conda-forge / biom-format-feedstock

A conda-smithy repository for biom-format.

About biom-format-feedstock

Feedstock license: BSD-3-Clause

Home: http://biom-format.org/

Package license: BSD-3-Clause

Summary: Biological Observation Matrix (BIOM) format

Development: https://github.com/biocore/biom-format

Current build status

Azure

Variant Status linux_64_python3.10.____cpython linux_64_python3.11.____cpython linux_64_python3.12.____cpython linux_64_python3.8.____cpython linux_64_python3.9.____cpython osx_64_python3.10.____cpython osx_64_python3.11.____cpython osx_64_python3.12.____cpython osx_64_python3.8.____cpython osx_64_python3.9.____cpython win_64_python3.10.____cpython win_64_python3.11.____cpython win_64_python3.12.____cpython win_64_python3.8.____cpython win_64_python3.9.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing biom-format

Installing biom-format from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, biom-format can be installed with conda:

conda install biom-format

or with mamba:

mamba install biom-format

It is possible to list all of the versions of biom-format available on your platform with conda:

conda search biom-format --channel conda-forge

or with mamba:

mamba search biom-format --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search biom-format --channel conda-forge

# List packages depending on `biom-format`:
mamba repoquery whoneeds biom-format --channel conda-forge

# List dependencies of `biom-format`:
mamba repoquery depends biom-format --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge Anaconda-Cloud channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating biom-format-feedstock

If you would like to improve the biom-format recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/biom-format-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @nsoranzo
• @synapticarbors
• @wasade

biom-format-feedstock's Issues

`biom convert` fail using this channel, but works on bioconda

Issue: This command fails with this error:

$ biom convert -i OTU_converted.txt -o OTU.biom --to-json             --process-obs-metadata sc_separated --table-type "OTU table"

Traceback (most recent call last):
  File "/people/bris469/bin/anaconda/envs/hundo_env/bin/biom", line 11, in <module>
    sys.exit(cli())
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/biom/cli/table_converter.py", line 129, in convert
    table_type, process_obs_metadata, tsv_metadata_formatter)
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/biom/cli/table_converter.py", line 207, in _convert
    write_biom_table(result, fmt, output_filepath)
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/biom/cli/util.py", line 26, in write_biom_table
    f.write(table.to_json(biom.parse.generatedby()))
  File "/people/bris469/bin/anaconda/envs/hundo_env/lib/python3.6/site-packages/biom/table.py", line 4278, in to_json
    raise TableException("Unsupported matrix data type.")

Environment (conda list):

