search

saeyslab / harpy

https://harpy.readthedocs.io/en/latest/
Other
7 stars 1 forks source link

Test failure for transcripts #14

Closed berombau closed 4 months ago

berombau commented 5 months ago 
pytest
FAILED src/sparrow/_tests/test_plot/test_plot_annotation.py::test_score_genes - KeyError: 1
FAILED src/sparrow/_tests/test_plot/test_plot_transcripts.py::test_analyse_genes_left_out - KeyError: "None of [Index(['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',\n       '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24',\n       '25', '26', '27', ...
FAILED src/sparrow/_tests/test_table/test_annotation.py::test_score_genes - KeyError: 1
ArneDefauw commented 4 months ago

I can not reproduce this test failure. Maybe something to do with pandas or anndata version? Can you give me result of conda env export?

berombau commented 4 months ago

Mmmh, yeah could be

Conda env
``` name: harpy prefix: /opt/homebrew/Caskroom/mambaforge/base/envs/harpy channels: - pytorch - conda-forge dependencies: - affine=2.4.0=pyhd8ed1ab_0 - alabaster=0.7.16=pyhd8ed1ab_0 - aom=3.5.0=h7ea286d_0 - app-model=0.2.4=pyhd8ed1ab_0 - appdirs=1.4.4=pyh9f0ad1d_0 - appnope=0.1.4=pyhd8ed1ab_0 - arpack=3.7.0=h58ebc17_2 - array-api-compat=1.4.1=pyhd8ed1ab_0 - asciitree=0.3.3=py_2 - asttokens=2.4.1=pyhd8ed1ab_0 - attrs=23.2.0=pyh71513ae_0 - babel=2.14.0=pyhd8ed1ab_0 - bioformats_jar=2020.5.27=pyhd8ed1ab_0 - blosc=1.21.5=hc338f07_0 - boost-cpp=1.78.0=hf1d6563_2 - branca=0.7.1=pyhd8ed1ab_0 - brotli=1.0.9=h1a8c8d9_9 - brotli-bin=1.0.9=h1a8c8d9_9 - brotli-python=1.0.9=py310h0f1eb42_9 - brunsli=0.1=h9f76cd9_0 - bzip2=1.0.8=h93a5062_5 - c-ares=1.27.0=h93a5062_0 - c-blosc2=2.13.2=ha57e6be_0 - ca-certificates=2024.2.2=hf0a4a13_0 - cached-property=1.5.2=hd8ed1ab_1 - cached_property=1.5.2=pyha770c72_1 - cachey=0.2.1=pyh9f0ad1d_0 - cairo=1.16.0=h73a0509_1014 - certifi=2024.2.2=pyhd8ed1ab_0 - cfitsio=4.2.0=h2f961c4_0 - charls=2.3.4=hbdafb3b_0 - click=8.1.7=unix_pyh707e725_0 - click-plugins=1.1.1=py_0 - cligj=0.7.2=pyhd8ed1ab_1 - cloudpickle=3.0.0=pyhd8ed1ab_0 - colorama=0.4.6=pyhd8ed1ab_0 - comm=0.2.1=pyhd8ed1ab_0 - contourpy=1.2.0=py310hd137fd4_0 - curl=8.1.2=h912dcd9_0 - cycler=0.12.1=pyhd8ed1ab_0 - cytoolz=0.12.3=py310hd125d64_0 - dav1d=1.2.1=hb547adb_0 - debugpy=1.8.1=py310h692a8b6_0 - decorator=5.1.1=pyhd8ed1ab_0 - docstring_parser=0.15=pyhd8ed1ab_0 - docutils=0.17.1=py310hbe9552e_4 - exceptiongroup=1.2.0=pyhd8ed1ab_2 - executing=2.0.1=pyhd8ed1ab_0 - expat=2.5.0=hb7217d7_1 - fasteners=0.17.3=pyhd8ed1ab_0 - ffmpeg=5.1.2=gpl_hf318d42_106 - fiona=1.9.1=py310h2e51ddd_0 - folium=0.16.0=pyhd8ed1ab_0 - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - font-ttf-inconsolata=3.000=h77eed37_0 - font-ttf-source-code-pro=2.038=h77eed37_0 - font-ttf-ubuntu=0.83=h77eed37_1 - fontconfig=2.14.2=h82840c6_0 - fonts-conda-ecosystem=1=0 - fonts-conda-forge=1=0 - fonttools=4.49.0=py310hd125d64_0 - freetype=2.12.1=hadb7bae_2 - freetype-py=2.4.0=pyhd8ed1ab_0 - freexl=1.0.6=h1a8c8d9_1 - fsspec=2023.6.0=pyh1a96a4e_0 - gdal=3.6.2=py310h0b34360_1 - geopandas=0.12.2=pyhd8ed1ab_0 - geopandas-base=0.12.2=pyha770c72_0 - geos=3.11.1=hb7217d7_0 - geotiff=1.7.1=heeaeb2e_5 - gettext=0.21.1=h0186832_0 - giflib=5.2.1=h1a8c8d9_3 - glib=2.78.1=h9e231a4_0 - glib-tools=2.78.1=h9e231a4_0 - glpk=5.0=h6d7a090_0 - gmp=6.3.0=h965bd2d_0 - gnutls=3.7.9=hd26332c_0 - graphite2=1.3.13=h9f76cd9_1001 - gst-plugins-base=1.22.7=h040e9b9_0 - gstreamer=1.22.7=hd492984_0 - h5py=3.8.0=nompi_py310h3419284_100 - harfbuzz=6.0.0=hddbc195_0 - hdf4=4.2.15=h1a38d6a_5 - hdf5=1.12.2=nompi_ha7af310_101 - heapdict=1.0.1=py_0 - hsluv=5.0.4=pyhd8ed1ab_0 - icu=70.1=h6b3803e_0 - idna=3.6=pyhd8ed1ab_0 - imagecodecs=2022.12.24=py310hdf9a3a5_0 - imageio=2.34.0=pyh4b66e23_0 - imagesize=1.4.1=pyhd8ed1ab_0 - importlib-metadata=7.0.1=pyha770c72_0 - importlib_metadata=7.0.1=hd8ed1ab_0 - importlib_resources=6.1.2=pyhd8ed1ab_0 - in-n-out=0.1.9=pyhd8ed1ab_0 - ipykernel=6.29.3=pyh3cd1d5f_0 - ipython=8.22.2=pyh707e725_0 - jasper=2.0.33=hc3cd1e9_1 - jedi=0.19.1=pyhd8ed1ab_0 - jgo=1.0.5=pyhd8ed1ab_0 - jinja2=3.1.3=pyhd8ed1ab_0 - joblib=1.3.2=pyhd8ed1ab_0 - jpeg=9e=h1a8c8d9_3 - jpype1=1.5.0=py310h21239e6_1 - json-c=0.16=hc449e50_0 - jsonschema=4.21.1=pyhd8ed1ab_0 - jsonschema-specifications=2023.12.1=pyhd8ed1ab_0 - jupyter_core=5.7.1=py310hbe9552e_0 - jxrlib=1.1=h93a5062_3 - kealib=1.5.0=hfd766a6_0 - kiwisolver=1.4.5=py310h38f39d4_1 - krb5=1.20.1=h69eda48_0 - lame=3.100=h1a8c8d9_1003 - lazy_loader=0.3=pyhd8ed1ab_0 - lcms2=2.15=h481adae_0 - leidenalg=0.9.1=py310h0f1eb42_0 - lerc=4.0.0=h9a09cb3_0 - libaec=1.1.2=h13dd4ca_1 - libavif=0.11.1=h9f83d30_2 - libblas=3.9.0=21_osxarm64_openblas - libbrotlicommon=1.0.9=h1a8c8d9_9 - libbrotlidec=1.0.9=h1a8c8d9_9 - libbrotlienc=1.0.9=h1a8c8d9_9 - libcblas=3.9.0=21_osxarm64_openblas - libclang=14.0.6=default_h5dc8d65_1 - libclang13=14.0.6=default_hc7183e1_1 - libcurl=8.1.2=h912dcd9_0 - libcxx=16.0.6=h4653b0c_0 - libdap4=3.20.6=h8510809_2 - libdeflate=1.14=h1a8c8d9_0 - libedit=3.1.20191231=hc8eb9b7_2 - libev=4.33=h93a5062_2 - libexpat=2.5.0=hb7217d7_1 - libffi=3.4.2=h3422bc3_5 - libgdal=3.6.2=hf9f7efc_1 - libgfortran=5.0.0=13_2_0_hd922786_3 - libgfortran5=13.2.0=hf226fd6_3 - libglib=2.78.1=hd9b11f9_0 - libiconv=1.17=h0d3ecfb_2 - libidn2=2.3.7=h93a5062_0 - libkml=1.3.0=h4f02115_1016 - liblapack=3.9.0=21_osxarm64_openblas - liblapacke=3.9.0=21_osxarm64_openblas - libllvm14=14.0.6=hd1a9a77_4 - libllvm15=15.0.7=h62b9111_1 - libnetcdf=4.8.1=nompi_h2510be2_106 - libnghttp2=1.58.0=ha4dd798_0 - libogg=1.3.4=h27ca646_1 - libopenblas=0.3.26=openmp_h6c19121_0 - libopencv=4.7.0=py310h57d381e_0 - libopus=1.3.1=h27ca646_1 - libpng=1.6.43=h091b4b1_0 - libpq=15.2=h1a28acd_0 - libprotobuf=3.21.12=ha614eb4_2 - librttopo=1.1.0=h844f84d_12 - libsodium=1.0.18=h27ca646_1 - libspatialindex=1.9.3=hbdafb3b_4 - libspatialite=5.0.1=h558e587_22 - libsqlite=3.45.1=h091b4b1_0 - libssh2=1.11.0=h7a5bd25_0 - libtasn1=4.19.0=h1a8c8d9_0 - libtiff=4.5.0=heb92581_0 - libunistring=0.9.10=h3422bc3_0 - libvorbis=1.3.7=h9f76cd9_0 - libvpx=1.11.0=hc470f4d_3 - libwebp-base=1.3.2=hb547adb_0 - libxcb=1.13=h9b22ae9_1004 - libxml2=2.10.3=h67585b2_4 - libzip=1.10.1=ha0bc3c6_3 - libzlib=1.2.13=h53f4e23_5 - libzopfli=1.0.3=h9f76cd9_0 - llvm-openmp=17.0.6=hcd81f8e_0 - llvmlite=0.42.0=py310hf7687f1_1 - locket=1.0.0=pyhd8ed1ab_0 - lz4-c=1.9.4=hb7217d7_0 - magicgui=0.8.1=pyhd8ed1ab_0 - mapclassify=2.6.1=pyhd8ed1ab_0 - markupsafe=2.1.5=py310hd125d64_0 - matplotlib-base=3.8.3=py310h2439c42_0 - matplotlib-inline=0.1.6=pyhd8ed1ab_0 - maven=3.9.6=hce30654_0 - mdurl=0.1.2=pyhd8ed1ab_0 - metis=5.1.1=hebf3989_2 - mpfr=4.2.1=h9546428_0 - msgpack-python=1.0.7=py310hd137fd4_0 - munch=4.0.0=pyhd8ed1ab_0 - munkres=1.1.4=pyh9f0ad1d_0 - mypy_extensions=1.0.0=pyha770c72_0 - mysql-common=8.0.33=hf9e6398_6 - mysql-libs=8.0.33=he3dca8b_6 - napari=0.4.18=pyh9208f05_3 - napari-console=0.0.9=pyh9208f05_0 - napari-plugin-engine=0.2.0=pyhd8ed1ab_2 - napari-svg=0.1.10=pyhd8ed1ab_0 - natsort=8.4.0=pyhd8ed1ab_0 - ncurses=6.4=h463b476_2 - nest-asyncio=1.6.0=pyhd8ed1ab_0 - nettle=3.9.1=h40ed0f5_0 - networkx=3.2.1=pyhd8ed1ab_0 - npe2=0.7.4=pyhd8ed1ab_0 - nspr=4.35=hb7217d7_0 - nss=3.98=h5ce2875_0 - numba=0.59.0=py310hdf1f89a_1 - numcodecs=0.12.1=py310hd5a4765_0 - numpydoc=1.5.0=pyhd8ed1ab_0 - opencv=4.7.0=py310hb6292c7_0 - openh264=2.3.1=hb7217d7_2 - openjdk=11.0.22=h3fcba2d_0 - openjpeg=2.5.0=hbc2ba62_2 - openssl=3.1.5=h0d3ecfb_0 - p11-kit=0.24.1=h29577a5_0 - packaging=23.2=pyhd8ed1ab_0 - pandas=2.2.1=py310h401b61c_0 - parso=0.8.3=pyhd8ed1ab_0 - partd=1.4.1=pyhd8ed1ab_0 - patsy=0.5.6=pyhd8ed1ab_0 - pcre=8.45=hbdafb3b_0 - pcre2=10.40=hb34f9b4_0 - pexpect=4.9.0=pyhd8ed1ab_0 - pickleshare=0.7.5=py_1003 - pillow=9.4.0=py310h5a7539a_1 - pint=0.23=pyhd8ed1ab_0 - pip=22.2.2=pyhd8ed1ab_0 - pixman=0.43.4=hebf3989_0 - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1 - platformdirs=4.2.0=pyhd8ed1ab_0 - ply=3.11=py_1 - pooch=1.8.1=pyhd8ed1ab_0 - poppler=22.12.0=h9564b9f_1 - poppler-data=0.4.12=hd8ed1ab_0 - postgresql=15.2=h45c140d_0 - proj=9.1.0=h13f728c_1 - prompt-toolkit=3.0.42=pyha770c72_0 - psutil=5.9.8=py310hd125d64_0 - psygnal=0.9.5=pyhd8ed1ab_0 - pthread-stubs=0.4=h27ca646_1001 - ptyprocess=0.7.0=pyhd3deb0d_0 - pure_eval=0.2.2=pyhd8ed1ab_0 - py-opencv=4.7.0=py310h69fb684_0 - pyconify=0.1.6=pyhd8ed1ab_0 - pydantic=1.10.13=py310hd125d64_1 - pydantic-compat=0.1.1=pyhd8ed1ab_0 - pygments=2.17.2=pyhd8ed1ab_0 - pynndescent=0.5.11=pyhca7485f_0 - pyopengl=3.1.6=pyhd8ed1ab_1 - pyparsing=3.1.1=pyhd8ed1ab_0 - pyproj=3.4.1=py310hce8d790_0 - pyproject_hooks=1.0.0=pyhd8ed1ab_0 - pyqt=5.15.7=py310h7aaa74b_3 - pyqt5-sip=12.11.0=py310h0f1eb42_3 - pysocks=1.7.1=pyha2e5f31_6 - python=3.10.13=h2469fbe_0_cpython - python-build=1.1.1=pyhd8ed1ab_0 - python-dateutil=2.9.0=pyhd8ed1ab_0 - python-tzdata=2024.1=pyhd8ed1ab_0 - python_abi=3.10=4_cp310 - pytorch=1.13.0=py3.10_0 - pytz=2024.1=pyhd8ed1ab_0 - pywavelets=1.4.1=py310h280b8fa_1 - pyyaml=6.0.1=py310h2aa6e3c_1 - pyzmq=25.1.2=py310hbb13138_0 - qt-main=5.15.8=hfe8d25c_6 - qtconsole-base=5.5.1=pyha770c72_0 - qtpy=2.4.1=pyhd8ed1ab_0 - rasterio=1.3.4=py310h2a1f202_0 - readline=8.2=h92ec313_1 - referencing=0.33.0=pyhd8ed1ab_0 - requests=2.31.0=pyhd8ed1ab_0 - rich=13.7.1=pyhd8ed1ab_0 - rpds-py=0.18.0=py310hf632f72_0 - rtree=1.2.0=py310ha3239f5_0 - scanpy=1.9.4=pyhd8ed1ab_0 - scikit-learn=1.4.1.post1=py310h7ef31dd_0 - scipy=1.12.0=py310hf4b343e_2 - scyjava=1.9.1=pyhd8ed1ab_0 - seaborn=0.13.0=hd8ed1ab_0 - seaborn-base=0.13.0=pyhd8ed1ab_0 - session-info=1.0.0=pyhd8ed1ab_0 - setuptools=69.1.1=pyhd8ed1ab_0 - shapely=2.0.1=py310h9356385_0 - shellingham=1.5.4=pyhd8ed1ab_0 - sip=6.8.3=py310h692a8b6_0 - six=1.16.0=pyh6c4a22f_0 - snappy=1.1.10=h17c5cce_0 - snowballstemmer=2.2.0=pyhd8ed1ab_0 - snuggs=1.4.7=py_0 - sphinx=4.5.0=pyh6c4a22f_0 - sphinxcontrib-applehelp=1.0.4=pyhd8ed1ab_0 - sphinxcontrib-devhelp=1.0.2=py_0 - sphinxcontrib-htmlhelp=2.0.1=pyhd8ed1ab_0 - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0 - sphinxcontrib-qthelp=1.0.3=py_0 - sphinxcontrib-serializinghtml=1.1.5=pyhd8ed1ab_2 - sqlite=3.45.1=hf2abe2d_0 - stack_data=0.6.2=pyhd8ed1ab_0 - statsmodels=0.14.1=py310h50ce23c_0 - stdlib-list=0.10.0=pyhd8ed1ab_0 - suitesparse=5.10.1=h88be0ae_2 - superqt=0.6.1=pyh9208f05_0 - svt-av1=1.4.1=h7ea286d_0 - tbb=2021.10.0=h1995070_2 - texttable=1.7.0=pyhd8ed1ab_0 - threadpoolctl=3.3.0=pyhc1e730c_0 - tifffile=2022.10.10=pyhd8ed1ab_0 - tiledb=2.13.2=h9bd36d0_0 - tk=8.6.13=h5083fa2_1 - toml=0.10.2=pyhd8ed1ab_0 - tomli=2.0.1=pyhd8ed1ab_0 - tomli-w=1.0.0=pyhd8ed1ab_0 - toolz=0.12.1=pyhd8ed1ab_0 - tornado=6.4=py310hd125d64_0 - tqdm=4.66.2=pyhd8ed1ab_0 - traitlets=5.14.1=pyhd8ed1ab_0 - typer=0.9.0=pyhd8ed1ab_0 - typing-extensions=4.10.0=hd8ed1ab_0 - typing_extensions=4.10.0=pyha770c72_0 - tzcode=2024a=h93a5062_0 - tzdata=2024a=h0c530f3_0 - umap-learn=0.5.5=py310hbe9552e_1 - unicodedata2=15.1.0=py310h2aa6e3c_0 - uriparser=0.9.7=h13dd4ca_1 - vispy=0.12.2=py310hb614ae6_0 - wcwidth=0.2.13=pyhd8ed1ab_0 - wheel=0.42.0=pyhd8ed1ab_0 - wrapt=1.16.0=py310hd125d64_0 - x264=1!164.3095=h57fd34a_2 - x265=3.5=hbc6ce65_3 - xerces-c=3.2.4=h627aa08_1 - xorg-libxau=1.0.11=hb547adb_0 - xorg-libxdmcp=1.1.3=h27ca646_0 - xyzservices=2023.10.1=pyhd8ed1ab_0 - xz=5.2.6=h57fd34a_0 - yaml=0.2.5=h3422bc3_2 - zeromq=4.3.5=hebf3989_1 - zfp=1.0.1=ha8f4885_0 - zipp=3.17.0=pyhd8ed1ab_0 - zlib=1.2.13=h53f4e23_5 - zlib-ng=2.0.7=h1a8c8d9_0 - zstd=1.5.5=h4f39d0f_0 - pip: - accessible-pygments==0.0.4 - aicsimageio==4.14.0 - aiobotocore==2.5.4 - aiofiles==22.1.0 - aiohttp==3.9.3 - aioitertools==0.11.0 - aiosignal==1.3.1 - aiosqlite==0.20.0 - alpineer==0.1.10 - anndata==0.10.3 - antlr4-python3-runtime==4.9.3 - anyio==4.3.0 - argon2-cffi==23.1.0 - argon2-cffi-bindings==21.2.0 - ark-analysis==0.7.0 - arrow==1.3.0 - async-timeout==4.0.3 - autopep8==2.0.4 - basicpy==1.0.0 - beautifulsoup4==4.12.3 - bleach==6.1.0 - bokeh==3.3.4 - botocore==1.31.17 - cachetools==5.3.3 - cellpose==2.2.3 - cffi==1.16.0 - chardet==5.2.0 - charset-normalizer==2.1.1 - cmasher==1.8.0 - cmocean==4.0.3 - colorcet==3.1.0 - colorlog==6.8.2 - colorspacious==1.1.2 - coverage==7.4.3 - cython==0.29.37 - dask==2023.9.3 - dask-image==2023.8.1 - datasets==2.19.1 - datashader==0.16.0 - defusedxml==0.7.1 - deprecated==1.2.14 - dill==0.3.8 - distlib==0.3.8 - distributed==2023.9.3 - docrep==0.3.2 - elementpath==4.3.0 - entrypoints==0.4 - fastjsonschema==2.19.1 - fastremap==1.14.1 - fcsparser==0.2.8 - feather-format==0.4.1 - filelock==3.13.1 - flowsom==0.0.1 - fqdn==1.5.1 - frozenlist==1.4.1 - hdbscan==0.8.33 - huggingface-hub==0.23.0 - hydra-colorlog==1.2.0 - hydra-core==1.2.0 - hydra-submitit-launcher==1.2.0 - igraph==0.10.8 - inflect==7.0.0 - iniconfig==2.0.0 - ipylab==1.0.0 - ipympl==0.9.4 - ipython-genutils==0.2.0 - ipywidgets==8.1.2 - isoduration==20.11.0 - jax==0.4.6 - jaxlib==0.4.6 - jmespath==1.0.1 - json5==0.9.25 - jsonpointer==2.4 - jupyter-cache==0.6.1 - jupyter-client==7.4.9 - jupyter-events==0.10.0 - jupyter-server==2.14.0 - jupyter-server-fileid==0.9.2 - jupyter-server-terminals==0.5.3 - jupyter-server-ydoc==0.8.0 - jupyter-ydoc==0.2.5 - jupyterlab==3.6.7 - jupyterlab-pygments==0.3.0 - jupyterlab-server==2.27.1 - jupyterlab-widgets==3.0.10 - lamin-utils==0.13.0 - latexcodec==2.0.1 - loguru==0.7.2 - lxml==4.9.4 - markdown-it-py==2.2.0 - matplotlib-scalebar==0.8.1 - mdit-py-plugins==0.3.5 - mistune==3.0.2 - mudata==0.2.3 - multidict==6.0.5 - multipledispatch==1.0.0 - multiprocess==0.70.16 - multiscale-spatial-image==0.11.2 - myst-nb==0.17.2 - myst-parser==0.18.1 - napari-clusters-plotter==0.7.3 - napari-matplotlib==2.0.1 - napari-skimage-regionprops==0.10.1 - napari-spatialdata==0.3.1 - napari-tools-menu==0.1.19 - napari-workflows==0.2.10 - nbclassic==1.0.0 - nbclient==0.7.4 - nbconvert==7.16.4 - nbformat==5.9.2 - nbproject==0.10.1 - notebook==6.5.7 - notebook-shim==0.2.4 - nptyping==2.5.0 - numpy==1.23.5 - ome-types==0.5.0 - ome-zarr==0.8.4.dev0 - omegaconf==2.3.0 - omnipath==1.0.8 - opencv-python-headless==4.9.0.80 - opt-einsum==3.3.0 - orjson==3.9.15 - overrides==7.7.0 - palettable==3.3.3 - pandocfilters==1.5.1 - param==2.0.2 - pims==0.6.1 - pluggy==1.4.0 - prometheus-client==0.20.0 - pyarrow==15.0.0 - pyarrow-hotfix==0.6 - pybtex==0.24.0 - pybtex-docutils==1.0.3 - pycodestyle==2.11.1 - pycparser==2.22 - pyct==0.5.0 - pydata-sphinx-theme==0.13.3 - pyflowsom==0.1.15 - pygeos==0.14 - pyproject-api==1.6.1 - pyrootutils==1.0.4 - pytest==8.0.2 - pytest-cov==4.1.0 - pytest-qt==4.4.0 - python-dotenv==1.0.1 - python-igraph==0.10.8 - python-json-logger==2.0.7 - pytometry==0.1.4 - readfcs==1.1.7 - resource-backed-dask-array==0.1.0 - rfc3339-validator==0.1.4 - rfc3986-validator==0.1.1 - roifile==2024.1.10 - s3fs==2023.6.0 - scienceplots==2.1.1 - scikit-image==0.19.3 - send2trash==1.8.3 - slicerator==1.1.0 - sniffio==1.3.1 - sortedcontainers==2.4.0 - soupsieve==2.5 - sparrow==0.0.1 - spatial-image==0.3.0 - spatial-lda==0.1.3 - spatialdata==0.1.dev953+gc120a4d - spatialdata-plot==0.1.1.dev5+g66ba049.d20240416 - sphinx-autodoc-typehints==1.19.1 - sphinx-book-theme==1.0.1 - sphinx-copybutton==0.5.2 - sphinx-design==0.4.1 - sphinx-rtd-theme==1.3.0 - sphinxcontrib-bibtex==2.6.2 - sphinxcontrib-jquery==4.1 - sqlalchemy==2.0.28 - squidpy==1.3.1 - submitit==1.4.5 - tabulate==0.9.0 - tblib==3.0.0 - terminado==0.18.1 - tinycss2==1.2.1 - tox==4.13.0 - types-python-dateutil==2.9.0.20240316 - universal-pathlib==0.2.2 - uri-template==1.3.0 - urllib3==1.26.18 - validators==0.22.0 - virtualenv==20.25.1 - voronoi-diagram-for-polygons==0.1.6 - webcolors==1.13 - webencodings==0.5.1 - websocket-client==1.8.0 - widgetsnbextension==4.0.10 - xarray==2022.12.0 - xarray-dataclasses==1.5.0 - xarray-datatree==0.0.12 - xarray-schema==0.0.3 - xarray-spatial==0.3.5 - xmlschema==3.0.2 - xmltodict==0.13.0 - xsdata==24.2.1 - xxhash==3.4.1 - y-py==0.6.2 - yarl==1.9.4 - ypy-websocket==0.8.4 - zarr==2.15.0 - zict==3.0.0 - zstandard==0.22.0 ```
ArneDefauw commented 4 months ago

Mmmh, yeah could be Conda env

ok, I will try to reproduce it

ArneDefauw commented 4 months ago

fixed by https://github.com/saeyslab/harpy/commit/b80524660db4f5064fa8137f121ac30abc03fa51

the spatialdata object used for unit testing got corrupted (more specifically the var names of the table layer) when copying from mac to linux (i.e. git push, git clone...). Now we create the table in the fixture, which solves the problem.