lifelines conda packages <0.29 need to specify scipy <1.14 requirement

[hermidalc]

Solution to issue cannot be found in the documentation.

• [X] I checked the documentation.

Issue

For all lifelines conda packages <0.29, you need to specify scipy <1.14 requirement, otherwise you will get this error below because as of 1.14 integrate.trapz is gone

File "/home/hermidalc/soft/miniforge3/envs/sksurv-bio-workflows-r41/lib/python3.10/site-packages/lifelines/fitters/__init__.py", line 21, in <module>
    from scipy.integrate import trapz
ImportError: cannot import name 'trapz' from 'scipy.integrate'

Installed packages

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.9                hd590300_0    conda-forge
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h2372a71_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
astor                     0.8.1              pyh9f0ad1d_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
autograd                  1.6.2              pyhd8ed1ab_0    conda-forge
autograd-gamma            0.5.0              pyh9f0ad1d_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
binutils_impl_linux-64    2.40                 ha1999f0_7    conda-forge
bioconductor-affy         1.72.0            r41hc0cfd56_2    bioconda
bioconductor-affyio       1.64.0            r41hc0cfd56_2    bioconda
bioconductor-affyplm      1.70.0            r41hc0cfd56_2    bioconda
bioconductor-annotate     1.72.0            r41hdfd78af_0    bioconda
bioconductor-annotationdbi 1.56.2            r41hdfd78af_0    bioconda
bioconductor-apeglm       1.16.0            r41hc247a5b_2    bioconda
bioconductor-aroma.light  3.24.0            r41hdfd78af_0    bioconda
bioconductor-biobase      2.54.0            r41hc0cfd56_2    bioconda
bioconductor-biocfilecache 2.2.0             r41hdfd78af_0    bioconda
bioconductor-biocgenerics 0.40.0            r41hdfd78af_0    bioconda
bioconductor-biocio       1.4.0             r41hdfd78af_0    bioconda
bioconductor-biocparallel 1.28.3            r41hc247a5b_1    bioconda
bioconductor-biomart      2.50.0            r41hdfd78af_0    bioconda
bioconductor-biostrings   2.62.0            r41hc0cfd56_2    bioconda
bioconductor-delayedarray 0.20.0            r41hc0cfd56_2    bioconda
bioconductor-deseq2       1.34.0            r41hc247a5b_3    bioconda
bioconductor-edaseq       2.28.0            r41hdfd78af_0    bioconda
bioconductor-edger        3.36.0            r41hc247a5b_2    bioconda
bioconductor-gcrma        2.66.0            r41hc0cfd56_2    bioconda
bioconductor-genefilter   1.76.0            r41h38f54d8_2    bioconda
bioconductor-geneplotter  1.72.0            r41hdfd78af_0    bioconda
bioconductor-genomeinfodb 1.30.1            r41hdfd78af_0    bioconda
bioconductor-genomeinfodbdata 1.2.7             r41hdfd78af_2    bioconda
bioconductor-genomicalignments 1.30.0            r41hc0cfd56_2    bioconda
bioconductor-genomicfeatures 1.46.1            r41hdfd78af_0    bioconda
bioconductor-genomicranges 1.46.1            r41hc0cfd56_1    bioconda
bioconductor-iranges      2.28.0            r41hc0cfd56_2    bioconda
bioconductor-keggrest     1.34.0            r41hdfd78af_0    bioconda
bioconductor-limma        3.50.3            r41hc0cfd56_0    bioconda
bioconductor-matrixgenerics 1.6.0             r41hdfd78af_0    bioconda
bioconductor-nanostringdiff 1.24.0            r41hc247a5b_2    bioconda
bioconductor-preprocesscore 1.56.0            r41hc0cfd56_3    bioconda
bioconductor-rhtslib      1.26.0            r41hc0cfd56_2    bioconda
bioconductor-rsamtools    2.10.0            r41hc247a5b_2    bioconda
bioconductor-rtracklayer  1.54.0            r41hd029910_0    bioconda
bioconductor-ruvseq       1.28.0            r41hdfd78af_0    bioconda
bioconductor-s4vectors    0.32.4            r41hc0cfd56_0    bioconda
bioconductor-shortread    1.52.0            r41hc247a5b_2    bioconda
bioconductor-summarizedexperiment 1.24.0            r41hdfd78af_0    bioconda
bioconductor-sva          3.42.0            r41hc0cfd56_2    bioconda
bioconductor-xvector      0.34.0            r41hc0cfd56_2    bioconda
bioconductor-zlibbioc     1.40.0            r41hc0cfd56_2    bioconda
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.28.1               hd590300_0    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            hbbf8b49_1016    conda-forge
certifi                   2024.6.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.1           py310hd41b1e2_0    conda-forge
curl                      8.4.0                hca28451_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.8.2           py310h76e45a6_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
