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Quirks installing spatialdata with pixi
Dear spatialdata devs,
I just switched to pixi, and really like it. However I am running with some issues specifically with spatialdata. I don't want to enforce this as a standard I understand why you prefer having pip install in the README. I just wanted to reach out in case you would know why this is happening. Feel free to disregard and tell me to use mamba hehe.
After testing a variety of install commands I figured out one that installs `spatialdata 0.2.5.post0' reliably. I will still post this in case it can help someone else, or devs could make this work more seamless :)
- Reproduce using pixi (version 0.39.2)
pixi init
pixi add python pandas anndata numpy spatialdata spatialdata-plot ipykernel
✔ Added python >=3.12.8,<3.13
✔ Added pandas >=2.2.3,<3
✔ Added anndata >=0.11.3,<0.12
✔ Added numpy >=1.26.4,<2
✔ Added spatialdata >=0.2.3,<0.3
✔ Added spatialdata-plot >=0.2.7,<0.3
✔ Added ipykernel >=6.29.5,<7
pixi list
❯ pixi list
Package Version Build Size Kind Source
aiohappyeyeballs 2.4.6 pyhd8ed1ab_0 18.8 KiB conda aiohappyeyeballs
aiohttp 3.11.12 py312h998013c_0 868.3 KiB conda aiohttp
aiosignal 1.3.2 pyhd8ed1ab_0 12.9 KiB conda aiosignal
anndata 0.11.3 pyhd8ed1ab_0 110.3 KiB conda anndata
aom 3.9.1 h7bae524_0 2.1 MiB conda aom
appnope 0.1.4 pyhd8ed1ab_1 9.8 KiB conda appnope
array-api-compat 1.10.0 pyhd8ed1ab_0 37.5 KiB conda array-api-compat
asciitree 0.3.3 py_2 6 KiB conda asciitree
asttokens 3.0.0 pyhd8ed1ab_1 27.5 KiB conda asttokens
attrs 25.1.0 pyh71513ae_0 55 KiB conda attrs
aws-c-auth 0.8.1 hfc2798a_0 90.4 KiB conda aws-c-auth
aws-c-cal 0.8.1 hc8a0bd2_3 39 KiB conda aws-c-cal
aws-c-common 0.10.6 h5505292_0 216.7 KiB conda aws-c-common
aws-c-compression 0.3.0 hc8a0bd2_5 17.6 KiB conda aws-c-compression
aws-c-event-stream 0.5.0 h54f970a_11 46 KiB conda aws-c-event-stream
aws-c-http 0.9.2 h96aa502_4 149.4 KiB conda aws-c-http
aws-c-io 0.15.3 haba67d1_6 132.9 KiB conda aws-c-io
aws-c-mqtt 0.11.0 h24f418c_12 131.2 KiB conda aws-c-mqtt
aws-c-s3 0.7.9 hf37e03c_1 96.4 KiB conda aws-c-s3
aws-c-sdkutils 0.2.2 hc8a0bd2_0 48.7 KiB conda aws-c-sdkutils
aws-checksums 0.2.2 hc8a0bd2_4 68.5 KiB conda aws-checksums
aws-crt-cpp 0.29.9 ha81f72f_2 230.4 KiB conda aws-crt-cpp
aws-sdk-cpp 1.11.489 h0e5014b_0 2.7 MiB conda aws-sdk-cpp
azure-core-cpp 1.14.0 hd50102c_0 287.4 KiB conda azure-core-cpp
azure-identity-cpp 1.10.0 hc602bab_0 163 KiB conda azure-identity-cpp
azure-storage-blobs-cpp 12.13.0 h7585a09_1 428.4 KiB conda azure-storage-blobs-cpp
azure-storage-common-cpp 12.8.0 h9ca1f76_1 118.4 KiB conda azure-storage-common-cpp
azure-storage-files-datalake-cpp 12.12.0 hcdd55da_1 191.4 KiB conda azure-storage-files-datalake-cpp
blosc 1.21.6 h7dd00d9_1 32.8 KiB conda blosc
bokeh 3.6.3 pyhd8ed1ab_0 4.3 MiB conda bokeh
branca 0.8.1 pyhd8ed1ab_0 28.9 KiB conda branca
brotli 1.1.0 hd74edd7_2 19.1 KiB conda brotli
brotli-bin 1.1.0 hd74edd7_2 16.4 KiB conda brotli-bin
brotli-python 1.1.0 py312hde4cb15_2 331.4 KiB conda brotli-python
brunsli 0.1 h9f76cd9_0 174.1 KiB conda brunsli
bzip2 1.0.8 h99b78c6_7 120 KiB conda bzip2
c-ares 1.34.4 h5505292_0 175.3 KiB conda c-ares
c-blosc2 2.15.2 h9cbb436_1 242.2 KiB conda c-blosc2
