From 34b5987838a97ec9636a9e3babea063773665722 Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Sun, 14 Apr 2024 03:39:54 +0000
Subject: [PATCH 1/2] Automated updates to seed environment: shotgun

---
 2024.5/shotgun/passed/seed-environment-conda.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/2024.5/shotgun/passed/seed-environment-conda.yml b/2024.5/shotgun/passed/seed-environment-conda.yml
index 002831d7..5d24f525 100644
--- a/2024.5/shotgun/passed/seed-environment-conda.yml
+++ b/2024.5/shotgun/passed/seed-environment-conda.yml
@@ -51,3 +51,4 @@ dependencies:
 extras:
   variant_override:
     qiime2_epoch: '2024.5'
+# modified: 2024-04-14

From 18e4a9024211521d3459608ae6f6335371db7da6 Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Sun, 14 Apr 2024 06:20:34 +0000
Subject: [PATCH 2/2] Update conda environments
 (Prepare-2024.5/shotgun/2024-04-14)

---
 .../qiime2-shotgun-macos-latest-conda.yml     | 54 ++++++++++--------
 .../qiime2-shotgun-ubuntu-latest-conda.yml    | 56 ++++++++++---------
 .../shotgun/passed/seed-environment-conda.yml |  5 +-
 .../shotgun/staged/seed-environment-conda.yml |  4 +-
 4 files changed, 64 insertions(+), 55 deletions(-)

diff --git a/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml b/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml
index eb3304d8..741df311 100644
--- a/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml
+++ b/2024.5/shotgun/passed/qiime2-shotgun-macos-latest-conda.yml
@@ -121,9 +121,8 @@ dependencies:
 - contourpy=1.1.1
 - cryptography=42.0.5
 - curl=7.88.1
-- cutadapt=4.7
+- cutadapt=4.8
 - cycler=0.12.1
-- cython=3.0.10
 - debugpy=1.8.1
 - decorator=4.4.2
 - defusedxml=0.7.1
@@ -150,18 +149,19 @@ dependencies:
 - fontconfig=2.14.2
 - fonts-conda-ecosystem=1
 - fonts-conda-forge=1
-- fonttools=4.50.0
+- fonttools=4.51.0
 - formulaic=1.0.1
 - fqdn=1.5.1
 - freetype=2.12.1
 - fribidi=1.0.10
 - future=1.0.0
 - gawk=5.3.0
-- gettext=0.21.1
+- gettext=0.22.5
+- gettext-tools=0.22.5
 - gffutils=0.10.1
 - gfortran_impl_osx-64=11.4.0
 - gfortran_osx-64=11.4.0
-- giflib=5.2.1
+- giflib=5.2.2
 - glimmerhmm=3.0.4
 - globus-sdk=3.39.0
 - glpk=5.0
@@ -194,7 +194,7 @@ dependencies:
 - isoduration=20.11.0
 - jedi=0.19.1
 - jinja2=3.1.3
-- joblib=1.3.2
+- joblib=1.4.0
 - jpeg=9e
 - jq=1.7.1
 - jsonlines=3.0.0
@@ -205,7 +205,7 @@ dependencies:
 - jupyter_client=7.4.9
 - jupyter_core=5.7.2
 - jupyter_events=0.10.0
-- jupyter_server=2.13.0
+- jupyter_server=2.14.0
 - jupyter_server_terminals=0.5.3
 - jupyterlab_pygments=0.3.0
 - jupyterlab_widgets=3.0.10