ecos                      2.0.14          py310h261611a_0    conda-forge
eli5                      0.13.0             pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.6.2                h59595ed_0    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_2    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.53.0          py310hc51659f_0    conda-forge
formulaic                 1.0.1              pyhd8ed1ab_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
gcc_impl_linux-64         14.1.0               h3c94d91_0    conda-forge
gdk-pixbuf                2.42.10              h6b639ba_2    conda-forge
gettext                   0.22.5               h59595ed_2    conda-forge
gettext-tools             0.22.5               h59595ed_2    conda-forge
gfortran_impl_linux-64    14.1.0               he4a1faa_0    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
glib                      2.78.1               hfc55251_0    conda-forge
glib-tools                2.78.1               hfc55251_0    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
graphlib-backport         1.0.3              pyhd8ed1ab_0    conda-forge
graphviz                  8.1.0                h28d9a01_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.22.5               hf7dbed1_0    conda-forge
gstreamer                 1.22.5               h98fc4e7_0    conda-forge
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h977cf35_4    conda-forge
gxx_impl_linux-64         14.1.0               h2879b86_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
harfbuzz                  7.3.0                hdb3a94d_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.7                pyhd8ed1ab_0    conda-forge
importlib-metadata        8.0.0              pyha770c72_0    conda-forge
importlib_metadata        8.0.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
interface_meta            1.3.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.26.0             pyh707e725_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py310hff52083_0    conda-forge
jsonschema                4.22.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.22.0             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py310hff52083_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.1             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.2             pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_17    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py310hd41b1e2_1    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.15                 haa2dc70_1    conda-forge
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libasprintf               0.22.5               h661eb56_2    conda-forge
libasprintf-devel         0.22.5               h661eb56_2    conda-forge
libblas                   3.9.0            22_linux64_mkl    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcap                    2.69                 h0f662aa_0    conda-forge
libcblas                  3.9.0            22_linux64_mkl    conda-forge
libclang                  15.0.7          default_h127d8a8_5    conda-forge
libclang13                15.0.7          default_h5d6823c_5    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.3                h59595ed_0    conda-forge
libgcc-devel_linux-64     14.1.0             h5d3d1c9_100    conda-forge
libgcc-ng                 14.1.0               h77fa898_0    conda-forge
libgcrypt                 1.11.0               h4ab18f5_0    conda-forge
libgd                     2.3.3                hfa28ad5_6    conda-forge
libgettextpo              0.22.5               h59595ed_2    conda-forge
libgettextpo-devel        0.22.5               h59595ed_2    conda-forge
libgfortran-ng            14.1.0               h69a702a_0    conda-forge
libgfortran5              14.1.0               hc5f4f2c_0    conda-forge
libglib                   2.78.1               hebfc3b9_0    conda-forge
libgomp                   14.1.0               h77fa898_0    conda-forge
libgpg-error              1.50                 h4f305b6_0    conda-forge
libhwloc                  2.9.3           default_h554bfaf_1009    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             2.1.5.1              hd590300_1    conda-forge
liblapack                 3.9.0            22_linux64_mkl    conda-forge
libllvm15                 15.0.7               h5cf9203_3    conda-forge
libnghttp2                1.58.0               h47da74e_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libogg                    1.3.5                h4ab18f5_0    conda-forge
