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 supportedDescribe 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'
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 :)
pixi list
Describe the bug
Trying to install spatialdata with pixi fails.
This same command worked before.
Expected behavior
A working environment
Desktop:
similar things I have tried
This actually worked!
Making it work with all the packages I want: