PREP: pin pyzotero to prevent downgrade (moshpit/linux-64)

Author: lizgehret

2026.10/moshpit/passed/rachis-moshpit-linux-64-conda.yml

@@ -17,7 +17,7 @@ dependencies:
 - arpack=3.9.1
 - array-api-compat=1.15.0
 - asttokens=3.0.2
-- atpublic=7.0.0
+- atpublic=9.0.0
 - attrs=26.1.0
 - augustus=3.5.0
 - aws-c-auth=0.9.0
@@ -39,7 +39,7 @@ dependencies:
 - azure-storage-common-cpp=12.8.0
 - azure-storage-files-datalake-cpp=12.12.0
 - babel=2.18.0
-- backports.zstd=1.7.0
+- backports.zstd=1.8.0
 - bamtools=2.5.3
 - bbmap=39.80
 - bc=1.07.1
@@ -82,7 +82,7 @@ dependencies:
 - bioconductor-zlibbioc=1.52.0
 - biom-format=2.1.17
 - biopython=1.86
-- bitarray=3.11.0
+- bitarray=3.12.1
 - bitstring=4.4.0
 - blast=2.16.0
 - boost-cpp=1.85.0
@@ -118,7 +118,7 @@ dependencies:
 - commonmark=0.9.2
 - conda-pack=0.9.1
 - contourpy=1.4.0
-- cpython=3.12.14
+- cpython=3.12.15
 - curl=8.18.0
 - cutadapt=5.2
 - cycler=0.12.1
@@ -149,7 +149,7 @@ dependencies:
 - feedparser=6.0.14
 - feedparser-sgmllib=2.1.0
 - filelock=3.32.6
-- flufl.lock=9.2.0
+- flufl.lock=10.0.0
 - font-ttf-dejavu-sans-mono=2.37
 - font-ttf-inconsolata=3.000
 - font-ttf-source-code-pro=2.038
@@ -175,7 +175,7 @@ dependencies:
 - glog=0.7.1
 - glpk=5.0
 - gmp=6.3.0
-- gmpy2=2.3.1
+- gmpy2=2.3.2
 - gperftools=2.18.90
 - graphite2=1.3.15
 - gridss=2.13.2
@@ -197,13 +197,13 @@ dependencies:
 - icu=75.1
 - idna=3.20
 - igraph=0.10.16
-- ijson=3.5.1
+- ijson=3.6.0
 - imagesize=2.0.1
 - importlib-metadata=9.0.1
 - importlib_metadata=9.0.1
 - importlib_resources=7.1.0
 - inflate64=1.0.4
-- iniconfig=2.3.0
+- iniconfig=2.3.1
 - insilicoseq=2.0.1
 - interface_meta=1.3.0
 - iow=1.0.8
@@ -212,7 +212,7 @@ dependencies:
 - ipywidgets=8.1.9
 - isa-l=2.32.1
 - isodate=0.7.2
-- jedi=0.20.0
+- jedi=0.20.1
 - jinja2=3.1.6
 - joblib=1.6.0
 - jq=1.8.2
@@ -260,7 +260,7 @@ dependencies:
 - libcxsparse=4.4.1
 - libdeflate=1.22
 - libdrm=2.4.129
-- libedit=3.1.20250104
+- libedit=3.1.20260512
 - libegl=1.7.0
 - libev=4.33
 - libevent=2.1.12
@@ -300,14 +300,14 @@ dependencies:
 - libnsl=2.0.1
 - libntlm=1.8
 - libopengl=1.7.0
-- libopenssl-static=3.6.4
+- libopenssl-static=3.6.5
 - libparquet=16.1.0
 - libparu=1.0.0
 - libpciaccess=0.19
 - libpng=1.6.59
 - libpq=17.7
 - libprotobuf=5.29.3
-- libpython=3.12.14
+- libpython=3.12.15
 - librbio=4.3.4
 - libre2-11=2025.06.26
 - libsanitizer=16.2.0
@@ -336,7 +336,7 @@ dependencies:
 - libxml2=2.13.9
 - libxslt=1.1.43
 - libzlib=1.3.2
-- llvm-openmp=23.1.2
+- llvm-openmp=23.1.3
 - loguru=0.7.3
 - lp_solve=5.5.2.11
 - lxml=6.0.2
@@ -375,7 +375,7 @@ dependencies:
 - mysql-common=9.0.1
 - mysql-connector-c=6.1.11
 - mysql-libs=9.0.1
-- narwhals=2.26.0
+- narwhals=2.27.1
 - natsort=8.4.0
 - ncbi-datasets-pyclient=18.18.0
 - ncbi-vdb=3.4.1
@@ -390,14 +390,14 @@ dependencies:
 - openjpeg=2.5.3
 - openldap=2.6.10
 - openmpi=4.1.6
-- openssl=3.6.4
+- openssl=3.6.5
 - optree=0.20.0
 - orc=2.1.1
 - packaging=26.3
 - pandas=2.3.3
-- pandera=0.33.1
-- pandera-base=0.33.1
-- pandoc=3.12
+- pandera=0.34.1
+- pandera-base=0.34.1
+- pandoc=3.12.1
 - pango=1.56.3
 - parsl=2026.2.23
 - parso=0.8.7
@@ -408,7 +408,7 @@ dependencies:
 - pcre2=10.44
 - perl=5.32.1
 - perl-app-cpanminus=1.7048
-- perl-archive-tar=3.12
+- perl-archive-tar=3.14
 - perl-b-cow=0.007
 - perl-carp=1.50
 - perl-class-method-modifiers=2.13
@@ -471,20 +471,20 @@ dependencies:
 - perl-types-serialiser=1.01
 - perl-xml-parser=2.44_01
 - perl-yaml=1.30
-- petl=1.7.28
+- petl=1.7.29
 - pexpect=4.9.0
 - pigz=2.8
 - pillow=11.3.0
 - pip=26.2.1
 - pixman=0.46.4
-- platformdirs=4.12.2
+- platformdirs=4.13.0
 - plotly=7.1.0
 - pluggy=1.6.0
 - pockets=0.9.1
-- polars=1.44.2
