From a39e7736f7034ad292c40d93415e18e34b74cc21 Mon Sep 17 00:00:00 2001 From: q2d2 Date: Fri, 15 Mar 2024 16:39:01 +0000 Subject: [PATCH] Automated updates to latest resolved environment files: 2024.5 shotgun --- .../qiime2-shotgun-macos-latest-conda.yml | 252 ++++++++--------- .../qiime2-shotgun-ubuntu-latest-conda.yml | 258 +++++++++--------- 2 files changed, 263 insertions(+), 247 deletions(-) diff --git a/latest/passed/qiime2-shotgun-macos-latest-conda.yml b/latest/passed/qiime2-shotgun-macos-latest-conda.yml index 6b6521f0..1f858aaf 100644 --- a/latest/passed/qiime2-shotgun-macos-latest-conda.yml +++ b/latest/passed/qiime2-shotgun-macos-latest-conda.yml @@ -1,16 +1,16 @@ channels: -- https://packages.qiime2.org/qiime2/2024.2/shotgun/passed +- https://packages.qiime2.org/qiime2/2024.5/shotgun/passed - bioconda - conda-forge - defaults dependencies: - _r-mutex=1.0.1 - altair=5.2.0 -- anyio=4.2.0 +- anyio=4.3.0 - appdirs=1.4.4 -- appnope=0.1.3 -- argcomplete=3.2.1 -- argh=0.31.0 +- appnope=0.1.4 +- argcomplete=3.2.3 +- argh=0.31.2 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - aria2=1.36.0 @@ -89,19 +89,19 @@ dependencies: - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 -- busco=5.6.1 +- busco=5.5.0 - bwa=0.7.17 - bwidget=1.9.14 - bzip2=1.0.8 -- c-ares=1.25.0 -- ca-certificates=2023.11.17 -- cachecontrol=0.13.1 +- c-ares=1.27.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.16.0 - cctools_osx-64=973.0.1 - cdbtools=0.99 -- certifi=2023.11.17 +- certifi=2024.2.2 - cffi=1.16.0 - charset-normalizer=3.3.2 - circos=0.69.9 @@ -114,32 +114,34 @@ dependencies: - clangxx_osx-64=17.0.6 - click=8.1.7 - colorama=0.4.6 -- comm=0.2.1 +- comm=0.2.2 - compiler-rt=17.0.6 - compiler-rt_osx-64=17.0.6 - conda-pack=0.7.0 - contourpy=1.1.1 -- cryptography=42.0.0 +- cryptography=42.0.5 - curl=7.88.1 - cutadapt=4.6 - cycler=0.12.1 -- cython=3.0.7 -- debugpy=1.8.0 +- cython=3.0.9 +- debugpy=1.8.1 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=4.5.2 -- diamond=2.1.8 -- dill=0.3.7 +- diamond=2.1.9 +- dill=0.3.8 - dnaio=1.2.0 - easel=0.49 - eggnog-mapper=2.1.12 - emperor=1.0.4 -- entrez-direct=16.2 +- entrez-direct=21.6 +- entrezpy=2.1.3 - entrypoints=0.4 - exceptiongroup=1.2.0 - executing=2.0.1 -- expat=2.5.0 +- expat=2.6.1 - fastcluster=1.2.6 +- feedparser=6.0.11 - flufl.lock=7.1 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 @@ -148,12 +150,12 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.47.2 +- fonttools=4.49.0 - formulaic=1.0.1 - fqdn=1.5.1 - freetype=2.12.1 - fribidi=1.0.10 -- future=0.18.3 +- future=1.0.0 - gawk=5.3.0 - gettext=0.21.1 - gffutils=0.10.1 @@ -161,7 +163,7 @@ dependencies: - gfortran_osx-64=11.4.0 - giflib=5.2.1 - glimmerhmm=3.0.4 -- globus-sdk=3.34.0 +- globus-sdk=3.39.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 @@ -177,16 +179,16 @@ dependencies: - icu=70.1 - idna=3.6 - ijson=3.2.3 -- importlib-metadata=7.0.1 -- importlib_resources=6.1.1 +- importlib-metadata=7.0.2 +- importlib_resources=6.3.0 - iniconfig=2.0.0 - insilicoseq=1.5.4 - interface_meta=1.3.0 - iow=1.0.5 -- ipykernel=6.29.0 +- ipykernel=6.29.3 - ipython=8.12.2 - ipython_genutils=0.2.0 -- ipywidgets=8.1.1 +- ipywidgets=8.1.2 - isa-l=2.31.0 - isl=0.25 - isoduration=20.11.0 @@ -201,14 +203,14 @@ dependencies: - jsonschema-specifications=2023.12.1 - jsonschema-with-format-nongpl=4.21.1 - jupyter_client=7.4.9 -- jupyter_core=5.7.1 -- jupyter_events=0.9.0 -- jupyter_server=2.12.5 -- jupyter_server_terminals=0.5.2 +- jupyter_core=5.7.2 +- jupyter_events=0.9.1 +- jupyter_server=2.13.0 +- jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 -- jupyterlab_widgets=3.0.9 +- jupyterlab_widgets=3.0.10 - k8=0.2.5 -- kaiju=1.10.0 +- kaiju=1.10.1 - kiwisolver=1.4.5 - kraken2=2.1.3 - krb5=1.20.1 @@ -227,7 +229,7 @@ dependencies: - libdeflate=1.13 - libedit=3.1.20191231 - libev=4.33 -- libexpat=2.5.0 +- libexpat=2.6.1 - libffi=3.4.4 - libgd=2.3.3 - libgfortran=5.0.0 @@ -235,17 +237,17 @@ dependencies: - libgfortran5=13.2.0 - libglib=2.78.1 - libiconv=1.17 -- libidn2=2.3.4 +- libidn2=2.3.7 - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 - libllvm17=17.0.6 - libnghttp2=1.58.0 -- libopenblas=0.3.26 -- libpng=1.6.39 +- libopenblas=0.3.25 +- libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 -- libsqlite=3.44.2 +- libsqlite=3.45.2 - libssh2=1.11.0 - libtiff=4.4.0 - libunistring=0.9.10 @@ -264,7 +266,7 @@ dependencies: - lz4=4.3.3 - lz4-c=1.9.4 - make=4.3 -- markupsafe=2.1.4 +- markupsafe=2.1.5 - matplotlib=3.6.0 - matplotlib-base=3.6.0 - matplotlib-inline=0.1.6 @@ -272,44 +274,46 @@ dependencies: - metabat2=2.15 - metaeuk=6.a5d39d9 - metis=5.1.1 -- minimap2=2.26 -- miniprot=0.12 +- minimap2=2.27 +- miniprot=0.13 - mistune=3.0.2 - mmseqs2=15.6f452 - mpc=1.3.1 - mpfr=4.2.1 +- mpi=1.0 - msgpack-python=1.0.7 - munkres=1.1.4 - natsort=8.4.0 - nbclassic=1.0.0 -- nbclient=0.8.0 -- nbconvert=7.14.2 -- nbconvert-core=7.14.2 -- nbconvert-pandoc=7.14.2 -- nbformat=5.9.2 -- ncbi-datasets-pylib=16.3.0 +- nbclient=0.10.0 +- nbconvert=7.16.2 +- nbconvert-core=7.16.2 +- nbconvert-pandoc=7.16.2 +- nbformat=5.10.2 +- ncbi-datasets-pylib=16.6.0 - ncbi-vdb=3.0.0 - ncurses=6.4 - nest-asyncio=1.6.0 - networkx=3.1 - nlopt=2.7.1 - notebook=6.5.5 -- notebook-shim=0.2.3 +- notebook-shim=0.2.4 - numba=0.58.1 - numpy=1.24.4 - oniguruma=6.9.9 - openjdk=21.0.2 - openjpeg=2.5.0 -- openssl=3.2.0 -- overrides=7.6.0 -- packaging=23.2 +- openssl=3.2.1 +- overrides=7.7.0 +- packaging=24.0 - pandas=1.5.3 -- pandoc=3.1.3 +- pandoc=3.1.12.2 - pandocfilters=1.5.0 - pango=1.50.14 - paramiko=3.4.0 - parsl=2023.12.4 - parso=0.8.3 +- pathlib=1.0.1 - patsy=0.5.3 - pbzip2=1.1.13 - pcre=8.45 @@ -378,18 +382,18 @@ dependencies: - perl-types-serialiser=1.01 - perl-xml-parser=2.44_01 - perl-yaml=1.30 -- pexpect=4.8.0 +- pexpect=4.9.0 - pickleshare=0.7.5 - pigz=2.8 - pillow=9.2.0 -- pip=23.3.2 -- pixman=0.43.0 +- pip=24.0 +- pixman=0.43.4 - pkgutil-resolve-name=1.3.10 -- platformdirs=4.1.0 -- pluggy=1.3.0 -- pooch=1.8.0 +- platformdirs=4.2.0 +- pluggy=1.4.0 +- pooch=1.8.1 - prodigal=2.6.3 -- prometheus_client=0.19.0 +- prometheus_client=0.20.0 - prompt-toolkit=3.0.42 - prompt_toolkit=3.0.42 - protobuf=3.20.3 @@ -405,43 +409,46 @@ dependencies: - pynndescent=0.5.11 - pyobjc-core=10.1 - pyobjc-framework-cocoa=10.1 -- pyparsing=3.1.1 +- pyparsing=3.1.2 - pysam=0.21.0 - pysocks=1.7.1 -- pytest=7.4.4 +- pytest=8.1.1 - python=3.8.18 - python-dateutil=2.8.2 +- python-dotenv=1.0.1 - python-fastjsonschema=2.19.1 -- python-isal=1.5.3 +- python-isal=1.6.1 - python-json-logger=2.0.7 - python_abi=3.8 -- pytz=2023.3.post1 +- pytz=2024.1 - pyvcf3=1.0.3 - pyyaml=6.0.1 - pyzmq=24.0.1 -- q2-assembly=2023.11.0.dev0+10.gfa7d842 -- q2-composition=2023.11.0.dev0+2.g89c2a1c -- q2-cutadapt=2023.11.0.dev0+3.gc78541c -- q2-demux=2023.11.0.dev0+4.g59b2378 -- q2-diversity=2023.11.0.dev0+2.g7171c05 -- q2-diversity-lib=2023.11.0.dev0+3.g5a1b4a6 -- q2-emperor=2023.11.0.dev0+2.g706f4c4 -- q2-feature-classifier=2023.11.0.dev0+2.g7f9f1c8 -- q2-feature-table=2023.11.0.dev0+8.g9f87ffb -- q2-longitudinal=2023.11.0.dev0+3.gd55ee50 -- q2-metadata=2023.11.0.dev0+1.g5ac3877 -- q2-moshpit=2023.11.0.dev0+25.g03a2702 -- q2-mystery-stew=2023.11.0.dev0+2.g1836c05 -- q2-quality-control=2023.11.0.dev0+2.g0d8aba5 -- q2-quality-filter=2023.11.0.dev0+1.g032ad25 -- q2-sample-classifier=2023.11.0.dev0+3.g7aef7e7 -- q2-sapienns=2023.11.0.dev0+3.g474f133 -- q2-taxa=2023.11.0.dev0+1.g1efb0b0 -- q2-types=2023.11.0.dev0+2.g1827eab -- q2-types-genomics=2023.11.0.dev0+8.g3b993ed -- q2cli=2023.11.0.dev0+13.g246f054 -- q2templates=2023.11.0.dev0+1.gba531e6 -- qiime2=2023.11.0.dev0+16.gc95b12b +- pyzotero=1.5.18 +- q2-assembly=2024.5.0.dev0 +- q2-composition=2024.5.0.dev0 +- q2-cutadapt=2024.5.0.dev0 +- q2-demux=2024.5.0.dev0 +- q2-diversity=2024.5.0.dev0+1.g99a0cca +- q2-diversity-lib=2024.5.0.dev0 +- q2-emperor=2024.5.0.dev0 +- q2-feature-classifier=2024.5.0.dev0 +- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-fondue=2024.5.0.dev0 +- q2-longitudinal=2024.5.0.dev0 +- q2-metadata=2024.5.0.dev0 +- q2-moshpit=2024.5.0.dev0+1.gdf1301d +- q2-mystery-stew=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0 +- q2-quality-filter=2024.5.0.dev0 +- q2-sample-classifier=2024.5.0.dev0 +- q2-sapienns=2024.5.0.dev0 +- q2-taxa=2024.5.0.dev0 +- q2-types=2024.5.0.dev0+4.g823b5a4 +- q2-vsearch=2024.5.0.dev0 +- q2cli=2024.5.0.dev0 +- q2templates=2024.5.0.dev0 +- qiime2=2024.5.0.dev0+1.g6306962 - quast=5.2.0 - r-ade4=1.7_22 - r-ape=5.7_1 @@ -458,13 +465,13 @@ dependencies: - r-bit64=4.0.5 - r-bitops=1.0_7 - r-blob=1.2.4 -- r-boot=1.3_28.1 +- r-boot=1.3_30 - r-brio=1.1.4 - r-broom=1.0.5 - r-bslib=0.6.1 - r-cachem=1.0.8 - r-cairo=1.6_0 -- r-callr=3.7.3 +- r-callr=3.7.5 - r-cellranger=1.1.0 - r-checkmate=2.3.1 - r-class=7.3_22 @@ -476,15 +483,15 @@ dependencies: - r-cpp11=0.4.7 - r-crayon=1.5.2 - r-curl=4.3.3 -- r-cvxr=1.0_11 -- r-data.table=1.14.10 -- r-dbi=1.2.1 +- r-cvxr=1.0_12 +- r-data.table=1.15.2 +- r-dbi=1.2.2 - r-dbplyr=2.4.0 -- r-deldir=2.0_2 +- r-deldir=2.0_4 - r-desc=1.4.3 - r-desctools=0.99.51 - r-diffobj=0.3.5 -- r-digest=0.6.34 +- r-digest=0.6.35 - r-doparallel=1.0.17 - r-dorng=1.8.6 - r-dplyr=1.1.4 @@ -510,7 +517,7 @@ dependencies: - r-foreign=0.8_86 - r-formatr=1.14 - r-formula=1.2_5 -- r-frictionless=1.0.2 +- r-frictionless=1.0.3 - r-fs=1.6.3 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 @@ -519,7 +526,7 @@ dependencies: - r-generics=0.1.3 - r-getopt=1.20.4 - r-ggbeeswarm=0.7.2 -- r-ggplot2=3.4.4 +- r-ggplot2=3.5.0 - r-ggrastr=1.0.2 - r-ggrepel=0.9.5 - r-gld=2.6.6 @@ -532,7 +539,7 @@ dependencies: - r-gtable=0.3.4 - r-haven=2.5.4 - r-highr=0.10 -- r-hmisc=5.1_1 +- r-hmisc=5.1_2 - r-hms=1.1.3 - r-htmltable=2.4.2 - r-htmltools=0.5.7 @@ -540,7 +547,7 @@ dependencies: - r-httr=1.4.7 - r-ids=1.0.1 - r-igraph=1.4.2 -- r-interp=1.1_5 +- r-interp=1.1_6 - r-irlba=2.3.5.1 - r-isoband=0.2.7 - r-iterators=1.0.14 @@ -601,8 +608,8 @@ dependencies: - r-rcolorbrewer=1.1_3 - r-rcpp=1.0.12 - r-rcppannoy=0.0.22 -- r-rcppeigen=0.3.3.9.4 -- r-rcpphnsw=0.5.0 +- r-rcppeigen=0.3.4.0.0 +- r-rcpphnsw=0.6.0 - r-rcppml=0.3.7 - r-rcppprogress=0.4.2 - r-rcurl=1.98_1.12 @@ -627,25 +634,25 @@ dependencies: - r-rstudioapi=0.15.0 - r-rsvd=1.0.5 - r-rtsne=0.17 -- r-rvest=1.0.3 +- r-rvest=1.0.4 - r-sass=0.4.8 - r-scales=1.3.0 - r-scs=3.2.4 - r-selectr=0.4_2 - r-sitmo=2.0.2 - r-snow=0.4_4 -- r-sp=2.1_2 +- r-sp=2.1_3 - r-statmod=1.5.0 - r-stringdist=0.9.10 - r-stringi=1.7.12 - r-stringr=1.5.1 -- r-survival=3.5_7 +- r-survival=3.5_8 - r-sys=3.4.2 - r-systemfonts=1.0.5 - r-testthat=3.2.1 - r-textshaping=0.3.6 - r-tibble=3.2.1 -- r-tidyr=1.3.0 +- r-tidyr=1.3.1 - r-tidyselect=1.2.0 - r-tidytree=0.4.6 - r-tidyverse=1.3.2 @@ -658,24 +665,24 @@ dependencies: - r-vctrs=0.6.5 - r-vegan=2.6_4 - r-vipor=0.4.7 -- r-viridis=0.6.4 +- r-viridis=0.6.5 - r-viridislite=0.4.2 - r-vroom=1.6.5 - r-waldo=0.5.2 - r-withr=3.0.0 -- r-xfun=0.41 +- r-xfun=0.42 - r-xml=3.99_0.14 - r-xml2=1.3.3 - r-xtable=1.8_4 - r-yaml=2.3.8 -- r-yulab.utils=0.1.3 +- r-yulab.utils=0.1.4 - readline=8.2 -- referencing=0.32.1 +- referencing=0.33.0 - requests=2.31.0 -- rescript=2023.11.0.dev0+45.g51df26b +- rescript=2024.5.0.dev0+2.ga0df425 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 -- rpds-py=0.17.1 +- rpds-py=0.18.0 - samtools=1.18 - scikit-bio=0.5.8 - scikit-learn=0.24.1 @@ -685,14 +692,15 @@ dependencies: - send2trash=1.8.2 - sepp=4.3.10 - setproctitle=1.3.3 -- setuptools=69.0.3 +- setuptools=69.2.0 +- sgmllib3k=1.0.0 - sigtool=0.1.3 - simplejson=3.19.2 - six=1.16.0 -- sniffio=1.3.0 +- sniffio=1.3.1 - soupsieve=2.5 - spades=3.15.2 -- sqlite=3.44.2 +- sqlite=3.45.2 - stack_data=0.6.2 - statsmodels=0.14.0 - suitesparse=5.10.1 @@ -700,22 +708,22 @@ dependencies: - tar=1.34 - tbb=2021.10.0 - tblib=3.0.0 -- terminado=0.18.0 -- threadpoolctl=3.2.0 +- terminado=0.18.1 +- threadpoolctl=3.3.0 - tinycss2=1.2.1 - tk=8.6.13 - tktable=2.10 - toml=0.10.2 - tomli=2.0.1 -- tomlkit=0.12.3 -- toolz=0.12.0 -- tornado=6.3.3 -- tqdm=4.66.1 +- tomlkit=0.12.4 +- toolz=0.12.1 +- tornado=6.4 +- tqdm=4.66.2 - traitlets=5.9.0 - typeguard=2.13.3 -- types-python-dateutil=2.8.19.20240106 -- typing-extensions=4.9.0 -- typing_extensions=4.9.0 +- types-python-dateutil=2.8.19.20240311 +- typing-extensions=4.10.0 +- typing_extensions=4.10.0 - typing_utils=0.1.0 - tzlocal=2.1 - ucsc-fatotwobit=366 @@ -723,7 +731,7 @@ dependencies: - umap-learn=0.5.4 - unicodedata2=15.1.0 - unifrac=1.3 -- unifrac-binaries=1.3.1 +- unifrac-binaries=1.3.2 - uri-template=1.3.0 - urllib3=1.26.18 - vsearch=2.27.0 @@ -733,11 +741,11 @@ dependencies: - websocket-client=1.7.0 - wget=1.20.3 - wheel=0.42.0 -- widgetsnbextension=4.0.9 +- widgetsnbextension=4.0.10 - wrapt=1.16.0 - xlsxwriter=3.1.9 - xmltodict=0.13.0 -- xopen=1.8.0 +- xopen=1.9.0 - xorg-kbproto=1.0.7 - xorg-libice=1.0.10 - xorg-libsm=1.2.3 diff --git a/latest/passed/qiime2-shotgun-ubuntu-latest-conda.yml b/latest/passed/qiime2-shotgun-ubuntu-latest-conda.yml index aa983cd9..fbf047c8 100644 --- a/latest/passed/qiime2-shotgun-ubuntu-latest-conda.yml +++ b/latest/passed/qiime2-shotgun-ubuntu-latest-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.2/shotgun/passed +- https://packages.qiime2.org/qiime2/2024.5/shotgun/passed - bioconda - conda-forge - defaults @@ -10,10 +10,10 @@ dependencies: - _sysroot_linux-64_curr_repodata_hack=3 - alsa-lib=1.2.8 - altair=5.2.0 -- anyio=4.2.0 +- anyio=4.3.0 - appdirs=1.4.4 -- argcomplete=3.2.1 -- argh=0.31.0 +- argcomplete=3.2.3 +- argh=0.31.2 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - aria2=1.36.0 @@ -96,48 +96,50 @@ dependencies: - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 -- busco=5.6.1 +- busco=5.5.0 - bwa=0.7.17 - bwidget=1.9.14 - bzip2=1.0.8 -- c-ares=1.25.0 -- ca-certificates=2023.11.17 -- cachecontrol=0.13.1 +- c-ares=1.27.0 +- ca-certificates=2024.2.2 +- cachecontrol=0.14.0 - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.16.0 - cdbtools=0.99 -- certifi=2023.11.17 +- certifi=2024.2.2 - cffi=1.16.0 - charset-normalizer=3.3.2 - circos=0.69.9 - click=8.1.7 - colorama=0.4.6 -- comm=0.2.1 +- comm=0.2.2 - conda-pack=0.7.0 - contourpy=1.1.1 - cryptography=39.0.0 -- curl=7.87.0 +- curl=7.88.1 - cutadapt=4.6 - cycler=0.12.1 -- cython=3.0.7 +- cython=3.0.9 - dbus=1.13.6 -- debugpy=1.8.0 +- debugpy=1.8.1 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=4.5.2 - diamond=2.1.8 -- dill=0.3.7 +- dill=0.3.8 - dnaio=1.2.0 - easel=0.49 - eggnog-mapper=2.1.12 - emperor=1.0.4 -- entrez-direct=16.2 +- entrez-direct=21.6 +- entrezpy=2.1.3 - entrypoints=0.4 - exceptiongroup=1.2.0 - executing=2.0.1 -- expat=2.5.0 +- expat=2.6.1 - fastcluster=1.2.6 +- feedparser=6.0.11 - fftw=3.3.10 - flufl.lock=7.1 - font-ttf-dejavu-sans-mono=2.37 @@ -147,12 +149,12 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.47.2 +- fonttools=4.49.0 - formulaic=1.0.1 - fqdn=1.5.1 - freetype=2.12.1 - fribidi=1.0.10 -- future=0.18.3 +- future=1.0.0 - gawk=5.3.0 - gcc_impl_linux-64=13.2.0 - gettext=0.21.1 @@ -162,7 +164,7 @@ dependencies: - glib=2.78.1 - glib-tools=2.78.1 - glimmerhmm=3.0.4 -- globus-sdk=3.34.0 +- globus-sdk=3.39.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 @@ -171,7 +173,7 @@ dependencies: - gsl=2.7 - gst-plugins-base=1.21.3 - gstreamer=1.21.3 -- gstreamer-orc=0.4.34 +- gstreamer-orc=0.4.38 - gxx_impl_linux-64=13.2.0 - h5py=3.8.0 - harfbuzz=6.0.0 @@ -182,16 +184,16 @@ dependencies: - icu=70.1 - idna=3.6 - ijson=3.2.3 -- importlib-metadata=7.0.1 -- importlib_resources=6.1.1 +- importlib-metadata=7.0.2 +- importlib_resources=6.3.0 - iniconfig=2.0.0 - insilicoseq=1.5.4 - interface_meta=1.3.0 - iow=1.0.5 -- ipykernel=6.29.0 +- ipykernel=6.29.3 - ipython=8.12.2 - ipython_genutils=0.2.0 -- ipywidgets=8.1.1 +- ipywidgets=8.1.2 - isa-l=2.31.0 - isoduration=20.11.0 - jack=1.9.22 @@ -206,14 +208,14 @@ dependencies: - jsonschema-specifications=2023.12.1 - jsonschema-with-format-nongpl=4.21.1 - jupyter_client=7.4.9 -- jupyter_core=5.7.1 -- jupyter_events=0.9.0 -- jupyter_server=2.12.5 -- jupyter_server_terminals=0.5.2 +- jupyter_core=5.7.2 +- jupyter_events=0.9.1 +- jupyter_server=2.13.0 +- jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 -- jupyterlab_widgets=3.0.9 +- jupyterlab_widgets=3.0.10 - k8=0.2.5 -- kaiju=1.10.0 +- kaiju=1.10.1 - kernel-headers_linux-64=3.10.0 - keyutils=1.6.1 - kiwisolver=1.4.5 @@ -233,13 +235,13 @@ dependencies: - libclang=15.0.7 - libclang13=15.0.7 - libcups=2.3.3 -- libcurl=7.87.0 +- libcurl=7.88.1 - libdb=6.2.32 - libdeflate=1.13 - libedit=3.1.20191231 - libev=4.33 - libevent=2.1.10 -- libexpat=2.5.0 +- libexpat=2.6.1 - libffi=3.4.2 - libflac=1.4.3 - libgcc-devel_linux-64=13.2.0 @@ -250,26 +252,26 @@ dependencies: - libgfortran5=13.2.0 - libglib=2.78.1 - libgomp=13.2.0 -- libgpg-error=1.47 +- libgpg-error=1.48 - libhwloc=2.9.1 - libiconv=1.17 -- libidn2=2.3.4 +- libidn2=2.3.7 - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 - libllvm15=15.0.7 -- libnghttp2=1.51.0 +- libnghttp2=1.52.0 - libnsl=2.0.1 - libogg=1.3.4 -- libopenblas=0.3.26 +- libopenblas=0.3.25 - libopus=1.3.1 -- libpng=1.6.39 +- libpng=1.6.43 - libpq=15.1 - libprotobuf=3.20.3 - libsanitizer=13.2.0 - libsndfile=1.2.2 - libsodium=1.0.18 -- libsqlite=3.44.2 +- libsqlite=3.45.2 - libssh2=1.10.0 - libstdcxx-devel_linux-64=13.2.0 - libstdcxx-ng=13.2.0 @@ -296,7 +298,7 @@ dependencies: - lz4=4.3.3 - lz4-c=1.9.4 - make=4.3 -- markupsafe=2.1.4 +- markupsafe=2.1.5 - matplotlib=3.6.0 - matplotlib-base=3.6.0 - matplotlib-inline=0.1.6 @@ -304,12 +306,13 @@ dependencies: - metabat2=2.15 - metaeuk=6.a5d39d9 - metis=5.1.0 -- minimap2=2.26 -- miniprot=0.12 +- minimap2=2.27 +- miniprot=0.13 - mistune=3.0.2 - mmseqs2=15.6f452 - mpfr=4.2.1 - mpg123=1.32.4 +- mpi=1.0 - msgpack-python=1.0.7 - munkres=1.1.4 - mysql-common=8.0.32 @@ -317,21 +320,21 @@ dependencies: - mysql-libs=8.0.32 - natsort=8.4.0 - nbclassic=1.0.0 -- nbclient=0.8.0 -- nbconvert=7.14.2 -- nbconvert-core=7.14.2 -- nbconvert-pandoc=7.14.2 -- nbformat=5.9.2 -- ncbi-datasets-pylib=16.3.0 +- nbclient=0.10.0 +- nbconvert=7.16.2 +- nbconvert-core=7.16.2 +- nbconvert-pandoc=7.16.2 +- nbformat=5.10.2 +- ncbi-datasets-pylib=16.6.0 - ncbi-vdb=3.0.0 - ncurses=6.4 - nest-asyncio=1.6.0 - networkx=3.1 - nlopt=2.7.1 - notebook=6.5.5 -- notebook-shim=0.2.3 +- notebook-shim=0.2.4 - nspr=4.35 -- nss=3.97 +- nss=3.98 - numba=0.58.1 - numpy=1.24.4 - oniguruma=6.9.9 @@ -339,15 +342,16 @@ dependencies: - openjpeg=2.5.0 - openmp=8.0.1 - openssl=1.1.1w -- overrides=7.6.0 -- packaging=23.2 +- overrides=7.7.0 +- packaging=24.0 - pandas=1.5.3 -- pandoc=3.1.3 +- pandoc=3.1.12.2 - pandocfilters=1.5.0 - pango=1.50.14 - paramiko=3.4.0 - parsl=2023.12.4 - parso=0.8.3 +- pathlib=1.0.1 - patsy=0.5.3 - pbzip2=1.1.13 - pcre=8.45 @@ -416,19 +420,19 @@ dependencies: - perl-types-serialiser=1.01 - perl-xml-parser=2.44_01 - perl-yaml=1.30 -- pexpect=4.8.0 +- pexpect=4.9.0 - pickleshare=0.7.5 - pigz=2.8 - pillow=9.2.0 -- pip=23.3.2 -- pixman=0.43.0 +- pip=24.0 +- pixman=0.43.2 - pkgutil-resolve-name=1.3.10 -- platformdirs=4.1.0 -- pluggy=1.3.0 +- platformdirs=4.2.0 +- pluggy=1.4.0 - ply=3.11 -- pooch=1.8.0 +- pooch=1.8.1 - prodigal=2.6.3 -- prometheus_client=0.19.0 +- prometheus_client=0.20.0 - prompt-toolkit=3.0.42 - prompt_toolkit=3.0.42 - protobuf=3.20.3 @@ -443,45 +447,48 @@ dependencies: - pyjwt=2.8.0 - pynacl=1.5.0 - pynndescent=0.5.11 -- pyparsing=3.1.1 +- pyparsing=3.1.2 - pyqt=5.15.7 - pyqt5-sip=12.11.0 - pysam=0.21.0 - pysocks=1.7.1 -- pytest=7.4.4 +- pytest=8.1.1 - python=3.8.15 - python-dateutil=2.8.2 +- python-dotenv=1.0.1 - python-fastjsonschema=2.19.1 -- python-isal=1.5.3 +- python-isal=1.6.1 - python-json-logger=2.0.7 - python_abi=3.8 -- pytz=2023.3.post1 +- pytz=2024.1 - pyvcf3=1.0.3 - pyyaml=6.0.1 - pyzmq=24.0.1 -- q2-assembly=2023.11.0.dev0+10.gfa7d842 -- q2-composition=2023.11.0.dev0+2.g89c2a1c -- q2-cutadapt=2023.11.0.dev0+3.gc78541c -- q2-demux=2023.11.0.dev0+4.g59b2378 -- q2-diversity=2023.11.0.dev0+2.g7171c05 -- q2-diversity-lib=2023.11.0.dev0+3.g5a1b4a6 -- q2-emperor=2023.11.0.dev0+2.g706f4c4 -- q2-feature-classifier=2023.11.0.dev0+2.g7f9f1c8 -- q2-feature-table=2023.11.0.dev0+8.g9f87ffb -- q2-longitudinal=2023.11.0.dev0+3.gd55ee50 -- q2-metadata=2023.11.0.dev0+1.g5ac3877 -- q2-moshpit=2023.11.0.dev0+25.g03a2702 -- q2-mystery-stew=2023.11.0.dev0+2.g1836c05 -- q2-quality-control=2023.11.0.dev0+2.g0d8aba5 -- q2-quality-filter=2023.11.0.dev0+1.g032ad25 -- q2-sample-classifier=2023.11.0.dev0+3.g7aef7e7 -- q2-sapienns=2023.11.0.dev0+3.g474f133 -- q2-taxa=2023.11.0.dev0+1.g1efb0b0 -- q2-types=2023.11.0.dev0+2.g1827eab -- q2-types-genomics=2023.11.0.dev0+8.g3b993ed -- q2cli=2023.11.0.dev0+13.g246f054 -- q2templates=2023.11.0.dev0+1.gba531e6 -- qiime2=2023.11.0.dev0+16.gc95b12b +- pyzotero=1.5.18 +- q2-assembly=2024.5.0.dev0 +- q2-composition=2024.5.0.dev0 +- q2-cutadapt=2024.5.0.dev0 +- q2-demux=2024.5.0.dev0 +- q2-diversity=2024.5.0.dev0+1.g99a0cca +- q2-diversity-lib=2024.5.0.dev0 +- q2-emperor=2024.5.0.dev0 +- q2-feature-classifier=2024.5.0.dev0 +- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-fondue=2024.5.0.dev0 +- q2-longitudinal=2024.5.0.dev0 +- q2-metadata=2024.5.0.dev0 +- q2-moshpit=2024.5.0.dev0+1.gdf1301d +- q2-mystery-stew=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0 +- q2-quality-filter=2024.5.0.dev0 +- q2-sample-classifier=2024.5.0.dev0 +- q2-sapienns=2024.5.0.dev0 +- q2-taxa=2024.5.0.dev0 +- q2-types=2024.5.0.dev0+4.g823b5a4 +- q2-vsearch=2024.5.0.dev0 +- q2cli=2024.5.0.dev0 +- q2templates=2024.5.0.dev0 +- qiime2=2024.5.0.dev0+1.g6306962 - qt-main=5.15.6 - quast=5.2.0 - r-ade4=1.7_22 @@ -499,13 +506,13 @@ dependencies: - r-bit64=4.0.5 - r-bitops=1.0_7 - r-blob=1.2.4 -- r-boot=1.3_28.1 +- r-boot=1.3_30 - r-brio=1.1.4 - r-broom=1.0.5 - r-bslib=0.6.1 - r-cachem=1.0.8 - r-cairo=1.6_0 -- r-callr=3.7.3 +- r-callr=3.7.5 - r-cellranger=1.1.0 - r-checkmate=2.3.0 - r-class=7.3_22 @@ -517,15 +524,15 @@ dependencies: - r-cpp11=0.4.7 - r-crayon=1.5.2 - r-curl=4.3.3 -- r-cvxr=1.0_11 -- r-data.table=1.14.10 -- r-dbi=1.2.1 +- r-cvxr=1.0_12 +- r-data.table=1.15.2 +- r-dbi=1.2.2 - r-dbplyr=2.4.0 -- r-deldir=2.0_2 +- r-deldir=2.0_4 - r-desc=1.4.3 - r-desctools=0.99.51 - r-diffobj=0.3.5 -- r-digest=0.6.34 +- r-digest=0.6.35 - r-doparallel=1.0.17 - r-dorng=1.8.6 - r-dplyr=1.1.4 @@ -551,7 +558,7 @@ dependencies: - r-foreign=0.8_86 - r-formatr=1.14 - r-formula=1.2_5 -- r-frictionless=1.0.2 +- r-frictionless=1.0.3 - r-fs=1.6.3 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 @@ -560,7 +567,7 @@ dependencies: - r-generics=0.1.3 - r-getopt=1.20.4 - r-ggbeeswarm=0.7.2 -- r-ggplot2=3.4.4 +- r-ggplot2=3.5.0 - r-ggrastr=1.0.2 - r-ggrepel=0.9.5 - r-gld=2.6.6 @@ -573,7 +580,7 @@ dependencies: - r-gtable=0.3.4 - r-haven=2.5.4 - r-highr=0.10 -- r-hmisc=5.1_1 +- r-hmisc=5.1_2 - r-hms=1.1.3 - r-htmltable=2.4.2 - r-htmltools=0.5.7 @@ -581,7 +588,7 @@ dependencies: - r-httr=1.4.7 - r-ids=1.0.1 - r-igraph=1.4.2 -- r-interp=1.1_5 +- r-interp=1.1_6 - r-irlba=2.3.5.1 - r-isoband=0.2.7 - r-iterators=1.0.14 @@ -642,11 +649,11 @@ dependencies: - r-rcolorbrewer=1.1_3 - r-rcpp=1.0.12 - r-rcppannoy=0.0.22 -- r-rcppeigen=0.3.3.9.4 -- r-rcpphnsw=0.5.0 +- r-rcppeigen=0.3.4.0.0 +- r-rcpphnsw=0.6.0 - r-rcppml=0.3.7 - r-rcppprogress=0.4.2 -- r-rcurl=1.98_1.10 +- r-rcurl=1.98_1.12 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 @@ -668,25 +675,25 @@ dependencies: - r-rstudioapi=0.15.0 - r-rsvd=1.0.5 - r-rtsne=0.17 -- r-rvest=1.0.3 +- r-rvest=1.0.4 - r-sass=0.4.8 - r-scales=1.3.0 - r-scs=3.2.4 - r-selectr=0.4_2 - r-sitmo=2.0.2 - r-snow=0.4_4 -- r-sp=2.1_2 +- r-sp=2.1_3 - r-statmod=1.5.0 - r-stringdist=0.9.10 - r-stringi=1.7.12 - r-stringr=1.5.1 -- r-survival=3.5_7 +- r-survival=3.5_8 - r-sys=3.4.2 - r-systemfonts=1.0.5 - r-testthat=3.2.1 - r-textshaping=0.3.6 - r-tibble=3.2.1 -- r-tidyr=1.3.0 +- r-tidyr=1.3.1 - r-tidyselect=1.2.0 - r-tidytree=0.4.6 - r-tidyverse=1.3.2 @@ -699,26 +706,26 @@ dependencies: - r-vctrs=0.6.5 - r-vegan=2.6_4 - r-vipor=0.4.7 -- r-viridis=0.6.4 +- r-viridis=0.6.5 - r-viridislite=0.4.2 - r-vroom=1.6.5 - r-waldo=0.5.2 - r-withr=3.0.0 -- r-xfun=0.41 +- r-xfun=0.42 - r-xml=3.99_0.14 - r-xml2=1.3.3 - r-xtable=1.8_4 - r-yaml=2.3.8 -- r-yulab.utils=0.1.3 +- r-yulab.utils=0.1.4 - readline=8.2 -- referencing=0.32.1 +- referencing=0.33.0 - repeatmasker=4.1.5 - requests=2.31.0 -- rescript=2023.11.0.dev0+45.g51df26b +- rescript=2024.5.0.dev0+2.ga0df425 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rmblast=2.14.1 -- rpds-py=0.17.1 +- rpds-py=0.18.0 - samtools=1.18 - scikit-bio=0.5.8 - scikit-learn=0.24.1 @@ -729,14 +736,15 @@ dependencies: - send2trash=1.8.2 - sepp=4.3.10 - setproctitle=1.3.3 -- setuptools=69.0.3 +- setuptools=69.2.0 +- sgmllib3k=1.0.0 - simplejson=3.19.2 - sip=6.7.12 - six=1.16.0 -- sniffio=1.3.0 +- sniffio=1.3.1 - soupsieve=2.5 - spades=3.15.2 -- sqlite=3.44.2 +- sqlite=3.45.2 - stack_data=0.6.2 - statsmodels=0.14.0 - suitesparse=5.10.1 @@ -744,23 +752,23 @@ dependencies: - tar=1.34 - tbb=2021.9.0 - tblib=3.0.0 -- terminado=0.18.0 -- threadpoolctl=3.2.0 +- terminado=0.18.1 +- threadpoolctl=3.3.0 - tinycss2=1.2.1 - tk=8.6.13 - tktable=2.10 - toml=0.10.2 - tomli=2.0.1 -- tomlkit=0.12.3 -- toolz=0.12.0 -- tornado=6.3.3 -- tqdm=4.66.1 +- tomlkit=0.12.4 +- toolz=0.12.1 +- tornado=6.4 +- tqdm=4.66.2 - traitlets=5.9.0 - trf=4.09.1 - typeguard=2.13.3 -- types-python-dateutil=2.8.19.20240106 -- typing-extensions=4.9.0 -- typing_extensions=4.9.0 +- types-python-dateutil=2.8.19.20240311 +- typing-extensions=4.10.0 +- typing_extensions=4.10.0 - typing_utils=0.1.0 - tzlocal=2.1 - ucsc-fatotwobit=447 @@ -768,7 +776,7 @@ dependencies: - umap-learn=0.5.4 - unicodedata2=15.1.0 - unifrac=1.3 -- unifrac-binaries=1.3.1 +- unifrac-binaries=1.3.2 - uri-template=1.3.0 - urllib3=1.26.18 - vsearch=2.27.0 @@ -778,7 +786,7 @@ dependencies: - websocket-client=1.7.0 - wget=1.20.3 - wheel=0.42.0 -- widgetsnbextension=4.0.9 +- widgetsnbextension=4.0.10 - wrapt=1.16.0 - xcb-util=0.4.0 - xcb-util-image=0.4.0 @@ -788,7 +796,7 @@ dependencies: - xkeyboard-config=2.38 - xlsxwriter=3.1.9 - xmltodict=0.13.0 -- xopen=1.8.0 +- xopen=1.9.0 - xorg-fixesproto=5.0 - xorg-inputproto=2.3.2 - xorg-kbproto=1.0.7