Open
Description
Describe the bug
The following work fine:
pytest --cov=torchgeo.datasets tests/datasets/test_landcoverai.py
coverage run --source=torchgeo.datasets -m pytest tests/datasets/test_landcoverai.py
The following raise an error, possibly due to an import reload:
pytest --cov=torchgeo.datasets.landcoverai tests/datasets/test_landcoverai.py
coverage run --source=torchgeo.datasets.landcoverai -m pytest tests/datasets/test_landcoverai.py
Specifically, I see errors like the following:
ImportError while loading conftest '/Users/Adam/torchgeo/tests/conftest.py'.
tests/conftest.py:10: in <module>
import torchvision
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torchvision/__init__.py:10: in <module>
from torchvision import _meta_registrations, datasets, io, models, ops, transforms, utils # usort:skip
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torchvision/_meta_registrations.py:25: in <module>
@register_meta("roi_align")
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torchvision/_meta_registrations.py:19: in wrapper
get_meta_lib().impl(getattr(getattr(torch.ops.torchvision, op_name), overload_name), fn)
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/library.py:322: in impl
raise RuntimeError(
E RuntimeError: This is not allowed since there's already a kernel registered from python overriding roi_align's behavior for Meta dispatch key and torchvision namespace.
or:
ImportError while loading conftest '/Users/Adam/torchgeo/tests/conftest.py'.
tests/conftest.py:9: in <module>
import torch
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/__init__.py:1795: in <module>
from torch._tensor import Tensor # usort: skip
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/_tensor.py:21: in <module>
from torch.overrides import (
../spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/overrides.py:1757: in <module>
has_torch_function = _add_docstr(
E RuntimeError: function '_has_torch_function' already has a docstring
I also see warnings related to reloading numpy, so I'm guessing this is related. In fact, torch does not seem to support being reloaded:
>>> from importlib import reload
>>> import torch
>>> torch = reload(torch)
Traceback (most recent call last):
File "<python-input-2>", line 1, in <module>
torch = reload(torch)
File "/Users/Adam/spack/opt/spack/darwin-sequoia-m2/apple-clang-16.0.0/python-3.13.2-j7e4p3aq54ba6lpgvoyrwzbsxq3m74gl/lib/python3.13/importlib/__init__.py", line 129, in reload
_bootstrap._exec(spec, module)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 866, in _exec
File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "/Users/Adam/spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/__init__.py", line 2623, in <module>
class _TritonLibrary:
...<10 lines>...
return cls.ops_table[(op_key, dispatch_key)]
File "/Users/Adam/spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/__init__.py", line 2624, in _TritonLibrary
lib = torch.library.Library("triton", "DEF")
File "/Users/Adam/spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/torch/library.py", line 93, in __init__
self.m: Optional[Any] = torch._C._dispatch_library(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
kind, ns, dispatch_key, filename, lineno
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
RuntimeError: Only a single TORCH_LIBRARY can be used to register the namespace triton; please put all of your definitions in a single TORCH_LIBRARY block. If you were trying to specify implementations, consider using TORCH_LIBRARY_IMPL (which can be duplicated). If you really intended to define operators for a single namespace in a distributed way, you can use TORCH_LIBRARY_FRAGMENT to explicitly indicate this. Previous registration of TORCH_LIBRARY was registered at /dev/null:2623; latest registration was registered at /dev/null:2623It seems that something, somewhere in coverage.py is trying to reload(torch) or reload(torchvision), which is not supported. I'm very curious why this only happens when reporting coverage for a single file (module) instead of a directory (package).