ca-certificates 2025.1.31 hf0a4a13_0 154.7 KiB conda ca-certificates
cached-property 1.5.2 hd8ed1ab_1 4 KiB conda cached-property
cached_property 1.5.2 pyha770c72_1 10.8 KiB conda cached_property
certifi 2024.12.14 pyhd8ed1ab_0 157.9 KiB conda certifi
cffi 1.17.1 py312h0fad829_0 274.6 KiB conda cffi
charls 2.4.2 h13dd4ca_0 113.5 KiB conda charls
charset-normalizer 3.4.1 pyhd8ed1ab_0 46.3 KiB conda charset-normalizer
click 8.1.8 pyh707e725_0 82.7 KiB conda click
cloudpickle 3.1.1 pyhd8ed1ab_0 25.3 KiB conda cloudpickle
colorama 0.4.6 pyhd8ed1ab_1 26.4 KiB conda colorama
colorcet 3.1.0 pyhd8ed1ab_1 169.9 KiB conda colorcet
comm 0.2.2 pyhd8ed1ab_1 11.8 KiB conda comm
contourpy 1.3.1 py312hb23fbb9_0 239.9 KiB conda contourpy
cpython 3.12.8 py312hd8ed1ab_1 43.7 KiB conda cpython
cycler 0.12.1 pyhd8ed1ab_1 13.1 KiB conda cycler
cytoolz 1.0.1 py312hea69d52_0 330.9 KiB conda cytoolz
dask 2025.1.0 pyhd8ed1ab_0 7.4 KiB conda dask
dask-core 2025.1.0 pyhd8ed1ab_0 939.3 KiB conda dask-core
dask-image 2024.5.3 pyhd8ed1ab_0 65.8 KiB conda dask-image
datashader 0.17.0 pyhd8ed1ab_0 16.4 MiB conda datashader
dav1d 1.2.1 hb547adb_0 309 KiB conda dav1d
debugpy 1.8.12 py312hd8f9ff3_0 2.4 MiB conda debugpy
decorator 5.1.1 pyhd8ed1ab_1 13.7 KiB conda decorator
deprecated 1.2.18 pyhd8ed1ab_0 14 KiB conda deprecated
distributed 2025.1.0 pyhd8ed1ab_0 783.4 KiB conda distributed
exceptiongroup 1.2.2 pyhd8ed1ab_1 20 KiB conda exceptiongroup
executing 2.1.0 pyhd8ed1ab_1 27.7 KiB conda executing
fasteners 0.19 pyhd8ed1ab_1 20.2 KiB conda fasteners
filelock 3.17.0 pyhd8ed1ab_0 17.1 KiB conda filelock
folium 0.19.4 pyhd8ed1ab_0 78.5 KiB conda folium
fonttools 4.56.0 py312h998013c_0 2.6 MiB conda fonttools
freetype 2.12.1 hadb7bae_2 582.5 KiB conda freetype
freexl 2.0.0 h3ab3353_2 52.1 KiB conda freexl
frozenlist 1.5.0 py312h998013c_1 55.9 KiB conda frozenlist
fsspec 2023.6.0 pyh1a96a4e_0 115.5 KiB conda fsspec
geopandas 1.0.1 pyhd8ed1ab_3 7.4 KiB conda geopandas
geopandas-base 1.0.1 pyha770c72_3 233.7 KiB conda geopandas-base
geos 3.13.0 hf9b8971_0 1.4 MiB conda geos
geotiff 1.7.3 h82bf549_3 111.1 KiB conda geotiff
gflags 2.2.2 hf9b8971_1005 80.2 KiB conda gflags
giflib 5.2.2 h93a5062_0 69.9 KiB conda giflib
glog 0.7.1 heb240a5_0 109.6 KiB conda glog
gmp 6.3.0 h7bae524_2 356.6 KiB conda gmp
gmpy2 2.1.5 py312h524cf62_3 144.5 KiB conda gmpy2
h2 4.2.0 pyhd8ed1ab_0 52.6 KiB conda h2
h5py 3.12.1 nompi_py312h34530d4_103 1.1 MiB conda h5py
hdf5 1.14.4 nompi_ha698983_105 3.3 MiB conda hdf5
hpack 4.1.0 pyhd8ed1ab_0 30 KiB conda hpack
hyperframe 6.1.0 pyhd8ed1ab_0 17 KiB conda hyperframe
icu 75.1 hfee45f7_0 11.3 MiB conda icu
idna 3.10 pyhd8ed1ab_1 48.6 KiB conda idna
imagecodecs 2024.12.30 py312h8857d0e_0 1.8 MiB conda imagecodecs
imageio 2.37.0 pyhfb79c49_0 286.4 KiB conda imageio
importlib-metadata 8.6.1 pyha770c72_0 28.5 KiB conda importlib-metadata
ipykernel 6.29.5 pyh57ce528_0 116.8 KiB conda ipykernel
ipython 8.32.0 pyh907856f_0 621.8 KiB conda ipython
jedi 0.19.2 pyhd8ed1ab_1 823.9 KiB conda jedi
jinja2 3.1.5 pyhd8ed1ab_0 109.9 KiB conda jinja2
joblib 1.4.2 pyhd8ed1ab_1 215.1 KiB conda joblib
json-c 0.18 he4178ee_0 72 KiB conda json-c
jupyter_client 8.6.3 pyhd8ed1ab_1 103.8 KiB conda jupyter_client
jupyter_core 5.7.2 pyh31011fe_1 56.3 KiB conda jupyter_core
jxrlib 1.1 h93a5062_3 193.2 KiB conda jxrlib
kiwisolver 1.4.8 py312h2c4a281_0 59.9 KiB conda kiwisolver
krb5 1.21.3 h237132a_0 1.1 MiB conda krb5
lazy-loader 0.4 pyhd8ed1ab_2 15.9 KiB conda lazy-loader
lazy_loader 0.4 pyhd8ed1ab_2 6.5 KiB conda lazy_loader
lcms2 2.17 h7eeda09_0 207.2 KiB conda lcms2
legacy-api-wrap 1.4.1 pyhd8ed1ab_0 14.8 KiB conda legacy-api-wrap
lerc 4.0.0 h9a09cb3_0 210.7 KiB conda lerc
libabseil 20240722.0 cxx17_h07bc746_4 1.1 MiB conda libabseil
libaec 1.1.3 hebf3989_0 27.8 KiB conda libaec
libarchive 3.7.7 h3b16cec_3 754.7 KiB conda libarchive
libarrow 19.0.0 h819e3af_8_cpu 5.3 MiB conda libarrow
libarrow-acero 19.0.0 hf07054f_8_cpu 488.6 KiB conda libarrow-acero
libarrow-dataset 19.0.0 hf07054f_8_cpu 489.3 KiB conda libarrow-dataset
libarrow-substrait 19.0.0 h4239455_8_cpu 439.1 KiB conda libarrow-substrait
libavif16 1.1.1 h45b7238_2 94.5 KiB conda libavif16
libblas 3.9.0 28_h10e41b3_openblas 16.4 KiB conda libblas
libbrotlicommon 1.1.0 hd74edd7_2 66.8 KiB conda libbrotlicommon
libbrotlidec 1.1.0 hd74edd7_2 27.7 KiB conda libbrotlidec
libbrotlienc 1.1.0 hd74edd7_2 273.1 KiB conda libbrotlienc
libcblas 3.9.0 28_hb3479ef_openblas 16.4 KiB conda libcblas
libcrc32c 1.1.2 hbdafb3b_0 18.3 KiB conda libcrc32c
libcurl 8.11.1 h73640d1_0 376.1 KiB conda libcurl
libcxx 19.1.7 ha82da77_0 511.2 KiB conda libcxx
libde265 1.0.15 h2ffa867_0 271.3 KiB conda libde265
libdeflate 1.23 hec38601_0 52.9 KiB conda libdeflate
libedit 3.1.20250104 pl5321hafb1f1b_0 105.2 KiB conda libedit
libev 4.33 h93a5062_2 104.9 KiB conda libev
libevent 2.1.12 h2757513_1 359.5 KiB conda libevent
libexpat 2.6.4 h286801f_0 63.2 KiB conda libexpat
libffi 3.4.6 h1da3d7d_0 35.5 KiB conda libffi
libgdal-core 3.10.1 h9ef0d2d_2 8.1 MiB conda libgdal-core
libgfortran 5.0.0 13_2_0_hd922786_3 107.6 KiB conda libgfortran
libgfortran5 13.2.0 hf226fd6_3 974 KiB conda libgfortran5
libgoogle-cloud 2.34.0 hdbe95d5_0 857.6 KiB conda libgoogle-cloud
libgoogle-cloud-storage 2.34.0 h7081f7f_0 516.8 KiB conda libgoogle-cloud-storage
libgrpc 1.67.1 h0a426d6_1 5.1 MiB conda libgrpc
libheif 1.19.5 gpl_h297b2c4_100 419.6 KiB conda libheif
libhwloc 2.11.2 default_hbce5d74_1001 2.2 MiB conda libhwloc
libhwy 1.1.0 h2ffa867_0 443 KiB conda libhwy
libiconv 1.17 h0d3ecfb_2 660.6 KiB conda libiconv
libjpeg-turbo 3.0.0 hb547adb_1 534.7 KiB conda libjpeg-turbo
libjxl 0.11.1 h562e088_0 852 KiB conda libjxl
libkml 1.3.0 he250239_1021 274.8 KiB conda libkml
liblapack 3.9.0 28_hc9a63f6_openblas 16.4 KiB conda liblapack
libllvm15 15.0.7 h2621b3d_4 21 MiB conda libllvm15
liblzma 5.6.4 h39f12f2_0 96.6 KiB conda liblzma
libnghttp2 1.64.0 h6d7220d_0 553.4 KiB conda libnghttp2
libopenblas 0.3.28 openmp_hf332438_1 4 MiB conda libopenblas
libopentelemetry-cpp 1.18.0 h0c05b2d_1 517.2 KiB conda libopentelemetry-cpp
libopentelemetry-cpp-headers 1.18.0 hce30654_1 313.1 KiB conda libopentelemetry-cpp-headers
libparquet 19.0.0 h636d7b7_8_cpu 872.5 KiB conda libparquet
libpng 1.6.46 h3783ad8_0 260.3 KiB conda libpng
libprotobuf 5.28.3 h3bd63a1_1 2.2 MiB conda libprotobuf
libre2-11 2024.07.02 h07bc746_2 163.2 KiB conda libre2-11
librttopo 1.1.0 ha2cf0f4_17 186.6 KiB conda librttopo
libsodium 1.0.20 h99b78c6_0 161.1 KiB conda libsodium
