New upstream version 1.75+dfsg

  - SET PATH=C:\Py;C:\Py\Scripts;C:\Py\Library\bin;%PATH%

  - conda config --set always_yes yes

  - conda update conda

  - conda install setuptools numpy mysql-connector-python psycopg2 matplotlib networkx reportlab scipy coverage

  - if "PY_MAJOR_VER"=="2" conda install unittest2

# Pinning pillow==5.4.1 as version 6 breaks on current latest reportlab

# https://bitbucket.org/rptlab/reportlab/issues/176/incompatibility-with-pillow-600

  - conda install setuptools numpy psycopg2 matplotlib networkx reportlab scipy coverage pillow==5.4.1

# Pinning mysql-connector-python==8.0.13 for Python 3 as 8.0.16 breaks our tests

# https://github.com/biopython/biopython/issues/2120

# We don't install mysql-connector-python for Python 2

  - if "%PY_MAJOR_VER%"=="3" conda install mysql-connector-python==8.0.13

  - python setup.py build

test_script:

# =================================================

# flake8:

#   pycodestyle: E### (error), W### (warning)

#   pyflake:     F### (error)

# pydocstyle: D1## - Missing Docstrings

#             D2## - Whitespace Issues

#             D4## - Docstring Content issues

# flake8-bugbear: B###

# flake8-quotes: Q###

# flake8-commas: C#### (in case installed locally)

# flake8-black : BLK### (in case installed locally)

# flake8-pie : PIE### (in case installed locally)

# =================================================

[flake8]

doctests = True

# Exclude some file types and folders that shouldn't be checked:

exclude = .svn,CVS,.bzr,.hg,.git,__pycache__,.tox,.github,build,

ignore =

    # =============================================================

    # Biopython's 'standard' ignores we can agree to always accept:

    # =============================================================

    D203, # 1 blank line required before class docstring

          # deliberately ignore in favour of passing D211: No blank lines

          # allowed before class docstring

    W503, # line-break before binary operator

          # deliberately ignore (in favour of some day enforcing W504?)

    # ===========================================

    # Ignores that we have to accept for a while:

    # ===========================================

    E123, # closing bracket does not match indentation of opening bracket's line

          # TODO? (main/Bio/Tests: 3/91/31 occurrences)

    E203, # whitespace before ':'

          # gives false positives after running black, see

          # https://github.com/PyCQA/pycodestyle/issues/373

    E501, # line too long

          # Maybe we find a sensible limit, e.g. 88 (black) and enforce it

    W504, # line break after binary operator (Bio/Tests/Scripts: 225/119/7) TODO?

    B007, # Loop control variable not used within the loop body.

          # If this is intended, start the name with an underscore

    # =========================================

    # 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

    # 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

# =============================

# per-file-ignores error codes:

# =============================

#Bio/*:E122 continuation line missing indentation or outdented TODO? (264 occurrences)

#      E126 continuation line over-indented for hanging indent TODO?  (54 occurrences)

#      F401 module imported but unused TODO? (107 occurrences)

#      F841 local variable is assigned to but never used TODO? (55 occurrences)

#      D105 missing docstring magic method (121 occurrences)

#      B009 do not call getattr with a constant attribute value,

#           it is not any safer than normal property access

#      B010 do not call setattr with a constant attribute value,

#           it is not any safer than normal property access

#      B011 do not call assert False since python -O removes these calls;

#           instead callers should raise AssertionError().

#      C812 missing trailing comma

#      C815 missing trailing comma in Python 3.5+

#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)

#        D102 missing docstring in public method (956 occurrences)

#        D103 missing docstring in public functions (52 occurrences)

#        B009 do not call getattr with a constant attribute value,

#             it is not any safer than normal property access

#        B010 do not call setattr with a constant attribute value,

#             it is not any safer than normal property access

#        B011 do not call assert False since python -O removes these calls;

#             instead callers should raise AssertionError()

#        C812 missing trailing comma

# =======================

# flake8-quotes settings:

# =======================

inline-quotes = double

# MMTF is a binary file format,

Tests/PDB/4CUP.mmtf binary

# UCSC Nib files are binary:

Tests/Nib/test_bigendian.nib binary

Tests/Nib/test_littleendian.nib binary

Bio/Alphabet @peterjc

Bio/Align/* @peterjc

Bio/Align/_aligners.c @mdehoon

Bio/AlignIO/* @peterjc

Tests/test_AlignIO* @peterjc

- [ ] I hereby agree to dual licence this and any previous contributions under both

the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_.

- [ ] I have read the ``CONTRIBUTING.rst`` file and understand that AppVeyor and

TravisCI will be used to confirm the Biopython unit tests and ``flake8`` style

checks pass with these changes.

- [ ] I have read the ``CONTRIBUTING.rst`` file, have run ``flake8`` locally, and

understand that AppVeyor and TravisCI will be used to confirm the Biopython unit

tests and style checks pass with these changes.

- [ ] I have added my name to the alphabetical contributors listings in the files

``NEWS.rst`` and ``CONTRIB.rst`` as part of this pull request, am listed