To Reproduce
> pip install torchgeo # to install the dependencies
> git clone https://github.com/microsoft/torchgeo.git # to get the tests
> cd torchgeo
> coverage run --source=torchgeo.datasets.landcoverai -m pytest tests/datasets/test_landcoverai.py> coverage debug sys
-- sys -------------------------------------------------------
coverage_version: 7.2.6
coverage_module: /Users/Adam/spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages/coverage/__init__.py
tracer: -none-
CTracer: unavailable
plugins.file_tracers: -none-
plugins.configurers: -none-
plugins.context_switchers: -none-
configs_attempted: .coveragerc
setup.cfg
tox.ini
pyproject.toml
configs_read: -none-
config_file: None
config_contents: -none-
data_file: -none-
python: 3.13.2 (main, Feb 8 2025, 15:35:03) [Clang 16.0.0 (clang-1600.0.26.6)]
platform: macOS-15.3-arm64-arm-64bit-Mach-O
implementation: CPython
executable: /Users/Adam/spack/var/spack/environments/default/.spack-env/._view/xrnxxkbbchrixacht7gsgdzjxsu6eyqh/bin/python3
def_encoding: utf-8
fs_encoding: utf-8
pid: 6835
cwd: /Users/Adam/torchgeo
path: /Users/Adam/spack/var/spack/environments/default/.spack-env/._view/xrnxxkbbchrixacht7gsgdzjxsu6eyqh/bin
/Users/Adam/spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages
/Users/Adam/spack/opt/spack/darwin-sequoia-m2/apple-clang-16.0.0/python-3.13.2-j7e4p3aq54ba6lpgvoyrwzbsxq3m74gl/lib/python313.zip
/Users/Adam/spack/opt/spack/darwin-sequoia-m2/apple-clang-16.0.0/python-3.13.2-j7e4p3aq54ba6lpgvoyrwzbsxq3m74gl/lib/python3.13
/Users/Adam/spack/opt/spack/darwin-sequoia-m2/apple-clang-16.0.0/python-3.13.2-j7e4p3aq54ba6lpgvoyrwzbsxq3m74gl/lib/python3.13/lib-dynload
/Users/Adam/spack/var/spack/environments/default/.spack-env/._view/xrnxxkbbchrixacht7gsgdzjxsu6eyqh/lib/python3.13/site-packages
environment: HOME = /Users/Adam
PYTHONPATH = /Users/Adam/spack/var/spack/environments/default/.spack-env/view/lib/python3.13/site-packages
SPACK_PYTHON = /Users/Adam/spack/var/spack/environments/default/.spack-env/view/bin/python3
command_line: /Users/Adam/spack/var/spack/environments/default/.spack-env/view/bin/coverage debug sys
sqlite3_sqlite_version: 3.46.0
sqlite3_temp_store: 0
sqlite3_compile_options: ATOMIC_INTRINSICS=1, COMPILER=clang-16.0.0, DEFAULT_AUTOVACUUM,
DEFAULT_CACHE_SIZE=-2000, DEFAULT_FILE_FORMAT=4,
DEFAULT_JOURNAL_SIZE_LIMIT=-1, DEFAULT_MMAP_SIZE=0, DEFAULT_PAGE_SIZE=4096,
DEFAULT_PCACHE_INITSZ=20, DEFAULT_RECURSIVE_TRIGGERS,
DEFAULT_SECTOR_SIZE=4096, DEFAULT_SYNCHRONOUS=2,
DEFAULT_WAL_AUTOCHECKPOINT=1000, DEFAULT_WAL_SYNCHRONOUS=2,
DEFAULT_WORKER_THREADS=0, DIRECT_OVERFLOW_READ, ENABLE_COLUMN_METADATA,
ENABLE_FTS3, ENABLE_FTS4, ENABLE_FTS5, ENABLE_GEOPOLY,
ENABLE_MATH_FUNCTIONS, ENABLE_RTREE, MALLOC_SOFT_LIMIT=1024,