libopenblas               0.3.27          pthreads_h413a1c8_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libosqp                   0.6.3                h59595ed_0    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
libpq                     15.4                 hfc447b1_2    conda-forge
libqdldl                  0.1.5                h27087fc_1    conda-forge
librsvg                   2.56.3               h98fae49_0    conda-forge
libsanitizer              14.1.0               hcba0ae0_0    conda-forge
libsndfile                1.2.2                hc60ed4a_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  14.1.0             h5d3d1c9_100    conda-forge
libstdcxx-ng              14.1.0               hc0a3c3a_0    conda-forge
libsystemd0               255                  h3516f8a_1    conda-forge
libtiff                   4.5.1                h8b53f26_1    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.3.1                hbf2b3c1_0    conda-forge
libwebp-base              1.3.1                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxkbcommon              1.6.0                h5d7e998_0    conda-forge
libxml2                   2.11.5               h0d562d8_0    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
lifelines                 0.27.8             pyhd8ed1ab_0    conda-forge
llvm-openmp               18.1.8               hf5423f3_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                2.1.5           py310h2372a71_0    conda-forge
matplotlib                3.9.0           py310hff52083_0    conda-forge
matplotlib-base           3.9.0           py310h0b1de36_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mkl                       2024.2.0           ha957f24_663    conda-forge
mpg123                    1.32.6               h59595ed_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.33               hf1915f5_6    conda-forge
mysql-libs                8.0.33               hca2cd23_6    conda-forge
natsort                   8.4.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  h59595ed_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
nlopt                     2.7.1           py310h236f06b_5    conda-forge
notebook                  7.2.1              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.101                h593d115_0    conda-forge
numexpr                   2.7.3           py310hb5077e9_1    conda-forge
numpy                     1.26.4          py310hb13e2d6_0    conda-forge
openjpeg                  2.5.0                hfec8fc6_2    conda-forge
openssl                   3.1.6                h4ab18f5_0    conda-forge
osqp                      0.6.7.post0     py310hf9f9076_0    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3           py310h9b08913_1    conda-forge
pandoc                    2.19.2               h32600fe_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.14              heaa33ce_1    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.0          py310h582fbeb_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
ply                       3.11               pyhd8ed1ab_2    conda-forge
pooch                     1.8.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
psutil                    6.0.0           py310hc51659f_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio-client         16.1                 hb77b528_5    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.9          py310h04931ad_5    conda-forge
pyqt5-sip                 12.12.2         py310hc6cd4ac_5    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.13         hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-graphviz           0.20.3             pyh717bed2_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    4_cp310    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_1    conda-forge
pyzmq                     26.0.3          py310h6883aea_0    conda-forge
qdldl-python              0.1.5.post2     py310hcc13569_1    conda-forge
qhull                     2020.2               h4bd325d_2    conda-forge
qt-main                   5.15.8              h7fe3ca9_15    conda-forge
r-ashr                    2.2_54            r41h7525677_1    conda-forge
r-askpass                 1.1               r41h06615bd_3    conda-forge
r-assertthat              0.2.1             r41hc72bb7e_3    conda-forge
r-backports               1.4.1             r41h06615bd_1    conda-forge
r-base                    4.1.3               hb1b9b86_10    conda-forge
r-base64enc               0.1_3           r41h06615bd_1005    conda-forge
