All Sphinx tests are incorrectly reported as failing

[eschluntz]

Describe the bug

Every single FAIL_TO_PASS and PASS_TO_PASS test case is being marked as a failure in the report.json for every single task from the Sphinx repo, on swebench Verified. Looking at test_output.txt it looks as if many are actually passing...

I also noticed that the patch.diff includes many changes to setup.py and tox.ini, even though for this test my agent only edited a single line (adding a comment). I'm not sure if that's intentional with the build steps for the sphinx task, or something could be wrong with my setup.

Steps/Code to Reproduce

python run.py \
  --model_name claude-sonnet-3.5 \
  --split test \
  --per_instance_cost_limit 10.0 \
  --cache_task_images \   # NOTE: i tried removing this as well and had the same results
  --data_path princeton-nlp/SWE-bench_Verified \
  --instance_filter sphinx-doc__sphinx-7454 \
  --suffix v1.1

My agent did nothing but view some files and add a comment:

THOUGHT:
Now I'll add the test comment to the first line after the shebang:
ACTION (str_replace_editor):
command:
str_replace

path:
/repo/utils/bump_version.py

old_str:
#!/usr/bin/env python3


new_str:
#!/usr/bin/env python3
# this is a test


OBSERVATION:
The file /repo/utils/bump_version.py has been edited. Here's the result of running `cat -n` on a snippet of the edited file:
     1  #!/usr/bin/env python3
     2  # this is a test
     3
     4  import argparse
     5  import os
     6  import re
     7  import sys
Review the changes and make sure they are as expected (correct indentation, no duplicate lines, etc). Edit the file again if necessary.
2024-10-04 20:32:53,980 - httpx - INFO - HTTP Request: POST https://api.anthropic.com/v1/messages "HTTP/1.1 200 OK"
THOUGHT:
Great! I've successfully added the comment "# this is a test" to the bump_version.py file. The changes look correct - the comment was inserted on line 2 right after the shebang line, with proper spacing.
No tool use. Submitting.
INFO     Found submission: 

Grading:

python -m swebench.harness.run_evaluation     \
  --split test \
  --dataset_name princeton-nlp/SWE-bench_Verified \
  --max_workers 24 \
  --predictions_path ...../all_preds.jsonl

Expected Results

For a noop change like this, I would expect all of the PASS_TO_PASS tests to pass

Actual Results

Report.json:

{
    "sphinx-doc__sphinx-7454": {
        "patch_is_None": false,
        "patch_exists": true,
        "patch_successfully_applied": true,
        "resolved": false,
        "tests_status": {
            "FAIL_TO_PASS": {
                "success": [],
                "failure": [
                    "tests/test_domain_py.py::test_parse_annotation"
                ]
            },
            "PASS_TO_PASS": {
                "success": [],
                "failure": [
                    "tests/test_domain_py.py::test_function_signatures",
                    "tests/test_domain_py.py::test_domain_py_xrefs",
                    "tests/test_domain_py.py::test_domain_py_objects",
                    "tests/test_domain_py.py::test_resolve_xref_for_properties",
                    "tests/test_domain_py.py::test_domain_py_find_obj",
                    "tests/test_domain_py.py::test_get_full_qualified_name",
                    "tests/test_domain_py.py::test_pyfunction_signature",
                    "tests/test_domain_py.py::test_pyfunction_signature_full",
                    "tests/test_domain_py.py::test_pyfunction_signature_full_py38",
                    "tests/test_domain_py.py::test_optional_pyfunction_signature",
                    "tests/test_domain_py.py::test_pyexception_signature",
                    "tests/test_domain_py.py::test_exceptions_module_is_ignored",
                    "tests/test_domain_py.py::test_pydata_signature",
                    "tests/test_domain_py.py::test_pydata_signature_old",
                    "tests/test_domain_py.py::test_pyobject_prefix",
                    "tests/test_domain_py.py::test_pydata",
                    "tests/test_domain_py.py::test_pyfunction",
                    "tests/test_domain_py.py::test_pymethod_options",
                    "tests/test_domain_py.py::test_pyclassmethod",
                    "tests/test_domain_py.py::test_pystaticmethod",
                    "tests/test_domain_py.py::test_pyattribute",
                    "tests/test_domain_py.py::test_pydecorator_signature",
                    "tests/test_domain_py.py::test_pydecoratormethod_signature",
                    "tests/test_domain_py.py::test_module_index",
                    "tests/test_domain_py.py::test_module_index_submodule",
                    "tests/test_domain_py.py::test_module_index_not_collapsed",
                    "tests/test_domain_py.py::test_modindex_common_prefix"
                ]
            },
            "FAIL_TO_FAIL": {
                "success": [],
                "failure": []
            },
            "PASS_TO_FAIL": {
                "success": [],
                "failure": []
            }
        }
    }
}

test_output.txt:

+ source /opt/miniconda3/bin/activate
++ _CONDA_ROOT=/opt/miniconda3
++ . /opt/miniconda3/etc/profile.d/conda.sh
+++ export CONDA_EXE=/opt/miniconda3/bin/conda
+++ CONDA_EXE=/opt/miniconda3/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+++ CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+++ '[' -z '' ']'
+++ export CONDA_SHLVL=0
+++ CONDA_SHLVL=0
+++ '[' -n '' ']'
+++++ dirname /opt/miniconda3/bin/conda
++++ dirname /opt/miniconda3/bin
+++ PATH=/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export PATH
+++ '[' -z '' ']'
+++ PS1=
++ conda activate
++ local cmd=activate
++ case "$cmd" in
++ __conda_activate activate
++ '[' -n '' ']'
++ local ask_conda
+++ PS1=
+++ __conda_exe shell.posix activate
+++ /opt/miniconda3/bin/conda shell.posix activate
++ ask_conda='PS1='\''(base) '\''
export PATH='\''/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
++ eval 'PS1='\''(base) '\''
export PATH='\''/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
+++ PS1='(base) '
+++ export PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export CONDA_PREFIX=/opt/miniconda3
+++ CONDA_PREFIX=/opt/miniconda3
+++ export CONDA_SHLVL=1
+++ CONDA_SHLVL=1
+++ export CONDA_DEFAULT_ENV=base
+++ CONDA_DEFAULT_ENV=base
+++ export 'CONDA_PROMPT_MODIFIER=(base) '
+++ CONDA_PROMPT_MODIFIER='(base) '
+++ export CONDA_EXE=/opt/miniconda3/bin/conda
+++ CONDA_EXE=/opt/miniconda3/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+++ CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
++ __conda_hashr
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
+ conda activate testbed
+ local cmd=activate
+ case "$cmd" in
+ __conda_activate activate testbed
+ '[' -n '' ']'
+ local ask_conda
++ PS1='(base) '
++ __conda_exe shell.posix activate testbed
++ /opt/miniconda3/bin/conda shell.posix activate testbed
+ ask_conda='PS1='\''(testbed) '\''
export PATH='\''/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3/envs/testbed'\''
export CONDA_SHLVL='\''2'\''
export CONDA_DEFAULT_ENV='\''testbed'\''
export CONDA_PROMPT_MODIFIER='\''(testbed) '\''
export CONDA_PREFIX_1='\''/opt/miniconda3'\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
+ eval 'PS1='\''(testbed) '\''
export PATH='\''/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3/envs/testbed'\''
export CONDA_SHLVL='\''2'\''
export CONDA_DEFAULT_ENV='\''testbed'\''
export CONDA_PROMPT_MODIFIER='\''(testbed) '\''
export CONDA_PREFIX_1='\''/opt/miniconda3'\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
++ PS1='(testbed) '
++ export PATH=/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export CONDA_PREFIX=/opt/miniconda3/envs/testbed
++ CONDA_PREFIX=/opt/miniconda3/envs/testbed
++ export CONDA_SHLVL=2
++ CONDA_SHLVL=2
++ export CONDA_DEFAULT_ENV=testbed
++ CONDA_DEFAULT_ENV=testbed
++ export 'CONDA_PROMPT_MODIFIER=(testbed) '
++ CONDA_PROMPT_MODIFIER='(testbed) '
++ export CONDA_PREFIX_1=/opt/miniconda3
++ CONDA_PREFIX_1=/opt/miniconda3
++ export CONDA_EXE=/opt/miniconda3/bin/conda
++ CONDA_EXE=/opt/miniconda3/bin/conda
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
++ CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ cd /testbed
+ git config --global --add safe.directory /testbed
+ cd /testbed
+ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   utils/bump_version.py

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	setup.py.orig
	tox.ini.orig

no changes added to commit (use "git add" and/or "git commit -a")
+ git show
commit aca3f825f2e4a8817190f3c885a242a285aa0dba
Merge: e9e4aa8cf a6dcbc7b6
Author: Takeshi KOMIYA <i.tkomiya@gmail.com>
Date:   Fri Apr 10 01:13:03 2020 +0900

    Merge pull request #7442 from tk0miya/7435_typehints_not_suppressed_for_class
    
    Fix #7435: autodoc_typehints doesn't suppress typehints for classes/methods

diff --cc CHANGES
index 0ac1502c5,c0370d82d..e0923b433
--- a/CHANGES
+++ b/CHANGES
@@@ -22,9 -22,9 +22,11 @@@ Bugs fixe
  * #7418: std domain: duplication warning for glossary terms is case insensitive
  * #7438: C++, fix merging overloaded functions in parallel builds.
  * #7422: autodoc: fails with ValueError when using autodoc_mock_imports
+ * #7435: autodoc: ``autodoc_typehints='description'`` doesn't suppress typehints
+   in signature for classes/methods
  * #7423: crashed when giving a non-string object to logger
 +* #7479: html theme: Do not include xmlns attribute with HTML 5 doctype
 +* #7426: html theme: Escape some links in HTML templates
  
