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conda-forge / qgis-feedstock

A conda-smithy repository for qgis.
BSD 3-Clause "New" or "Revised" License
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macOS: import from scipy fails and starts new QGIS instance #405

Open jakimowb opened 4 months ago

jakimowb commented 4 months ago

Solution to issue cannot be found in the documentation.

Issue

I create a new empty conda environment with QGIS and scipy as:

mamba create -n example
mamba activate example
conda config --add channels conda-forge
conda config --set channel_priority strict
mamba install qgis scipy

When I now start QGIS and from scipy.interpolate import interp1d from the python shell, (the first) QGIS gets stucked and starts a second QGIS instance.

First QGIS

The first QGIS instance does not respond anymore, until the second is closed:

image

It shows the following python shell stacktrace:

# Python Console
# Use iface to access QGIS API interface or type '?' for more info
# Security warning: typing commands from an untrusted source can harm your computer
from scipy.interpolate import interp1d
Traceback (most recent call last):
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/code.py", line 90, in runcode
    exec(code, self.locals)
  File "<input>", line 1, in <module>
  File "/Users/jakimowb/miniforge3/envs/example/share/qgis/python/qgis/utils.py", line 888, in _import
    mod = _builtin_import(name, globals, locals, fromlist, level)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/site-packages/scipy/__init__.py", line 67, in <module>
    from scipy._lib import _pep440
  File "/Users/jakimowb/miniforge3/envs/example/share/qgis/python/qgis/utils.py", line 888, in _import
    mod = _builtin_import(name, globals, locals, fromlist, level)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/site-packages/scipy/_lib/__init__.py", line 12, in <module>
    from scipy._lib._testutils import PytestTester
  File "/Users/jakimowb/miniforge3/envs/example/share/qgis/python/qgis/utils.py", line 888, in _import
    mod = _builtin_import(name, globals, locals, fromlist, level)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/site-packages/scipy/_lib/_testutils.py", line 21, in <module>
    _tags = list(sys_tags())
            ^^^^^^^^^^^^^^^^
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/site-packages/packaging/tags.py", line 543, in sys_tags
    yield from cpython_tags(warn=warn)
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/site-packages/packaging/tags.py", line 212, in cpython_tags
    platforms = list(platforms or platform_tags())
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/jakimowb/miniforge3/envs/example/lib/python3.12/site-packages/packaging/tags.py", line 412, in mac_platforms
    version = cast("MacVersion", tuple(map(int, version_str.split(".")[:2])))
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: ''

Second QGIS

The new QGIS instance shows several warnings & errors in the log panel. Users/jakimow is the current directory from which the 1st qgis instance was started from shell:

General Log:

2024-02-22T11:41:07     WARNING    Unable to load /Users/jakimowb/-sS
2024-02-22T11:41:07     WARNING    Unable to load /Users/jakimowb/-c
2024-02-22T11:41:07     WARNING    Unable to load /Users/jakimowb/import platform; print(platform.mac_ver()[0])

Messages Log:

2024-02-22T11:41:07     CRITICAL    Authentication System : DISABLED. Resources authenticating via the system can not be accessed
2024-02-22T11:41:07     CRITICAL    Invalid Data Source : /Users/jakimowb/-sS is not a valid or recognized data source.
2024-02-22T11:41:07     CRITICAL    Invalid Data Source : /Users/jakimowb/-c is not a valid or recognized data source.
2024-02-22T11:41:07     CRITICAL    Invalid Data Source : /Users/jakimowb/import platform; print(platform.mac_ver()[0]) is not a valid or recognized data source.

