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61 Commits

Author SHA1 Message Date
ruff-isort
de0bb21fb3 Apply isort (forcing single lines, not sorting by type) via ruff 
$ ruff check --fix --select=I \
  --config=lint.isort.force-single-line=true \
  --config=lint.isort.order-by-type=false \
  BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py

Using ruff version 0.4.10
 2024-06-26 15:31:39 +09:00
Peter Cock
0938871295 black v23.9.1 
Had to tweak four conflicts with D202
 2023-10-05 08:47:54 +01:00
mdehoon
e812f38bfb replace numpy by np in some test scripts (#4418) 
* update

* update

* update

* update

* update

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---------

Co-authored-by: Michiel de Hoon <mdehoon@madpc2s-MacBook-Pro.local>
 2023-08-14 18:31:48 +09:00
Adam Vandergriff
8d9d20d09c change test_cluster type to builtin float 2022-12-22 10:08:02 +00:00
Adam Vandergriff
3b4804d79c fixed additional instance of deprecated type 2022-12-22 10:08:02 +00:00
Sergio
7dc2fb357c Apply black style to test_Cluster.py, version 19.10b0. (#3089) 
* Apply black style to test_Cluster.py, version 19.10b0.
* disable black format on some matrices to preserve line breaks
 2020-07-24 11:39:00 +01:00
mdehoon
fef0cae7c7 update test_Cluster.py for python3 (#2658) 2020-02-09 17:30:23 +09:00
Peter Cock
34dbd86f7d Avoid flake8 str concatenation warning 2019-12-28 19:20:44 +00:00
mdehoon
0f10cf5657 fix indentation (#2452) 2019-12-28 22:57:27 +09:00
mdehoon
12f7276f7a convert Bio.Cluster to python3 only (#2451) 
* convert Bio.Cluster to python3 only
* report NaN
 2019-12-28 11:29:01 +00:00
mdehoon
98bb06c7fb fix clustercentroids (#2231) 
* fix clustercentroids

* adding tests for clustercentroids

* getting started on transpose

* starting Transpose=True

* add checks for transpose=True

* make travis happy
 2019-08-29 12:56:13 +09:00
unify
1b9e569a7f Using tool unify to convert Tests/ to use double quotes 
Using https://github.com/myint/unify for this:

$ unify --quote \" --in-place Tests/*.py Tests/*/*.py
 2019-08-02 14:10:22 +01:00
peterjc
e4fc1f9511 flake8 E241 - fixed with autopep8 
autopep8 -i --select E241 *.py
 2019-04-23 10:35:56 +01:00
peterjc
846c8f1cc6 flake8 D100: Automatically added docstrings 
Done with the following ad-hoc script:

"""In-place fix for D100 Missing docstring in public module."""
import os
import sys

def fix(lines, docstring):
    answer = []
    # 0 = preamble
    # 1 = waiting for it
    # 2 = seen module docstring
    state = 0
    for line in lines:
        if state == 0 and line.startswith("#") or not line.strip():
            # hashbang or licence block
            pass
        elif state == 0 and line.lstrip().startswith('"""'):
            state = 2
        elif state == 2:
            pass
        else:
            # Insert docstring
            answer.append('"""%s"""\n\n' % docstring)
            state = 2
        answer.append(line)
    return answer

for f in sys.argv[1:]:
    print(f)
    with open(f) as handle:
        old = list(handle)
    name = os.path.basename(f)
    assert name.endswith(".py")
    name = name[:-3].replace("_", " ")
    if name.startswith("test "):
        name = "Tests for %s" % name[5:]
    if not name.endswith(" tool"):
        name += " module"
    new = fix(old, name + ".")
    with open(f, "w") as handle:
        for line in new:
            handle.write(line)
print("Done")
 2019-04-23 10:27:31 +01:00
peterjc
6825235bac flake8 E303 too many blank lines 2018-11-21 13:59:22 +00:00
Michiel de Hoon
158bb2e02e add test using default weight 2018-11-21 13:59:22 +00:00
Sergio
1268821636 Fill in missing licence headers in Python files (#1714) 
This avoids changing files which should be ready to dual license.
 2018-07-11 08:57:12 +01:00
peterjc
ae31f56d1b Need to test for numpy in test_Cluster.py 
Even if we have a numpy check in Bio.Cluster, due
to the way it gets imported in the test we need
to have our own check her first anyway.
 2018-06-22 11:44:20 +01:00
mdehoon
12341ae713 Cluster tests (#1631) 
* fix documentation, cleanup, and one bug fix

