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"safe_dump()" has been removed error using conda skeleton pypi pod5 #5258

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Mathias-Boulanger opened this issue Mar 26, 2024 · 7 comments
Closed
2 tasks done

"safe_dump()" has been removed error using conda skeleton pypi pod5 #5258

Mathias-Boulanger opened this issue Mar 26, 2024 · 7 comments
Labels
source::community catch-all for issues filed by community members stale::closed [bot] closed after being marked as stale stale [bot] marked as stale due to inactivity type::support neither a bug nor feature, is really just a user having questions or difficulty somewhere

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@Mathias-Boulanger
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Checklist

  • I added a descriptive title
  • I searched open reports and couldn't find a duplicate

What happened?

Dear conda devs,

It's my first time trying to contribute to conda framework by creating a conda package.
The idea is to just create a package for the Nanopore pod5 python tool kit available on PyPi.

For this purpose I used this command: conda skeleton pypi --version 0.3.10 pod5 but I got this error:

Traceback (most recent call last):
  File "/tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pod5-0.3.10/setup.py", line 15, in <module>
    setuptools.setup()
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/setuptools/__init__.py", line 104, in setup
    return distutils.core.setup(**attrs)
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 220, in setup
    fn.write(yaml.safe_dump(data, encoding=None))
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/ruamel/yaml/main.py", line 1260, in safe_dump
    error_deprecation('safe_dump', 'dump', arg="typ='safe', pure=True")
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/ruamel/yaml/main.py", line 1039, in error_deprecation
    raise AttributeError(s, name=None)
AttributeError: 
"safe_dump()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.dump(...)

instead of file "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 220

        fn.write(yaml.safe_dump(data, encoding=None))

If I understood correctly this is the setuptools package that using a deprecated syntax yaml.safe_dump() from the ruamel/yaml package.

Do you have any idea how to fix this?
Please let me know if I posted this on the wrong repo or if I should address this issue to anyone else...

Thank you for your help.

Full error log:

conda skeleton pypi --version 0.3.10 pod5
Using url https://files.pythonhosted.org/packages/69/b0/b5c4ca9cec24b982e72d5c805a9605e7eab4e39333c8cc77295a5eae412d/pod5-0.3.10.tar.gz (64 KB) for pod5.
Downloading pod5
PyPI URL:  https://files.pythonhosted.org/packages/69/b0/b5c4ca9cec24b982e72d5c805a9605e7eab4e39333c8cc77295a5eae412d/pod5-0.3.10.tar.gz
Using cached download
Unpacking pod5...
done
working in /tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz
Reloading output folder: ...working... done
Solving environment (_h_env): ...working... done

## Package Plan ##

  environment location: /g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place


The following NEW packages will be INSTALLED:

