From 0145cc4f246dfbe4829a35796ab867f5536b662a Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Fri, 1 Nov 2024 19:57:11 +0000
Subject: [PATCH] Update conda environments (Prepare-2025.4-pathogenome)

---
 .../qiime2-pathogenome-macos-latest-conda.yml | 54 +++++++++----------
 ...qiime2-pathogenome-ubuntu-latest-conda.yml | 50 ++++++++---------
 .../passed/seed-environment-conda.yml         | 38 ++++++-------
 .../staged/seed-environment-conda.yml         | 38 ++++++-------
 4 files changed, 90 insertions(+), 90 deletions(-)

diff --git a/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml b/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml
index 4eebd6a2..7034e852 100644
--- a/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml
+++ b/2025.4/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed
+- https://packages.qiime2.org/qiime2/2025.4/pathogenome/passed
 - conda-forge
 - bioconda
 dependencies:
@@ -53,7 +53,7 @@ dependencies:
 - biom-format=2.1.15
 - biopython=1.84
 - blast=2.16.0
-- bleach=6.1.0
+- bleach=6.2.0
 - bowtie2=2.5.1
 - brotli=1.1.0
 - brotli-bin=1.1.0
@@ -179,7 +179,7 @@ dependencies:
 - libcblas=3.9.0
 - libclang-cpp18.1=18.1.7
 - libcurl=8.8.0
-- libcxx=19.1.2
+- libcxx=19.1.3
 - libdeflate=1.20
 - libedit=3.1.20191231
 - libev=4.33
@@ -192,7 +192,7 @@ dependencies:
 - libgfortran-devel_osx-64=12.3.0
 - libgfortran5=13.2.0
 - libglib=2.80.2
-- libhwloc=2.11.1
+- libhwloc=2.11.2
 - libiconv=1.17
 - libidn2=2.3.7
 - libintl=0.22.5
@@ -216,7 +216,7 @@ dependencies:
 - libxml2=2.12.7
 - libxslt=1.1.39
 - libzlib=1.2.13
-- llvm-openmp=19.1.2
+- llvm-openmp=19.1.3
 - llvm-tools=18.1.7
 - lxml=5.2.2
 - lz4=4.3.3
@@ -353,23 +353,23 @@ dependencies:
 - pyvcf3=1.0.3
 - pyyaml=6.0.2
 - pyzmq=24.0.1
-- q2-amrfinderplus=2024.10.0
-- q2-assembly=2024.10.0
-- q2-demux=2024.10.0
-- q2-feature-classifier=2024.10.0
-- q2-feature-table=2024.10.0
-- q2-longitudinal=2024.10.0
-- q2-metadata=2024.10.0
-- q2-mystery-stew=2024.10.0
-- q2-quality-control=2024.10.0
-- q2-sample-classifier=2024.10.0
-- q2-taxa=2024.10.0
-- q2-types=2024.10.0
-- q2-viromics=2024.10.0
-- q2-vizard=2024.10.0
-- q2cli=2024.10.1
-- q2templates=2024.10.0
-- qiime2=2024.10.1
+- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede
+- q2-assembly=2025.4.0.dev0
+- q2-demux=2025.4.0.dev0
+- q2-feature-classifier=2025.4.0.dev0
+- q2-feature-table=2025.4.0.dev0
+- q2-longitudinal=2025.4.0.dev0
+- q2-metadata=2025.4.0.dev0
+- q2-mystery-stew=2025.4.0.dev0
+- q2-quality-control=2025.4.0.dev0
+- q2-sample-classifier=2025.4.0.dev0
+- q2-taxa=2025.4.0.dev0
+- q2-types=2025.4.0.dev0
+- q2-viromics=2025.4.0.dev0+2.g48e387f
+- q2-vizard=2025.4.0.dev0
+- q2cli=2025.4.0.dev0+1.g0ac7869
+- q2templates=2025.4.0.dev0
+- qiime2=2025.4.0.dev0+1.gab00603
 - quast=5.2.0
 - r-abind=1.4_5
 - r-argparser=0.7.2
@@ -414,7 +414,7 @@ dependencies:
 - r-fontawesome=0.5.2
 - r-forcats=1.0.0
 - r-formatr=1.14
-- r-fs=1.6.4
+- r-fs=1.6.5
 - r-futile.logger=1.4.3
 - r-futile.options=1.0.1
 - r-gargle=1.5.2
@@ -520,10 +520,10 @@ dependencies:
 - readline=8.2
 - referencing=0.35.1
 - requests=2.32.3
-- rescript=2024.10.0
+- rescript=2025.4.0.dev0
 - rfc3339-validator=0.1.4
 - rfc3986-validator=0.1.1
-- rpds-py=0.20.0
+- rpds-py=0.20.1
 - rpsbproc=0.5.0
