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Pytest discovery hangs in Remote SSH #25553
Description
Type: Bug
Behaviour
Pytest discovery hangs infinitely
Steps to reproduce:
- Enter Remote SSH server through Remote Tunneling
- Load project in server
- Enter pytest discovery
Python Log Output
# Diagnostic data
2025-10-31 08:07:46.111 [info] Experiment 'pythonSurveyNotification' is active
2025-10-31 08:07:47.174 [info] Native locator: Refresh started
2025-10-31 08:07:52.690 [info] > conda info --json
2025-10-31 08:08:01.605 [info] > pyenv which python
2025-10-31 08:08:01.605 [info] cwd: .
2025-10-31 08:08:01.719 [info] Active interpreter [/scratch/project/tcr_ml/gnn_release]: /scratch/project_mnt/S0163/gnn_env/bin/python
2025-10-31 08:08:01.971 [info] Native locator: Refresh finished in 14797 ms
2025-10-31 08:08:03.224 [info] Starting Pylance language server.
2025-10-31 08:08:17.059 [debug] Testing: Refreshing all test data
2025-10-31 08:08:17.060 [info] Discover tests for workspace name: gnn_release - uri: /scratch/project/tcr_ml/gnn_release
2025-10-31 08:08:17.074 [debug] Starting Test Discovery named pipe
2025-10-31 08:09:43.105 [debug] Testing: Manually triggered test refresh
2025-10-31 08:09:43.105 [debug] Testing: Clearing all discovered tests
2025-10-31 08:09:43.105 [debug] Testing: Forcing test data refresh
2025-10-31 08:09:43.105 [debug] Testing: Refreshing all test data
2025-10-31 08:09:43.105 [info] Discover tests for workspace name: gnn_release - uri: /scratch/project/tcr_ml/gnn_release
2025-10-31 08:09:43.106 [error] Test discovery already in progress, not starting a new one.
Pytest output commandline
(gnn_env) uqachoo1@bun129: gnn_release:$ pytest --collect-only -v
=================================================================================================== test session starts ===================================================================================================
platform linux -- Python 3.11.8, pytest-8.4.2, pluggy-1.6.0 -- /scratch/project_mnt/S0163/gnn_env/bin/python
cachedir: .pytest_cache
rootdir: /scratch/project_mnt/S0163/gnn_release
configfile: pyproject.toml
testpaths: tests
plugins: anyio-4.11.0, mock-3.15.1, xdist-3.8.0, cov-7.0.0
collected 43 items
<Dir gnn_release>
<Package tests>
<Package generate_edge_tests>
<Module test_api.py>
<Function test_write_edges_file_for_pdb_success>
<Function test_write_edges_file_for_pdb_missing>
<Function test_write_edges_file_for_pdb_invalid_extension>
<Function test_generate_edges_from_pdb_file_invokes_writer>
<Function test_generate_edges_from_pdb_dir_uses_executor>
<Function test_generate_edges_from_tar_creates_archive>
<Function test_generate_edges_from_tar_keep_expanded>
<Function test_generate_edges_from_tar_dir>
<Function test_generate_edges_from_pdb_file_raises_file_not_found>
<Function test_generate_edges_from_pdb_file_raises_value_error_for_non_pdb>
<Module test_generate_edge.py>
<Function test_load_pdb_structure_success>
<Function test_load_pdb_structure_failure_logs_and_returns_none>
<Function test_basic_same_chain_and_inclusive_cutoff>
<Function test_prefers_cb_over_ca>
<Function test_ca_fallback_when_no_cb>
<Function test_residues_without_ca_are_ignored>
<Function test_different_chains_not_compared>
<Function test_multiple_models_are_independent>
<Function test_alternate_parser_basic>
<Function test_edges_text_basic>
<Function test_edges_text_multiple_pairs_and_order>
<Module test_io.py>
<Function test_iter_target_pdbs_filters_by_token_patterns>
<Function test_load_pdb_structure_success_and_failure>
<Package generate_graph_tests>
<Module test_encoding.py>
<Function test_load_pca_encoding_preserves_single_letter_index>
<Function test_load_pca_encoding_maps_three_letter_codes>
<Module test_graph_dataset.py>
<Function test_raw_and_processed_file_names_normalization>
<Function test_process_single_txt_and_len_get>
<Function test_process_tar_gz_multiple_graphs>
<Module test_io.py>
<Function test_list_edge_txts_finds_only_txt_files_non_recursive>
<Function test_list_edge_txts_accepts_str_path>
<Function test_list_edge_txts_is_case_sensitive_by_default>
<Function test_parse_edges_basic_spaces_and_tabs>