@@ -218,6 +218,8 @@ dependencies:
 - ld64_osx-64=711
 - lerc=4.0.0
 - libaec=1.1.3
+- libasprintf=0.22.5
+- libasprintf-devel=0.22.5
 - libblas=3.9.0
 - libbrotlicommon=1.1.0
 - libbrotlidec=1.1.0
@@ -232,12 +234,16 @@ dependencies:
 - libexpat=2.6.2
 - libffi=3.4.4
 - libgd=2.3.3
+- libgettextpo=0.22.5
+- libgettextpo-devel=0.22.5
 - libgfortran=5.0.0
 - libgfortran-devel_osx-64=11.4.0
 - libgfortran5=13.2.0
 - libglib=2.78.1
 - libiconv=1.17
 - libidn2=2.3.7
+- libintl=0.22.5
+- libintl-devel=0.22.5
 - liblapack=3.9.0
 - liblapacke=3.9.0
 - libllvm14=14.0.6
@@ -257,7 +263,7 @@ dependencies:
 - libxml2=2.10.3
 - libxslt=1.1.37
 - libzlib=1.2.13
-- llvm-openmp=18.1.2
+- llvm-openmp=18.1.3
 - llvm-tools=17.0.6
 - llvmlite=0.41.1
 - lockfile=0.12.2
@@ -289,9 +295,9 @@ dependencies:
 - nbconvert=7.16.3
 - nbconvert-core=7.16.3
 - nbconvert-pandoc=7.16.3
-- nbformat=5.10.3
+- nbformat=5.10.4
 - ncbi-datasets-pylib=16.6.0
-- ncbi-vdb=3.0.0
+- ncbi-vdb=3.1.0
 - ncurses=6.4.20240210
 - nest-asyncio=1.6.0
 - networkx=3.1
@@ -307,12 +313,12 @@ dependencies:
 - overrides=7.7.0
 - packaging=24.0
 - pandas=1.5.3
-- pandoc=3.1.12.3
+- pandoc=3.1.13
 - pandocfilters=1.5.0
 - pango=1.50.14
 - paramiko=3.4.0
 - parsl=2023.12.4
-- parso=0.8.3
+- parso=0.8.4
 - pathlib=1.0.1
 - patsy=0.5.3
 - pbzip2=1.1.13
@@ -332,7 +338,7 @@ dependencies:
 - perl-constant=1.33
 - perl-dbi=1.643
 - perl-digest-perl-md5=1.9
-- perl-encode=3.19
+- perl-encode=3.21
 - perl-exporter=5.74
 - perl-exporter-tiny=1.002002
 - perl-extutils-config=0.008
@@ -419,7 +425,7 @@ dependencies:
 - python-fastjsonschema=2.19.1
 - python-isal=1.6.1
 - python-json-logger=2.0.7
-- python-zlib-ng=0.4.1
+- python-zlib-ng=0.4.2
 - python_abi=3.8
 - pytz=2024.1
 - pyvcf3=1.0.3
@@ -445,7 +451,7 @@ dependencies:
 - 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-types=2024.5.0.dev0+5.gd24a69d
 - q2-vsearch=2024.5.0.dev0
 - q2cli=2024.5.0.dev0
 - q2templates=2024.5.0.dev0
@@ -501,7 +507,7 @@ dependencies:
 - r-e1071=1.7_14
 - r-ecosolver=0.5.5
 - r-ellipsis=0.3.2
-- r-emmeans=1.10.0
+- r-emmeans=1.10.1
 - r-energy=1.7_11
 - r-estimability=1.4.1
 - r-evaluate=0.23
@@ -543,7 +549,7 @@ dependencies:
 - r-hmisc=5.1_2
 - r-hms=1.1.3
 - r-htmltable=2.4.2
-- r-htmltools=0.5.8
+- r-htmltools=0.5.8.1
 - r-htmlwidgets=1.6.4
 - r-httr=1.4.7
 - r-ids=1.0.1
@@ -555,7 +561,7 @@ dependencies:
 - r-jpeg=0.1_10
 - r-jquerylib=0.1.4
 - r-jsonlite=1.8.8
-- r-knitr=1.45
+- r-knitr=1.46
 - r-labeling=0.4.3
 - r-lambda.r=1.2.4
 - r-lattice=0.22_6
@@ -569,7 +575,7 @@ dependencies:
 - r-magrittr=2.0.3
 - r-mass=7.3_60.0.1
 - r-matrix=1.6_5
-- r-matrixstats=1.2.0
+- r-matrixstats=1.3.0
 - r-memoise=2.0.1
 - r-mgcv=1.9_1
 - r-mime=0.12
@@ -679,7 +685,7 @@ dependencies:
 - readline=8.2
 - referencing=0.34.0
 - requests=2.31.0
-- rescript=2024.5.0.dev0+2.ga0df425
+- rescript=2024.5.0.dev0+3.g6e87cfe
 - rfc3339-validator=0.1.4
 - rfc3986-validator=0.1.1
 - rpds-py=0.18.0
@@ -689,7 +695,7 @@ dependencies:
 - scipy=1.10.0
 - seaborn=0.12.2
 - seaborn-base=0.12.2
-- send2trash=1.8.2
+- send2trash=1.8.3
 - sepp=4.3.10
 - setproctitle=1.3.3
 - setuptools=69.2.0
@@ -722,8 +728,8 @@ dependencies:
 - traitlets=5.9.0
 - typeguard=2.13.3
 - types-python-dateutil=2.9.0.20240316
-- typing-extensions=4.10.0
-- typing_extensions=4.10.0
+- typing-extensions=4.11.0
+- typing_extensions=4.11.0
 - typing_utils=0.1.0
 - tzlocal=2.1
 - ucsc-fatotwobit=366
@@ -734,7 +740,7 @@ dependencies:
 - unifrac-binaries=1.3.2
 - uri-template=1.3.0
 - urllib3=1.26.18
-- vsearch=2.27.0
+- vsearch=2.27.1
 - wcwidth=0.2.13
 - webcolors=1.13
 - webencodings=0.5.1
diff --git a/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml b/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml
index cfc03f8b..573ba7d5 100644
--- a/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml
+++ b/2024.5/shotgun/passed/qiime2-shotgun-ubuntu-latest-conda.yml
@@ -88,7 +88,7 @@ dependencies:
 - bioconductor-zlibbioc=1.44.0
 - biom-format=2.1.14
 - biopython=1.78
-- blast=2.14.1
+- blast=2.15.0
 - bleach=6.1.0
 - boost-cpp=1.74.0
 - bowtie2=2.5.1
@@ -118,15 +118,14 @@ dependencies:
 - contourpy=1.1.1
 - cryptography=39.0.0
 - curl=7.87.0
-- cutadapt=4.7
+- cutadapt=4.8
 - cycler=0.12.1
-- cython=3.0.10
 - dbus=1.13.6
 - debugpy=1.8.1
 - decorator=4.4.2
 - defusedxml=0.7.1
 - dendropy=4.5.2
-- diamond=2.1.8
+- diamond=2.1.9
 - dill=0.3.8
 - dnaio=1.2.0
 - easel=0.49
@@ -149,7 +148,7 @@ dependencies:
 - fontconfig=2.14.2
 - fonts-conda-ecosystem=1
 - fonts-conda-forge=1
-- fonttools=4.50.0
+- fonttools=4.51.0
 - formulaic=1.0.1
 - fqdn=1.5.1
 - freetype=2.12.1
@@ -157,10 +156,11 @@ dependencies:
 - future=1.0.0
 - gawk=5.3.0
 - gcc_impl_linux-64=13.2.0
-- gettext=0.21.1
+- gettext=0.22.5
+- gettext-tools=0.22.5
 - gffutils=0.10.1
 - gfortran_impl_linux-64=13.2.0
-- giflib=5.2.1
+- giflib=5.2.2
 - glib=2.78.1
 - glib-tools=2.78.1
 - glimmerhmm=3.0.4
@@ -199,7 +199,7 @@ dependencies:
 - jack=1.9.22
 - jedi=0.19.1
 - jinja2=3.1.3
-- joblib=1.3.2
+- joblib=1.4.0
 - jpeg=9e
 - jq=1.7.1
 - jsonlines=3.0.0
@@ -210,7 +210,7 @@ dependencies:
 - jupyter_client=7.4.9