 - rsync=3.3.0
 - samtools=1.21
@@ -534,7 +534,7 @@ dependencies:
 - seaborn-base=0.12.2
 - send2trash=1.8.3
 - setproctitle=1.3.3
-- setuptools=75.1.0
+- setuptools=75.3.0
 - shortuuid=1.0.13
 - sigtool=0.1.3
 - simplejson=3.19.3
@@ -546,7 +546,7 @@ dependencies:
 - statsmodels=0.14.4
 - tapi=1100.0.11
 - tar=1.34
-- tbb=2021.13.0
+- tbb=2022.0.0
 - tblib=3.0.0
 - terminado=0.18.1
 - threadpoolctl=3.5.0
diff --git a/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml b/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml
index f7a2afa9..14b8eb84 100644
--- a/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml
+++ b/2025.4/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed
+- https://packages.qiime2.org/qiime2/2025.4/pathogenome/passed
 - conda-forge
 - bioconda
 dependencies:
@@ -59,7 +59,7 @@ dependencies:
 - biom-format=2.1.15
 - biopython=1.84
 - blast=2.16.0
-- bleach=6.1.0
+- bleach=6.2.0
 - bowtie2=2.5.1
 - brotli=1.1.0
 - brotli-bin=1.1.0
@@ -206,7 +206,7 @@ dependencies:
 - libglib=2.80.2
 - libgomp=14.2.0
 - libgpg-error=1.50
-- libhwloc=2.11.1
+- libhwloc=2.11.2
 - libiconv=1.17
 - libidn2=2.3.7
 - libjpeg-turbo=3.0.0
@@ -386,23 +386,23 @@ dependencies:
 - pyvcf3=1.0.3
 - pyyaml=6.0.2
 - pyzmq=24.0.1
-- q2-amrfinderplus=2024.10.0
-- q2-assembly=2024.10.0
-- q2-demux=2024.10.0
-- q2-feature-classifier=2024.10.0
-- q2-feature-table=2024.10.0
-- q2-longitudinal=2024.10.0
-- q2-metadata=2024.10.0
-- q2-mystery-stew=2024.10.0
-- q2-quality-control=2024.10.0
-- q2-sample-classifier=2024.10.0
-- q2-taxa=2024.10.0
-- q2-types=2024.10.0
-- q2-viromics=2024.10.0
-- q2-vizard=2024.10.0
-- q2cli=2024.10.1
-- q2templates=2024.10.0
-- qiime2=2024.10.1
+- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede
+- q2-assembly=2025.4.0.dev0
+- q2-demux=2025.4.0.dev0
+- q2-feature-classifier=2025.4.0.dev0
+- q2-feature-table=2025.4.0.dev0
+- q2-longitudinal=2025.4.0.dev0
+- q2-metadata=2025.4.0.dev0
+- q2-mystery-stew=2025.4.0.dev0
+- q2-quality-control=2025.4.0.dev0
+- q2-sample-classifier=2025.4.0.dev0
+- q2-taxa=2025.4.0.dev0
+- q2-types=2025.4.0.dev0
+- q2-viromics=2025.4.0.dev0+2.g48e387f
+- q2-vizard=2025.4.0.dev0
+- q2cli=2025.4.0.dev0+1.g0ac7869
+- q2templates=2025.4.0.dev0
+- qiime2=2025.4.0.dev0+1.gab00603
 - qt-main=5.15.8
 - quast=5.2.0
 - r-abind=1.4_5
@@ -448,7 +448,7 @@ dependencies:
 - r-fontawesome=0.5.2
 - r-forcats=1.0.0
 - r-formatr=1.14
-- r-fs=1.6.4
+- r-fs=1.6.5
 - r-futile.logger=1.4.3
 - r-futile.options=1.0.1
 - r-gargle=1.5.2
@@ -555,11 +555,11 @@ dependencies:
 - referencing=0.35.1
 - repeatmasker=4.1.7p1
 - requests=2.32.3
-- rescript=2024.10.0
+- rescript=2025.4.0.dev0
 - rfc3339-validator=0.1.4
 - rfc3986-validator=0.1.1
 - rmblast=2.14.1
-- rpds-py=0.20.0
+- rpds-py=0.20.1
 - rpsbproc=0.5.0
 - rsync=3.3.0
 - samtools=1.21
@@ -571,7 +571,7 @@ dependencies:
 - sed=4.8
 - send2trash=1.8.3
 - setproctitle=1.3.3
-- setuptools=75.1.0
+- setuptools=75.3.0
 - shortuuid=1.0.13
 - simplejson=3.19.3
 - sip=6.7.12
@@ -583,7 +583,7 @@ dependencies:
 - statsmodels=0.14.4
 - sysroot_linux-64=2.17
 - tar=1.34
-- tbb=2021.13.0
+- tbb=2022.0.0
 - tblib=3.0.0
 - terminado=0.18.1
 - threadpoolctl=3.5.0
diff --git a/2025.4/pathogenome/passed/seed-environment-conda.yml b/2025.4/pathogenome/passed/seed-environment-conda.yml
