Quirks installing spatialdata with pixi

[josenimo]

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 :)

1. 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
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python                            3.12.8        hc22306f_1_cpython             12.4 MiB   conda  python
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python_abi                        3.12          5_cp312                        6.1 KiB    conda  python_abi
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qhull                             2020.2        h420ef59_5                     504.3 KiB  conda  qhull
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re2                               2024.07.02    h6589ca4_2                     26.2 KiB   conda  re2
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rich                              13.9.4        pyhd8ed1ab_1                   181.3 KiB  conda  rich
scanpy                            1.10.4        pyhd8ed1ab_0                   1.9 MiB    conda  scanpy
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six                               1.17.0        pyhd8ed1ab_0                   16 KiB     conda  six
sleef                             3.8           h8391f65_0                     571 KiB    conda  sleef
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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
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stdlib-list                       0.11.0        pyhd8ed1ab_1                   25.7 KiB   conda  stdlib-list
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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
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tqdm                              4.67.1        pyhd8ed1ab_1                   87.4 KiB   conda  tqdm
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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
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uriparser                         0.9.8         h00cdb27_0                     39.7 KiB   conda  uriparser
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wcwidth                           0.2.13        pyhd8ed1ab_1                   31.8 KiB   conda  wcwidth
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x265                              3.5           hbc6ce65_3                     1.7 MiB    conda  x265
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xarray-spatial                    0.4.0         pyhd8ed1ab_1                   1.6 MiB    conda  xarray-spatial
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xyzservices                       2025.1.0      pyhd8ed1ab_0                   47.5 KiB   conda  xyzservices
yaml                              0.2.5         h3422bc3_2                     86 KiB     conda  yaml
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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
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❯ 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'

[josenimo]

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 prefix-dev/pixi#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.

[LucaMarconato]

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: conda-forge/spatialdata-feedstock#14 (comment).

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. spatial-image/multiscale-spatial-image#106

NotImplementedError: The legacy implementation is no longer supported

This is caused by this bug here: dask/dask#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.

[josenimo]

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.

[LucaMarconato]

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: spatial-image/multiscale-spatial-image#105 (comment) 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.