  Testing
  --------
+ git diff aca3f825f2e4a8817190f3c885a242a285aa0dba
diff --git a/utils/bump_version.py b/utils/bump_version.py
old mode 100755
new mode 100644
index b829877b6..981f9292e
--- a/utils/bump_version.py
+++ b/utils/bump_version.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# this is a test
 
 import argparse
 import os
+ source /opt/miniconda3/bin/activate
++ _CONDA_ROOT=/opt/miniconda3
++ . /opt/miniconda3/etc/profile.d/conda.sh
+++ export CONDA_EXE=/opt/miniconda3/bin/conda
+++ CONDA_EXE=/opt/miniconda3/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+++ CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+++ '[' -z x ']'
++ conda activate
++ local cmd=activate
++ case "$cmd" in
++ __conda_activate activate
++ '[' -n '' ']'
++ local ask_conda
+++ PS1='(testbed) '
+++ __conda_exe shell.posix activate
+++ /opt/miniconda3/bin/conda shell.posix activate
++ ask_conda='PS1='\''(base) '\''
export PATH='\''/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3'\''
export CONDA_SHLVL='\''3'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_PREFIX_2='\''/opt/miniconda3/envs/testbed'\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
++ eval 'PS1='\''(base) '\''
export PATH='\''/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3'\''
export CONDA_SHLVL='\''3'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_PREFIX_2='\''/opt/miniconda3/envs/testbed'\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
+++ PS1='(base) '
+++ export PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ PATH=/opt/miniconda3/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export CONDA_PREFIX=/opt/miniconda3
+++ CONDA_PREFIX=/opt/miniconda3
+++ export CONDA_SHLVL=3
+++ CONDA_SHLVL=3
+++ export CONDA_DEFAULT_ENV=base
+++ CONDA_DEFAULT_ENV=base
+++ export 'CONDA_PROMPT_MODIFIER=(base) '
+++ CONDA_PROMPT_MODIFIER='(base) '
+++ export CONDA_PREFIX_2=/opt/miniconda3/envs/testbed
+++ CONDA_PREFIX_2=/opt/miniconda3/envs/testbed
+++ export CONDA_EXE=/opt/miniconda3/bin/conda
+++ CONDA_EXE=/opt/miniconda3/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+++ CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
++ __conda_hashr
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
+ conda activate testbed
+ local cmd=activate
+ case "$cmd" in
+ __conda_activate activate testbed
+ '[' -n '' ']'
+ local ask_conda
++ PS1='(base) '
++ __conda_exe shell.posix activate testbed
++ /opt/miniconda3/bin/conda shell.posix activate testbed
+ ask_conda='PS1='\''(testbed) '\''
export PATH='\''/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3/envs/testbed'\''
export CONDA_SHLVL='\''4'\''
export CONDA_DEFAULT_ENV='\''testbed'\''
export CONDA_PROMPT_MODIFIER='\''(testbed) '\''
export CONDA_PREFIX_3='\''/opt/miniconda3'\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
+ eval 'PS1='\''(testbed) '\''
export PATH='\''/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/miniconda3/envs/testbed'\''
export CONDA_SHLVL='\''4'\''
export CONDA_DEFAULT_ENV='\''testbed'\''
export CONDA_PROMPT_MODIFIER='\''(testbed) '\''
export CONDA_PREFIX_3='\''/opt/miniconda3'\''
export CONDA_EXE='\''/opt/miniconda3/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/miniconda3/bin/python'\'''
++ PS1='(testbed) '
++ export PATH=/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/opt/miniconda3/envs/testbed/bin:/opt/miniconda3/condabin:/opt/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export CONDA_PREFIX=/opt/miniconda3/envs/testbed
++ CONDA_PREFIX=/opt/miniconda3/envs/testbed
++ export CONDA_SHLVL=4
++ CONDA_SHLVL=4
++ export CONDA_DEFAULT_ENV=testbed
++ CONDA_DEFAULT_ENV=testbed
++ export 'CONDA_PROMPT_MODIFIER=(testbed) '
++ CONDA_PROMPT_MODIFIER='(testbed) '
++ export CONDA_PREFIX_3=/opt/miniconda3
++ CONDA_PREFIX_3=/opt/miniconda3
++ export CONDA_EXE=/opt/miniconda3/bin/conda
++ CONDA_EXE=/opt/miniconda3/bin/conda
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
++ CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ python -m pip install -e '.[test]'
Obtaining file:///testbed
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: sphinxcontrib-applehelp in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.0.4)
Requirement already satisfied: sphinxcontrib-devhelp in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.0.2)
Requirement already satisfied: sphinxcontrib-jsmath in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (2.0.1)
Requirement already satisfied: sphinxcontrib-serializinghtml in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.1.5)
Requirement already satisfied: sphinxcontrib-qthelp in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.0.3)
Requirement already satisfied: Jinja2>=2.3 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (2.11.3)
Requirement already satisfied: Pygments>=2.0 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (2.18.0)
Requirement already satisfied: docutils>=0.12 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (0.21.2)
Requirement already satisfied: snowballstemmer>=1.1 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (2.2.0)
Requirement already satisfied: babel>=1.3 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (2.16.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (0.7.11)
Requirement already satisfied: imagesize in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.4.1)
Requirement already satisfied: requests>=2.5.0 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (2.32.3)
Requirement already satisfied: setuptools in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (72.1.0)
Requirement already satisfied: packaging in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (24.1)
Requirement already satisfied: pytest in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (8.3.3)
Requirement already satisfied: pytest-cov in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (5.0.0)
Requirement already satisfied: html5lib in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.1)
Requirement already satisfied: typed_ast in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (1.5.5)
Requirement already satisfied: cython in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Sphinx==3.0.1.dev20241004) (3.0.11)
Requirement already satisfied: MarkupSafe>=0.23 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from Jinja2>=2.3->Sphinx==3.0.1.dev20241004) (2.0.1)
Requirement already satisfied: charset-normalizer<4,>=2 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx==3.0.1.dev20241004) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx==3.0.1.dev20241004) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx==3.0.1.dev20241004) (2.2.3)
Requirement already satisfied: certifi>=2017.4.17 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from requests>=2.5.0->Sphinx==3.0.1.dev20241004) (2024.8.30)
Requirement already satisfied: six>=1.9 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from html5lib->Sphinx==3.0.1.dev20241004) (1.16.0)
Requirement already satisfied: webencodings in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from html5lib->Sphinx==3.0.1.dev20241004) (0.5.1)
Requirement already satisfied: iniconfig in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from pytest->Sphinx==3.0.1.dev20241004) (2.0.0)
Requirement already satisfied: pluggy<2,>=1.5 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from pytest->Sphinx==3.0.1.dev20241004) (1.5.0)
Requirement already satisfied: exceptiongroup>=1.0.0rc8 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from pytest->Sphinx==3.0.1.dev20241004) (1.2.2)
Requirement already satisfied: tomli>=1 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from pytest->Sphinx==3.0.1.dev20241004) (2.0.1)
Requirement already satisfied: coverage>=5.2.1 in /opt/miniconda3/envs/testbed/lib/python3.9/site-packages (from coverage[toml]>=5.2.1->pytest-cov->Sphinx==3.0.1.dev20241004) (7.6.1)
Installing collected packages: Sphinx
  Attempting uninstall: Sphinx
    Found existing installation: Sphinx 3.0.1.dev20241004
    Uninstalling Sphinx-3.0.1.dev20241004:
      Successfully uninstalled Sphinx-3.0.1.dev20241004
  DEPRECATION: Legacy editable install of Sphinx[test]==3.0.1.dev20241004 from file:///testbed (setup.py develop) is deprecated. pip 25.0 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457
  Running setup.py develop for Sphinx
Successfully installed Sphinx
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ git checkout aca3f825f2e4a8817190f3c885a242a285aa0dba tests/test_domain_py.py
Updated 0 paths from 20b75ba95
+ git apply -v -
Checking patch tests/test_domain_py.py...
Applied patch tests/test_domain_py.py cleanly.
+ tox --current-env -epy39 -v -- tests/test_domain_py.py
py39: commands[0]> pytest --durations 25 tests/test_domain_py.py
============================= test session starts ==============================
platform linux -- Python 3.9.19, pytest-8.3.3, pluggy-1.5.0
cachedir: .tox/py39/.pytest_cache
libraries: Sphinx-3.0.1+/aca3f825f, docutils-0.21.2
base tempdir: /tmp/pytest-of-root/pytest-0
rootdir: /testbed
configfile: setup.cfg
plugins: cov-5.0.0
collected 28 items

