diff --git a/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml b/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml index faac3ca2..561dab5e 100644 --- a/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml +++ b/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml @@ -5,10 +5,11 @@ channels: dependencies: - _r-mutex=1.0.1 - altair=5.5.0 +- annotated-types=0.7.0 - anyio=4.7.0 - appdirs=1.4.4 - appnope=0.1.4 -- argcomplete=3.5.1 +- argcomplete=3.5.2 - argh=0.31.3 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 @@ -75,10 +76,10 @@ dependencies: - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 -- bwidget=1.9.14 +- bwidget=1.10.1 - bzip2=1.0.8 -- c-ares=1.34.3 -- ca-certificates=2024.8.30 +- c-ares=1.34.4 +- ca-certificates=2024.12.14 - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.18.0 @@ -104,10 +105,10 @@ dependencies: - contourpy=1.3.1 - cryptography=44.0.0 - curl=8.8.0 -- cutadapt=4.9 +- cutadapt=5.0 - cycler=0.12.1 - deblur=1.1.1 -- debugpy=1.8.9 +- debugpy=1.8.11 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=5.0.1 @@ -131,7 +132,7 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.55.2 +- fonttools=4.55.3 - formulaic=1.0.2 - fqdn=1.5.1 - freetype=2.12.1 @@ -265,9 +266,11 @@ dependencies: - mpc=1.3.1 - mpfr=4.2.1 - mpi=1.0.1 +- multimethod=1.9.1 - munkres=1.1.4 - muscle=3.8.1551 -- narwhals=1.15.2 +- mypy_extensions=1.0.0 +- narwhals=1.18.3 - natsort=8.4.0 - nbclassic=1.1.0 - nbclient=0.10.1 @@ -290,7 +293,9 @@ dependencies: - overrides=7.7.0 - packaging=24.2 - pandas=2.2.2 -- pandoc=3.5 +- pandera=0.21.1 +- pandera-base=0.21.1 +- pandoc=3.6 - pandocfilters=1.5.0 - pango=1.54.0 - paramiko=3.5.0 @@ -328,7 +333,7 @@ dependencies: - pigz=2.8 - pillow=10.3.0 - pip=24.3.1 -- pixman=0.43.4 +- pixman=0.44.2 - pkgutil-resolve-name=1.3.10 - platformdirs=4.3.6 - pluggy=1.5.0 @@ -341,6 +346,8 @@ dependencies: - ptyprocess=0.7.0 - pure_eval=0.2.3 - pycparser=2.22 +- pydantic=2.10.3 +- pydantic-core=2.27.1 - pyfaidx=0.8.1.3 - pygments=2.18.0 - pyhmmer=0.10.15 @@ -376,24 +383,24 @@ dependencies: - q2-diversity-lib=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 - q2-fragment-insertion=2025.4.0.dev0 - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 - q2-mystery-stew=2025.4.0.dev0 - q2-phylogeny=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 -- q2-quality-filter=2025.4.0.dev0 +- q2-quality-filter=2025.4.0.dev0+1.g5d1e22f - q2-sample-classifier=2025.4.0.dev0 - q2-stats=2025.4.0.dev0+1.g253c0f6 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0+2.g12602ac +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2galaxy=2025.4.0.dev0 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+4.ge8e66ba +- qiime2=2025.4.0.dev0+5.gdb970dd - r-abind=1.4_5 - r-ade4=1.7_22 - r-ape=5.8 @@ -420,7 +427,7 @@ dependencies: - r-class=7.3_22 - r-cli=3.6.3 - r-clipr=0.8.0 -- r-cluster=2.1.6 +- r-cluster=2.1.8 - r-codetools=0.2_20 - r-colorspace=2.1_1 - r-conflicted=1.2.0 @@ -507,7 +514,7 @@ dependencies: - r-lme4=1.1_35.5 - r-lmertest=3.1_3 - r-lmom=3.2 -- r-lubridate=1.9.3 +- r-lubridate=1.9.4 - r-magrittr=2.0.3 - r-mass=7.3_60.0.1 - r-matrix=1.6_5 @@ -625,6 +632,7 @@ dependencies: - rfc3986=2.0.0 - rfc3986-validator=0.1.1 - rich=13.9.4 +- rnanorm=2.1.0 - rpds-py=0.22.3 - rpsbproc=0.5.0 - samtools=1.21 @@ -671,6 +679,7 @@ dependencies: - types-python-dateutil=2.9.0.20241206 - typing-extensions=4.12.2 - typing_extensions=4.12.2 +- typing_inspect=0.9.0 - typing_utils=0.1.0 - tzdata=2024b - tzlocal=2.1 @@ -692,7 +701,7 @@ dependencies: - wrapt=1.17.0 - xmltodict=0.14.2 - xopen=2.0.2 -- xorg-libxau=1.0.11 +- xorg-libxau=1.0.12 - xorg-libxdmcp=1.1.5 - xz=5.6.3 - xz-gpl-tools=5.6.3 diff --git a/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml b/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml index d344e2c1..d2386056 100644 --- a/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml +++ b/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml @@ -8,9 +8,10 @@ dependencies: - _r-mutex=1.0.1 - alsa-lib=1.2.11 - altair=5.5.0 +- annotated-types=0.7.0 - anyio=4.7.0 - appdirs=1.4.4 -- argcomplete=3.5.1 +- argcomplete=3.5.2 - argh=0.31.3 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 @@ -79,10 +80,10 @@ dependencies: - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 -- bwidget=1.9.14 +- bwidget=1.10.1 - bzip2=1.0.8 -- c-ares=1.34.3 -- ca-certificates=2024.8.30 +- c-ares=1.34.4 +- ca-certificates=2024.12.14 - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.18.0 @@ -98,11 +99,11 @@ dependencies: - contourpy=1.3.1 - cryptography=44.0.0 - curl=8.8.0 -- cutadapt=4.9 +- cutadapt=5.0 - cycler=0.12.1 - dbus=1.13.6 - deblur=1.1.1 -- debugpy=1.8.9 +- debugpy=1.8.11 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=5.0.1 @@ -126,7 +127,7 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.55.2 +- fonttools=4.55.3 - formulaic=1.0.2 - fqdn=1.5.1 - freetype=2.12.1 @@ -289,11 +290,13 @@ dependencies: - mpfr=4.2.1 - mpg123=1.32.9 - mpi=1.0.1 +- multimethod=1.9.1 - munkres=1.1.4 - muscle=3.8.1551 +- mypy_extensions=1.0.0 - mysql-common=8.3.0 - mysql-libs=8.3.0 -- narwhals=1.15.2 +- narwhals=1.18.3 - natsort=8.4.0 - nbclassic=1.1.0 - nbclient=0.10.1 @@ -318,7 +321,9 @@ dependencies: - overrides=7.7.0 - packaging=24.2 - pandas=2.2.2 -- pandoc=3.5 +- pandera=0.21.1 +- pandera-base=0.21.1 +- pandoc=3.6 - pandocfilters=1.5.0 - pango=1.54.0 - paramiko=3.5.0 @@ -356,7 +361,7 @@ dependencies: - pigz=2.8 - pillow=10.3.0 - pip=24.3.1 -- pixman=0.43.2 +- pixman=0.44.2 - pkgutil-resolve-name=1.3.10 - platformdirs=4.3.6 - pluggy=1.5.0 @@ -371,6 +376,8 @@ dependencies: - pulseaudio-client=17.0 - pure_eval=0.2.3 - pycparser=2.22 +- pydantic=2.10.3 +- pydantic-core=2.27.1 - pyfaidx=0.8.1.3 - pygments=2.18.0 - pyhmmer=0.10.15 @@ -406,24 +413,24 @@ dependencies: - q2-diversity-lib=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 - q2-fragment-insertion=2025.4.0.dev0 - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 - q2-mystery-stew=2025.4.0.dev0 - q2-phylogeny=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 -- q2-quality-filter=2025.4.0.dev0 +- q2-quality-filter=2025.4.0.dev0+1.g5d1e22f - q2-sample-classifier=2025.4.0.dev0 - q2-stats=2025.4.0.dev0+1.g253c0f6 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0+2.g12602ac +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2galaxy=2025.4.0.dev0 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+4.ge8e66ba +- qiime2=2025.4.0.dev0+5.gdb970dd - qt-main=5.15.8 - r-abind=1.4_5 - r-ade4=1.7_22 @@ -451,7 +458,7 @@ dependencies: - r-class=7.3_22 - r-cli=3.6.3 - r-clipr=0.8.0 -- r-cluster=2.1.6 +- r-cluster=2.1.8 - r-codetools=0.2_20 - r-colorspace=2.1_1 - r-conflicted=1.2.0 @@ -538,7 +545,7 @@ dependencies: - r-lme4=1.1_35.5 - r-lmertest=3.1_3 - r-lmom=3.2 -- r-lubridate=1.9.3 +- r-lubridate=1.9.4 - r-magrittr=2.0.3 - r-mass=7.3_60.0.1 - r-matrix=1.6_5 @@ -656,6 +663,7 @@ dependencies: - rfc3986=2.0.0 - rfc3986-validator=0.1.1 - rich=13.9.4 +- rnanorm=2.1.0 - rpds-py=0.22.3 - rpsbproc=0.5.0 - samtools=1.21 @@ -704,6 +712,7 @@ dependencies: - types-python-dateutil=2.9.0.20241206 - typing-extensions=4.12.2 - typing_extensions=4.12.2 +- typing_inspect=0.9.0 - typing_utils=0.1.0 - tzdata=2024b - tzlocal=2.1 @@ -734,10 +743,10 @@ dependencies: - xorg-fixesproto=5.0 - xorg-inputproto=2.3.2 - xorg-kbproto=1.0.7 -- xorg-libice=1.1.1 -- xorg-libsm=1.2.4 +- xorg-libice=1.1.2 +- xorg-libsm=1.2.5 - xorg-libx11=1.8.9 -- xorg-libxau=1.0.11 +- xorg-libxau=1.0.12 - xorg-libxdmcp=1.1.5 - xorg-libxext=1.3.4 - xorg-libxfixes=5.0.3 diff --git a/2025.4/amplicon/passed/seed-environment-conda.yml b/2025.4/amplicon/passed/seed-environment-conda.yml index 3d1e7954..ed18387d 100644 --- a/2025.4/amplicon/passed/seed-environment-conda.yml +++ b/2025.4/amplicon/passed/seed-environment-conda.yml @@ -25,24 +25,24 @@ dependencies: - q2-diversity=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 - q2-fragment-insertion=2025.4.0.dev0 - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 - q2-mystery-stew=2025.4.0.dev0 - q2-phylogeny=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 -- q2-quality-filter=2025.4.0.dev0 +- q2-quality-filter=2025.4.0.dev0+1.g5d1e22f - q2-sample-classifier=2025.4.0.dev0 - q2-stats=2025.4.0.dev0+1.g253c0f6 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0+2.g12602ac +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2galaxy=2025.4.0.dev0 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+4.ge8e66ba +- qiime2=2025.4.0.dev0+5.gdb970dd - r-base=4.3.3 - r-reticulate=1.36.0 - rescript=2025.4.0.dev0+2.g16a48fa diff --git a/2025.4/amplicon/staged/seed-environment-conda.yml b/2025.4/amplicon/staged/seed-environment-conda.yml index 3f9b4f68..8830df18 100644 --- a/2025.4/amplicon/staged/seed-environment-conda.yml +++ b/2025.4/amplicon/staged/seed-environment-conda.yml @@ -26,24 +26,24 @@ dependencies: - q2-diversity=2025.4.0.dev0 - q2-emperor=2025.4.0.dev0 - q2-feature-classifier=2025.4.0.dev0 -- q2-feature-table=2025.4.0.dev0 +- q2-feature-table=2025.4.0.dev0+1.gcb009e7 - q2-fragment-insertion=2025.4.0.dev0 - q2-longitudinal=2025.4.0.dev0 - q2-metadata=2025.4.0.dev0 - q2-mystery-stew=2025.4.0.dev0 - q2-phylogeny=2025.4.0.dev0 - q2-quality-control=2025.4.0.dev0 -- q2-quality-filter=2025.4.0.dev0 +- q2-quality-filter=2025.4.0.dev0+1.g5d1e22f - q2-sample-classifier=2025.4.0.dev0 - q2-stats=2025.4.0.dev0+1.g253c0f6 - q2-taxa=2025.4.0.dev0 - q2-types=2025.4.0.dev0 -- q2-vizard=2025.4.0.dev0+2.g12602ac +- q2-vizard=2025.4.0.dev0+65.g1e59022 - q2-vsearch=2025.4.0.dev0 - q2cli=2025.4.0.dev0+1.g0ac7869 - q2galaxy=2025.4.0.dev0 - q2templates=2025.4.0.dev0 -- qiime2=2025.4.0.dev0+4.ge8e66ba +- qiime2=2025.4.0.dev0+5.gdb970dd - r-base=4.3.3 - r-reticulate=1.36.0 - rescript=2025.4.0.dev0+2.g16a48fa