AttributeError: 'TestURLConstruction' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?

[sagitter]

Hi all.

Setup

I am reporting a problem with Biopython be9f39d, Python 3.12.0~b2 in Fedora 39 (GCC-13.1.1):

Expected behaviour

No error

Actual behaviour

Python version: 3.12.0b2 (main, Jun 13 2023, 00:00:00) [GCC 13.1.1 20230511 (Red Hat 13.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-0.1.20230615gitbe9f39d.fc39.aarch64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-0.1.20230615gitbe9f39d.fc39.aarch64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
test_Entrez ... /builddir/build/BUILDROOT/python-biopython-1.82-0.1.20230615gitbe9f39d.fc39.aarch64/usr/lib64/python3.12/site-packages/Bio/Entrez/__init__.py:694: UserWarning: 
            Email address is not specified.
            To make use of NCBI's E-utilities, NCBI requires you to specify your
            email address with each request.  As an example, if your email address
            is A.N.Other@example.com, you can specify it as follows:
               from Bio import Entrez
               Entrez.email = 'A.N.Other@example.com'
            In case of excessive usage of the E-utilities, NCBI will attempt to contact
            a user at the email address provided before blocking access to the
            E-utilities.
  warnings.warn(
FAIL
test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ERROR
test_default_params (test_Entrez.TestURLConstruction.test_default_params)
Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok
test_email_warning (test_Entrez.TestURLConstruction.test_email_warning)
Test issuing warning when user does not specify email address. ... ok
test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok
test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key)
Test checking whether a Request object specifies an API key. ... ok
======================================================================
ERROR: test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILD/biopython-be9f39d56d55d3f93c113cc20d2971bd91f84426/Tests/test_Entrez.py", line 212, in test_construct_cgi_epost2
    check_request_ids(self, query, variables["id"])
  File "/builddir/build/BUILD/biopython-be9f39d56d55d3f93c113cc20d2971bd91f84426/Tests/test_Entrez.py", line 129, in check_request_ids
    testcase.assertEquals(len(params["id"]), 1)
    ^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestURLConstruction' object has no attribute 'assertEquals'. Did you mean: 'assertEqual'?
----------------------------------------------------------------------
Ran 1 test in 4.165 seconds
FAILED (failures = 1)

Steps to reproduce

Full build log: output.txt

#4312

[peterjc]

Looks like I missed that during #2319.

Do you want to submit a pull request fixing this?

[sagitter]

Sorry for late reply; following patch is working against biopython-1.81:

--- a/Tests/test_Entrez.orig.py	2023-02-13 04:07:42.000000000 +0100
+++ b/Tests/test_Entrez.py	2023-06-30 14:42:58.177365639 +0200
@@ -126,7 +126,7 @@
     :type params: dict
     :param expected: Expected set of IDs, as colleciton of strings.
     """
-    testcase.assertEquals(len(params["id"]), 1)
+    testcase.assertEqual(len(params["id"]), 1)
     ids_str = params["id"][0]
     # Compare up to ordering
     testcase.assertCountEqual(ids_str.split(","), expected)

[peterjc]

Would it be simple for you to turn that into a pull request on GitHub? For a tiny change like this I tend to do it all in their web-interface.

(I can make the change myself, but attributing it to you is more work)

[sagitter]

Would it be simple for you to turn that into a pull request on GitHub? For a tiny change like this I tend to do it all in their web-interface.

(I can make the change myself, but attributing it to you is more work)

Done