All plugins are disabled. Open the plugin manager fails with:

image

System tested on

macBook Pro, 2020 1,4 GHz Quad-Core Intel Core i5 macOS 14.3.1 Sonoma

QGIS version 3.34.3-Prizren QGIS code branch Release 3.34
Qt version 5.15.8
Python version 3.12.2
GDAL/OGR version 3.8.3
PROJ version 9.3.1
EPSG Registry database version v10.098 (2023-11-24)
GEOS version 3.12.1-CAPI-1.18.1
SQLite version 3.45.1
PDAL version 2.6.3
PostgreSQL client version unknown
SpatiaLite version 5.1.0
QWT version 6.2.0
QScintilla2 version 2.14.1
OS version macOS 10.16
       

Active Python plugins processing | 2.12.99 grassprovider | 2.12.99 db_manager | 0.1.20 MetaSearch | 0.3.6

Installed packages

# packages in environment at /Users/jakimowb/miniforge3/envs/example:
#
# Name                    Version                   Build  Channel
azure-core-cpp            1.10.3               hbb1e571_1    conda-forge
azure-storage-blobs-cpp   12.10.0              he51d815_0    conda-forge
azure-storage-common-cpp  12.5.0               hf4badfb_2    conda-forge
blosc                     1.21.5               heccf04b_0    conda-forge
brotli-python             1.1.0           py312heafc425_1    conda-forge
bzip2                     1.0.8                h10d778d_5    conda-forge
c-ares                    1.26.0               h10d778d_0    conda-forge
ca-certificates           2024.2.2             h8857fd0_0    conda-forge
cairo                     1.18.0               h99e66fa_0    conda-forge
ceres-solver              2.2.0                haa0d064_2    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cfitsio                   4.3.1                h60fb419_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
coverage                  7.4.2           py312h41838bb_0    conda-forge
curl                      8.5.0                h726d00d_0    conda-forge
draco                     1.5.7                h7728843_0    conda-forge
eigen                     3.4.0                h1c7c39f_0    conda-forge
exiv2                     0.28.2               h239cba9_0    conda-forge
expat                     2.5.0                hf0c8a7f_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_1    conda-forge
fontconfig                2.14.2               h5bb23bf_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               h60636b9_2    conda-forge
freexl                    2.0.0                h3ec172f_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gdal                      3.8.3           py312h1be6df0_2    conda-forge
geos                      3.12.1               h93d8f39_0    conda-forge
geotiff                   1.7.1               h509af15_15    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gflags                    2.2.2             hb1e8313_1004    conda-forge
giflib                    5.2.1                hb7f2c08_3    conda-forge
glib                      2.78.4               h2d185b6_0    conda-forge
glib-tools                2.78.4               h2d185b6_0    conda-forge
glog                      0.7.0                h31b1b29_0    conda-forge
gmp                       6.3.0                h93d8f39_0    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
gst-plugins-base          1.22.9               h3fb38fc_0    conda-forge
gstreamer                 1.22.9               hf63bbb8_0    conda-forge
hdf4                      4.2.15               h8138101_7    conda-forge
hdf5                      1.14.3          nompi_h691f4bf_100    conda-forge
httplib2                  0.22.0             pyhd8ed1ab_0    conda-forge
icu                       73.2                 hf5e326d_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
jinja2                    3.1.3              pyhd8ed1ab_0    conda-forge
json-c                    0.17                 h8e11ae5_0    conda-forge
kealib                    1.5.3                h5f07ac3_0    conda-forge
khronos-opencl-icd-loader 2023.04.17           hb7f2c08_0    conda-forge
krb5                      1.21.2               hb884880_0    conda-forge
laz-perf                  3.4.0                h1c7c39f_0    conda-forge
lcms2                     2.16                 ha2f27b4_0    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libabseil                 20230802.1      cxx17_h048a20a_0    conda-forge
libaec                    1.1.2                he965462_1    conda-forge
libarchive                3.7.2                hd35d340_1    conda-forge
libblas                   3.9.0           21_osx64_openblas    conda-forge
libboost-headers          1.84.0               h694c41f_1    conda-forge
libbrotlicommon           1.1.0                h0dc2134_1    conda-forge