tests/test_domain_py.py ......F.....................                     [100%]

=================================== FAILURES ===================================
____________________________ test_parse_annotation _____________________________

    def test_parse_annotation():
        doctree = _parse_annotation("int")
        assert_node(doctree, ([pending_xref, "int"],))
        assert_node(doctree[0], pending_xref, refdomain="py", reftype="class", reftarget="int")
    
        doctree = _parse_annotation("List[int]")
        assert_node(doctree, ([pending_xref, "List"],
                              [desc_sig_punctuation, "["],
                              [pending_xref, "int"],
                              [desc_sig_punctuation, "]"]))
    
        doctree = _parse_annotation("Tuple[int, int]")
        assert_node(doctree, ([pending_xref, "Tuple"],
                              [desc_sig_punctuation, "["],
                              [pending_xref, "int"],
                              [desc_sig_punctuation, ", "],
                              [pending_xref, "int"],
                              [desc_sig_punctuation, "]"]))
    
        doctree = _parse_annotation("Callable[[int, int], int]")
        assert_node(doctree, ([pending_xref, "Callable"],
                              [desc_sig_punctuation, "["],
                              [desc_sig_punctuation, "["],
                              [pending_xref, "int"],
                              [desc_sig_punctuation, ", "],
                              [pending_xref, "int"],
                              [desc_sig_punctuation, "]"],
                              [desc_sig_punctuation, ", "],
                              [pending_xref, "int"],
                              [desc_sig_punctuation, "]"]))
    
        # None type makes an object-reference (not a class reference)
        doctree = _parse_annotation("None")
        assert_node(doctree, ([pending_xref, "None"],))
>       assert_node(doctree[0], pending_xref, refdomain="py", reftype="obj", reftarget="None")

tests/test_domain_py.py:273: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

node = <pending_xref: <#text: 'None'>>
cls = <class 'sphinx.addnodes.pending_xref'>, xpath = ''
kwargs = {'refdomain': 'py', 'reftarget': 'None', 'reftype': 'obj'}
key = 'reftype', value = 'obj'