r-bbmle                   1.0.25            r41hc72bb7e_1    conda-forge
r-bdsmatrix               1.3_6             r41h06615bd_1    conda-forge
r-bh                      1.81.0_1          r41hc72bb7e_0    conda-forge
r-biocmanager             1.30.21           r41hc72bb7e_0    conda-forge
r-bit                     4.0.5             r41h06615bd_0    conda-forge
r-bit64                   4.0.5             r41h06615bd_1    conda-forge
r-bitops                  1.0_7             r41h06615bd_1    conda-forge
r-blob                    1.2.4             r41hc72bb7e_0    conda-forge
r-boot                    1.3_28.1          r41hc72bb7e_0    conda-forge
r-broom                   1.0.5             r41hc72bb7e_0    conda-forge
r-bslib                   0.5.0             r41hc72bb7e_0    conda-forge
r-cachem                  1.0.8             r41h57805ef_0    conda-forge
r-callr                   3.7.3             r41hc72bb7e_0    conda-forge
r-caret                   6.0_94            r41h133d619_0    conda-forge
r-cellranger              1.1.0           r41hc72bb7e_1005    conda-forge
r-class                   7.3_22            r41h57805ef_0    conda-forge
r-cli                     3.6.1             r41h38f115c_0    conda-forge
r-clipr                   0.8.0             r41hc72bb7e_1    conda-forge
r-clock                   0.7.0             r41ha503ecb_0    conda-forge
r-cluster                 2.1.4             r41h8da6f51_0    conda-forge
r-coda                    0.19_4            r41hc72bb7e_1    conda-forge
r-codetools               0.2_19            r41hc72bb7e_0    conda-forge
r-colorspace              2.1_0             r41h133d619_0    conda-forge
r-commonmark              1.9.0             r41h133d619_0    conda-forge
r-conflicted              1.2.0             r41h785f33e_0    conda-forge
r-cpp11                   0.4.7             r41hc72bb7e_0    conda-forge
r-crayon                  1.5.2             r41hc72bb7e_1    conda-forge
r-crul                    1.4.0             r41h785f33e_0    conda-forge
r-curl                    4.3.3             r41hf9611b0_2    conda-forge
r-data.table              1.14.8            r41h133d619_0    conda-forge
r-dbi                     1.1.3             r41hc72bb7e_1    conda-forge
r-dbplyr                  2.3.2             r41hc72bb7e_0    conda-forge
r-deldir                  1.0_9             r41h61816a4_0    conda-forge
r-diagram                 1.6.5             r41ha770c72_1    conda-forge
r-digest                  0.6.31            r41h38f115c_0    conda-forge
r-dplyr                   1.1.2             r41ha503ecb_0    conda-forge
r-dtplyr                  1.3.1             r41hc72bb7e_0    conda-forge
r-e1071                   1.7_13            r41h38f115c_0    conda-forge
r-ellipsis                0.3.2             r41h06615bd_1    conda-forge
r-emdbook                 1.3.12            r41hc72bb7e_2    conda-forge
r-essentials              4.1             r41hd8ed1ab_2003    conda-forge
r-etrunct                 0.1             r41hc72bb7e_1004    conda-forge
r-evaluate                0.21              r41hc72bb7e_0    conda-forge
r-fansi                   1.0.4             r41h133d619_0    conda-forge
r-farver                  2.1.1             r41h7525677_1    conda-forge
r-fastmap                 1.1.1             r41h38f115c_0    conda-forge
r-filelock                1.0.2           r41h133d619_1003    conda-forge
r-fnn                     1.1.3.2           r41h38f115c_0    conda-forge
r-fontawesome             0.5.1             r41hc72bb7e_0    conda-forge
r-forcats                 1.0.0             r41hc72bb7e_0    conda-forge
r-foreach                 1.5.2             r41hc72bb7e_1    conda-forge
r-foreign                 0.8_84            r41h133d619_0    conda-forge
r-formatr                 1.14              r41hc72bb7e_0    conda-forge
r-fs                      1.6.2             r41ha503ecb_0    conda-forge
r-futile.logger           1.4.3           r41hc72bb7e_1004    conda-forge
r-futile.options          1.0.1           r41hc72bb7e_1003    conda-forge
r-future                  1.32.0            r41hc72bb7e_0    conda-forge
r-future.apply            1.11.0            r41hc72bb7e_0    conda-forge
r-gargle                  1.4.0             r41h785f33e_0    conda-forge
r-generics                0.1.3             r41hc72bb7e_1    conda-forge
r-ggplot2                 3.4.2             r41hc72bb7e_0    conda-forge
r-gistr                   0.9.0             r41hc72bb7e_1    conda-forge
r-glmnet                  4.1_7             r41haa30946_0    conda-forge