libspatialite 5.1.0 hf92fc0a_12 2.8 MiB conda libspatialite
libsqlite 3.48.0 h3f77e49_1 832.8 KiB conda libsqlite
libssh2 1.11.1 h9cc3647_0 272.5 KiB conda libssh2
libthrift 0.21.0 h64651cc_0 316.7 KiB conda libthrift
libtiff 4.7.0 h551f018_3 361.9 KiB conda libtiff
libtorch 2.5.1 cpu_generic_he9b55c7_13 27 MiB conda libtorch
libutf8proc 2.10.0 hda25de7_0 81.7 KiB conda libutf8proc
libuv 1.50.0 h5505292_0 409.1 KiB conda libuv
libwebp-base 1.5.0 h2471fea_0 283.2 KiB conda libwebp-base
libxcb 1.17.0 hdb1d25a_0 316.1 KiB conda libxcb
libxml2 2.13.5 h178c5d8_1 569.2 KiB conda libxml2
libzlib 1.3.1 h8359307_2 45.3 KiB conda libzlib
libzopfli 1.0.3 h9f76cd9_0 144.4 KiB conda libzopfli
llvm-openmp 19.1.7 hdb05f8b_0 274.2 KiB conda llvm-openmp
llvmlite 0.44.0 py312h728bc31_0 399.5 KiB conda llvmlite
locket 1.0.0 pyhd8ed1ab_0 8.1 KiB conda locket
lz4 4.3.3 py312hf263c89_2 103 KiB conda lz4
lz4-c 1.10.0 h286801f_1 145.3 KiB conda lz4-c
lzo 2.10 h93a5062_1001 128.4 KiB conda lzo
mapclassify 2.8.1 pyhd8ed1ab_1 55.4 KiB conda mapclassify
markdown-it-py 3.0.0 pyhd8ed1ab_1 62.9 KiB conda markdown-it-py
markupsafe 3.0.2 py312h998013c_1 23.5 KiB conda markupsafe
matplotlib-base 3.10.0 py312hdbc7e53_0 7.6 MiB conda matplotlib-base
matplotlib-inline 0.1.7 pyhd8ed1ab_1 14.1 KiB conda matplotlib-inline
matplotlib-scalebar 0.9.0 pyhd8ed1ab_0 20.7 KiB conda matplotlib-scalebar
mdurl 0.1.2 pyhd8ed1ab_1 14.1 KiB conda mdurl
minizip 4.0.7 hff1a8ea_3 75.8 KiB conda minizip
mpc 1.3.1 h8f1351a_1 102.3 KiB conda mpc
mpfr 4.2.1 hb693164_3 337.4 KiB conda mpfr
mpmath 1.3.0 pyhd8ed1ab_1 429.4 KiB conda mpmath
msgpack-python 1.1.0 py312h6142ec9_0 88.7 KiB conda msgpack-python
multidict 6.1.0 py312hdb8e49c_1 54.7 KiB conda multidict
multipledispatch 0.6.0 pyhd8ed1ab_1 16.8 KiB conda multipledispatch
multiscale-spatial-image 1.0.0 pyhd8ed1ab_2 23.8 KiB conda multiscale-spatial-image
munkres 1.1.4 pyh9f0ad1d_0 12.2 KiB conda munkres
natsort 8.4.0 pyh29332c3_1 38.1 KiB conda natsort
ncurses 6.5 h5e97a16_3 778.3 KiB conda ncurses
nest-asyncio 1.6.0 pyhd8ed1ab_1 11.3 KiB conda nest-asyncio
networkx 3.4.2 pyh267e887_2 1.2 MiB conda networkx
nlohmann_json 3.11.3 h00cdb27_1 120.4 KiB conda nlohmann_json
nomkl 1.0 h5ca1d4c_0 3.8 KiB conda nomkl
numba 0.61.0 py312hdf12f13_1 5.6 MiB conda numba
numcodecs 0.15.0 py312hcb1e3ce_0 674.7 KiB conda numcodecs
numpy 1.26.4 py312h8442bc7_0 5.8 MiB conda numpy
ome-zarr 0.10.3 pyhd8ed1ab_1 36.8 KiB conda ome-zarr
openjpeg 2.5.3 h8a3d83b_0 311.9 KiB conda openjpeg
openssl 3.4.0 h81ee809_1 2.8 MiB conda openssl
orc 2.0.3 h0ff2369_2 428.2 KiB conda orc
packaging 24.2 pyhd8ed1ab_2 58.8 KiB conda packaging
pandas 2.2.3 py312hcd31e36_1 13.8 MiB conda pandas
param 2.2.0 pyhd8ed1ab_0 102.3 KiB conda param
parso 0.8.4 pyhd8ed1ab_1 73.5 KiB conda parso
partd 1.4.2 pyhd8ed1ab_0 20.4 KiB conda partd
patsy 1.0.1 pyhd8ed1ab_1 182.2 KiB conda patsy
pcre2 10.44 h297a79d_2 604.5 KiB conda pcre2
pexpect 4.9.0 pyhd8ed1ab_1 52.3 KiB conda pexpect
pickleshare 0.7.5 pyhd8ed1ab_1004 11.5 KiB conda pickleshare
pillow 11.1.0 py312h50aef2c_0 40.9 MiB conda pillow
pims 0.7 pyhd8ed1ab_1 69.7 KiB conda pims
platformdirs 4.3.6 pyhd8ed1ab_1 20 KiB conda platformdirs
pooch 1.8.2 pyhd8ed1ab_1 52.8 KiB conda pooch
