplore/scripts/PBcount.py
@@ -9,7 +9,7 @@
 
 
 # Use print as a function for python 3 compatibility
-from __future__ import print_function
+
 
 # Standard modules
 import os

diff --git a/pbxplore/scripts/PBstat.py b/pbxplore/scripts/PBstat.py
@@ -13,7 +13,7 @@
 # Modules
 # ============================================================================
 # Use print as a function for python 3 compatibility
-from __future__ import print_function
+
 
 # Standard modules
 import os
@@ -25,7 +25,7 @@
 
 # Weblogolib is an optional requirement
 try:
-    import weblogolib
+    import weblogo
 except:
     IS_WEBLOGO = False
 else:

diff --git a/pbxplore/structure/PDB.py b/pbxplore/structure/PDB.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Standard modules
 import os

diff --git a/pbxplore/structure/loader.py b/pbxplore/structure/loader.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import absolute_import, print_function
+
 import sys
 
 # Local module

diff --git a/pbxplore/structure/structure.py b/pbxplore/structure/structure.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from __future__ import print_function, absolute_import
+
 
 # Standard module
 import math

diff --git a/pbxplore/tests/__init__.py b/pbxplore/tests/__init__.py
@@ -37,7 +37,7 @@ def system_info():
     module_info("numpy")
     module_info("MDAnalysis")
     module_info("matplotlib")
-    module_info("weblogolib")
+    module_info("weblogo")
 
     py_version = sys.version.replace('\n', '')
     print("Python version {0}".format(py_version))