    _libgcc_mutex:    0.1-conda_forge            conda-forge
    _openmp_mutex:    4.5-2_gnu                  conda-forge
    bzip2:            1.0.8-hd590300_5           conda-forge
    ca-certificates:  2024.2.2-hbcca054_0        conda-forge
    ld_impl_linux-64: 2.40-h41732ed_0            conda-forge
    libffi:           3.4.2-h7f98852_5           conda-forge
    libgcc-ng:        13.2.0-h807b86a_5          conda-forge
    libgomp:          13.2.0-h807b86a_5          conda-forge
    libnsl:           2.0.1-hd590300_0           conda-forge
    libsqlite:        3.45.2-h2797004_0          conda-forge
    libuuid:          2.38.1-h0b41bf4_0          conda-forge
    libxcrypt:        4.4.36-hd590300_1          conda-forge
    libzlib:          1.2.13-hd590300_5          conda-forge
    ncurses:          6.4.20240210-h59595ed_0    conda-forge
    openssl:          3.2.1-hd590300_1           conda-forge
    patch:            2.7.6-h7f98852_1002        conda-forge
    pip:              24.0-pyhd8ed1ab_0          conda-forge
    python:           3.10.14-hd12c33a_0_cpython conda-forge
    python_abi:       3.10-4_cp310               conda-forge
    readline:         8.2-h8228510_1             conda-forge
    ruamel.yaml:      0.18.6-py310h2372a71_0     conda-forge
    ruamel.yaml.clib: 0.2.8-py310h2372a71_0      conda-forge
    setuptools:       69.2.0-pyhd8ed1ab_0        conda-forge
    tk:               8.6.13-noxft_h4845f30_101  conda-forge
    tzdata:           2024a-h0c530f3_0           conda-forge
    wheel:            0.43.0-pyhd8ed1ab_0        conda-forge
    xz:               5.2.6-h166bdaf_0           conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Applying patch: /tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pypi-distutils.patch
Applying patch: /tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pypi-distutils.patch with args:
['-Np0', '-i', '/tmp/tmp3o9vl1x7/pypi-distutils.patch.native', '--binary']
checking file core.py
Hunk #1 succeeded at 167 with fuzz 2 (offset 1 line).
patching file core.py
Hunk #1 succeeded at 167 with fuzz 2 (offset 1 line).
Applying patch: /tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pypi-distutils.patch
Applying patch: /tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pypi-distutils.patch with args:
['-Np0', '-i', '/tmp/tmpvxaywyu2/pypi-distutils.patch.native', '--binary']
checking file core.py
Hunk #1 succeeded at 187 with fuzz 2 (offset 21 lines).
patching file core.py
Hunk #1 succeeded at 187 with fuzz 2 (offset 21 lines).
Traceback (most recent call last):
  File "/tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pod5-0.3.10/setup.py", line 15, in <module>
    setuptools.setup()
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/setuptools/__init__.py", line 104, in setup
    return distutils.core.setup(**attrs)
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 220, in setup
    fn.write(yaml.safe_dump(data, encoding=None))
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/ruamel/yaml/main.py", line 1260, in safe_dump
    error_deprecation('safe_dump', 'dump', arg="typ='safe', pure=True")
  File "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/ruamel/yaml/main.py", line 1039, in error_deprecation
    raise AttributeError(s, name=None)
AttributeError: 
"safe_dump()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.dump(...)

instead of file "/g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 220

        fn.write(yaml.safe_dump(data, encoding=None))


$PYTHONPATH = /tmp/tmpgogymv1econda_skeleton_pod5-0.3.10.tar.gz/pod5-0.3.10:/g/krebs/boulanger/Scripts/PythonScripts:

Leaving build/test directories:
  Work:
 /g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/work 
  Test:
 /g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/test_tmp 
Leaving build/test environments:
  Test:
source activate  /g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ 
  Build:
source activate  /g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_build_env 


Error: command failed: /g/krebs/boulanger/miniconda3/conda-bld/skeleton_1711470458614/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python setup.py install

Conda Info

active environment : bioconda
    active env location : /g/krebs/boulanger/miniconda3/envs/bioconda
            shell level : 1
       user config file : /home/boulange/.condarc
 populated config files : /home/boulange/.condarc
          conda version : 24.3.0
    conda-build version : 24.3.0
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen
                          __conda=24.3.0=0
                          __glibc=2.28=0
                          __linux=4.18.0=0
                          __unix=0=0
       base environment : /g/krebs/boulanger/miniconda3  (writable)
      conda av data dir : /g/krebs/boulanger/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /g/krebs/boulanger/miniconda3/pkgs
                          /home/boulange/.conda/pkgs
       envs directories : /g/krebs/boulanger/miniconda3/envs
                          /home/boulange/.conda/envs
               platform : linux-64
             user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/4.18.0-477.13.1.el8_8.x86_64 rocky/8.8 glibc/2.28 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
                UID:GID : 24562:718
             netrc file : None
           offline mode : False

Conda Config

==> /home/boulange/.condarc <==
auto_activate_base: False
channels:
  - conda-forge
  - bioconda
  - r
  - defaults