 - jupyter_core=5.7.2
 - jupyter_events=0.10.0
-- jupyter_server=2.13.0
+- jupyter_server=2.14.0
 - jupyter_server_terminals=0.5.3
 - jupyterlab_pygments=0.3.0
 - jupyterlab_widgets=3.0.10
@@ -226,6 +226,8 @@ dependencies:
 - ld_impl_linux-64=2.40
 - lerc=4.0.0
 - libaec=1.1.3
+- libasprintf=0.22.5
+- libasprintf-devel=0.22.5
 - libblas=3.9.0
 - libbrotlicommon=1.1.0
 - libbrotlidec=1.1.0
@@ -248,6 +250,8 @@ dependencies:
 - libgcc-ng=13.2.0
 - libgcrypt=1.10.3
 - libgd=2.3.3
+- libgettextpo=0.22.5
+- libgettextpo-devel=0.22.5
 - libgfortran-ng=13.2.0
 - libgfortran5=13.2.0
 - libglib=2.78.1
@@ -311,7 +315,7 @@ dependencies:
 - mistune=3.0.2
 - mmseqs2=15.6f452
 - mpfr=4.2.1
-- mpg123=1.32.4
+- mpg123=1.32.6
 - mpi=1.0
 - msgpack-python=1.0.7
 - munkres=1.1.4
@@ -324,9 +328,9 @@ dependencies:
 - nbconvert=7.16.3
 - nbconvert-core=7.16.3
 - nbconvert-pandoc=7.16.3
-- nbformat=5.10.3
+- nbformat=5.10.4
 - ncbi-datasets-pylib=16.6.0
-- ncbi-vdb=3.0.0
+- ncbi-vdb=3.1.0
 - ncurses=6.4.20240210
 - nest-asyncio=1.6.0
 - networkx=3.1
@@ -345,12 +349,12 @@ dependencies:
 - overrides=7.7.0
 - packaging=24.0
 - pandas=1.5.3
-- pandoc=3.1.12.3
+- pandoc=3.1.13
 - pandocfilters=1.5.0
 - pango=1.50.14
 - paramiko=3.4.0
 - parsl=2023.12.4
-- parso=0.8.3
+- parso=0.8.4
 - pathlib=1.0.1
 - patsy=0.5.3
 - pbzip2=1.1.13
@@ -370,7 +374,7 @@ dependencies:
 - perl-constant=1.33
 - perl-dbi=1.643
 - perl-digest-perl-md5=1.9
-- perl-encode=3.19
+- perl-encode=3.21
 - perl-exporter=5.74
 - perl-exporter-tiny=1.002002
 - perl-extutils-config=0.008
@@ -459,7 +463,7 @@ dependencies:
 - python-fastjsonschema=2.19.1
 - python-isal=1.6.1
 - python-json-logger=2.0.7
-- python-zlib-ng=0.4.1
+- python-zlib-ng=0.4.2
 - python_abi=3.8
 - pytz=2024.1
 - pyvcf3=1.0.3
@@ -485,7 +489,7 @@ dependencies:
 - 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-types=2024.5.0.dev0+5.gd24a69d
 - q2-vsearch=2024.5.0.dev0
 - q2cli=2024.5.0.dev0
 - q2templates=2024.5.0.dev0
@@ -542,7 +546,7 @@ dependencies:
 - r-e1071=1.7_14
 - r-ecosolver=0.5.5
 - r-ellipsis=0.3.2
-- r-emmeans=1.10.0
+- r-emmeans=1.10.1
 - r-energy=1.7_11
 - r-estimability=1.4.1
 - r-evaluate=0.23
@@ -584,7 +588,7 @@ dependencies:
 - r-hmisc=5.1_2
 - r-hms=1.1.3
 - r-htmltable=2.4.2
-- r-htmltools=0.5.8
+- r-htmltools=0.5.8.1
 - r-htmlwidgets=1.6.4
 - r-httr=1.4.7
 - r-ids=1.0.1
@@ -596,7 +600,7 @@ dependencies:
 - r-jpeg=0.1_10
 - r-jquerylib=0.1.4
 - r-jsonlite=1.8.8
-- r-knitr=1.45
+- r-knitr=1.46
 - r-labeling=0.4.3
 - r-lambda.r=1.2.4
 - r-lattice=0.22_6
@@ -610,7 +614,7 @@ dependencies:
 - r-magrittr=2.0.3
 - r-mass=7.3_60.0.1
 - r-matrix=1.6_5
-- r-matrixstats=1.2.0
+- r-matrixstats=1.3.0
 - r-memoise=2.0.1
 - r-mgcv=1.9_1
 - r-mime=0.12
@@ -721,7 +725,7 @@ dependencies:
 - referencing=0.34.0
 - repeatmasker=4.1.5
 - requests=2.31.0
-- rescript=2024.5.0.dev0+2.ga0df425
+- rescript=2024.5.0.dev0+3.g6e87cfe
 - rfc3339-validator=0.1.4
 - rfc3986-validator=0.1.1
 - rmblast=2.14.1
@@ -733,7 +737,7 @@ dependencies:
 - seaborn=0.12.2
 - seaborn-base=0.12.2
 - sed=4.8
-- send2trash=1.8.2
+- send2trash=1.8.3
 - sepp=4.3.10
 - setproctitle=1.3.3
 - setuptools=69.2.0
@@ -767,8 +771,8 @@ dependencies:
 - trf=4.09.1
 - typeguard=2.13.3
 - types-python-dateutil=2.9.0.20240316
-- typing-extensions=4.10.0
-- typing_extensions=4.10.0
+- typing-extensions=4.11.0
+- typing_extensions=4.11.0
 - typing_utils=0.1.0
 - tzlocal=2.1
 - ucsc-fatotwobit=447
@@ -779,7 +783,7 @@ dependencies:
 - unifrac-binaries=1.3.2
 - uri-template=1.3.0
 - urllib3=1.26.18
-- vsearch=2.27.0
+- vsearch=2.27.1
 - wcwidth=0.2.13
 - webcolors=1.13
 - webencodings=0.5.1
diff --git a/2024.5/shotgun/passed/seed-environment-conda.yml b/2024.5/shotgun/passed/seed-environment-conda.yml
index 5d24f525..e1bb65c0 100644
--- a/2024.5/shotgun/passed/seed-environment-conda.yml
+++ b/2024.5/shotgun/passed/seed-environment-conda.yml
@@ -34,13 +34,13 @@ dependencies:
 - 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-types=2024.5.0.dev0+5.gd24a69d
 - q2-vsearch=2024.5.0.dev0
 - q2cli=2024.5.0.dev0
 - q2templates=2024.5.0.dev0
 - qiime2=2024.5.0.dev0+1.g6306962
 - r-base=4.2.2
-- rescript=2024.5.0.dev0+2.ga0df425
+- rescript=2024.5.0.dev0+3.g6e87cfe
 - scikit-bio=0.5.8
 - scikit-learn=0.24.1
 - scipy=1.10.0
@@ -51,4 +51,3 @@ dependencies:
 extras:
   variant_override:
     qiime2_epoch: '2024.5'
-# modified: 2024-04-14
diff --git a/2024.5/shotgun/staged/seed-environment-conda.yml b/2024.5/shotgun/staged/seed-environment-conda.yml
index 445e7e30..a38f8521 100644
--- a/2024.5/shotgun/staged/seed-environment-conda.yml
+++ b/2024.5/shotgun/staged/seed-environment-conda.yml
@@ -35,13 +35,13 @@ dependencies:
 - q2-sapienns=2024.5.0.dev0
 - q2-taxa=2024.5.0.dev0
 - q2-types-genomics=2023.11.0.dev0+8.g3b993ed
-- q2-types=2024.5.0.dev0+4.g823b5a4
+- q2-types=2024.5.0.dev0+5.gd24a69d
 - q2-vsearch=2024.5.0.dev0
 - q2cli=2024.5.0.dev0
 - q2templates=2024.5.0.dev0
 - qiime2=2024.5.0.dev0+1.g6306962
 - r-base=4.2.2
-- rescript=2024.5.0.dev0+2.ga0df425
+- rescript=2024.5.0.dev0+3.g6e87cfe
 - scikit-bio=0.5.8
 - scikit-learn=0.24.1
 - scipy=1.10.0