+- polars=2.0.0
 - polars-lts-cpu=1.34.0.deprecated
-- polars-runtime-32=1.44.2
-- polars-runtime-compat=1.44.2
+- polars-runtime-32=2.0.0
+- polars-runtime-compat=2.0.0
 - popt=1.19
 - pplacer=1.1.alpha19
 - prank=251117
@@ -503,25 +503,25 @@ dependencies:
 - pybind11=3.1.0
 - pybind11-global=3.1.0
 - pycoverm=0.6.2
-- pycparser=3.0
+- pycparser=3.11
 - pycryptodomex=3.23.0
-- pydantic=2.13.5
-- pydantic-core=2.46.5
+- pydantic=2.14.1
+- pydantic-core=2.50.1
 - pygments=2.21.0
 - pyhmmer=0.12.3
-- pymongo=4.18.2
+- pymongo=4.18.3
 - pyparsing=3.3.3
 - pyppmd=1.1.0
 - pyrodigal=3.7.1
 - pysam=0.23.3
 - pyside6=6.9.0
 - pysocks=1.7.1
 - pytest=9.1.1
-- python=3.12.14
+- python=3.12.15
 - python-abi3=3.12
 - python-dateutil=2.9.0.post0
 - python-dotenv=1.2.4
-- python-gil=3.12.14
+- python-gil=3.12.15
 - python-igraph=0.11.9
 - python-isal=1.8.0
 - python-kaleido=0.2.1
@@ -530,23 +530,23 @@ dependencies:
 - python-zlib-ng=1.0.0
 - python_abi=3.12
 - pytorch=2.7.1
-- pytz=2026.4
+- pytz=2026.5
 - pyyaml=6.0.3
 - pyzmq=27.2.0
 - pyzotero=1.14.0
 - pyzstd=0.19.1
-- q2-annotate=2026.10.0.dev0+2.gc9767e1
+- q2-annotate=2026.10.0.dev0+3.g635d2f9
 - q2-assembly=2026.10.0.dev0+4.g09721e9
 - q2-cutadapt=2026.10.0.dev0+3.gac415ae
 - q2-demux=2026.10.0.dev0
-- q2-fastp=2026.10.0.dev0+3.g5af2543
-- q2-feature-table=2026.10.0.dev0+14.g9c210db
-- q2-fondue=2026.10.0.dev0+2.g2691f25
-- q2-mag=2026.10.0.dev0+3.g438963a
+- q2-fastp=2026.10.0.dev0+4.g6b7a512
+- q2-feature-table=2026.10.0.dev0+15.gdb39e84
+- q2-fondue=2026.10.0.dev0+3.g44e2b25
+- q2-mag=2026.10.0.dev0+5.gee16594
 - q2-metadata=2026.10.0.dev0+1.g8a56980
 - q2-mystery-stew=2026.10.0.dev0
 - q2-quality-control=2026.10.0.dev0
-- q2-sapienns=2026.10.0.dev0
+- q2-sapienns=2026.10.0.dev0+1.g7fd5c82
 - q2-sourmash=2026.10.0.dev0
 - q2-taxa=2026.10.0.dev0+2.g4d075c9
 - q2-types=2026.10.0.dev0+2.g861f127
@@ -700,7 +700,7 @@ dependencies:
 - r-xml=3.99_0.17
 - r-xml2=1.4.0
 - r-yaml=2.3.12
-- rachis=2026.10.0.dev0+7.g8923e91
+- rachis=2026.10.0.dev0+8.ged1c2d0
 - rachis-cli=2026.10.0.dev0+1.ge730ca2
 - raxml=8.2.13
 - re2=2025.06.26
@@ -717,7 +717,7 @@ dependencies:
 - rmblast=2.14.1
 - rnanorm=2.1.0
 - roman-numerals=4.1.0
-- rpds-py=2026.6.3
+- rpds-py=2026.9.1
 - rpsbproc=0.5.1
 - rsync=3.4.4
 - ruby=3.4.2
@@ -745,7 +745,7 @@ dependencies:
 - sniffio=1.3.1
 - snowballstemmer=3.1.1
 - sortedcontainers=2.4.0
-- soupsieve=2.10
+- soupsieve=3.0.3
 - sourmash-minimal=4.9.4
 - sourmash_plugin_branchwater=0.9.15
 - spades=4.2.0
@@ -758,7 +758,7 @@ dependencies:
 - sphinxcontrib-napoleon=0.7
 - sphinxcontrib-qthelp=2.0.0
 - sphinxcontrib-serializinghtml=2.0.0
-- sqlalchemy=2.1.3
+- sqlalchemy=2.1.4
 - sqlite=3.53.4
 - stack_data=0.6.3
 - statsmodels=0.15.0
@@ -771,20 +771,20 @@ dependencies:
 - tbb=2021.13.0
 - tblib=3.2.2
 - text-unidecode=1.3
-- texttable=1.7.0
+- texttable=1.7.1
 - threadpoolctl=3.7.0
 - tibs=0.5.7
 - tiktoken=0.14.0
 - tk=8.6.13
 - tktable=2.10
-- tomli=2.4.1
+- tomli=2.5.0
 - tomlkit=0.15.1
 - tornado=6.5.10
 - tqdm=4.67.3
 - traitlets=5.16.1
 - trf=4.10.0rc2
 - typeguard=4.6.0
-- typer=0.27.2
+- typer=0.27.3
 - typing-extensions=4.16.0
 - typing-inspection=0.4.4
 - typing_extensions=4.16.0
@@ -799,12 +799,12 @@ dependencies:
 - unzip=6.0
 - urllib3=2.5.0
 - usearch=12.0_beta
-- validators=0.35.0
+- validators=0.36.0
 - vamb=5.0.4
 - vambcore=0.1.2
 - vsearch=2.30.4
 - wayland=1.26.0
-- wcwidth=0.9.1
+- wcwidth=0.9.2
 - wget=1.21.4
 - wheel=0.48.0
 - whenever=0.11.0
@@ -841,7 +841,7 @@ dependencies:
 - xz-gpl-tools=5.8.3
 - xz-tools=5.8.3
 - yaml=0.2.5
-- yq=4.4.0
+- yq=4.4.5
 - zeromq=4.3.5
 - zipfile-deflate64=0.2.0
 - zipp=4.1.1