Conda list

# packages in environment at /g/krebs/boulanger/miniconda3/envs/bioconda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiofiles                  0.8.0              pyhd8ed1ab_0    conda-forge
aioftp                    0.12.0                     py_0    conda-forge
aiohttp                   3.8.6            py39hd1e30aa_1    conda-forge
aiohttp-jinja2            1.4.2              pyhd8ed1ab_0    conda-forge
aiohttp-security          0.4.0                      py_0    conda-forge
aiohttp-session           2.7.0                      py_0    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
alabaster                 0.7.16             pyhd8ed1ab_0    conda-forge
amqp                      5.2.0              pyhd8ed1ab_1    conda-forge
anaconda-client           1.6.14                     py_0    conda-forge
anyio                     3.7.1              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argh                      0.26.2          pyh9f0ad1d_1002    conda-forge
async-timeout             4.0.3              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
backoff                   2.2.1              pyhd8ed1ab_0    conda-forge
backports.zoneinfo        0.2.1            py39hf3d152e_8    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
billiard                  4.2.0            py39hd1e30aa_0    conda-forge
bioconda-utils            2.13.0             pyh7cba7a3_0    bioconda
boa                       0.15.1             pyhd8ed1ab_0    conda-forge
boltons                   23.1.1             pyhd8ed1ab_0    conda-forge
boto3                     1.34.70            pyhd8ed1ab_0    conda-forge
botocore                  1.34.70         pyge38_1234567_0    conda-forge
brotli-python             1.1.0            py39h3d6467e_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.27.0               hd590300_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cachetools                3.0.0                      py_0    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
celery                    5.3.6              pyhd8ed1ab_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0           py39h7a31438_0    conda-forge
chardet                   5.2.0            py39hf3d152e_1    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
click-didyoumean          0.3.1              pyhd8ed1ab_0    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
click-repl                0.3.0              pyhd8ed1ab_0    conda-forge
clyent                    1.2.2              pyhd8ed1ab_2    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
colorlog                  4.8.0            py39hf3d152e_3    conda-forge
conda                     23.3.1           py39hf3d152e_0    conda-forge
conda-build               3.24.0           py39hf3d152e_1    conda-forge
conda-forge-pinning       2023.05.06.13.08.41      hd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
conda-verify              3.1.1           py39hf3d152e_1006    conda-forge
containers-common         0.57.0               ha770c72_0    conda-forge
cryptography              42.0.5           py39hd4f0224_0    conda-forge
curl                      8.6.0                hca28451_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
deprecated                1.2.14             pyh1a96a4e_0    conda-forge
diskcache                 5.6.3              pyhd8ed1ab_0    conda-forge
docutils                  0.19             py39hf3d152e_1    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
expat                     2.6.2                h59595ed_0    conda-forge
filelock                  3.13.3             pyhd8ed1ab_0    conda-forge
fmt                       9.1.0                h924138e_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_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
frozenlist                1.4.1            py39hd1e30aa_0    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
galaxy-lib                19.5.2             pyh864c0ab_1    bioconda
gdk-pixbuf                2.42.10              h829c605_5    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gidgethub                 3.0.0                      py_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
git                       2.44.0          pl5321h709897a_0    conda-forge
gitdb2                    3.0.2                      py_0    conda-forge
gitpython                 3.0.8                      py_0    conda-forge
glob2                     0.7                        py_0    conda-forge
gpgme                     1.18.0               h27087fc_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  9.0.0                h78e8752_1    conda-forge
gtk2                      2.24.33              h280cfa0_4    conda-forge
gts                       0.7.6                h977cf35_4    conda-forge
harfbuzz                  8.3.0                h3d44ed6_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        7.1.0              pyha770c72_0    conda-forge
involucro                 1.1.3                ha8f183a_0    conda-forge
jinja2                    2.11.3             pyhd8ed1ab_2    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.24             pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4              py39hf3d152e_3    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter_core              5.7.2            py39hf3d152e_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kombu                     5.3.5            py39hf3d152e_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaio                    0.3.113              h166bdaf_0    conda-forge
libarchive                3.6.2                h039dbb9_1    conda-forge
libassuan                 2.5.7                h59595ed_0    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcurl                   8.6.0                hca28451_0    conda-forge
libdeflate                1.20                 hd590300_0    conda-forge
libdevmapper              2.02.187             h7f98852_1    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgd                     2.3.3                h119a65a_9    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libglib                   2.80.0               hf2295e7_1    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libgpg-error              1.48                 h71f35ed_0    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
