New upstream version 1.76+dfsg (95c11d7f) · Commits · Debian Med / python-biopython

.flake8

+6 −6

Original line number	Diff line number	Diff line
		@@ -40,20 +40,19 @@ ignore =
		# =========================================
		# Optional ignores for local installations:
		# =========================================
		BLK100, # Black would make changes, only on local installations (so far)
		PIE781, # Assigning to temp variable and then returning, not enforcing

		# ========================
		# Folder specific ignores:
		# ========================
		per-file-ignores =
		Bio/*:E122,E126,F401,F841,D105,B009,B010,B011,C812,C815
		Tests/*:F401,F841,D101,D102,D103,B009,B010,B011,C812
		Bio/*:E122,E126,F401,F841,D105,B009,B010,B011,C812,C815,BLK100
		Tests/*:F401,F841,D101,D102,D103,B009,B010,B011,C812,BLK100

		# Due to a bug in flake8, we need the following lines for running the
		# pre-commit hook. If you made edits above, please change also here!
		/Bio/*:E122,E126,F401,F841,D105,B009,B010,B011,C812,C815
		/Tests/*:F401,F841,D101,D102,D103,B009,B010,B011,C812
		/Bio/*:E122,E126,F401,F841,D105,B009,B010,B011,C812,C815,BLK100
		/Tests/*:F401,F841,D101,D102,D103,B009,B010,B011,C812,BLK100

		# =============================
		# per-file-ignores error codes:
		@@ -71,6 +70,7 @@ per-file-ignores =
		# instead callers should raise AssertionError().
		# C812 missing trailing comma
		# C815 missing trailing comma in Python 3.5+
		# BLK100 Black would make changes
		#Tests/*:F401 module imported but unused TODO? (88 occurrences)
		# F841 local variable is assigned to but never used TODO? (64 occurrences)
		# D101 missing docstring in public class (207 occurrences)
		@@ -83,7 +83,7 @@ per-file-ignores =
		# B011 do not call assert False since python -O removes these calls;
		# instead callers should raise AssertionError()
		# C812 missing trailing comma

		# BLK100 Black would make changes
		# =======================
		# flake8-quotes settings:
		# =======================

.gitignore

+6 −5

Original line number	Diff line number	Diff line
		@@ -25,7 +25,6 @@ dist
		#Ignore all compiled python files (e.g. from running the unit tests):
		*.pyc
		*.pyo
		*.py{}
		*.py-e

		#Ignore all Jython class files (present if using Jython)
		@@ -60,6 +59,8 @@ Tests/biosql.ini
		Tests/BioSQL/temp_sqlite.db
		Tests/BioSQL/temp_sqlite.db-journal
		Tests/Cluster/cyano_result*
		# Created by Tests/test_BWA_tool.py:
		Tests/out.bam

		#TODO - The Tutorial doctests should leave example files after
		#running Tests/test_Tutorial.py

.travis-tox.ini

+4 −4

Original line number	Diff line number	Diff line
		@@ -55,6 +55,7 @@ whitelist_externals =
		# (But must compile numpy for PyPy right now)
		install_command = pip install --only-binary=scipy {opts} {packages}
		deps =
		numpy
		#Lines startings xxx: are filtered by the environment.
		#Leaving py36 without any dependencies (even numpy)
		cover: coverage
		@@ -69,9 +70,7 @@ deps =
		py27,py35: mysql-connector-python-rf
		py35,py37: mysqlclient
		py27,py35,pypy: rdflib
		pypy,pypy3: numpy==1.12.1
		pypy,pypy3: mysqlclient
		py27,py35,py37: numpy
		py37: scipy
		py27: networkx
		py37: matplotlib
		@@ -101,6 +100,8 @@ deps =
		flake8-rst-docstrings
		flake8-comprehensions
		flake8-bugbear;python_version>="3.5"
		flake8-implicit-str-concat;python_version>="3.5"
		flake8-black;python_version>="3.6"
		flake8-quotes
		restructuredtext_lint
		doc8
		@@ -140,10 +141,9 @@ commands =
		python setup.py sdist --formats=gztar,zip

