Add support for terminal_columns in Alignment formatting, issue 5035 by data2code · Pull Request #5070 · biopython/biopython

data2code · 2025-09-19T20:22:41Z

[ X] I hereby agree to dual licence this and any previous contributions under both
the Biopython License Agreement AND the BSD 3-Clause License.
[ X] I have read the CONTRIBUTING.rst file, have run pre-commit
locally, and understand that continuous integration checks 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
already, or do not wish to be listed. (This acknowledgement is optional.)

Modify Bio.Align.init.py to support terminal_columns. If not specified, use all available terminal columns to show the alignment, otherwise, use user-specified value. Add Tests/test_Align_Alignment_format.py.

Fix the syntax for assert in test_Align_Alignment_format.py

mdehoon · 2025-09-20T00:31:34Z

@data2code Can you have a look at the failing checks?

data2code · 2025-09-20T02:24:18Z

I don't know what's wrong. I ran "pytest Tests/test_Align_Alignment_format.py" and it was clean.

mdehoon · 2025-09-22T06:35:14Z

@data2code Have a look at the failing checks as shown on this web page.
All tests must pass, not just the new test in test_Align_Alignment_format.py.

…yle check

data2code · 2025-09-23T05:03:52Z

I believe I have fixed the style issue in the test script. The error currently is in the main code.
https://ci.appveyor.com/project/biopython/biopython/builds/52789718

I don't feel comfortable to add this new attribute to the Alignment class, as I am unfamiliar with the BioPython code base.
I am not sure I am the right person to create this PR.

peterjc · 2025-09-23T08:24:46Z

The errors look like a problem not creating an attribute when the object is created? eg

File "C:\Py\Lib\site-packages\Bio\Align\__init__.py", line 2305, in _format_pretty
    if self.terminal_columns is None:
       ^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Alignment' object has no attribute 'terminal_columns'

Black is still not happy - this could be the version of black:

black....................................................................Failed
- hook id: black
- exit code: 1

would reformat Tests/test_Align_Alignment_format.py

We still use black 24.10.0 for trailing whitespace in doctests.

mdehoon · 2025-09-23T10:36:44Z

The errors look like a problem not creating an attribute when the object is created? eg

File "C:\Py\Lib\site-packages\Bio\Align_init_.py", line 2305, in _format_pretty
> if self.terminal_columns is None:
> ^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Alignment' object has no attribute 'terminal_columns'

The Alignment class needs a class variable terminal_columns that is None by default.

data2code · 2025-09-24T04:58:25Z

Not sure what I can do here. The Pre-commit.ci gives failures without providing me the accurate feedback.

mdehoon · 2025-09-24T11:19:10Z

@data2code Check the failing tests as shown on this web page, where it says "4 failing checks"

data2code · 2025-09-24T13:16:54Z

@mdehoon I only see failure flags without details. I am not a biopython developer; instead, I am a user who made a feature request. I am afraid I have done what I can with the issue. Could someone from the developer team help take over? Thanks.

mdehoon · 2025-09-24T13:21:54Z

@data2code

Could someone from the developer team help take over?

There is no developer team. We are all just volunteers.

What happens if you click on the first failure (where it says "CI / style (pull_request)") ?

data2code · 2025-09-24T14:40:40Z

This is all I see. An error without useful details.

peterjc · 2025-09-24T17:12:09Z

Two files are not following the automated style checking using the tool black, which is part of the pre-commit checks we expect you te run locally. See https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst

peterjc · 2025-09-24T17:13:37Z

The main tests are looking better though, from AppVeyor which runs the tests on Windows:

======================================================================
ERROR: test_Align_Alignment_format
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\projects\biopython\Tests\run_tests.py", line 266, in runTest
    raise RuntimeError(f"No tests found in {name}")
RuntimeError: No tests found in test_Align_Alignment_format
----------------------------------------------------------------------
Ran 501 tests in 576.243 seconds

peterjc · 2025-09-24T17:14:47Z

Bio/Align/__init__.py

 import sys
 import types
 import warnings
+import shutil


This would ideally be a few lines up (alphabetical sorting of standard library imports).

peterjc · 2025-09-24T17:15:34Z

Bio/Align/__init__.py

        position_width = 10
-        line_width = 80
+
+        # support custom column size, see issue 5035


I think the comment is redundant and could be removed.

peterjc · 2025-09-24T17:16:38Z

Tests/test_Align_Alignment_format.py

@@ -0,0 +1,40 @@
+"""Tests for controling the number of terminal columns
+   Issue #5035
+"""


This is not formatted in the expected style, but there are bigger issues with your test.

peterjc · 2025-09-24T17:18:12Z

Tests/test_Align_Alignment_format.py

+#                   0 -||||||...||||--|...|--|...||..|-|....|..|.|--|--|||.||.|-------|--------------|.||.|---|-||---------||-------------||.|.|.|.||-. 129
+# query             0 DVQLQESGPGLVKP--SQSQSLTCTVTGYSITSDYAWNWIRQFP--GNKLEWMGYMS-------Y--------------SGSTRY---NPSLRSRISITRDTSKNQFFLQLKSVTTEDTATYFCARG-W 100
+# 
+assert (len(str(best_alignment).split("\n")) == 4), "Expecting alignment to be output as one group."


You have not defined any tests using the unittest framework, thus the error No tests found in test_Align_Alignment_format.

See https://biopython.org/docs/latest/Tutorial/chapter_testing.html

Also I think this need not be an entire new file.

data2code · 2025-09-24T17:44:42Z

@peterjc Thank you, that's very helpful.

data2code · 2025-09-24T17:57:14Z

@peterjc The test looks good on my local:

$ python Tests/test_Align_Alignment_format.py
test_terminal_columns (main.TestAlignmentFormat.test_terminal_columns) ... ok

Ran 1 test in 0.001s

OK

Any pointers for what to work on next? Thank you!

peterjc · 2025-09-24T23:08:11Z

Fix the black style. Move the test into an appropriate existing Bio.Align test file. At that point we can ask GitHub Actions to run the full test suite (and see if the Circle CI apparent timeout is related to your changes or not).

[I have not considered the value of the change itself yet, as others seem to have.]

…ack style

data2code · 2025-09-27T04:57:55Z

I believe the test error was not due to the code I added to the test file. The error was triggered by other tests in the same file.

codecov · 2025-09-27T07:09:35Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.93%. Comparing base (be97b2d) to head (9fba345).
⚠️ Report is 8 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5070      +/-   ##
==========================================
- Coverage   85.44%   77.93%   -7.52%     
==========================================
  Files         286      282       -4     
  Lines       59908    59430     -478     
==========================================
- Hits        51189    46316    -4873     
- Misses       8719    13114    +4395

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

mdehoon · 2025-09-27T12:14:49Z

Bio/Align/__init__.py

        position_width = 10
-        line_width = 80
+
+        if not hasattr(self, "terminal_columns") or self.terminal_columns is None:


It is better to have a class variable terminal_columns on the Alignment class.

data2code · 2025-09-27T21:58:10Z

@mdehoon Updated. Thanks for the suggestion.

mdehoon · 2025-09-28T01:16:04Z

@data2code Have a look at https://docs.python.org/3/tutorial/classes.html#class-and-instance-variables

data2code · 2025-09-28T02:36:08Z

Okay, move it to a class attribute. Thanks.

mdehoon · 2025-09-28T13:31:26Z

Tests/test_Align_Alignment.py

+        #                 120 .|.|.||-. 129
+        # query            92 TYFCARG-W 100
+        #
+        self.assertEqual(len(str(best_alignment).split("\n")), 12)


Why not just test str(best_alignment) explicitly (using triple quotes)?

IMHO, this test should not be checking the exact alignment itself, but instead focus on the row count. The exact alginment might be altered in the future due small changes in alignment algorithm or the naming of the "target", "query" or other small formatting changes. The exact alignment should be checked by other test cases, while this test focuses on row counts. I hope it makes sense.

If at some point some bug is introduced that causes the printed alignment to be incorrect, then your test may not capture it, if it only checks the number of lines.

The algorithm by definition generates the optimal alignment. Even if there are any changes to the algorithm, the generated optimal alignment will still be the same.

… tests

data2code · 2025-09-29T05:17:25Z

@mdehoon You have a valid point in believing the algorithm won't change, however, the formatting itself can change. E.g., someone may decided instead of using query and target, print Q and T instead. Then this test will break. Anyway, this test is to check the alignment layout, not the exact content of the alignment itself. There are other tests that change the validity of the content of the alignment. I think it's best for this test to focus on the formatting not the content. If it is okay with everyone, we should close this thread. I have learned a lot from this PR, thank you and Peter for your patience! Really appreciate all the guidance and feedback.

Add support for terminal_columns in Alignment formatting, issue 5035

4ae4b5a

data2code requested a review from mdehoon as a code owner September 19, 2025 20:22

Update test_Align_Alignment_format.py

b392e42

Fix the syntax for assert in test_Align_Alignment_format.py

imporve Tests/test_Align_Alignment_format.py

3e895ef

add spaces in Tests/test_Align_Alignment_format.py required by the st…

a36be93

…yle check

check for if terminal_columns is defined in Bio/Align/__init__.py

8374c81

peterjc reviewed Sep 24, 2025

View reviewed changes

peterjc requested changes Sep 24, 2025

View reviewed changes

Improve test script to use unittest

518de3c

Move TestAlignmentFormat into Tests/test_Align_Alignment.py, fixed bl…

3a1f356

…ack style

mdehoon reviewed Sep 27, 2025

View reviewed changes

Add terminal_columns to the Alignment class as a new attribute

63a6686

move terminal_columns into a class attribute

9fba345

mdehoon reviewed Sep 28, 2025

View reviewed changes

set terminal_columns to 80 to ensure backward compatibility for other…

3dbba05

… tests

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data2code commented Sep 19, 2025

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