proj 9.5.1 h1318a7e_0 2.5 MiB conda proj
prometheus-cpp 1.3.0 h0967b3e_0 169.2 KiB conda prometheus-cpp
prompt-toolkit 3.0.50 pyha770c72_0 265.5 KiB conda prompt-toolkit
propcache 0.2.1 py312h998013c_1 49.7 KiB conda propcache
psutil 6.1.1 py312hea69d52_0 483.8 KiB conda psutil
pthread-stubs 0.4 hd74edd7_1002 8.2 KiB conda pthread-stubs
ptyprocess 0.7.0 pyhd8ed1ab_1 19 KiB conda ptyprocess
pure_eval 0.2.3 pyhd8ed1ab_1 16.3 KiB conda pure_eval
pyarrow 19.0.0 py312h1f38498_0 24.8 KiB conda pyarrow
pyarrow-core 19.0.0 py312hc40f475_0_cpu 4.2 MiB conda pyarrow-core
pybind11 2.13.6 pyh1ec8472_2 182 KiB conda pybind11
pybind11-global 2.13.6 pyh415d2e4_2 174.9 KiB conda pybind11-global
pycparser 2.22 pyh29332c3_1 107.5 KiB conda pycparser
pyct 0.5.0 pyhd8ed1ab_1 19.7 KiB conda pyct
pygments 2.19.1 pyhd8ed1ab_0 867.8 KiB conda pygments
pynndescent 0.5.13 pyhd8ed1ab_1 48.5 KiB conda pynndescent
pyogrio 0.10.0 py312hfd5e53c_1 550.9 KiB conda pyogrio
pyparsing 3.2.1 pyhd8ed1ab_0 90.9 KiB conda pyparsing
pyproj 3.7.0 py312h1ab748d_0 482.9 KiB conda pyproj
pysocks 1.7.1 pyha55dd90_7 20.6 KiB conda pysocks
python 3.12.8 hc22306f_1_cpython 12.4 MiB conda python
python-dateutil 2.9.0.post0 pyhff2d567_1 217.3 KiB conda python-dateutil
python-tzdata 2025.1 pyhd8ed1ab_0 140.4 KiB conda python-tzdata
python_abi 3.12 5_cp312 6.1 KiB conda python_abi
pytorch 2.5.1 cpu_generic_py312_h49ed405_13 25 MiB conda pytorch
pytz 2024.1 pyhd8ed1ab_0 184.1 KiB conda pytz
pywavelets 1.8.0 py312he0011b7_0 3.5 MiB conda pywavelets
pyyaml 6.0.2 py312h998013c_2 187.6 KiB conda pyyaml
pyzmq 26.2.1 py312hf4875e0_0 356.1 KiB conda pyzmq
qhull 2020.2 h420ef59_5 504.3 KiB conda qhull
rav1e 0.6.6 h69fbcac_2 1.5 MiB conda rav1e
re2 2024.07.02 h6589ca4_2 26.2 KiB conda re2
readline 8.2 h92ec313_1 244.5 KiB conda readline
requests 2.32.3 pyhd8ed1ab_1 57.3 KiB conda requests
rich 13.9.4 pyhd8ed1ab_1 181.3 KiB conda rich
scanpy 1.10.4 pyhd8ed1ab_0 1.9 MiB conda scanpy
scikit-image 0.25.1 py312hcb1e3ce_0 10.1 MiB conda scikit-image
scikit-learn 1.6.1 py312h39203ce_0 9.3 MiB conda scikit-learn
scipy 1.15.1 py312hb7ffdcd_0 15.2 MiB conda scipy
seaborn 0.13.2 hd8ed1ab_3 6.7 KiB conda seaborn
seaborn-base 0.13.2 pyhd8ed1ab_3 222.5 KiB conda seaborn-base
session-info 1.0.0 pyhd8ed1ab_0 11.9 KiB conda session-info
setuptools 75.8.0 pyhff2d567_0 757.4 KiB conda setuptools
shapely 2.0.7 py312ha6455e5_0 525 KiB conda shapely
six 1.17.0 pyhd8ed1ab_0 16 KiB conda six
sleef 3.8 h8391f65_0 571 KiB conda sleef
slicerator 1.1.0 pyhd8ed1ab_1 15.4 KiB conda slicerator
snappy 1.2.1 h98b9ce2_1 35 KiB conda snappy
sortedcontainers 2.4.0 pyhd8ed1ab_1 28 KiB conda sortedcontainers
spatial-image 1.1.0 pyhd8ed1ab_1 13.2 KiB conda spatial-image
spatialdata 0.2.3 pyhd8ed1ab_0 121.2 KiB conda spatialdata
spatialdata-plot 0.2.7 pyhd8ed1ab_1 41.9 KiB conda spatialdata-plot
sqlite 3.48.0 hd7222ec_1 837.9 KiB conda sqlite
stack_data 0.6.3 pyhd8ed1ab_1 26.4 KiB conda stack_data
statsmodels 0.14.4 py312h755e627_0 11.3 MiB conda statsmodels
stdlib-list 0.11.0 pyhd8ed1ab_1 25.7 KiB conda stdlib-list
svt-av1 2.3.0 hf24288c_0 1.3 MiB conda svt-av1
sympy 1.13.3 pyh2585a3b_105 4.3 MiB conda sympy
tbb 2022.0.0 h0cbf7ec_0 115.1 KiB conda tbb
tblib 3.0.0 pyhd8ed1ab_1 17 KiB conda tblib