* cosmetic changes only

* fixing Travis errors

* fixing Travis errors

* fixing Travis errors

* fixing Travis errors

* rewrote Tree index code
 2018-04-29 15:30:26 +09:00
mdehoon
1b2d7dfc87 Cluster version 1.55, first trial (#1599) 
Updating to the C Clustering Library version 1.55. This allows compiling Bio.Cluster without numpy being present (numpy is still needed at runtime).
 2018-04-14 10:01:54 +09:00
Peter Cock
c9721f453e PEP8 whitespace 2017-08-21 10:49:34 +01:00
Michiel de Hoon
9f7fd3eb4c C Clustering Library 1.53. This adds the sort method to Trees, improves the cut method, and fixes some minor bugs. 2017-08-19 15:24:51 +09:00
Peter Cock
fd1c57adb4 autopep8 --in-place --select E305 Tests/*.py 
Taking advantage of autopep8 being updated to fix
https://github.com/hhatto/autopep8/issues/304
 2017-04-20 17:15:31 +01:00
peterjc
e5bbe09052 Remove duplicated line, my mistake 2017-02-08 11:11:35 +00:00
Adam Novak
2a3735a591 Not using lambdas just to pass arguments to assertEquals. 2017-02-08 10:29:42 +00:00
Peter Cock
a112181dfc Fix remaining pep8 E124 failures under Tests/ 2016-06-15 11:01:14 +01:00
Peter Cock
ae8b8ecbfb Avoid naked except clauses. 
Would also catch KeyboardInterupt, rightly flagged by QualifiedCode.com
as worth fixing.

Also minor PEP8 white space fixes.
 2016-01-04 20:45:18 +09:00
Peter Cock
838a8e1984 Selective use of autopep8 to remove whitespace after commas 
Numerous examples still present where the white space is used
to make a data-structure much easier to read (arrays etc).

Part of tackling GitHub issue #406
 2015-01-07 04:43:14 +00:00
Peter Cock
a87df70051 PEP8 white space in Tests 
autopep8 --select E225,E226,E261,E302 -i Tests/*.py
 2015-01-04 04:24:47 +00:00
carlosp420
db6bc30338 PEP8 fixes rest of test files 2014-11-16 22:13:26 +09:00
Peter Cock
b67cebf60e Fix common PEP8 violation in unittest verbosity argument 2014-11-11 14:38:37 +09:00
peterjc
b0496b342e autopep8 E203 - Remove extraneous whitespace (colon related) 
$ autopep8 -r -i --select E203 ...

Note did not apply changes to e.g. Tests/test_Crystal.py and
Bio/SCOP/Raf.py where colon used for numpy array access, nor
auto-generated files like Bio/SubsMat/MatrixInfo.py
 2014-10-27 14:28:03 +00:00
peterjc
82272b1f36 autopep8 E265 - Format block comments. 
$ autopep8 --version
autopep8 1.0.4
$ autopep8 -r -i --select E265 ...
 2014-10-27 14:27:12 +00:00
peterjc
c7811df35b Test Bio.Cluster error handling. 
See previous commit and also Debian issue https://bugs.debian.org/751277
where this part of the C code was failing on Python 3 under PowerPC,
dicussion also CC'd to the Biopython mailing list.

This closes GitHub issue #340.
 2014-08-30 13:33:47 +09:00
Peter Cock
3e0f34a2ad Switch import testing order for Bio.Cluster test 2014-04-27 13:15:12 +01:00
peterjc
14977ce666 Apply 2to3 ws_comma fixer (white space changes) 
$ 2to3 --no-diffs -n -w -f ws_comma Bio BioSQL Tests Doc Scripts
 2013-10-05 13:59:54 +01:00
Christian Brueffer
87a3a3ae92 Remove superfluous commas. 2013-03-29 17:44:19 +00:00
Christian Brueffer
fd82a0a7a7 Add blank lines where needed (PEP8 E302). 2012-12-06 10:43:43 +08:00
Christian Brueffer
9dfec35649 Zap redundant backslashes between brackets (PEP8 E502). 2012-12-05 10:14:03 +00:00
Christian Brueffer
9c76921b91 Remove excessive blank lines (PEP8 E303). 2012-12-05 09:22:22 +00:00
Christian Brueffer
b1c859788e Trim EOL whitespace (PEP8 W291, W293), batch 3. 2012-12-04 19:22:28 +08:00
Christian Brueffer
5192d13e01 Fix whitespace before and after operators (PEP8 E221 and E222). 
Whitespace was left intact in places where it helps readability.
 2012-12-04 09:02:37 +00:00
Christian Brueffer
145615b416 Avoid chaining commands by ";" and ";" at the end of statements. 
Fixes PEP8 E702 multiple statements on one line (semicolon)
 2012-12-03 19:30:45 +08:00
Michiel de Hoon
750e1b602a C Clustering Library version 1.50. Can be used with Python 3 2010-12-25 10:52:38 +09:00
peterjc
cb1f54499c Use ImportError subclass for missing Python dependencies (see Gentoo Bug 313125 with pydoc) 2010-10-18 14:40:43 +01:00
Michiel de Hoon
f53f212808 C Clustering Library version 1.49; Don't test eigenvectors for eigenvalues equal to zero 2010-04-05 22:05:39 +09:00
mdehoon
f05f8b5194 C Clustering Library version 1.48; adding better support for principal component analysis. 2010-03-29 12:49:55 +09:00
Peter
9252f1c129 No code changes. Removing white space before ':' character to match PEP8. Added a few missing license statements too. 2009-11-11 11:44:41 +00:00
mdehoon
fd3059dca8 C Clustering Library version 1.46. 2009-05-30 07:47:41 +00:00
mdehoon
8c8545b5b0 Simplifying test_Cluster.py. 2009-02-03 12:06:29 +00:00