<Function test_parse_edges_ignores_blank_and_whitespace_only_lines>
<Function test_parse_edges_trims_leading_and_trailing_whitespace>
<Function test_parse_edges_unicode_and_non_ascii_tokens>
<Function test_parse_edges_empty_file_returns_empty_list>
<Function test_parse_edges_missing_file_raises>
<Module test_import.py>
<Function test_can_import_package>
<Package utils_tests>
<Module test_common_utils.py>
<Function test_is_within_directory_true_and_false>
<Function test_safe_extract_tar_gz_allows_safe_and_blocks_traversal>
<Function test_make_archive_calls_subprocess_run>
<Function test_tmp_root_returns_subdirectory_of_system_temp>
<Function test_cleanup_uses_shutil_rmtree>
==================================================================================================== warnings summary =====================================================================================================
../gnn_env/lib/python3.11/site-packages/torch_geometric/typing.py:54
/scratch/project_mnt/S0163/gnn_env/lib/python3.11/site-packages/torch_geometric/typing.py:54: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /scratch/project_mnt/S0163/gnn_env/lib/python3.11/site-packages/libpyg.so)
warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
../gnn_env/lib/python3.11/site-packages/torch_geometric/typing.py:110
/scratch/project_mnt/S0163/gnn_env/lib/python3.11/site-packages/torch_geometric/typing.py:110: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /scratch/project_mnt/S0163/gnn_env/lib/python3.11/site-packages/libpyg.so)
warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
===================================================================================================== tests coverage ======================================================================================================
_____________________________________________________________________________________ coverage: platform linux, python 3.11.8-final-0 _____________________________________________________________________________________
Name Stmts Miss Cover Missing
--------------------------------------------------------------------------
src/tcrgnn/__init__.py 8 4 50% 8-12
src/tcrgnn/edge_gen/__init__.py 0 0 100%
src/tcrgnn/edge_gen/_io.py 15 8 47% 22, 41-47
src/tcrgnn/edge_gen/api.py 52 35 33% 52-63, 86-93, 119-127, 143-152, 168-169
src/tcrgnn/edge_gen/cli.py 0 0 100%
src/tcrgnn/edge_gen/generate_edge.py 58 43 26% 38-44, 75-88, 111-139, 174-178
src/tcrgnn/fold_backend/__init__.py 0 0 100%
src/tcrgnn/graph_gen/__init__.py 0 0 100%
src/tcrgnn/graph_gen/_io.py 7 4 43% 18-19, 23-24
src/tcrgnn/graph_gen/api.py 14 14 0% 1-75
src/tcrgnn/graph_gen/build_graph.py 33 24 27% 22-37, 54-76, 104-105
src/tcrgnn/graph_gen/encodings.py 8 4 50% 55-59
src/tcrgnn/graph_gen/graph_dataset.py 47 28 40% 60-65, 80, 95, 116-149, 160, 176
src/tcrgnn/models/__init__.py 0 0 100%
src/tcrgnn/models/gatv2.py 20 20 0% 1-33
src/tcrgnn/plotting/__init__.py 0 0 100%
src/tcrgnn/plotting/api.py 14 14 0% 1-22
src/tcrgnn/plotting/charts.py 35 35 0% 1-52
src/tcrgnn/plotting/io.py 26 26 0% 1-48
src/tcrgnn/plotting/prepare.py 11 11 0% 1-20
src/tcrgnn/posthoc_adjustment/__init__.py 0 0 100%
src/tcrgnn/posthoc_adjustment/api.py 0 0 100%
src/tcrgnn/posthoc_adjustment/transform.py 104 104 0% 1-175
src/tcrgnn/training/__init__.py 0 0 100%
src/tcrgnn/training/config.py 21 2 90% 14-15
src/tcrgnn/training/data_loading.py 19 19 0% 1-33
src/tcrgnn/training/loop.py 50 39 22% 25-74
src/tcrgnn/utils/__init__.py 0 0 100%
src/tcrgnn/utils/_common_utils.py 25 15 40% 19-23, 43-49, 63, 75, 85
src/tcrgnn/utils/_device.py 11 11 0% 1-16
--------------------------------------------------------------------------
TOTAL 578 460 20%
============================================================================================== 43 tests collected in 11.78s ===============================================================================================
Test directory structure
Pyproject toml setup
[project]
name = "tcrgnn"
version = "0.1.0"
description = "GNN TCR Python Package"
authors = [{ name = "Amos Choo", email = "amos.choo@uq.edu.au" }]
dependencies = [
"torch_geometric==2.5.3",
"jupyter",
"matplotlib",
"seaborn",