threadpoolctl 3.5.0 pyhc1e730c_0 23 KiB conda threadpoolctl
tifffile 2025.1.10 pyhd8ed1ab_0 176.5 KiB conda tifffile
tk 8.6.13 h5083fa2_1 3 MiB conda tk
toolz 1.0.0 pyhd8ed1ab_1 51.2 KiB conda toolz
tornado 6.4.2 py312hea69d52_0 822.8 KiB conda tornado
tqdm 4.67.1 pyhd8ed1ab_1 87.4 KiB conda tqdm
traitlets 5.14.3 pyhd8ed1ab_1 107.5 KiB conda traitlets
typing-extensions 4.12.2 hd8ed1ab_1 9.8 KiB conda typing-extensions
typing_extensions 4.12.2 pyha770c72_1 38.7 KiB conda typing_extensions
tzdata 2025a h78e105d_0 120 KiB conda tzdata
umap-learn 0.5.7 py312h81bd7bf_1 185.7 KiB conda umap-learn
unicodedata2 16.0.0 py312hea69d52_0 400.1 KiB conda unicodedata2
uriparser 0.9.8 h00cdb27_0 39.7 KiB conda uriparser
urllib3 2.3.0 pyhd8ed1ab_0 97.8 KiB conda urllib3
wcwidth 0.2.13 pyhd8ed1ab_1 31.8 KiB conda wcwidth
wrapt 1.17.2 py312hea69d52_0 59.8 KiB conda wrapt
x265 3.5 hbc6ce65_3 1.7 MiB conda x265
xarray 2023.12.0 pyhd8ed1ab_0 707.6 KiB conda xarray
xarray-dataclasses 1.7.0 pyhd8ed1ab_1 17.6 KiB conda xarray-dataclasses
xarray-datatree 0.0.14 pyhd8ed1ab_0 55.9 KiB conda xarray-datatree
xarray-schema 0.0.3 pyhd8ed1ab_0 12 KiB conda xarray-schema
xarray-spatial 0.4.0 pyhd8ed1ab_1 1.6 MiB conda xarray-spatial
xerces-c 3.2.5 h92fc2f4_2 1.2 MiB conda xerces-c
xorg-libxau 1.0.12 h5505292_0 13.3 KiB conda xorg-libxau
xorg-libxdmcp 1.1.5 hd74edd7_0 18.1 KiB conda xorg-libxdmcp
xyzservices 2025.1.0 pyhd8ed1ab_0 47.5 KiB conda xyzservices
yaml 0.2.5 h3422bc3_2 86 KiB conda yaml
yarl 1.18.3 py312h998013c_1 142.1 KiB conda yarl
zarr 2.18.4 pyhd8ed1ab_0 156.7 KiB conda zarr
zeromq 4.3.5 hc1bb282_7 275 KiB conda zeromq
zfp 1.0.1 h1c5d8ea_2 195.4 KiB conda zfp
zict 3.0.0 pyhd8ed1ab_1 35.5 KiB conda zict
zipp 3.21.0 pyhd8ed1ab_1 21.3 KiB conda zipp
zlib 1.3.1 h8359307_2 75.8 KiB conda zlib
zlib-ng 2.2.4 h13dfb9a_0 85.3 KiB conda zlib-ng
zstandard 0.23.0 py312h15fbf35_1 323 KiB conda zstandard
zstd 1.5.6 hb46c0d2_0 395.6 KiB conda zstd
❯ pixi shell
❯ python
Python 3.12.8 | packaged by conda-forge | (main, Dec 5 2024, 14:19:53) [Clang 18.1.8 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import spatialdata
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/jnimoca/Jose_BI/spatialdata_test/.pixi/envs/default/lib/python3.12/site-packages/spatialdata/__init__.py", line 6, in <module>
import dask.dataframe as dd
File "/Users/jnimoca/Jose_BI/spatialdata_test/.pixi/envs/default/lib/python3.12/site-packages/dask/dataframe/__init__.py", line 14, in <module>
_dask_expr_enabled()
File "/Users/jnimoca/Jose_BI/spatialdata_test/.pixi/envs/default/lib/python3.12/site-packages/dask/dataframe/__init__.py", line 9, in _dask_expr_enabled
raise NotImplementedError("The legacy implementation is no longer supported")
NotImplementedError: The legacy implementation is no longer supported
Describe the bug Trying to install spatialdata with pixi fails. This same command worked before.
Expected behavior A working environment
Desktop:
- OS: macOS
- Version Sonoma 14.0
similar things I have tried
pixi add python spatialdata
#fails same as before
pixi add python
pixi add spatialdata --pypi
× failed to solve the pypi requirements of 'default' 'osx-arm64'
╰─▶ Build backend failed to determine requirements with `build_wheel()` (exit status: 1)