r-globals                 0.16.2            r41hc72bb7e_0    conda-forge
r-glue                    1.6.2             r41h06615bd_1    conda-forge
r-googledrive             2.1.0             r41hc72bb7e_0    conda-forge
r-googlesheets4           1.1.0             r41h785f33e_0    conda-forge
r-gower                   1.0.1             r41h133d619_0    conda-forge
r-gtable                  0.3.3             r41hc72bb7e_0    conda-forge
r-hardhat                 1.3.0             r41hc72bb7e_0    conda-forge
r-haven                   2.5.2             r41h38f115c_0    conda-forge
r-hexbin                  1.28.3            r41hac0b197_0    conda-forge
r-highr                   0.10              r41hc72bb7e_0    conda-forge
r-hms                     1.1.3             r41hc72bb7e_0    conda-forge
r-htmltools               0.5.5             r41h38f115c_0    conda-forge
r-htmlwidgets             1.6.2             r41hc72bb7e_0    conda-forge
r-httpcode                0.3.0             r41ha770c72_2    conda-forge
r-httpuv                  1.6.11            r41ha503ecb_0    conda-forge
r-httr                    1.4.6             r41hc72bb7e_0    conda-forge
r-hwriter                 1.3.2.1           r41hc72bb7e_1    conda-forge
r-ids                     1.0.1             r41hc72bb7e_2    conda-forge
r-interp                  1.1_4             r41h38f115c_0    conda-forge
r-invgamma                1.1               r41hc72bb7e_2    conda-forge
r-ipred                   0.9_14            r41h133d619_0    conda-forge
r-irdisplay               1.1               r41hd8ed1ab_1    conda-forge
r-irkernel                1.3.2             r41h785f33e_0    conda-forge
r-irlba                   2.3.5.1           r41h5f7b363_0    conda-forge
r-isoband                 0.2.7             r41h38f115c_1    conda-forge
r-iterators               1.0.14            r41hc72bb7e_1    conda-forge
r-jpeg                    0.1_10            r41h0de940f_2    conda-forge
r-jquerylib               0.1.4             r41hc72bb7e_1    conda-forge
r-jsonlite                1.8.5             r41h57805ef_0    conda-forge
r-kernsmooth              2.23_21           r41h13b3f57_0    conda-forge
r-knitr                   1.43              r41hc72bb7e_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_2    conda-forge
r-lambda.r                1.2.4             r41hc72bb7e_2    conda-forge
r-later                   1.3.1             r41ha503ecb_0    conda-forge
r-lattice                 0.21_8            r41h133d619_0    conda-forge
r-latticeextra            0.6_30            r41hc72bb7e_1    conda-forge
r-lava                    1.7.2.1           r41hc72bb7e_0    conda-forge
r-lazyeval                0.2.2             r41h06615bd_3    conda-forge
r-lifecycle               1.0.3             r41hc72bb7e_1    conda-forge
r-listenv                 0.9.0             r41hc72bb7e_0    conda-forge
r-lme4                    1.1_33            r41ha503ecb_0    conda-forge
r-lobstr                  1.1.2             r41h38f115c_2    conda-forge
r-locfit                  1.5_9.7           r41h133d619_0    conda-forge
r-lubridate               1.9.2             r41h133d619_1    conda-forge
r-magrittr                2.0.3             r41h06615bd_1    conda-forge
r-maps                    3.4.1             r41h06615bd_1    conda-forge
r-mass                    7.3_58.3          r41h133d619_0    conda-forge
r-matrix                  1.5_4.1           r41h316c678_0    conda-forge
r-matrixstats             1.0.0             r41h57805ef_0    conda-forge
r-memoise                 2.0.1             r41hc72bb7e_1    conda-forge
r-mgcv                    1.8_42            r41he1ae0d6_0    conda-forge
r-mime                    0.12              r41h06615bd_1    conda-forge
r-minqa                   1.2.5             r41hb13c81a_0    conda-forge
r-mixsqp                  0.3_48            r41h9f5de39_0    conda-forge
r-mnormt                  2.1.1             r41h8da6f51_0    conda-forge
r-modelmetrics            1.2.2.2           r41h7525677_2    conda-forge
r-modelr                  0.1.11            r41hc72bb7e_0    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1005    conda-forge
r-mvtnorm                 1.2_2             r41h61816a4_0    conda-forge
r-nlme                    3.1_162           r41hac0b197_0    conda-forge
r-nloptr                  2.0.3             r41hb13c81a_1    conda-forge
r-nnet                    7.3_19            r41h57805ef_0    conda-forge
r-numderiv                2016.8_1.1        r41hc72bb7e_4    conda-forge
r-openssl                 2.0.6             r41habfbb5e_0    conda-forge