    def assert_node(node: Node, cls: Any = None, xpath: str = "", **kwargs: Any) -> None:
        if cls:
            if isinstance(cls, list):
                assert_node(node, cls[0], xpath=xpath, **kwargs)
                if cls[1:]:
                    if isinstance(cls[1], tuple):
                        assert_node(node, cls[1], xpath=xpath, **kwargs)
                    else:
                        assert isinstance(node, nodes.Element), \
                            'The node%s does not have any children' % xpath
                        assert len(node) == 1, \
                            'The node%s has %d child nodes, not one' % (xpath, len(node))
                        assert_node(node[0], cls[1:], xpath=xpath + "[0]", **kwargs)
            elif isinstance(cls, tuple):
                assert isinstance(node, (list, nodes.Element)), \
                    'The node%s does not have any items' % xpath
                assert len(node) == len(cls), \
                    'The node%s has %d child nodes, not %r' % (xpath, len(node), len(cls))
                for i, nodecls in enumerate(cls):
                    path = xpath + "[%d]" % i
                    assert_node(node[i], nodecls, xpath=path, **kwargs)
            elif isinstance(cls, str):
                assert node == cls, 'The node %r is not %r: %r' % (xpath, cls, node)
            else:
                assert isinstance(node, cls), \
                    'The node%s is not subclass of %r: %r' % (xpath, cls, node)
    
        if kwargs:
            assert isinstance(node, nodes.Element), \
                'The node%s does not have any attributes' % xpath
    
            for key, value in kwargs.items():
                assert key in node, \
                    'The node%s does not have %r attribute: %r' % (xpath, key, node)
>               assert node[key] == value, \
                    'The node%s[%s] is not %r: %r' % (xpath, key, value, node[key])
E               AssertionError: The node[reftype] is not 'obj': 'class'

sphinx/testing/util.py:86: AssertionError
=============================== warnings summary ===============================
sphinx/util/docutils.py:45
  /testbed/sphinx/util/docutils.py:45: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    __version_info__ = tuple(LooseVersion(docutils.__version__).version)

sphinx/registry.py:22
  /testbed/sphinx/registry.py:22: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import iter_entry_points

../opt/miniconda3/envs/testbed/lib/python3.9/site-packages/pkg_resources/__init__.py:3144
../opt/miniconda3/envs/testbed/lib/python3.9/site-packages/pkg_resources/__init__.py:3144
../opt/miniconda3/envs/testbed/lib/python3.9/site-packages/pkg_resources/__init__.py:3144
../opt/miniconda3/envs/testbed/lib/python3.9/site-packages/pkg_resources/__init__.py:3144
  /opt/miniconda3/envs/testbed/lib/python3.9/site-packages/pkg_resources/__init__.py:3144: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

sphinx/directives/patches.py:15
  /testbed/sphinx/directives/patches.py:15: DeprecationWarning: The `docutils.parsers.rst.directive.html` module will be removed in Docutils 2.0. Since Docutils 0.18, the "Meta" node is defined in `docutils.parsers.rst.directives.misc`.
    from docutils.parsers.rst.directives import images, html, tables

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:210: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse():  # type: Node

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/i18n.py:88: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.translatable):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:110: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for ref in self.document.traverse(nodes.substitution_reference):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:131: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.target):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:150: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.block_quote):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:175: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.Element):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:222: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.index):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/references.py:30: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.substitution_definition):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:189: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.section):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:279: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.doctest_block):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/domains/citation.py:117: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.citation):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/domains/citation.py:136: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.citation_reference):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/builders/latex/transforms.py:37: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(matcher):  # type: nodes.Element

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:291: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(matcher):  # type: Element

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/util/compat.py:44: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.index):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/domains/index.py:52: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in document.traverse(addnodes.index):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/domains/math.py:85: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    self.data['has_equations'][docname] = any(document.traverse(math_node))

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/environment/collectors/asset.py:47: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in doctree.traverse(nodes.image):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/environment/collectors/asset.py:124: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in doctree.traverse(addnodes.download_reference):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/environment/collectors/title.py:46: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in doctree.traverse(nodes.section):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:301: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.system_message):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/__init__.py:384: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.manpage):

tests/test_domain_py.py: 28 warnings
  /testbed/sphinx/transforms/i18n.py:484: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for inline in self.document.traverse(matcher):  # type: nodes.inline

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/domains/cpp.py:6895: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(AliasNode):

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/transforms/post_transforms/__init__.py:71: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.pending_xref):

tests/test_domain_py.py: 42 warnings
  /testbed/sphinx/util/nodes.py:596: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in document.traverse(addnodes.only):

tests/test_domain_py.py: 32 warnings
  /testbed/sphinx/transforms/post_transforms/images.py:36: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.image):

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/transforms/post_transforms/__init__.py:214: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.desc_sig_element):

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/builders/latex/transforms.py:595: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(nodes.title):

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/builders/latex/transforms.py:597: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for i, index in enumerate(node.traverse(addnodes.index)):

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/transforms/post_transforms/code.py:44: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in self.document.traverse(addnodes.highlightlang):

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/transforms/post_transforms/code.py:99: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for lbnode in self.document.traverse(nodes.literal_block):  # type: nodes.literal_block