index 8ce428d2..16e77086 100644
--- a/2025.4/pathogenome/passed/seed-environment-conda.yml
+++ b/2025.4/pathogenome/passed/seed-environment-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released
+- https://packages.qiime2.org/qiime2/2025.4/pathogenome/passed
 - conda-forge
 - bioconda
 dependencies:
@@ -15,26 +15,26 @@ dependencies:
 - patsy=0.5.6
 - pysam=0.22.1
 - python=3.10
-- q2-amrfinderplus=2024.10.0
-- q2-assembly=2024.10.0
-- q2-demux=2024.10.0
-- q2-feature-classifier=2024.10.0
-- q2-feature-table=2024.10.0
-- q2-longitudinal=2024.10.0
-- q2-metadata=2024.10.0
-- q2-mystery-stew=2024.10.0
-- q2-quality-control=2024.10.0
-- q2-sample-classifier=2024.10.0
-- q2-taxa=2024.10.0
-- q2-types=2024.10.0
-- q2-viromics=2024.10.0
-- q2-vizard=2024.10.0
-- q2cli=2024.10.1
-- q2templates=2024.10.0
-- qiime2=2024.10.1
+- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede
+- q2-assembly=2025.4.0.dev0
+- q2-demux=2025.4.0.dev0
+- q2-feature-classifier=2025.4.0.dev0
+- q2-feature-table=2025.4.0.dev0
+- q2-longitudinal=2025.4.0.dev0
+- q2-metadata=2025.4.0.dev0
+- q2-mystery-stew=2025.4.0.dev0
+- q2-quality-control=2025.4.0.dev0
+- q2-sample-classifier=2025.4.0.dev0
+- q2-taxa=2025.4.0.dev0
+- q2-types=2025.4.0.dev0
+- q2-viromics=2025.4.0.dev0+2.g48e387f
+- q2-vizard=2025.4.0.dev0
+- q2cli=2025.4.0.dev0+1.g0ac7869
+- q2templates=2025.4.0.dev0
+- qiime2=2025.4.0.dev0+1.gab00603
 - r-base=4.3.3
 - r-reticulate=1.36.0
-- rescript=2024.10.0
+- rescript=2025.4.0.dev0
 - scikit-bio=0.6.0
 - scikit-learn=1.4.2
 - scipy=1.13.0
diff --git a/2025.4/pathogenome/staged/seed-environment-conda.yml b/2025.4/pathogenome/staged/seed-environment-conda.yml
index eb4a6112..d60f2af7 100644
--- a/2025.4/pathogenome/staged/seed-environment-conda.yml
+++ b/2025.4/pathogenome/staged/seed-environment-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released
+- https://packages.qiime2.org/qiime2/2025.4/pathogenome/staged
 - conda-forge
 - bioconda
 dependencies:
@@ -16,26 +16,26 @@ dependencies:
 - pysam=0.22.1
 - python=3.10
 - python_abi=3.9
-- q2-amrfinderplus=2024.10.0
-- q2-assembly=2024.10.0
-- q2-demux=2024.10.0
-- q2-feature-classifier=2024.10.0
-- q2-feature-table=2024.10.0
-- q2-longitudinal=2024.10.0
-- q2-metadata=2024.10.0
-- q2-mystery-stew=2024.10.0
-- q2-quality-control=2024.10.0
-- q2-sample-classifier=2024.10.0
-- q2-taxa=2024.10.0
-- q2-types=2024.10.0
-- q2-viromics=2024.10.0
-- q2-vizard=2024.10.0
-- q2cli=2024.10.1
-- q2templates=2024.10.0
-- qiime2=2024.10.1
+- q2-amrfinderplus=2025.4.0.dev0+2.ga45dede
+- q2-assembly=2025.4.0.dev0
+- q2-demux=2025.4.0.dev0
+- q2-feature-classifier=2025.4.0.dev0
+- q2-feature-table=2025.4.0.dev0
+- q2-longitudinal=2025.4.0.dev0
+- q2-metadata=2025.4.0.dev0
+- q2-mystery-stew=2025.4.0.dev0
+- q2-quality-control=2025.4.0.dev0
+- q2-sample-classifier=2025.4.0.dev0
+- q2-taxa=2025.4.0.dev0
+- q2-types=2025.4.0.dev0
+- q2-viromics=2025.4.0.dev0+2.g48e387f
+- q2-vizard=2025.4.0.dev0
+- q2cli=2025.4.0.dev0+1.g0ac7869
+- q2templates=2025.4.0.dev0
+- qiime2=2025.4.0.dev0+1.gab00603
 - r-base=4.3.3
 - r-reticulate=1.36.0
-- rescript=2024.10.0
+- rescript=2025.4.0.dev0
 - scikit-bio=0.6.0
 - scikit-learn=1.4.2
 - scipy=1.13.0