r-parallelly              1.36.0            r41hc72bb7e_0    conda-forge
r-pbdzmq                  0.3_9             r41hfae1697_0    conda-forge
r-pillar                  1.9.0             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_2    conda-forge
r-plogr                   0.2.0           r41hc72bb7e_1004    conda-forge
r-plyr                    1.8.8             r41h7525677_0    conda-forge
r-png                     0.1_8             r41h10cf519_0    conda-forge
r-prettyunits             1.1.1             r41hc72bb7e_2    conda-forge
r-proc                    1.18.2            r41ha503ecb_0    conda-forge
r-processx                3.8.1             r41h133d619_0    conda-forge
r-prodlim                 2023.03.31        r41h38f115c_0    conda-forge
r-progress                1.2.2             r41hc72bb7e_3    conda-forge
r-progressr               0.13.0            r41hc72bb7e_0    conda-forge
r-promises                1.2.0.1           r41h7525677_1    conda-forge
r-proxy                   0.4_27            r41h06615bd_1    conda-forge
r-pryr                    0.1.6             r41h38f115c_0    conda-forge
r-ps                      1.7.5             r41h133d619_0    conda-forge
r-purrr                   1.0.1             r41h133d619_0    conda-forge
r-quantmod                0.4.22            r41hc72bb7e_0    conda-forge
r-r.methodss3             1.8.2             r41hc72bb7e_1    conda-forge
r-r.oo                    1.25.0            r41hc72bb7e_1    conda-forge
r-r.utils                 2.12.2            r41hc72bb7e_0    conda-forge
r-r6                      2.5.1             r41hc72bb7e_1    conda-forge
r-ragg                    1.2.5             r41h85cdef0_1    conda-forge
r-randomforest            4.7_1.1           r41h8da6f51_1    conda-forge
r-rappdirs                0.3.3             r41h06615bd_1    conda-forge
r-rbokeh                  0.5.2             r41hc72bb7e_2    conda-forge
r-rcolorbrewer            1.1_3             r41h785f33e_1    conda-forge
r-rcpp                    1.0.10            r41h38f115c_0    conda-forge
r-rcpparmadillo           0.12.4.0.0        r41h08d816e_0    conda-forge
r-rcppeigen               0.3.3.9.3         r41h9f5de39_0    conda-forge
r-rcppnumerical           0.5_0             r41h38f115c_0    conda-forge
r-rcurl                   1.98_1.12         r41hf9611b0_1    conda-forge
r-readr                   2.1.4             r41h38f115c_0    conda-forge
r-readxl                  1.4.2             r41h81ef4d7_0    conda-forge
r-recipes                 1.0.6             r41hc72bb7e_0    conda-forge
r-recommended             4.1             r41hd8ed1ab_1005    conda-forge
r-rematch                 1.0.1           r41hc72bb7e_1005    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_2    conda-forge
r-repr                    1.1.6             r41h785f33e_0    conda-forge
r-reprex                  2.0.2             r41hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r41h7525677_2    conda-forge
r-restfulr                0.0.15            r41h73dbb54_0    bioconda
r-rjson                   0.2.21            r41h7525677_2    conda-forge
r-rlang                   1.1.1             r41ha503ecb_0    conda-forge
r-rmarkdown               2.22              r41hc72bb7e_0    conda-forge
r-rpart                   4.1.19            r41h06615bd_0    conda-forge
r-rsqlite                 2.3.1             r41h38f115c_0    conda-forge
r-rstudioapi              0.14              r41hc72bb7e_1    conda-forge
r-rvest                   1.0.3             r41hc72bb7e_1    conda-forge
r-sass                    0.4.6             r41ha503ecb_0    conda-forge
r-scales                  1.2.1             r41hc72bb7e_1    conda-forge
r-selectr                 0.4_2             r41hc72bb7e_2    conda-forge
r-shape                   1.4.6             r41ha770c72_1    conda-forge
r-shiny                   1.7.4             r41h785f33e_0    conda-forge
r-snow                    0.4_4             r41hc72bb7e_1    conda-forge
r-sourcetools             0.1.7_1           r41h38f115c_0    conda-forge
r-spatial                 7.3_16            r41h133d619_0    conda-forge
r-squarem                 2021.1            r41hc72bb7e_1    conda-forge
r-statmod                 1.5.0             r41h74f4db8_0    conda-forge
r-stringi                 1.7.12            r41hc0c3e09_1    conda-forge
r-stringr                 1.5.0             r41h785f33e_0    conda-forge
r-survival                3.5_5             r41h133d619_0    conda-forge
r-sys                     3.4.2             r41h57805ef_0    conda-forge
