Add recipe for taxidTools

[gregdenay]

Adds a recipe for the TaxidTools python package. This is a package to handle taxonomy definitions as hierarchical trees in native Python, allowing common operations such as lineage analysis, last common ancestor or consensus determination, branch filtering, pruning, normalization, import and export as JSON, etc...

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  run_exports:
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[gregdenay]

@BiocondaBot please add label

[gregdenay]

@BiocondaBot please update

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
noarch	taxidtools-2.2.3-pyhdfd78af_1.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>

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Docker image(s) built:

Package	Tag	CI	Install with docker
taxidtools	2.2.3--pyhdfd78af_1	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/taxidtools:2.2.3--pyhdfd78af_1.tar.gz | docker load

[martin-g]

The build has failed. Please investigate!

[gregdenay]

Need to wait for Azure problems to be fixed

[gregdenay]

Build fails locally with (only relevant part of the log):

$ bioconda-utils build --docker --mulled-test --packages taxidtools
14:02:06 BIOCONDA INFO (COMMAND) mulled-build build-and-test taxidtools=2.3.0--pyhdfd78af_0 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/lo             cal/env-activate.sh && pip check' --channels conda-forge,file:///home/debian/anaconda3/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /home/debian/anacon             da3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/involucro
14:02:06 BIOCONDA INFO (OUT) Executing: /home/debian/anaconda3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/involucro -v=2 -f /home/debian/anaconda3/env             s/bioconda/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/invfile.lua -set CHANNELS=conda-forge,file:///home/debian/anaconda3/envs/bioconda/conda-bld,bioc             onda,defaults -set TARGETS=taxidtools=2.3.0=pyhdfd78af_0 -set REPO=quay.io/biocontainers/taxidtools:2.3.0--pyhdfd78af_0 -set BINDS=build/dist:/usr/local/,/home/debia             n/anaconda3/envs/bioconda/conda-bld:/home/debian/anaconda3/envs/bioconda/conda-bld -set DEST_BASE_IMAGE=quay.io/bioconda/base-glibc-busybox-bash:3.0 -set CONDA_IMAGE             =quay.io/bioconda/create-env:latest -set 'TEST=bash -c '"'"'/usr/local/env-execute true && . /usr/local/env-activate.sh && pip check'"'"'' -set CONDA_BIN=conda build             -and-test
14:02:06 BIOCONDA INFO (ERR) [May 13 14:02:06] DEBU Run file [/home/debian/anaconda3/envs/bioconda/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/invfile.             lua]
14:02:06 BIOCONDA INFO (ERR) [May 13 14:02:06] INFO Invoke Task [build]
14:02:06 BIOCONDA INFO (ERR) [May 13 14:02:06] STEP Run image [quay.io/bioconda/create-env:latest] with command [[rm -rf /data/dist]]
14:02:06 BIOCONDA INFO (ERR) [May 13 14:02:06] DEBU Creating container [step-2c43582175]
14:02:06 BIOCONDA INFO (ERR) [May 13 14:02:06] DEBU Created container [bfb3a8e02bea step-2c43582175], starting it
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] DEBU Container [bfb3a8e02bea step-2c43582175] started, waiting for completion
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] DEBU Container [bfb3a8e02bea step-2c43582175] completed with exit code [0] as expected
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] DEBU Container [bfb3a8e02bea step-2c43582175] removed
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] STEP Run image [quay.io/bioconda/create-env:latest] with command [[/bin/sh -c conda install  -c 'conda-forge' -c 'file             :///home/debian/anaconda3/envs/bioconda/conda-bld' -c 'bioconda' -c 'defaults'  'taxidtools=2.3.0=pyhdfd78af_0' --strict-channel-priority -p /usr/local --copy --yes              --quiet&&create-env --conda=: /usr/local]]
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] DEBU Creating container [step-e5a68a9ac4]
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] DEBU Created container [1dac623c30df step-e5a68a9ac4], starting it
14:02:07 BIOCONDA INFO (ERR) [May 13 14:02:07] DEBU Container [1dac623c30df step-e5a68a9ac4] started, waiting for completion
..14:04:22 BIOCONDA INFO (ERR) [May 13 14:04:22] SOUT Collecting package metadata (repodata.json): ...working... done
14:04:25 BIOCONDA INFO (ERR) [May 13 14:04:25] SOUT Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
14:04:36 BIOCONDA INFO (ERR) [May 13 14:04:36] SOUT Solving environment: ...working...
14:04:36 BIOCONDA INFO (ERR) [May 13 14:04:36] SOUT Found conflicts! Looking for incompatible packages.
14:04:36 BIOCONDA INFO (ERR) [May 13 14:04:36] SOUT This can take several minutes.  Press CTRL-C to abort.
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SOUT failed
Examining conflict for python __glibc:   0%|          | 0/5 [00:00<?, ?it/s]                 0/5 [00:00<?, ?it/s]
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR UnsatisfiableError: The following specifications were found to be incompatible with your system:
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR - feature:/linux-64::__glibc==2.36=0
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR - python[version='>=3.9'] -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR Your installed version is: 2.36
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR Note that strict channel priority may have removed packages required for satisfiability.
14:04:38 BIOCONDA INFO (ERR) [May 13 14:04:38] SERR
14:04:46 BIOCONDA INFO (ERR) [May 13 14:04:46] ERRO Task processing failed: Unexpected exit code [1] of container [1dac623c30df step-e5a68a9ac4], container preserved
14:04:46 BIOCONDA INFO (OUT) ...
14:04:46 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test taxidtools=2.3.0--pyhdfd78af_0 -n biocontainers --test bash -c '/usr/local/env-execute true && /usr/local/env-activate.sh && pip check' --channels conda-forge,file:///home/debian/anaconda3/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /home/debian/anaconda3/es/bioconda/lib/python3.10/site-packages/bioconda_utils/involucro

14:04:46 BIOCONDA ERROR TEST FAILED: recipes/taxidtools
14:04:46 BIOCONDA INFO (COMMAND) conda build purge
14:04:46 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
14:04:46 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/taxidtools

Points to a weird version problem of __glibc