Merge pull request #41 from pombo-lab/v2.0.0-dev

V2.0.0 dev

.gitignore

@@ -9,6 +9,8 @@
 *.pyc
 *.pyd
 *.c
+lib/gamtools/cosegregation_internal.cpp
+lib/gamtools/mirnylib_numutils_internal.cpp
 
 # Packages #
 ############
@@ -47,9 +49,11 @@ docs/_build
 # py.test #
 ###########
 .cache/
+.pytest_cache/
 
 # tox #
 ###########
 .tox/
 .coverage
 .python-version
+coverage.xml

.pylintrc

@@ -34,15 +34,6 @@ unsafe-load-any-extension=no
 # run arbitrary code
 extension-pkg-whitelist=gamtools, numpy
 
-# Allow optimization of some AST trees. This will activate a peephole AST
-# optimizer, which will apply various small optimizations. For instance, it can
-# be used to obtain the result of joining multiple strings with the addition
-# operator. Joining a lot of strings can lead to a maximum recursion error in
-# Pylint and this flag can prevent that. It has one side effect, the resulting
-# AST will be different than the one from reality. This option is deprecated
-# and it will be removed in Pylint 2.0.
-optimize-ast=no
-
 
 [MESSAGES CONTROL]
 
@@ -65,7 +56,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=import-star-module-level,old-octal-literal,oct-method,print-statement,unpacking-in-except,parameter-unpacking,backtick,old-raise-syntax,old-ne-operator,long-suffix,dict-view-method,dict-iter-method,metaclass-assignment,next-method-called,raising-string,indexing-exception,raw_input-builtin,long-builtin,file-builtin,execfile-builtin,coerce-builtin,cmp-builtin,buffer-builtin,basestring-builtin,apply-builtin,filter-builtin-not-iterating,using-cmp-argument,useless-suppression,range-builtin-not-iterating,suppressed-message,no-absolute-import,old-division,cmp-method,reload-builtin,zip-builtin-not-iterating,intern-builtin,unichr-builtin,reduce-builtin,standarderror-builtin,unicode-builtin,xrange-builtin,coerce-method,delslice-method,getslice-method,setslice-method,input-builtin,round-builtin,hex-method,nonzero-method,map-builtin-not-iterating,no-member,fixme,anomalous-backslash-in-string,too-many-public-methods,no-self-use,useless-object-inheritance
+disable=no-member,fixme,anomalous-backslash-in-string,too-many-public-methods,useless-object-inheritance,superfluous-parens,consider-using-with,unsubscriptable-object,consider-using-f-string,unspecified-encoding
 
 
 [REPORTS]
@@ -75,12 +66,6 @@ disable=import-star-module-level,old-octal-literal,oct-method,print-statement,un
 # mypackage.mymodule.MyReporterClass.
 output-format=text
 
-# Put messages in a separate file for each module / package specified on the
-# command line instead of printing them on stdout. Reports (if any) will be
-# written in a file name "pylint_global.[txt|html]". This option is deprecated
-# and it will be removed in Pylint 2.0.
-files-output=no
-
 # Tells whether to display a full report or only the messages
 reports=yes
 
@@ -118,63 +103,33 @@ property-classes=abc.abstractproperty
 # Regular expression matching correct function names
 function-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for function names
-function-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct variable names
 variable-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for variable names
-variable-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct constant names
 const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
 
-# Naming hint for constant names
-const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
 # Regular expression matching correct attribute names
 attr-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for attribute names
-attr-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct argument names
 argument-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for argument names
-argument-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct class attribute names
 class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
 
-# Naming hint for class attribute names
-class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
 # Regular expression matching correct inline iteration names
 inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
 
-# Naming hint for inline iteration names
-inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
-
 # Regular expression matching correct class names
 class-rgx=[A-Z_][a-zA-Z0-9]+$
 
-# Naming hint for class names
-class-name-hint=[A-Z_][a-zA-Z0-9]+$
-
 # Regular expression matching correct module names
 module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 
-# Naming hint for module names
-module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
 # Regular expression matching correct method names
 method-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for method names
-method-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression which should only match function or class names that do
 # not require a docstring.
 no-docstring-rgx=^_
@@ -202,12 +157,6 @@ ignore-long-lines=^\s*(# )?<?https?://\S+>?$
 # else.
 single-line-if-stmt=no
 
-# List of optional constructs for which whitespace checking is disabled. `dict-
-# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
-# `trailing-comma` allows a space between comma and closing bracket: (a, ).
-# `empty-line` allows space-only lines.
-no-space-check=trailing-comma,dict-separator
-
 # Maximum number of lines in a module
 max-module-lines=1000
 

.travis.yml

@@ -1,15 +1,15 @@
 language: python
 python:
-  - '2.7'
-  - '3.5'
-  - '3.6'
-install:
-  - pip install --upgrade pip setuptools
-  - pip install tox tox-travis coveralls codeclimate-test-reporter
+  - '3.8'
+  - '3.9'
+before_install:
+  - pip3 install --upgrade pip setuptools
+  - pip3 install tox tox-travis cython codecov
+  - if [ $TRAVIS_PYTHON_VERSION -ne "3.7" ]; then pip3 install codeclimate-test-reporter; fi
 script:
   - tox
 after_success:
-  - coveralls
+  - codecov
 deploy:
   provider: pypi
   user: rob.beagrie

CHANGELOG.md

@@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.0.0] - 2020??
+### Added
+- Allow the doit dependencies database to be reset
+- Calculate coverage on individual bamfiles instead of all at once
+- Calculate intrinsic bias of a contact matrix
+- Added functions for calculating normalized pointwise mutual information (NPMI)
+- Added a CONTRIBUTORS file
+
+### Changed
+- Changed default matrix type from Dprime to NPMI
+- Use base-pair instead of read-count coverage for window calling
+- Use Orphan windows algorithm to call positive windows
+
 ## [1.1.1] - 2019-02-08
 ### Added
 - Added a CHANGELOG

CONTRIBUTORS.md

@@ -0,0 +1,8 @@
+Contributors
+============
+
+- Robert A. Beagrie
+- Alexander Kukalev
+- Thomas M. Sparks
+- Antonio Scialdone
+- Carlo Annunziatella

MANIFEST.in

@@ -1,5 +1,5 @@
 include README.md
-include lib/gamtools/*.pyx
 include lib/gamtools/tests/*.py
 include lib/gamtools/data/examples/*
 include lib/gamtools/data/scripts/*
+exclude lib/gamtools/*.pyx