r-systemfonts             1.0.4             r41h0ff29ef_1    conda-forge
r-textshaping             0.3.6             r41h24cd192_5    conda-forge
r-tibble                  3.2.1             r41h133d619_1    conda-forge
r-tidyr                   1.3.0             r41h38f115c_0    conda-forge
r-tidyselect              1.2.0             r41hc72bb7e_0    conda-forge
r-tidyverse               2.0.0             r41h785f33e_0    conda-forge
r-timechange              0.2.0             r41h38f115c_0    conda-forge
r-timedate                4022.108          r41hc72bb7e_0    conda-forge
r-tinytex                 0.45              r41hc72bb7e_0    conda-forge
r-tmvnsim                 1.0_2             r41h8da6f51_4    conda-forge
r-triebeard               0.4.1             r41h38f115c_0    conda-forge
r-truncnorm               1.0_9             r41h133d619_0    conda-forge
r-ttr                     0.24.3            r41h06615bd_1    conda-forge
r-tzdb                    0.4.0             r41ha503ecb_0    conda-forge
r-urltools                1.7.3             r41h7525677_3    conda-forge
r-utf8                    1.2.3             r41h133d619_0    conda-forge
r-uuid                    1.1_0             r41h06615bd_1    conda-forge
r-vctrs                   0.6.2             r41ha503ecb_0    conda-forge
r-viridislite             0.4.1             r41hc72bb7e_1    conda-forge
r-vroom                   1.6.3             r41ha503ecb_0    conda-forge
r-withr                   2.5.0             r41hc72bb7e_1    conda-forge
r-xfun                    0.39              r41ha503ecb_0    conda-forge
r-xml                     3.99_0.14         r41hc38eee6_1    conda-forge
r-xml2                    1.3.4             r41h1ad5fc0_1    conda-forge
r-xtable                  1.8_4             r41hc72bb7e_4    conda-forge
r-xts                     0.13.1            r41h133d619_0    conda-forge
r-yaml                    2.3.7             r41h133d619_0    conda-forge
r-zoo                     1.8_12            r41h133d619_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.18.1          py310he421c4c_0    conda-forge
rpy2                      3.4.5           py310r41h96516ba_3    conda-forge
scikit-learn              1.1.3           py310h0c3af53_1    conda-forge
scikit-survival           0.19.0.post1    py310h769672d_0    conda-forge
scipy                     1.14.0          py310h93e2701_0    conda-forge
seaborn                   0.13.2               hd8ed1ab_2    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_2    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                70.1.1             pyhd8ed1ab_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singledispatch            3.6.1              pyh44b312d_0    conda-forge
sip                       6.7.12          py310hc6cd4ac_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.1          py310h1f7b6fc_0    conda-forge
sysroot_linux-64          2.12                he073ed8_17    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tbb                       2021.11.0            h00ab1b0_1    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tktable                   2.10                 h8bc8fbc_6    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1           py310hc51659f_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
tzlocal                   5.2             py310hff52083_0    conda-forge
unicodedata2              15.1.0          py310h2372a71_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.6.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
wrapt                     1.16.0          py310h2372a71_0    conda-forge
xcb-util                  0.4.0                hd590300_1    conda-forge
xcb-util-image            0.4.0                h8ee46fc_1    conda-forge
xcb-util-keysyms          0.4.0                h8ee46fc_1    conda-forge
xcb-util-renderutil       0.3.9                hd590300_1    conda-forge
xcb-util-wm               0.4.1                h8ee46fc_1    conda-forge
xkeyboard-config          2.42                 h4ab18f5_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.9                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxt                1.3.0                hd590300_1    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xf86vidmodeproto     2.3.1             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.19.2             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                h4ab18f5_1    conda-forge
zstandard                 0.22.0          py310hab88d88_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Environment info