		[testenv:bdist_wheel]
		# This should use NumPy while compiling our C code...
		# This should not require NumPy while compiling our C code...
		skip_install = True
		deps =
		numpy
		commands =
		python setup.py bdist_wheel

.travis.yml

+68 −18

Original line number	Diff line number	Diff line
		@@ -62,31 +62,81 @@ matrix:
		- stage: test
		python: 2.7
		env: TOXENV=py27-cover
		addons:
		apt:
		packages:
		- &amd64_only_packages [ bwa, ]
		- *default_packages
		- stage: test
		python: 3.5
		env: TOXENV=py35-cover
		addons:
		apt:
		packages:
		- *amd64_only_packages
		- *default_packages
		- stage: test
		python: 3.6
		env: TOXENV=py36-cover
		addons:
		apt:
		packages:
		- *amd64_only_packages
		- *default_packages
		- stage: test
		python: 3.7
		env: TOXENV=py37-cover
		addons:
		apt:
		packages:
		- *amd64_only_packages
		- *default_packages
		- stage: test
		# TODO: Change this once a stable Python 3.8 is on TravisCI:
		python: 3.8-dev
		python: 3.8
		env: TOXENV=py38-cover
		addons:
		apt:
		packages:
		- *amd64_only_packages
		- *default_packages
		- stage: test
		python: 3.8
		env: TOXENV=py38-nocov
		arch: arm64
		services:
		addons:
		apt:
		packages:
		- stage: test
		python: 3.8
		env: TOXENV=py38-nocov
		arch: ppc64le
		- stage: test
		python: 3.8
		env: TOXENV=py38-cover
		arch: s390x
		- stage: test
		python: pypy
		env: TOXENV=pypy-nocov
		addons:
		apt:
		packages:
		- *amd64_only_packages
		- *default_packages
		- stage: test
		python: pypy3
		env: TOXENV=pypy3-nocov

		sudo: false
		addons:
		apt:
		packages:
		- bwa
		- *amd64_only_packages
		- *default_packages
		allow_failures:
		- arch: arm64

		addons:
		apt:
		packages: &default_packages
		- clustalo
		- clustalw
		- emboss
		@@ -102,8 +152,6 @@ addons:

		# We setup $HOME/bin and add it to the $PATH for extra binaries we're using.
		#
		# There is a phyml Ubuntu package, but currently too old.
		#
		# There is no GenePop Ubuntu pacakge, although it is in BioConda.
		#
		# We also need DSSP for testing but it is not available in the repositories.
		@@ -114,26 +162,28 @@ before_install:
		- pushd $HOME
		- mkdir -p bin
		- export PATH=$HOME/bin:$PATH
		- echo "Installing PhyML"
		- curl -L -O http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip
		- unzip PhyML-3.1.zip
		- mv PhyML-3.1/PhyML-3.1_linux64 bin/phyml
		#- echo "Installing dssp"
		#- curl -L -O ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
		#- mv dssp-2.0.4-linux-amd64 bin/dssp
		#- chmod a+x bin/dssp
		- echo "Installing Genepop"
		- curl -L -O https://anaconda.org/bioconda/genepop/4.5.1/download/linux-64/genepop-4.5.1-0.tar.bz2
		- \|
		if [ $TRAVIS_CPU_ARCH == amd64 ]; then
		echo "Installing Genepop"
		curl -L -O https://anaconda.org/bioconda/genepop/4.5.1/download/linux-64/genepop-4.5.1-0.tar.bz2
		# This will create ./bin/Genepop and a harmless ./info/ folder.
		- tar -jxvf genepop-4.5.1-0.tar.bz2
		tar -jxvf genepop-4.5.1-0.tar.bz2
		fi
		# Setup environment for t-coffee
		- mkdir -p $HOME/tcoffee_temp
		- export HOME_4_TCOFFEE=$HOME/tcoffee_temp
		- popd
		- cp Tests/biosql.ini.sample Tests/biosql.ini
		- psql -c "create database biosql_test;" -U postgres
		- psql -c "create user biosql_user with encrypted password 'biosql_pass';" -U postgres
		- psql -c "grant all privileges on database biosql_test to biosql_user;" -U postgres
		- \|
		if [ $TRAVIS_CPU_ARCH == amd64 ]; then
		psql -c "create database biosql_test;" -U postgres
		psql -c "create user biosql_user with encrypted password 'biosql_pass';" -U postgres
		psql -c "grant all privileges on database biosql_test to biosql_user;" -U postgres
		fi