MAX_ATTACHED=10, MAX_COLUMN=2000, MAX_COMPOUND_SELECT=500,
MAX_DEFAULT_PAGE_SIZE=8192, MAX_EXPR_DEPTH=1000, MAX_FUNCTION_ARG=127,
MAX_LENGTH=1000000000, MAX_LIKE_PATTERN_LENGTH=50000,
MAX_MMAP_SIZE=0x7fff0000, MAX_PAGE_COUNT=0xfffffffe, MAX_PAGE_SIZE=65536,
MAX_SQL_LENGTH=1000000000, MAX_TRIGGER_DEPTH=1000,
MAX_VARIABLE_NUMBER=32766, MAX_VDBE_OP=250000000, MAX_WORKER_THREADS=8,
MUTEX_PTHREADS, SYSTEM_MALLOC, TEMP_STORE=1, THREADSAFE=1> pip3 list
Package Version
----------------------------- ---------
aenum 3.1.12
affine 2.1.0
aiohttp 3.9.5
aiosignal 1.2.0
alabaster 0.7.16
altgraph 0.17.2
annotated-types 0.7.0
antlr4-python3-runtime 4.9.3
anyio 4.0.0
appdirs 1.4.4
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.3
asttokens 2.4.0
astunparse 1.6.3
async-lru 1.0.3
attrs 23.1.0
awscli 2.22.4
awscrt 0.20.9
Babel 2.15.0
beautifulsoup4 4.12.3
black 24.3.0
bleach 6.0.0
build 1.2.1
cachetools 5.2.0
Cartopy 0.24.1
certifi 2023.7.22
cffi 1.17.1
cftime 1.0.3.4
charset-normalizer 3.3.0
click 8.1.8
click-plugins 1.1.1
cligj 0.7.2
cmocean 4.0.3
colorama 0.4.6
comm 0.1.4
contourpy 1.3.0
coverage 7.2.6
cryptography 43.0.1
cycler 0.11.0
debugpy 1.6.7
decorator 5.1.1
defusedxml 0.7.1
distro 1.8.0
docstring_parser 0.15
docutils 0.19
editables 0.5
efficientnet_pytorch 0.7.1
einops 0.8.0
et_xmlfile 1.0.1
executing 2.1.0
fastjsonschema 2.16.3
filelock 3.12.4
fiona 1.10.1
flake8 6.1.0
fonttools 4.39.4
fqdn 1.5.1
frozenlist 1.5.0
fsspec 2024.10.0
future 0.18.2
GDAL 3.10.1
gdown 5.2.0
geocube 0.7.0
geopandas 1.0.1
gevent 24.11.1
greenlet 3.1.1
h5py 3.12.1
hatch-jupyter-builder 0.8.3
hatchling 1.25.0
hf_transfer 0.1.8
huggingface_hub 0.26.2
hydra-core 1.3.2
idna 3.4
imageio 2.35.1
imagesize 1.4.1
importlib_metadata 7.0.1
importlib_resources 5.12.0
iniconfig 2.0.0
InquirerPy 0.3.4
ipykernel 6.29.5
ipympl 0.9.4
ipython 8.17.2
ipython_genutils 0.2.0
ipywidgets 8.0.2
isoduration 20.11.0
isort 5.12.0
jaraco.classes 3.2.3
jedi 0.19.2
Jinja2 3.1.4
jmespath 1.0.1
joblib 1.4.2
json5 0.9.14
jsonargparse 4.35.0
jsonpointer 2.0
jsonschema 4.22.0
jsonschema-specifications 2023.12.1
jupyter_client 8.2.0
jupyter_core 5.3.0
jupyter-events 0.10.0
jupyter-lsp 2.2.0
jupyter_server 2.14.2
jupyter_server_terminals 0.4.4
jupyterlab 4.0.1
jupyterlab-pygments 0.2.2
jupyterlab_server 2.27.3
jupyterlab-widgets 3.0.3
keyring 24.3.0
kiwisolver 1.4.5
kornia 0.8.0
kornia_rs 0.1.0
laspy 2.5.4
lazy_loader 0.4
lightly 1.5.11
lightly_utils 0.0.2
lightning 2.4.0
lightning-utilities 0.11.2
lxml 5.3.0
macholib 1.15.2
markdown-it-py 3.0.0
MarkupSafe 2.1.3
matplotlib 3.10.0
matplotlib-inline 0.1.6
mccabe 0.7.0
mdurl 0.1.2
mistune 2.0.5
more-itertools 9.1.0
mpmath 1.3.0
multidict 6.1.0
munch 2.5.0
mypy 1.14.1
mypy_extensions 1.0.0
nbclient 0.6.7
nbconvert 7.14.1
nbformat 5.8.0