"networkx",
"biopython",
]
requires-python = ">=3.11"
readme = "README.md"
license = { text = "MIT" }
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"
[tool.pdm]
distribution = true
[tool.ruff]
line-length = 88
target-version = "py311"
exclude = ["old_folders"]
# Enable Ruff formatting (replaces Black)
[tool.ruff.format]
quote-style = "double" # or "single"
docstring-code-format = true
[tool.ruff.lint]
select = [
"E", # pycodestyle errors
"F", # pyflakes
"W", # warnings
"I", # import sorting
"UP", # pyupgrade
"B", # bugbear
"C4", # comprehensions
]
ignore = [
"E501", # optionally ignore line length if annoying
]
fixable = ["ALL"]
[tool.pytest.ini_options]
minversion = "8.0"
testpaths = ["tests"]
addopts = [
"-ra", # extra summary
"--strict-markers",
"--strict-config",
"--maxfail=1",
"--cov=tcrgnn",
"--cov-report=term-missing",
]
markers = [
"gpu: tests that require CUDA",
"slow: long running tests",
"integration: integration tests that touch disk or multiple modules",
]
[dependency-groups]
dev = [
"ruff>=0.14.2",
"pre-commit>=4.3.0",
"pytest>=8.4.2",
"pytest-cov>=7.0.0",
"pytest-xdist>=3.8.0",
"pytest-mock>=3.15.1",
]Extension version: 2025.16.0
VS Code version: Code 1.105.1 (7d842fb85a0275a4a8e4d7e040d2625abbf7f084, 2025-10-14T22:33:36.618Z)
OS version: Windows_NT arm64 10.0.26200
Modes:
Remote OS version: Linux x64 4.18.0-553.58.1.el8_10.x86_64
- Python version (& distribution if applicable, e.g. Anaconda): 3.12.11.final.0
- Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): System
- Value of the
python.languageServersetting: Default
User Settings
languageServer: "Pylance"
testing
• pytestArgs: "<placeholder>"
• pytestEnabled: true
Installed Extensions
| Extension Name | Extension Id | Version |
|---|---|---|
| copilot | Git | 1.388.0 |
| copilot-chat | Git | 0.32.4 |
| debugpy | ms- | 2025.14.1 |
| even-better-toml | tam | 0.21.2 |
| html-preview-vscode | geo | 0.2.5 |
| js-debug | ms- | 1.105.0 |
| jupyter | ms- | 2025.9.1 |
| jupyter-renderers | ms- | 1.3.0 |
| python | ms- | 2025.16.0 |
| rainbow-csv | mec | 3.23.0 |
| ruff | cha | 2025.28.0 |
| vscode-js-profile-table | ms- | 1.0.10 |
| vscode-jupyter-cell-tags | ms- | 0.1.9 |
| vscode-jupyter-slideshow | ms- | 0.1.6 |
| vscode-pylance | ms- | 2025.9.1 |
| vscode-python-envs | ms- | 1.10.0 |
System Info
| Item | Value |
|---|---|
| CPUs | Snapdragon(R) X Elite - X1E78100 - Qualcomm(R) Oryon(TM) CPU (12 x 2976) |
| GPU Status | 2d_canvas: enabled direct_rendering_display_compositor: disabled_off_ok gpu_compositing: enabled multiple_raster_threads: enabled_on opengl: enabled_on rasterization: enabled raw_draw: disabled_off_ok skia_graphite: disabled_off trees_in_viz: disabled_off video_decode: enabled video_encode: enabled vulkan: disabled_off webgl: enabled webgl2: enabled webgpu: enabled webnn: unavailable_software |
| Load (avg) | undefined |
| Memory (System) | 31.57GB (12.29GB free) |
| Process Argv | --crash-reporter-id 2029ef38-5638-40ab-aaa9-1893d0b014ab |
| Screen Reader | no |
| VM | 0% |
| Item | Value |
|---|---|
| Remote | bun133 |
| OS | Linux x64 4.18.0-553.58.1.el8_10.x86_64 |
| CPUs | AMD EPYC 9454 48-Core Processor (192 x 3799) |
| Memory (System) | 1510.91GB (1426.20GB free) |
| VM | 0% |
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3efgi100_wstrepl:31403338
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Activity
eleanorjboyd commentedon Nov 5, 2025
Hi! To confirm, does this work when you run it locally instead of over SSH? This info will help me investigate the following issue- thanks
amoschoomy commentedon Nov 10, 2025
Yes, I've cloned over the repository locally, and it can discover tests without issues
github-actions commentedon Dec 15, 2025
Hey Eleanor Boyd (@eleanorjboyd), this issue might need further attention.
Amos (@amoschoomy), you can help us out by closing this issue if the problem no longer exists, or adding more information.
github-actions commentedon Jan 15, 2026
Because we have not heard back with the information we requested, we are closing this issue for now. If you are able to provide the info later on, then we will be happy to re-open this issue to pick up where we left off.
Happy Coding!