$ conda list

# packages in environment at /people/bris469/bin/anaconda/envs/hundo_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
attrs                     19.1.0                   pypi_0    pypi
bbmap                     37.17                         1    bioconda
biom-format               2.1.6            py36h7eb728f_0    conda-forge
biopython                 1.73             py36h14c3975_0    conda-forge
blast                     2.9.0           pl526h979a64d_3    bioconda
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
certifi                   2019.6.16                py36_0    conda-forge
chardet                   3.0.4                    pypi_0    pypi
click                     6.7                        py_1    conda-forge
curl                      7.64.1               hf8cf82a_0    conda-forge
decorator                 4.4.0                    pypi_0    pypi
docutils                  0.14                  py36_1001    conda-forge
entrez-direct             11.0                    pl526_0    bioconda
expat                     2.2.5             he1b5a44_1003    conda-forge
fasttree                  2.1.10               h14c3975_3    bioconda
future                    0.17.1                py36_1000    conda-forge
hundo                     1.3.0                    pypi_0    pypi
idna                      2.8                      pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
jsonschema                3.0.1                    pypi_0    pypi
jupyter-core              4.5.0                    pypi_0    pypi
krb5                      1.16.3            h05b26f9_1001    conda-forge
libblas                   3.8.0               10_openblas    conda-forge
libcblas                  3.8.0               10_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
liblapack                 3.8.0               10_openblas    conda-forge
libopenblas               0.3.6                h6e990d7_4    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0  
mafft                     7.313                         1    bioconda
nbformat                  4.4.0                    pypi_0    pypi
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.16.4           py36h95a1406_0    conda-forge
openblas                  0.3.6                h6e990d7_4    conda-forge
openjdk                   11.0.1            h516909a_1016    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
pandas                    0.24.2           py36hb3f55d8_0    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-archive-tar          2.32                    pl526_0    bioconda
perl-base                 2.23                    pl526_1    bioconda
perl-business-isbn        3.004                   pl526_0    bioconda
perl-business-isbn-data   20140910.003            pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-bzip2   2.086           pl526hf484d3e_0    bioconda
perl-compress-raw-zlib    2.086           pl526h6bb024c_1    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-digest-hmac          1.03                    pl526_3    bioconda
perl-digest-md5           2.55                    pl526_0    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-encode-locale        1.05                    pl526_6    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-listing         6.04                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-html-parser          3.72            pl526h6bb024c_5    bioconda
perl-html-tagset          3.20                    pl526_3    bioconda
perl-html-tree            5.07                    pl526_1    bioconda
perl-http-cookies         6.04                    pl526_0    bioconda
perl-http-daemon          6.01                    pl526_1    bioconda
perl-http-date            6.02                    pl526_3    bioconda
perl-http-message         6.18                    pl526_0    bioconda
perl-http-negotiate       6.01                    pl526_3    bioconda
perl-io-compress          2.086           pl526hf484d3e_0    bioconda
perl-io-html              1.001                   pl526_2    bioconda
perl-io-socket-ssl        2.066                   pl526_0    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-libwww-perl          6.39                    pl526_0    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-lwp-mediatypes       6.04                    pl526_0    bioconda
perl-lwp-protocol-https   6.07                    pl526_4    bioconda
perl-mime-base64          3.15                    pl526_1    bioconda
perl-mozilla-ca           20180117                pl526_1    bioconda
perl-net-http             6.19                    pl526_0    bioconda
perl-net-ssleay           1.88            pl526h90d6eec_0    bioconda
perl-ntlm                 1.09                    pl526_4    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-scalar-list-utils    1.50            pl526h14c3975_0    bioconda
perl-socket               2.027                   pl526_1    bioconda
perl-storable             3.15            pl526h14c3975_0    bioconda
perl-test-requiresinternet 0.05                    pl526_0    bioconda
perl-time-local           1.28                    pl526_1    bioconda
perl-try-tiny             0.30                    pl526_1    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-uri                  1.76                    pl526_0    bioconda
perl-www-robotrules       6.02                    pl526_3    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44_01         pl526ha1d75be_1002    conda-forge
perl-xml-sax              1.02                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_3    bioconda
perl-xml-simple           2.25                    pl526_1    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
pigz                      2.3.4                         0    conda-forge
pip                       19.1.1                   py36_0    conda-forge
plotly                    3.7.0                    pypi_0    pypi
pyrsistent                0.15.3                   pypi_0    pypi
python                    3.6.7             h357f687_1005    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
pytz                      2019.1                     py_0    conda-forge
pyyaml                    5.1.1            py36h516909a_0    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
relatively                1.0.6                    pypi_0    pypi
requests                  2.22.0                   pypi_0    pypi
retrying                  1.3.3                    pypi_0    pypi
scipy                     1.3.0            py36h921218d_0    conda-forge
setuptools                41.0.1                   py36_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
sqlite                    3.28.0               hcee41ef_1    conda-forge
tk                        8.6.9             hed695b0_1002    conda-forge
traitlets                 4.3.2                    pypi_0    pypi
urllib3                   1.25.3                   pypi_0    pypi
vsearch                   2.13.1               h76f5088_0    bioconda
wheel                     0.33.4                   py36_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yaml                      0.1.7             h14c3975_1001    conda-forge
zip                       3.0                           0    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : hundo_env
    active env location : /people/bris469/bin/anaconda/envs/hundo_env
            shell level : 5
       user config file : /people/bris469/.condarc
 populated config files : /people/bris469/.condarc
          conda version : 4.7.5
    conda-build version : 3.10.9
         python version : 2.7.16.final.0
       virtual packages : 
       base environment : /people/bris469/bin/anaconda  (writable)
           channel URLs : 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
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /people/bris469/bin/anaconda/pkgs
                          /people/bris469/.conda/pkgs
       envs directories : /people/bris469/bin/anaconda/envs
                          /people/bris469/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.21.0 CPython/2.7.16 Linux/2.6.32-642.6.2.el6.x86_64 rhel/6.6 glibc/2.12
                UID:GID : 3859:100
             netrc file : None
           offline mode : False

---

Plot twist: the version of this package on bioconda totally works

$ git diff --no-index biom-no-work.txt biom-does-work.txt | grep biom
--- a/example/mothur_sop_silva/biom-no-work.txt
+++ b/example/mothur_sop_silva/biom-does-work.txt
-biom-format               2.1.6            py36h7eb728f_0    conda-forge
+biom-format               2.1.6                    py36_1    bioconda

I'll bump to 2.1.7 to see if that solves my problem.

See biocore/biom-format#816