nbmake 1.4.3
nbsphinx 0.8.8
nest_asyncio 1.6.0
netCDF4 1.7.2
networkx 3.1
notebook_shim 0.2.3
numpy 2.2.2
nvtx 0.2.5
odc-geo 0.1.2
omegaconf 2.3.0
openpyxl 3.1.2
overrides 7.3.1
packaging 24.2
pandas 2.2.3
pandocfilters 1.5.0
parso 0.8.4
pathspec 0.11.1
pexpect 4.9.0
pfzy 0.3.4
pillow 11.1.0
pip 21.2.4
pkginfo 1.9.6
planetary-computer 0.4.9
platformdirs 3.10.0
pluggy 1.5.0
pretrainedmodels 0.7.4
prometheus_client 0.17.0
prompt_toolkit 3.0.38
protobuf 3.13.0
psutil 6.1.1
ptyprocess 0.7.0
pure_eval 0.2.2
pybind11 2.13.6
pycocotools 2.0.8
pycodestyle 2.11.0
pycparser 2.21
pydantic 2.10.1
pydantic_core 2.27.1
pyflakes 3.1.0
Pygments 2.18.0
pyogrio 0.9.0
pyparsing 3.1.2
pyproj 3.7.0
pyproject_hooks 1.0.0
pyshp 2.3.1
PySocks 1.7.1
pystac 1.11.0
pystac-client 0.8.5
pytest 8.2.1
pytest-cov 4.0.0
python-dateutil 2.8.2
python-json-logger 2.0.7
pytorch-lightning 2.0.7
pytorch_sphinx_theme 0.0.24
pytz 2024.2
PyYAML 6.0.2
pyzmq 26.2.0
rasterio 1.4.3
readme_renderer 37.3
referencing 0.35.1
requests 2.32.3
requests-toolbelt 1.0.0
rfc3339_validator 0.1.4
rfc3986 2.0.0
rfc3986_validator 0.1.1
rich 13.7.1
rioxarray 0.17.0
rpds-py 0.20.0
Rtree 1.3.0
ruamel.yaml 0.17.16
ruamel.yaml.clib 0.2.12
ruff 0.9.1
safetensors 0.4.5
scikit-image 0.25.1
scikit-learn 1.6.1
scipy 1.15.1
seaborn 0.13.2
segmentation_models_pytorch 0.4.0
Send2Trash 1.8.3
setuptools 75.8.0
shapely 2.0.7
six 1.17.0
sniffio 1.3.0
snowballstemmer 2.2.0
soupsieve 2.4.1
Sphinx 7.3.7
sphinx-copybutton 0.2.12
sphinx_design 0.6.1
sphinx_rtd_theme 3.0.0
sphinxcontrib-applehelp 2.0.0
sphinxcontrib-devhelp 2.0.0
sphinxcontrib-htmlhelp 2.1.0
sphinxcontrib-jquery 4.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-programoutput 0.15
sphinxcontrib-qthelp 2.0.0
sphinxcontrib-serializinghtml 1.1.9
stack_data 0.6.2
sympy 1.13.1
terminado 0.17.1
threadpoolctl 3.1.0
tifffile 2024.8.30
timm 1.0.14
tinycss2 1.2.1
torch 2.6.0
torchgeo 0.6.2
torchmetrics 1.6.1
torchvision 0.21.0
tornado 6.3.3
tqdm 4.66.3
traitlets 5.14.3
trove-classifiers 2023.8.7
twine 6.0.1
typeshed_client 2.1.0
typing_extensions 4.12.2
tzdata 2023.3
uri_template 1.2.0
urllib3 1.26.20
wcwidth 0.2.7
webcolors 24.11.1
webencodings 0.5.1
websocket-client 1.8.0
wheel 0.41.2
widgetsnbextension 4.0.3
xarray 2024.7.0
yarl 1.9.2
zipp 3.17.0
zope.event 5.0
zope.interface 7.0.3Expected behavior
From what I can tell, reporting coverage for a single file is supported and should work: https://discuss.python.org/t/how-to-run-coverage-for-specific-file/46019
Additional context
The pytest-cov issue seems to go away when torchgeo is not installed on the system, but the coverage invocation fails regardless. This could be an issue in pytest or torch, but I figured I would first investigate where and why the import may be reloaded.