mamba version : 1.5.8
     active environment : sksurv-bio-workflows-r41
    active env location : /home/hermidalc/soft/miniforge3/envs/sksurv-bio-workflows-r41
            shell level : 1
       user config file : /home/hermidalc/.condarc
 populated config files : /home/hermidalc/soft/miniforge3/.condarc
                          /home/hermidalc/.condarc
          conda version : 24.5.0
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake
                          __conda=24.5.0=0
                          __glibc=2.37=0
                          __linux=6.8.9=0
                          __unix=0=0
       base environment : /home/hermidalc/soft/miniforge3  (writable)
      conda av data dir : /home/hermidalc/soft/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/hermidalc/soft/miniforge3/pkgs
                          /home/hermidalc/.conda/pkgs
       envs directories : /home/hermidalc/soft/miniforge3/envs
                          /home/hermidalc/.conda/envs
               platform : linux-64
             user-agent : conda/24.5.0 requests/2.32.3 CPython/3.10.14 Linux/6.8.9-100.fc38.x86_64 fedora/38 glibc/2.37 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

[CamDavidsonPilon]

Thanks for bringing this up @hermidalc. Hm, I'm not sure what the general solution is though.

When a dependency makes a breaking change (say from 0.x to 1.0), and the dependent library needs to update (from 1.x to 2.0) to resolve, the dependent library will require the dependency to be >=1.0 (via requirements.txt).

But, like you've brought up, the old dependent library 1.x hasn't changed its requirements. It feels both very right and very wrong to back to all 1.x versions and force the dependency to be <1.0, would you agree?

I'm not the first to experience this, so what's the recommended solution?

[hermidalc]

I'm not the first to experience this, so what's the recommended solution?

No one who's installed lifelines <0.29 (any lifelines version were you have import scipy.integrate.trapz would've ever gotten it to work without that immediate error when they ran their script without themselves forcing scipy <1.14 in their conda environment yaml if nothing else in their dependencies didn't already silently need that too.

So anyone installing lifelines <0.29 usually didn't get things working right out of the box, which I think would be frustrating to general users. I had to go manually search scipy for the newest version that still allowed import scipy.integrate.trapz to find <1.14 still supported it. So since lifelines install won't work out of the box I'm in favor of your conda install requirements specifying e.g. scipy >=1.2,<1.14, you already require minimum scipy you just need to add the second req. Then things will work out of the box as they should.

[hermidalc]

I also think a lot of conda package managers also just always add upper version limits to their deps to be <x.xx where x.xx is one minor number greater than the latest version they know works and they've tested with their package. Then you'll never run into this problem. This isn't perfect because if a later dep version will work in the future you will have to change this after testing that it does indeed work.

[hermidalc]

I also think a lot of conda package managers also just always add upper version limits to their deps to be <x.xx where x.xx is one minor number greater than the latest version they know works and they've tested with their package. Then you'll never run into this problem. This isn't perfect because if a later dep version will work in the future you will have to change this after testing that it does indeed work.

Maybe I'm wrong about this pariticular idea, nevermind. I don't see scikit-learn doing it https://github.com/conda-forge/scikit-learn-feedstock/blob/main/recipe/meta.yaml