liblief                   0.12.3               h27087fc_0    conda-forge
libmamba                  1.4.2                hcea66bb_0    conda-forge
libmambapy                1.4.2            py39hf0aba66_0    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.26          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
librsvg                   2.56.3               he3f83f7_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.28               hfc55251_1    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libtiff                   4.6.0                h1dd3fc0_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.3.2                h658648e_1    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.6               h232c23b_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.4.2            py39hc5d2bb1_0    conda-forge
markdown                  3.6                pyhd8ed1ab_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py39h3811e60_1    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
multidict                 6.0.5            py39hd1e30aa_0    conda-forge
nbformat                  5.10.3             pyhd8ed1ab_0    conda-forge
ncurses                   6.4.20240210         h59595ed_0    conda-forge
networkx                  2.8.8              pyhd8ed1ab_0    conda-forge
numpy                     1.19.5           py39hd249d9e_3    conda-forge
openssl                   3.2.1                hd590300_1    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandas                    1.4.4            py39h1832856_0    conda-forge
pango                     1.52.1               ha41ecd1_0    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
patchelf                  0.17.2               h58526e2_0    conda-forge
pcre2                     10.43                hcad00b1_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
pkginfo                   1.10.0             pyhd8ed1ab_0    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
prompt_toolkit            3.0.42               hd8ed1ab_0    conda-forge
psutil                    5.9.8            py39hd1e30aa_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
py-lief                   0.12.3           py39h5a03fae_0    conda-forge
pyaml                     17.12.1                    py_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6            py39hd1e30aa_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygithub                  1.59.1             pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pyjwt                     2.8.0              pyhd8ed1ab_1    conda-forge
pynacl                    1.5.0            py39hd1e30aa_3    conda-forge
pyopenssl                 24.0.0             pyhd8ed1ab_0    conda-forge
pyrsistent                0.20.0           py39hd1e30aa_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.19          h0755675_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.19.1             pyhd8ed1ab_0    conda-forge
python-libarchive-c       5.1              py39hf3d152e_0    conda-forge
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1            py39hd1e30aa_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
regex                     2022.7.9         py39hb9d737c_0    conda-forge
reproc                    14.2.4.post0         hd590300_1    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_1    conda-forge
requests                  2.29.0             pyhd8ed1ab_0    conda-forge
rich                      13.7.1             pyhd8ed1ab_0    conda-forge
ripgrep                   14.1.0               he8a937b_0    conda-forge
ruamel.yaml               0.17.40          py39hd1e30aa_0    conda-forge
ruamel.yaml.clib          0.2.8            py39hd1e30aa_0    conda-forge
ruamel_yaml               0.15.80         py39hd1e30aa_1009    conda-forge
s3transfer                0.10.1             pyhd8ed1ab_0    conda-forge
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
skopeo                    1.11.2               he5cbd37_0    conda-forge
smmap                     6.0.0              pyhd8ed1ab_1    conda-forge
smmap2                    3.0.1                      py_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    5.1.1              pyhd8ed1ab_1    conda-forge
sphinx-autodoc-typehints  1.19.2             pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.8              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.6              pyhd8ed1ab_0    conda-forge
sphinxcontrib-htmlhelp    2.0.5              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-qthelp      1.0.7              pyhd8ed1ab_0    conda-forge
sphinxcontrib-serializinghtml 1.1.10             pyhd8ed1ab_0    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
termcolor                 1.1.0              pyhd8ed1ab_3    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.1             pyhd8ed1ab_0    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.2             pyhd8ed1ab_0    conda-forge
typing-extensions         4.10.0               hd8ed1ab_0    conda-forge
typing_extensions         4.10.0             pyha770c72_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uritemplate               4.1.1              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.18            pyhd8ed1ab_0    conda-forge
vine                      5.1.0              pyhd8ed1ab_0    conda-forge
watchgod                  0.8.2              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0           py39hd1e30aa_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               1.8.7                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-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    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
yaml-cpp                  0.7.0                h59595ed_3    conda-forge
yarl                      1.9.4            py39hd1e30aa_0    conda-forge
yaspin                    2.0.0              pyhd8ed1ab_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstandard                 0.22.0           py39h6e5214e_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Additional Context