		# This is minimal and used under all stages

Bio/Align/Applications/_Dialign.py

+9 −9

Original line number	Diff line number	Diff line
		@@ -48,7 +48,7 @@ class DialignCommandline(AbstractCommandline):
		self.parameters = \
		[
		_Switch(["-afc", "afc"],
		"Creates additional output file '*.afc' "
		r"Creates additional output file '\*.afc' "
		"containing data of all fragments considered "
		"for alignment WARNING: this file can be HUGE !"),
		_Switch(["-afc_v", "afc_v"],
		@@ -70,7 +70,7 @@ class DialignCommandline(AbstractCommandline):
		_Switch(["-fa", "fa"],
		"Additional output file in FASTA format."),
		_Switch(["-ff", "ff"],
		"Creates file *.frg containing information about all "
		r"Creates file \*.frg containing information about all "
		"fragments that are part of the respective optimal "
		"pairwise alignmnets plus information about "
		"consistency in the multiple alignment"),
		@@ -78,10 +78,10 @@ class DialignCommandline(AbstractCommandline):
		"Output files are named <out_file>.<extension>.",
		equate=False),
		_Switch(["-fop", "fop"],
		"Creates file *.fop containing coordinates of all "
		r"Creates file \*.fop containing coordinates of all "
		"fragments that are part of the respective pairwise alignments."),
		_Switch(["-fsm", "fsm"],
		"Creates file *.fsm containing coordinates of all "
		r"Creates file \*.fsm containing coordinates of all "
		"fragments that are part of the final alignment"),
		_Switch(["-iw", "iw"],
		"Overlap weights switched off (by default, overlap "
		@@ -104,7 +104,7 @@ class DialignCommandline(AbstractCommandline):
		checker_function=lambda x: isinstance(x, int),
		equate=False),
		_Switch(["-lo", "lo"],
		"(Long Output) Additional file *.log with information "
		r"(Long Output) Additional file \*.log with information "
		"about fragments selected for pairwise alignment and "
		"about consistency in multi-alignment procedure."),
		_Switch(["-ma", "ma"],
		@@ -112,10 +112,10 @@ class DialignCommandline(AbstractCommandline):
		"N-fragments if nucleic acid sequences are aligned."),
		_Switch(["-mask", "mask"],
		"Residues not belonging to selected fragments are "
		"replaced by '*' characters in output alignment "
		r"replaced by '\*' characters in output alignment "
		"(rather than being printed in lower-case characters)"),
		_Switch(["-mat", "mat"],
		"Creates file *mat with substitution counts derived "
		r"Creates file \*mat with substitution counts derived "
		"from the fragments that have been selected for alignment."),
		_Switch(["-mat_thr", "mat_thr"],
		"Like '-mat' but only fragments with weight score "
		@@ -150,7 +150,7 @@ class DialignCommandline(AbstractCommandline):
		"are used only if up to 35 sequences are aligned since "
		"calculating overlap weights is time consuming)."),
		_Switch(["-pst", "pst"],
		"'print status'. Creates and updates a file *.sta with "
		r"'print status'. Creates and updates a file \*.sta with "
		"information about the current status of the program "
		"run. This option is recommended if large data sets "
		"are aligned since it allows the user to estimate the "
		@@ -161,7 +161,7 @@ class DialignCommandline(AbstractCommandline):
		"alignment or alignment of translated DNA fragments "
		"at the expense of sensitivity."),
		_Option(["-stars", "stars"],
		"Maximum number of '*' characters indicating degree "
		r"Maximum number of '\*' characters indicating degree "
		"of local similarity among sequences. By default, no "
		"stars are used but numbers between 0 and 9, instead.",
		checker_function=lambda x: x in range(0, 10),