2026.10/moshpit/passed/seed-environment-conda-linux.yml

@@ -36,18 +36,19 @@ dependencies:
 - pyarrow=16.1.0
 - pysam=0.23.3
 - python=3.12
-- q2-annotate=2026.10.0.dev0+2.gc9767e1
+- pyzotero=1.14.0
+- q2-annotate=2026.10.0.dev0+3.g635d2f9
 - q2-assembly=2026.10.0.dev0+4.g09721e9
 - q2-cutadapt=2026.10.0.dev0+3.gac415ae
 - q2-demux=2026.10.0.dev0
-- q2-fastp=2026.10.0.dev0+3.g5af2543
-- q2-feature-table=2026.10.0.dev0+14.g9c210db
-- q2-fondue=2026.10.0.dev0+2.g2691f25
-- q2-mag=2026.10.0.dev0+3.g438963a
+- q2-fastp=2026.10.0.dev0+4.g6b7a512
+- q2-feature-table=2026.10.0.dev0+15.gdb39e84
+- q2-fondue=2026.10.0.dev0+3.g44e2b25
+- q2-mag=2026.10.0.dev0+5.gee16594
 - q2-metadata=2026.10.0.dev0+1.g8a56980
 - q2-mystery-stew=2026.10.0.dev0
 - q2-quality-control=2026.10.0.dev0
-- q2-sapienns=2026.10.0.dev0
+- q2-sapienns=2026.10.0.dev0+1.g7fd5c82
 - q2-sourmash=2026.10.0.dev0
 - q2-taxa=2026.10.0.dev0+2.g4d075c9
 - q2-types=2026.10.0.dev0+2.g861f127
@@ -58,7 +59,7 @@ dependencies:
 - r-optparse=1.7.5
 - r-reticulate=1.45.0
 - rachis-cli=2026.10.0.dev0+1.ge730ca2
-- rachis=2026.10.0.dev0+7.g8923e91
+- rachis=2026.10.0.dev0+8.ged1c2d0
 - rescript=2026.10.0.dev0+8.gf7aa578
 - rnanorm=2.1.0
 - samtools=1.22.1