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@Mathias-Boulanger Mathias-Boulanger added the type::bug describes erroneous operation, use severity::* to classify the type label Mar 26, 2024
@github-project-automation github-project-automation bot moved this to 🆕 New in 🧭 Planning Mar 26, 2024
@jaimergp
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As a workaround, can you use grayskull instead of conda skeleton?

@Mathias-Boulanger
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Mathias-Boulanger commented Mar 28, 2024 •
edited
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Yes, I tried grayskull and I succeeded to create the recipe (and went through local test) for one of the dependency
of the pod5 package called: vbz-h5py-plugin.
But the recipe for the pod5 package failed upon testing mainly due to a dependency called lib-pod5 that is not available on conda-forge.

When I try to use grayskull to create lib-pod5 that is available on PyPi I got this error:

(condaforge) [boulange@seneca recipes]$ grayskull pypi lib-pod5



#### Initializing recipe for lib-pod5 (pypi) ####

Recovering metadata from pypi...
Traceback (most recent call last):
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/bin/grayskull", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/main.py", line 277, in main
    generate_recipes_from_list(args.pypi_packages, args)
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/main.py", line 300, in generate_recipes_from_list
    recipe, config = create_python_recipe(
                     ^^^^^^^^^^^^^^^^^^^^^
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/main.py", line 335, in create_python_recipe
    GrayskullFactory.create_recipe(
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/base/factory.py", line 46, in create_recipe
    GrayskullFactory.REGISTERED_STRATEGY[repo_type.lower()].fetch_data(
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 62, in fetch_data
    update_recipe(recipe, config, sections or ALL_SECTIONS)
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 499, in update_recipe
    metadata = get_metadata(recipe, config)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 350, in get_metadata
    sdist_metadata, pypi_metadata = get_origin_wise_metadata(config)
                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 234, in get_origin_wise_metadata
    pypi_metadata = get_pypi_metadata(config)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/g/krebs/boulanger/miniconda3/envs/condaforge/lib/python3.12/site-packages/grayskull/strategy/pypi.py", line 277, in get_pypi_metadata
    raise AttributeError(f"There is no sdist package on pypi for {config.name}.")
AttributeError: There is no sdist package on pypi for lib-pod5.

Thank you for your idea!

@jaimergp
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You can try to use the GH repo for lib-pod5 as a the source. That said, it looks like a C++ heavy package so it won't be one of those trivial packaging tasks :P

@Mathias-Boulanger
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Mathias-Boulanger commented Mar 28, 2024 •
edited
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Indeed, my first experience trying make conda package is not smooth as I though it would be...

The pod5 project is also located on GH here
Do you think I will have more chance to create recipe from this URL?

Thank you the suggestion.

@sfc-gh-srudenko
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fyi, same happens on conda skeleton pypi botocore or conda skeleton pypi click, lots of stuff is broken

@kenodegard kenodegard added type::support neither a bug nor feature, is really just a user having questions or difficulty somewhere source::community catch-all for issues filed by community members and removed type::bug describes erroneous operation, use severity::* to classify the type labels Jul 9, 2024
@jaimergp
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As a workaround, try using grayskull to generate your recipes from PyPI. conda skeleton is not really well maintained these days, as you can see.

@IroNEDR IroNEDR mentioned this issue Oct 4, 2024
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github-actions bot commented Oct 9, 2024

Hi there, thank you for your contribution!

This issue has been automatically marked as stale because it has not had recent activity. It will be closed automatically if no further activity occurs.

If you would like this issue to remain open please:

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Thanks!

@github-actions github-actions bot added the stale [bot] marked as stale due to inactivity label Oct 9, 2024
@github-actions github-actions bot added the stale::closed [bot] closed after being marked as stale label Oct 30, 2024
@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Oct 30, 2024
@github-project-automation github-project-automation bot moved this from 🆕 New to 🏁 Done in 🧭 Planning Oct 30, 2024
@noamraph noamraph mentioned this issue Nov 19, 2024
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