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/transforms/post_transforms/code.py:103: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for dbnode in self.document.traverse(nodes.doctest_block):  # type: nodes.doctest_block

tests/test_domain_py.py: 16 warnings
  /testbed/sphinx/environment/__init__.py:541: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for toctreenode in doctree.traverse(addnodes.toctree):

tests/test_domain_py.py: 22 warnings
  /testbed/sphinx/environment/adapters/toctree.py:204: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for subtocnode in toc.traverse(addnodes.toctree):

tests/test_domain_py.py: 11 warnings
  /testbed/sphinx/environment/adapters/toctree.py:262: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for refnode in newnode.traverse(nodes.reference):

tests/test_domain_py.py: 12 warnings
  /testbed/sphinx/util/nodes.py:348: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for img in node.traverse(nodes.image):

tests/test_domain_py.py: 12 warnings
  /testbed/sphinx/util/nodes.py:350: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for raw in node.traverse(nodes.raw):

tests/test_domain_py.py::test_domain_py_xrefs
  /testbed/tests/test_domain_py.py:81: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    refnodes = list(doctree.traverse(pending_xref))

tests/test_domain_py.py::test_domain_py_xrefs
  /testbed/tests/test_domain_py.py:99: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    refnodes = list(doctree.traverse(pending_xref))

tests/test_domain_py.py::test_domain_py_xrefs
  /testbed/tests/test_domain_py.py:128: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    refnodes = list(doctree.traverse(pending_xref))

tests/test_domain_py.py::test_resolve_xref_for_properties
  /testbed/sphinx/builders/html/__init__.py:415: DeprecationWarning: The frontend.OptionParser class will be replaced by a subclass of argparse.ArgumentParser in Docutils 0.21 or later.
    self.docsettings = OptionParser(

tests/test_domain_py.py: 72 warnings
  /opt/miniconda3/envs/testbed/lib/python3.9/optparse.py:1000: DeprecationWarning: The frontend.Option class will be removed in Docutils 0.21 or later.
    option = self.option_class(*args, **kwargs)

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /testbed/sphinx/builders/__init__.py:182: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in doctree.traverse(nodes.image):

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /testbed/sphinx/builders/html/__init__.py:827: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in doctree.traverse(nodes.image):

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /testbed/sphinx/environment/adapters/toctree.py:313: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for node in toc.traverse(nodes.reference):

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /opt/miniconda3/envs/testbed/lib/python3.9/site-packages/alabaster/layout.html:114: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
    _gaq.push(['_setAllowLinker', true]);

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /opt/miniconda3/envs/testbed/lib/python3.9/site-packages/alabaster/about.html:70: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /opt/miniconda3/envs/testbed/lib/python3.9/site-packages/alabaster/about.html:99: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /testbed/sphinx/environment/adapters/toctree.py:327: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for toctreenode in doctree.traverse(addnodes.toctree):

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /opt/miniconda3/envs/testbed/lib/python3.9/site-packages/alabaster/layout.html:215: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
tests/test_domain_py.py::test_resolve_xref_for_properties
  /opt/miniconda3/envs/testbed/lib/python3.9/site-packages/alabaster/layout.html:238: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
  <template>:33: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
  <template>:224: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
  <template>:386: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py::test_resolve_xref_for_properties
  <template>:401: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.

tests/test_domain_py.py: 24 warnings
  /testbed/sphinx/ext/todo.py:98: PendingDeprecationWarning: nodes.Node.traverse() is obsoleted by Node.findall().
    for todo in document.traverse(todo_node):

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================= slowest 25 durations =============================
0.27s setup    tests/test_domain_py.py::test_domain_py_xrefs
0.15s call     tests/test_domain_py.py::test_resolve_xref_for_properties
0.07s call     tests/test_domain_py.py::test_domain_py_xrefs
0.04s setup    tests/test_domain_py.py::test_pyfunction_signature_full_py38
0.04s setup    tests/test_domain_py.py::test_pyfunction_signature
0.02s call     tests/test_domain_py.py::test_pyfunction_signature_full_py38
0.01s setup    tests/test_domain_py.py::test_module_index_not_collapsed
0.01s setup    tests/test_domain_py.py::test_pydecoratormethod_signature
0.01s setup    tests/test_domain_py.py::test_pymethod_options
0.01s setup    tests/test_domain_py.py::test_pystaticmethod
0.01s setup    tests/test_domain_py.py::test_pydata
0.01s setup    tests/test_domain_py.py::test_pyexception_signature
0.01s setup    tests/test_domain_py.py::test_resolve_xref_for_properties
0.01s setup    tests/test_domain_py.py::test_optional_pyfunction_signature
0.01s setup    tests/test_domain_py.py::test_pydecorator_signature
0.01s setup    tests/test_domain_py.py::test_module_index
0.01s setup    tests/test_domain_py.py::test_pydata_signature
0.01s setup    tests/test_domain_py.py::test_pyattribute
0.01s setup    tests/test_domain_py.py::test_pyobject_prefix
0.01s setup    tests/test_domain_py.py::test_exceptions_module_is_ignored
0.01s setup    tests/test_domain_py.py::test_pydata_signature_old
0.01s setup    tests/test_domain_py.py::test_pyclassmethod
0.01s setup    tests/test_domain_py.py::test_pyfunction_signature_full
0.01s setup    tests/test_domain_py.py::test_module_index_submodule
0.01s setup    tests/test_domain_py.py::test_modindex_common_prefix
=========================== short test summary info ============================
FAILED tests/test_domain_py.py::test_parse_annotation - AssertionError: The n...
================= 1 failed, 27 passed, 1084 warnings in 1.11s ==================
py39: exit 1 (1.66 seconds) /testbed> pytest --durations 25 tests/test_domain_py.py pid=108
  py39: FAIL code 1 (1.68=setup[0.01]+cmd[1.66] seconds)
  evaluation failed :( (1.77 seconds)
+ git checkout aca3f825f2e4a8817190f3c885a242a285aa0dba tests/test_domain_py.py
Updated 1 path from 20b75ba95

run_instance.log:

2024-10-04 20:43:46,044 - INFO - Environment image sweb.env.x86_64.c6d251a05e0af7688b64fd:latest found for sphinx-doc__sphinx-7454
Building instance image sweb.eval.x86_64.sphinx-doc__sphinx-7454:latest for sphinx-doc__sphinx-7454
2024-10-04 20:44:03,489 - INFO - Creating container for sphinx-doc__sphinx-7454...
2024-10-04 20:44:03,511 - INFO - Container for sphinx-doc__sphinx-7454 created: 30206541dcdf4633a250302dd20a9840de78381c560736a4294dc0ec81f75ac6
2024-10-04 20:44:03,663 - INFO - Container for sphinx-doc__sphinx-7454 started: 30206541dcdf4633a250302dd20a9840de78381c560736a4294dc0ec81f75ac6
2024-10-04 20:44:03,663 - INFO - Intermediate patch for sphinx-doc__sphinx-7454 written to logs/run_evaluation/pr-writer/claude-sonnet-3.5__SWE-bench_Verified__default__t-0.00__p-0.95__c-10.00__install-1__sphinx-add-comment2/sphinx-doc__sphinx-7454/patch.diff, now applying to container...
2024-10-04 20:44:03,843 - INFO - Failed to apply patch to container, trying again...
2024-10-04 20:44:03,893 - INFO - >>>>> Applied Patch:
patching file setup.py
Reversed (or previously applied) patch detected!  Assuming -R.
patching file tox.ini
Reversed (or previously applied) patch detected!  Assuming -R.
patching file utils/bump_version.py

2024-10-04 20:44:04,115 - INFO - Git diff before:
diff --git a/utils/bump_version.py b/utils/bump_version.py
old mode 100755
new mode 100644
index b829877b6..981f9292e
--- a/utils/bump_version.py
+++ b/utils/bump_version.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# this is a test
 
 import argparse
 import os
2024-10-04 20:44:04,115 - INFO - Eval script for sphinx-doc__sphinx-7454 written to logs/run_evaluation/pr-writer/claude-sonnet-3.5__SWE-bench_Verified__default__t-0.00__p-0.95__c-10.00__install-1__sphinx-add-comment2/sphinx-doc__sphinx-7454/eval.sh; copying to container...
2024-10-04 20:44:07,709 - INFO - Test runtime: 3.47 seconds
2024-10-04 20:44:07,709 - INFO - Test output for sphinx-doc__sphinx-7454 written to logs/run_evaluation/pr-writer/claude-sonnet-3.5__SWE-bench_Verified__default__t-0.00__p-0.95__c-10.00__install-1__sphinx-add-comment2/sphinx-doc__sphinx-7454/test_output.txt
2024-10-04 20:44:07,753 - INFO - Git diff after:
diff --git a/utils/bump_version.py b/utils/bump_version.py
old mode 100755
new mode 100644
index b829877b6..981f9292e
--- a/utils/bump_version.py
+++ b/utils/bump_version.py
@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# this is a test
 
 import argparse
 import os
2024-10-04 20:44:07,753 - INFO - Grading answer for sphinx-doc__sphinx-7454...
2024-10-04 20:44:07,759 - INFO - report: {'sphinx-doc__sphinx-7454': {'patch_is_None': False, 'patch_exists': True, 'patch_successfully_applied': True, 'resolved': False, 'tests_status': {'FAIL_TO_PASS': {'success': [], 'failure': ['tests/test_domain_py.py::test_parse_annotation']}, 'PASS_TO_PASS': {'success': [], 'failure': ['tests/test_domain_py.py::test_function_signatures', 'tests/test_domain_py.py::test_domain_py_xrefs', 'tests/test_domain_py.py::test_domain_py_objects', 'tests/test_domain_py.py::test_resolve_xref_for_properties', 'tests/test_domain_py.py::test_domain_py_find_obj', 'tests/test_domain_py.py::test_get_full_qualified_name', 'tests/test_domain_py.py::test_pyfunction_signature', 'tests/test_domain_py.py::test_pyfunction_signature_full', 'tests/test_domain_py.py::test_pyfunction_signature_full_py38', 'tests/test_domain_py.py::test_optional_pyfunction_signature', 'tests/test_domain_py.py::test_pyexception_signature', 'tests/test_domain_py.py::test_exceptions_module_is_ignored', 'tests/test_domain_py.py::test_pydata_signature', 'tests/test_domain_py.py::test_pydata_signature_old', 'tests/test_domain_py.py::test_pyobject_prefix', 'tests/test_domain_py.py::test_pydata', 'tests/test_domain_py.py::test_pyfunction', 'tests/test_domain_py.py::test_pymethod_options', 'tests/test_domain_py.py::test_pyclassmethod', 'tests/test_domain_py.py::test_pystaticmethod', 'tests/test_domain_py.py::test_pyattribute', 'tests/test_domain_py.py::test_pydecorator_signature', 'tests/test_domain_py.py::test_pydecoratormethod_signature', 'tests/test_domain_py.py::test_module_index', 'tests/test_domain_py.py::test_module_index_submodule', 'tests/test_domain_py.py::test_module_index_not_collapsed', 'tests/test_domain_py.py::test_modindex_common_prefix']}, 'FAIL_TO_FAIL': {'success': [], 'failure': []}, 'PASS_TO_FAIL': {'success': [], 'failure': []}}}}
Result for sphinx-doc__sphinx-7454: resolved: False
2024-10-04 20:44:07,759 - INFO - Attempting to stop container sweb.eval.sphinx-doc__sphinx-7454.pr-writer...
2024-10-04 20:44:22,893 - INFO - Attempting to remove container sweb.eval.sphinx-doc__sphinx-7454.pr-writer...
2024-10-04 20:44:22,905 - INFO - Container sweb.eval.sphinx-doc__sphinx-7454.pr-writer removed.
2024-10-04 20:44:22,905 - INFO - Attempting to remove image sweb.eval.x86_64.sphinx-doc__sphinx-7454:latest...
2024-10-04 20:44:23,043 - INFO - Image sweb.eval.x86_64.sphinx-doc__sphinx-7454:latest removed.