libbrotlidec              1.1.0                h0dc2134_1    conda-forge
libbrotlienc              1.1.0                h0dc2134_1    conda-forge
libcblas                  3.9.0           21_osx64_openblas    conda-forge
libclang                  15.0.7          default_h6b1ee41_4    conda-forge
libclang13                15.0.7          default_h89cd682_4    conda-forge
libcrc32c                 1.1.2                he49afe7_0    conda-forge
libcurl                   8.5.0                h726d00d_0    conda-forge
libcxx                    16.0.6               hd57cbcb_0    conda-forge
libdeflate                1.19                 ha4e1b8e_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 h10d778d_2    conda-forge
libexpat                  2.5.0                hf0c8a7f_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgdal                   3.8.3                hf248df1_2    conda-forge
libgfortran               5.0.0           13_2_0_h97931a8_3    conda-forge
libgfortran5              13.2.0               h2873a65_3    conda-forge
libglib                   2.78.4               hab64008_0    conda-forge
libgoogle-cloud           2.12.0               he77a663_5    conda-forge
libgrpc                   1.60.1               h038e8f1_0    conda-forge
libhwloc                  2.9.3           default_h24e0189_1009    conda-forge
libiconv                  1.17                 hd75f5a5_2    conda-forge
libjpeg-turbo             3.0.0                h0dc2134_1    conda-forge
libkml                    1.3.0             hab3ca0e_1018    conda-forge
liblapack                 3.9.0           21_osx64_openblas    conda-forge
libllvm15                 15.0.7               hbedff68_4    conda-forge
libnetcdf                 4.9.2           nompi_h7760872_113    conda-forge
libnghttp2                1.58.0               h64cf6d3_1    conda-forge
libogg                    1.3.4                h35c211d_1    conda-forge
libopenblas               0.3.26          openmp_hfef2a42_0    conda-forge
libopus                   1.3.1                hc929b4f_1    conda-forge
libpng                    1.6.42               h92b6c6a_0    conda-forge
libpq                     16.2                 ha925e61_0    conda-forge
libprotobuf               4.25.1               hc4f2305_2    conda-forge
libre2-11                 2023.06.02           h4694dbf_0    conda-forge
librttopo                 1.1.0               hf05f67e_15    conda-forge
libspatialindex           1.9.3                he49afe7_4    conda-forge
libspatialite             5.1.0                hebe6af1_4    conda-forge
libsqlite                 3.45.1               h92b6c6a_0    conda-forge
libssh2                   1.11.0               hd019ec5_0    conda-forge
libtasn1                  4.19.0               hb7f2c08_0    conda-forge
libtiff                   4.6.0                h684deea_2    conda-forge
libvorbis                 1.3.7                h046ec9c_0    conda-forge
libwebp                   1.3.2                h44782d1_1    conda-forge
libwebp-base              1.3.2                h0dc2134_0    conda-forge
libxml2                   2.12.5               hc0ae0f7_0    conda-forge
libxslt                   1.1.39               h03b04e6_0    conda-forge
libzip                    1.10.1               hc158999_3    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
llvm-openmp               17.0.6               hb6ac08f_0    conda-forge
lxml                      5.1.0           py312h799ce31_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
lzo                       2.10              haf1e3a3_1000    conda-forge
markupsafe                2.1.5           py312h41838bb_0    conda-forge
metis                     5.1.0             he965462_1007    conda-forge
minizip                   4.0.4                h37d7099_0    conda-forge
mock                      5.1.0              pyhd8ed1ab_0    conda-forge
mpfr                      4.2.1                h0c69b56_0    conda-forge
mysql-common              8.0.33               h1d20c9b_6    conda-forge
mysql-libs                8.0.33               hed35180_6    conda-forge
ncurses                   6.4                  h93d8f39_2    conda-forge
nitro                     2.7.dev8             he965462_0    conda-forge
nose2                     0.9.2                      py_0    conda-forge
nspr                      4.35                 hea0b92c_0    conda-forge
nss                       3.98                 ha05da47_0    conda-forge
numpy                     1.26.4          py312he3a82b2_0    conda-forge
openjpeg                  2.5.0                ha4da562_3    conda-forge
openssl                   3.2.1                hd75f5a5_0    conda-forge