[stderr]
Traceback (most recent call last):
File "<string>", line 14, in <module>
requires = get_requires_for_build({})
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpIsYuEi/lib/python3.13/site-packages/setuptools/
build_meta.py", line 334, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpIsYuEi/lib/python3.13/site-packages/setuptools/
build_meta.py", line 304, in _get_build_requires
self.run_setup()
~~~~~~~~~~~~~~^^
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpIsYuEi/lib/python3.13/site-packages/setuptools/
build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpIsYuEi/lib/python3.13/site-packages/setuptools/
build_meta.py", line 320, in run_setup
exec(code, locals())
~~~~^^^^^^^^^^^^^^^^
File "<string>", line 50, in <module>
File "<string>", line 47, in _guard_py_ver
RuntimeError: Cannot install on Python version 3.13.1; only versions >=3.6,<3.10 are supported.
This actually worked!
❯ pixi init
✔ Created /Users/jnimoca/Jose_BI/sdata_test_5/pixi.toml
❯ pixi add "python>=3.6,<3.10"
✔ Added python>=3.6,<3.10
❯ pixi add spatialdata --pypi
✔ Added spatialdata >=0.2.5.post0, <0.3
Added these as pypi-dependencies.
❯ pixi shell
❯ python
Python 3.9.21 | packaged by conda-forge | (main, Dec 5 2024, 13:47:18)
[Clang 18.1.8 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import spatialdata
/Users/jnimoca/Jose_BI/sdata_test_5/.pixi/envs/default/lib/python3.9/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored
warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)
>>> spatialdata.SpatialData
<class 'spatialdata._core.spatialdata.SpatialData'>
>>> spatialdata.__version__
'0.2.5.post0'
Making it work with all the packages I want:
❯ pixi init
✔ Created /Users/jnimoca/Jose_BI/sdata_test_6/pixi.toml
❯ pixi add "python>=3.6,<3.10" pandas anndata numpy spatialdata spatialdata-plot ipykernel
✔ Added python>=3.6,<3.10
✔ Added pandas >=2.2.3,<3
✔ Added anndata >=0.10.9,<0.11
✔ Added numpy >=1.26.4,<2
✔ Added spatialdata >=0.2.3,<0.3
✔ Added spatialdata-plot >=0.2.7,<0.3
✔ Added ipykernel >=6.29.5,<7
❯ pixi shell
❯ python
Python 3.9.21 | packaged by conda-forge | (main, Dec 5 2024, 13:47:18)
[Clang 18.1.8 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import spatialdata
>>> spatialdata.SpatialData
<class 'spatialdata._core.spatialdata.SpatialData'>
>>> spatialdata.__version__
'0.2.3'
I now try to install the latest version, aka spatialdata 0.3 Unfortunately, I have not been able to make it work
First I tried to clone repo locally, and link it manually. I was not able to make this work. See https://github.com/prefix-dev/pixi/issues/1569
Second, I try linking the github repo directly
[pypi-dependencies]
spatialdata = { git = "https://github.com/scverse/spatialdata.git" }
This lead to the following issue:
[dependencies]
python = ">=3.6,<3.10"
[pypi-dependencies]
spatialdata = { git = "https://github.com/scverse/spatialdata.git" }
❯ pixi install
× failed to solve the pypi requirements of 'default' 'osx-arm64'
├─▶ failed to resolve pypi dependencies
╰─▶ Because the current Python version (3.9.21) does not satisfy Python>=3.10,<3.13 and
spatialdata==0.3.1.dev20+gc206323 depends on Python>=3.10,<3.13, we can conclude that
spatialdata==0.3.1.dev20+gc206323 cannot be used.
And because only spatialdata==0.3.1.dev20+gc206323 is available and you require
spatialdata, we can conclude that your requirements are unsatisfiable.
× failed to solve the pypi requirements of 'default' 'osx-arm64'
├─▶ failed to resolve pypi dependencies
╰─▶ Because the current Python version (3.9.21) does not satisfy Python>=3.10,<3.13 and
spatialdata==0.3.1.dev20+gc206323 depends on Python>=3.10,<3.13, we can conclude that
spatialdata==0.3.1.dev20+gc206323 cannot be used.
And because only spatialdata==0.3.1.dev20+gc206323 is available and you require
spatialdata, we can conclude that your requirements are unsatisfiable.
Following this comment I decide to force python >=3.10,<3.13, but it still ran into an error.
[dependencies]
python = ">=3.10,<3.13"
[pypi-dependencies]
spatialdata = { git = "https://github.com/scverse/spatialdata.git" }
❯ pixi install
× failed to solve the pypi requirements of 'default' 'osx-arm64'
╰─▶ Build backend failed to determine requirements with `build_wheel()` (exit status: 1)
[stderr]
Traceback (most recent call last):
File "<string>", line 14, in <module>
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-
v0/.tmpx6TjvT/lib/python3.12/site-packages/setuptools/build_meta.py", line 334, in
get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpx6TjvT/lib/
python3.12/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
self.run_setup()
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpx6TjvT/lib/
python3.12/site-packages/setuptools/build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
File "/Users/jnimoca/Library/Caches/rattler/cache/uv-cache/builds-v0/.tmpx6TjvT/lib/
python3.12/site-packages/setuptools/build_meta.py", line 320, in run_setup
exec(code, locals())
File "<string>", line 50, in <module>
File "<string>", line 47, in _guard_py_ver
RuntimeError: Cannot install on Python version 3.12.8; only versions >=3.6,<3.10 are
supported.
Hi, thanks for sharing this. @melonora and I are actually thinking to add a lockfile for pixi, so we started looking into it. This is mainly motivated by the fact that we cannot offer spatialdata on conda at the moment, due to dependencies (and dependencies of dependencies), not available. See more here: https://github.com/conda-forge/spatialdata-feedstock/pull/14#issuecomment-2648640172.
I'll comment the errors above:
RuntimeError: Cannot install on Python version 3.12.8; only versions >=3.6,<3.10 are supported.
I haven't seen this error before, not sure what's the problem here. 3.9 is quite a old version. I'll keep this error in mind in case I have an update to share.
spatialdata==0.3.1.dev20+gc206323 depends on Python>=3.10,<3.13, we can conclude tha
We restrict spatialdata to Python 3.13 because multiscale-spatial-image is currently restricted by 3.13. I was working on this right yesterday; currently having a problem (with pixi) on that repo. Please let me know if you have a solution for that. https://github.com/spatial-image/multiscale-spatial-image/pull/106
NotImplementedError: The legacy implementation is no longer supported
This is caused by this bug here: https://github.com/dask/dask/issues/11146. We currently have to restrict the versions of Dask we can depend on. We reached out to the pandas and dask devs and we are trying to work towards a solution.
Thank you @LucaMarconato and @melonora! Thank you for the context, and for working on it.
A lock file would be fantastic and user friendly solution.
If there is anything I can test on my side, please let me know. For now I will work with mamba/conda env.
Also, feel free to close this or move it into a discussion.
It sounds great! As a disclaimer, we are not working actively on this, but probably the sooner we have this the better.
For the moment I'd ask you please if you could try doing like what suggested in this post for the multiscale-spatial-image repo: https://github.com/spatial-image/multiscale-spatial-image/pull/105#issuecomment-2649134616 and give feedback there. My pixi gets stuck while trying to run pixi install -a. Not sure if there is a problem with my machine, with the env, or with the pixi version I'm using.