eval.sh:

#!/bin/bash
set -uxo pipefail
source /opt/miniconda3/bin/activate
conda activate testbed
cd /testbed
git config --global --add safe.directory /testbed
cd /testbed
git status
git show
git diff aca3f825f2e4a8817190f3c885a242a285aa0dba
source /opt/miniconda3/bin/activate
conda activate testbed
python -m pip install -e .[test]
git checkout aca3f825f2e4a8817190f3c885a242a285aa0dba tests/test_domain_py.py
git apply -v - <<'EOF_114329324912'
diff --git a/tests/test_domain_py.py b/tests/test_domain_py.py
--- a/tests/test_domain_py.py
+++ b/tests/test_domain_py.py
@@ -239,6 +239,7 @@ def test_get_full_qualified_name():
 def test_parse_annotation():
     doctree = _parse_annotation("int")
     assert_node(doctree, ([pending_xref, "int"],))
+    assert_node(doctree[0], pending_xref, refdomain="py", reftype="class", reftarget="int")
 
     doctree = _parse_annotation("List[int]")
     assert_node(doctree, ([pending_xref, "List"],
@@ -266,6 +267,12 @@ def test_parse_annotation():
                           [pending_xref, "int"],
                           [desc_sig_punctuation, "]"]))
 
+    # None type makes an object-reference (not a class reference)
+    doctree = _parse_annotation("None")
+    assert_node(doctree, ([pending_xref, "None"],))
+    assert_node(doctree[0], pending_xref, refdomain="py", reftype="obj", reftarget="None")
+
+
 
 def test_pyfunction_signature(app):
     text = ".. py:function:: hello(name: str) -> str"

EOF_114329324912
tox --current-env -epy39 -v -- tests/test_domain_py.py
git checkout aca3f825f2e4a8817190f3c885a242a285aa0dba tests/test_domain_py.py

System Information

Ubuntu
>>> uname -r
6.8.0-1013-gcp
>>> python --version
Python 3.12.3

[eschluntz]

from a little bit of digging, maybe the problem is that the tests are not being run with enough verbosity for some reason, and so the test harness is not picking up the PASS?

[eschluntz]

By comparing to successful run logs from the leaderboard, it looks my pytest command is wrong! It's missing the -rA which makes pytest print the test summary PASSs, which the grading harness looks for!

theirs: py39: commands[0]> pytest -rA --durations 25 tests/test_domain_py.py
ours: py39: commands[0]> pytest --durations 25 tests/test_domain_py.py

I think the patch that is supposed to apply that is failing. From run_instance.log:

patching file tox.ini
Reversed (or previously applied) patch detected!  Assuming -R.

MY patch.diff DOES include adding -rA, which maybe is conflicting with the test harness trying to do the same thing?

diff --git a/tox.ini b/tox.ini
index d9f040544..bf39854b6 100644
--- a/tox.ini
+++ b/tox.ini
@@ -28,7 +28,7 @@ extras =
 setenv =
     PYTHONWARNINGS = all,ignore::ImportWarning:importlib._bootstrap_external,ignore::DeprecationWarning:site,ignore::DeprecationWarning:distutils
 commands=
-    pytest --durations 25 {posargs}
+    pytest -rA --durations 25 {posargs}

My hypothesis at this point is that my containers did not get cleaned up somehow, and that's what's causing problems...

[eschluntz]

Ok, it's not the fault of dirty containers - those extra lines are coming from sphinx's pre-install steps applied by SWE-agent!
"sed -i 's/pytest/pytest -rA/' tox.ini"

This bug affects SWE-agent and you can see it in it's official submissions:
https://github.com/swe-bench/experiments/blob/main/evaluation/verified/20240620_sweagent_claude3.5sonnet/logs/sphinx-doc__sphinx-7440/report.json

(My agent is a fork of SWE-agent)

The fix is either:

1. SWE-agent should filter this out from the diff patchfile, so that swe-bench's grading script can cleanly re-apply it
2. swe-bench's grading script should be robust to the pre-install SED diffs already being present

[john-b-yang]

Please ignore the assignment. I will get to this issue in a timely manner.