owslib                    0.29.3             pyhd8ed1ab_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pcre2                     10.42                h0ad2156_0    conda-forge
pdal                      2.6.3                h82f9e37_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h73e2aa4_0    conda-forge
plotly                    5.19.0             pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
poppler                   24.02.0              h0c752f9_0    conda-forge
poppler-data              0.4.12               hd8ed1ab_0    conda-forge
postgresql                16.2                 hbd19fd8_0    conda-forge
proj                      9.3.1                h81faed2_0    conda-forge
psycopg2                  2.9.9           py312hca9e88b_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyproj                    3.6.1           py312h14d93e9_5    conda-forge
pyqt                      5.15.9          py312hd74d816_5    conda-forge
pyqt5-sip                 12.12.2         py312he36337a_5    conda-forge
pyqtwebkit                5.15.9          py312h5ae8335_2    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.12.2          h9f0c242_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.12                    4_cp312    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py312h104f124_1    conda-forge
qca                       2.3.8                h3036dd7_0    conda-forge
qgis                      3.34.3          py312h5fa82b5_2    conda-forge
qjson                     0.9.0             hed3eaa1_1009    conda-forge
qscintilla2               2.14.1          py312h12cbc42_0    conda-forge
qt-main                   5.15.8              h4385fff_19    conda-forge
qtkeychain                0.14.2               had6348c_0    conda-forge
qtwebkit                  5.212               h3b777d0_16    conda-forge
qwt                       6.2.0                hed3eaa1_6    conda-forge
re2                       2023.06.02           hd34609a_0    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
scipy                     1.12.0          py312h8adb940_2    conda-forge
setuptools                69.1.0             pyhd8ed1ab_1    conda-forge
sip                       6.7.12          py312h444b7ae_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.10               h225ccf5_0    conda-forge
sqlite                    3.45.1               h7461747_0    conda-forge
suitesparse               5.10.1               h4bf45ed_3    conda-forge
tbb                       2021.11.0            h7728843_1    conda-forge
tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge
tiledb                    2.19.1               h8fd0293_0    conda-forge
tk                        8.6.13               h1abcd95_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tzcode                    2024a                h10d778d_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uriparser                 0.9.7                hf0c8a7f_1    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xerces-c                  3.2.5                hbbe9ea5_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
zlib                      1.2.13               h8a1eda9_5    conda-forge
zstd                      1.5.5                h829000d_0    conda-forge

Environment info

active environment : example
    active env location : /Users/jakimowb/miniforge3/envs/example
            shell level : 1
       user config file : /Users/jakimowb/.condarc
 populated config files : /Users/jakimowb/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.10.13.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake
                          __conda=23.11.0=0
                          __osx=14.3.1=0
                          __unix=0=0
       base environment : /Users/jakimowb/miniforge3  (writable)
      conda av data dir : /Users/jakimowb/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/jakimowb/miniforge3/pkgs
                          /Users/jakimowb/.conda/pkgs
       envs directories : /Users/jakimowb/miniforge3/envs
                          /Users/jakimowb/.conda/envs
               platform : osx-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Darwin/23.3.0 OSX/14.3.1 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5
                UID:GID : 501:20
             netrc file : None
           offline mode : False
gillins commented 4 months ago

Weird. Fine under Linux, unfortunately I don't have OSX to test. Any ideas?

jakimowb commented 4 months ago

It might be caused by changes that were introduced with scipy 1.12.

As a workaround I use conda install "scipy<1.12"

gillins commented 4 months ago

Might be worth raising an issue with scipy-feedstock...