From de987ebca26e4cc0f5b7e3a78cd2d3deb67298f3 Mon Sep 17 00:00:00 2001
From: Q2-D2 <q2d2.noreply@gmail.com>
Date: Fri, 15 Mar 2024 14:22:21 -0700
Subject: [PATCH] [fmt] Automated Trial (Prepare) (#178)

* Automated updates to seed environment: fmt

* Update seed-environment-conda.yml

* Update seed-environment-conda.yml

* Update conda environments (Prepare-2024.5/fmt/2024-03-15)

---------

Co-authored-by: Evan Bolyen <ebolyen@gmail.com>
---
 .../passed/qiime2-fmt-macos-latest-conda.yml  | 104 +++++++++---------
 .../passed/qiime2-fmt-ubuntu-latest-conda.yml |  96 ++++++++--------
 2024.5/fmt/passed/seed-environment-conda.yml  |  16 +--
 2024.5/fmt/staged/seed-environment-conda.yml  |  14 +--
 4 files changed, 115 insertions(+), 115 deletions(-)

diff --git a/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml b/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml
index 34ef772f..8121ec31 100644
--- a/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml
+++ b/2024.5/fmt/passed/qiime2-fmt-macos-latest-conda.yml
@@ -1,11 +1,11 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.2/fmt/passed
+- https://packages.qiime2.org/qiime2/2024.5/fmt/passed
 - bioconda
 - conda-forge
 - defaults
 dependencies:
 - _r-mutex=1.0.1
-- anyio=4.2.0
+- anyio=4.3.0
 - appdirs=1.4.4
 - appnope=0.1.4
 - argon2-cffi=23.1.0
@@ -25,13 +25,13 @@ dependencies:
 - brotli-python=1.1.0
 - bwidget=1.9.14
 - bzip2=1.0.8
-- c-ares=1.26.0
+- 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
+- cctools_osx-64=986
 - certifi=2024.2.2
 - cffi=1.16.0
 - chardet=5.2.0
@@ -45,15 +45,15 @@ 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=42.0.3
+- cryptography=42.0.5
 - curl=7.88.1
 - cycler=0.12.1
-- cython=3.0.8
+- cython=3.0.9
 - debugpy=1.8.1
 - decorator=4.4.2
 - defusedxml=0.7.1
@@ -61,7 +61,7 @@ dependencies:
 - entrypoints=0.4
 - exceptiongroup=1.2.0
 - executing=2.0.1
-- expat=2.5.0
+- expat=2.6.2
 - flufl.lock=7.1
 - font-ttf-dejavu-sans-mono=2.37
 - font-ttf-inconsolata=3.000
@@ -78,7 +78,7 @@ dependencies:
 - gettext=0.21.1
 - gfortran_impl_osx-64=11.4.0
 - gfortran_osx-64=11.4.0
-- globus-sdk=3.37.0
+- globus-sdk=3.39.0
 - gmp=6.3.0
 - graphite2=1.3.13
 - gsl=2.7
@@ -91,11 +91,11 @@ dependencies:
 - icu=70.1
 - idna=3.6
 - ijson=3.2.3
-- importlib-resources=6.1.1
-- importlib_resources=6.1.1
+- importlib-resources=6.3.0
+- importlib_resources=6.3.0
 - iniconfig=2.0.0
 - iow=1.0.5
-- ipykernel=6.29.2
+- ipykernel=6.29.3
 - ipython=8.12.2
 - ipython_genutils=0.2.0
 - isl=0.25
@@ -110,15 +110,15 @@ 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
 - kiwisolver=1.4.5
 - krb5=1.20.1
 - lcms2=2.15
-- ld64_osx-64=609
+- ld64_osx-64=711
 - lerc=4.0.0
 - libaec=1.1.2
 - libblas=3.9.0
@@ -132,7 +132,7 @@ dependencies:
 - libdeflate=1.17
 - libedit=3.1.20191231
 - libev=4.33
-- libexpat=2.5.0
+- libexpat=2.6.2
 - libffi=3.4.4
 - libgfortran=5.0.0
 - libgfortran-devel_osx-64=11.4.0
@@ -144,9 +144,9 @@ dependencies:
 - libllvm17=17.0.6
 - libnghttp2=1.58.0
 - libopenblas=0.3.25
-- libpng=1.6.42
+- libpng=1.6.43
 - libsodium=1.0.18
-- libsqlite=3.45.1
+- libsqlite=3.45.2
 - libssh2=1.11.0
 - libtiff=4.5.0
 - libwebp-base=1.3.2
@@ -154,7 +154,7 @@ dependencies:
 - libxml2=2.10.3
 - libxslt=1.1.37
 - libzlib=1.2.13
-- llvm-openmp=17.0.6
+- llvm-openmp=18.1.1
 - llvm-tools=17.0.6
 - lockfile=0.12.2
 - lxml=4.9.2
@@ -162,7 +162,7 @@ dependencies:
 - lz4-c=1.9.4
 - make=4.3
 - markdown-it-py=3.0.0
-- marko=2.0.2
+- marko=2.0.3
 - markupsafe=2.1.5
 - matplotlib-base=3.7.3
 - matplotlib-inline=0.1.6
@@ -175,11 +175,11 @@ dependencies:
 - munkres=1.1.4
 - natsort=8.4.0
 - nbclassic=1.0.0
-- nbclient=0.8.0
-- nbconvert=7.16.0
-- nbconvert-core=7.16.0
-- nbconvert-pandoc=7.16.0
-- nbformat=5.9.2
+- nbclient=0.10.0
+- nbconvert=7.16.2
+- nbconvert-core=7.16.2
+- nbconvert-pandoc=7.16.2
+- nbformat=5.10.3
 - ncurses=6.4
 - nest-asyncio=1.6.0
 - networkx=3.1
@@ -189,25 +189,25 @@ dependencies:
 - openjpeg=2.5.0
 - openssl=3.2.1
 - overrides=7.7.0
-- packaging=23.2
+- packaging=24.0
 - pandas=1.5.3
-- pandoc=3.1.12
+- 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
 - pcre2=10.40
-- petl=1.7.14
+- petl=1.7.15
 - pexpect=4.9.0
 - pickleshare=0.7.5
 - pillow=9.4.0
 - pip=24.0
-- pixman=0.43.2
+- pixman=0.43.4
 - pkgutil-resolve-name=1.3.10
 - platformdirs=4.2.0
 - pluggy=1.4.0
-- pooch=1.8.0
+- pooch=1.8.1
 - prometheus_client=0.20.0
 - prompt-toolkit=3.0.42
 - prompt_toolkit=3.0.42
@@ -221,11 +221,11 @@ dependencies:
 - pynacl=1.5.0
 - pyobjc-core=10.1
 - pyobjc-framework-cocoa=10.1
-- pyparsing=3.1.1
+- pyparsing=3.1.2
 - pysocks=1.7.1
-- pytest=8.0.0
+- pytest=8.1.1
 - python=3.8.18
-- python-dateutil=2.8.2
+- python-dateutil=2.9.0
 - python-fastjsonschema=2.19.1
 - python-json-logger=2.0.7
 - python-slugify=8.0.4
@@ -233,13 +233,13 @@ dependencies:
 - pytz=2024.1
 - pyyaml=6.0.1
 - pyzmq=24.0.1
-- q2-fmt=2024.2.0
-- q2-mystery-stew=2024.2.0
-- q2-stats=2024.2.0
-- q2-types=2024.2.0
-- q2-vizard=2024.2.0
-- q2cli=2024.2.0
-- qiime2=2024.2.0
+- q2-fmt=2024.5.0.dev0
+- q2-mystery-stew=2024.5.0.dev0
+- q2-stats=2024.5.0.dev0
+- q2-types=2024.5.0.dev0+4.g823b5a4
+- q2-vizard=2024.5.0.dev0
+- q2cli=2024.5.0.dev0
+- qiime2=2024.5.0.dev0+1.g6306962
 - r-base=4.2.3
 - readline=8.2
 - referencing=0.33.0
@@ -247,7 +247,7 @@ dependencies:
 - rfc3339-validator=0.1.4
 - rfc3986=2.0.0
 - rfc3986-validator=0.1.1
-- rich=13.7.0
+- rich=13.7.1
 - rpds-py=0.18.0
 - samtools=1.18
 - scikit-bio=0.5.8
@@ -255,40 +255,40 @@ dependencies:
 - scipy=1.10.0
 - send2trash=1.8.2
 - setproctitle=1.3.3
-- setuptools=69.0.3
+- setuptools=69.2.0
 - shellingham=1.5.4
 - sigtool=0.1.3
 - simpleeval=0.9.13
 - six=1.16.0
-- sniffio=1.3.0
+- sniffio=1.3.1
 - soupsieve=2.5
 - stack_data=0.6.2
 - stringcase=1.2.0
 - tabulate=0.9.0
 - tapi=1100.0.11
 - tblib=3.0.0
-- terminado=0.18.0
+- terminado=0.18.1
 - text-unidecode=1.3
 - threadpoolctl=3.3.0
 - tinycss2=1.2.1
 - tk=8.6.13
 - tktable=2.10
 - tomli=2.0.1
-- tomlkit=0.12.3
-- tornado=6.3.3
+- tomlkit=0.12.4
+- tornado=6.4
 - traitlets=5.9.0
 - typeguard=2.13.3
 - typer=0.9.0
-- types-python-dateutil=2.8.19.20240106
-- typing-extensions=4.9.0
-- typing_extensions=4.9.0
+- types-python-dateutil=2.9.0.20240315
+- typing-extensions=4.10.0
+- typing_extensions=4.10.0
 - typing_utils=0.1.0
 - tzlocal=2.1
 - unicodedata2=15.1.0
 - unifrac=1.3
 - unifrac-binaries=1.3.2
 - uri-template=1.3.0
-- urllib3=2.2.0
+- urllib3=2.2.1
 - validators=0.22.0
 - wcwidth=0.2.13
 - webcolors=1.13
diff --git a/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml b/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml
index 77dea2e1..d54a3af3 100644
--- a/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml
+++ b/2024.5/fmt/passed/qiime2-fmt-ubuntu-latest-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.2/fmt/passed
+- https://packages.qiime2.org/qiime2/2024.5/fmt/passed
 - bioconda
 - conda-forge
 - defaults
@@ -7,7 +7,7 @@ dependencies:
 - _libgcc_mutex=0.1
 - _openmp_mutex=4.5
 - _r-mutex=1.0.1
-- anyio=4.2.0
+- anyio=4.3.0
 - appdirs=1.4.4
 - argon2-cffi=23.1.0
 - argon2-cffi-bindings=21.2.0
@@ -27,7 +27,7 @@ dependencies:
 - brotli-python=1.1.0
 - bwidget=1.9.14
 - bzip2=1.0.8
-- c-ares=1.26.0
+- c-ares=1.27.0
 - ca-certificates=2024.2.2
 - cachecontrol=0.14.0
 - cached-property=1.5.2
@@ -39,13 +39,13 @@ dependencies:
 - charset-normalizer=3.3.2
 - 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=42.0.3
+- cryptography=42.0.5
 - curl=8.1.2
 - cycler=0.12.1
-- cython=3.0.8
+- cython=3.0.9
 - debugpy=1.8.1
 - decorator=4.4.2
 - defusedxml=0.7.1
@@ -53,7 +53,7 @@ dependencies:
 - entrypoints=0.4
 - exceptiongroup=1.2.0
 - executing=2.0.1
-- expat=2.5.0
+- expat=2.6.2
 - flufl.lock=7.1
 - font-ttf-dejavu-sans-mono=2.37
 - font-ttf-inconsolata=3.000
@@ -70,7 +70,7 @@ dependencies:
 - gcc_impl_linux-64=13.2.0
 - gettext=0.21.1
 - gfortran_impl_linux-64=13.2.0
-- globus-sdk=3.37.0
+- globus-sdk=3.39.0
 - graphite2=1.3.13
 - gsl=2.7
 - gxx_impl_linux-64=13.2.0
@@ -82,11 +82,11 @@ dependencies:
 - icu=70.1
 - idna=3.6
 - ijson=3.2.3
-- importlib-resources=6.1.1
-- importlib_resources=6.1.1
+- importlib-resources=6.3.0
+- importlib_resources=6.3.0
 - iniconfig=2.0.0
 - iow=1.0.5
-- ipykernel=6.29.2
+- ipykernel=6.29.3
 - ipython=8.12.2
 - ipython_genutils=0.2.0
 - isodate=0.6.1
@@ -100,10 +100,10 @@ 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
 - kernel-headers_linux-64=2.6.32
 - keyutils=1.6.1
@@ -122,7 +122,7 @@ dependencies:
 - libdeflate=1.17
 - libedit=3.1.20191231
 - libev=4.33
-- libexpat=2.5.0
+- libexpat=2.6.2
 - libffi=3.4.2
 - libgcc-devel_linux-64=13.2.0
 - libgcc-ng=13.2.0
@@ -136,10 +136,10 @@ dependencies:
 - libnghttp2=1.58.0
 - libnsl=2.0.1
 - libopenblas=0.3.25
-- libpng=1.6.42
+- libpng=1.6.43
 - libsanitizer=13.2.0
 - libsodium=1.0.18
-- libsqlite=3.45.1
+- libsqlite=3.45.2
 - libssh2=1.11.0
 - libstdcxx-devel_linux-64=13.2.0
 - libstdcxx-ng=13.2.0
@@ -157,7 +157,7 @@ dependencies:
 - lz4-c=1.9.4
 - make=4.3
 - markdown-it-py=3.0.0
-- marko=2.0.2
+- marko=2.0.3
 - markupsafe=2.1.5
 - matplotlib-base=3.7.3
 - matplotlib-inline=0.1.6
@@ -168,11 +168,11 @@ dependencies:
 - munkres=1.1.4
 - natsort=8.4.0
 - nbclassic=1.0.0
-- nbclient=0.8.0
-- nbconvert=7.16.0
-- nbconvert-core=7.16.0
-- nbconvert-pandoc=7.16.0
-- nbformat=5.9.2
+- nbclient=0.10.0
+- nbconvert=7.16.2
+- nbconvert-core=7.16.2
+- nbconvert-pandoc=7.16.2
+- nbformat=5.10.3
 - ncurses=6.4
 - nest-asyncio=1.6.0
 - networkx=3.1
@@ -182,16 +182,16 @@ dependencies:
 - openjpeg=2.5.0
 - openssl=3.2.1
 - overrides=7.7.0
-- packaging=23.2
+- packaging=24.0
 - pandas=1.5.3
-- pandoc=3.1.12
+- 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
 - pcre2=10.40
-- petl=1.7.14
+- petl=1.7.15
 - pexpect=4.9.0
 - pickleshare=0.7.5
 - pillow=9.4.0
@@ -200,7 +200,7 @@ dependencies:
 - pkgutil-resolve-name=1.3.10
 - platformdirs=4.2.0
 - pluggy=1.4.0
-- pooch=1.8.0
+- pooch=1.8.1
 - prometheus_client=0.20.0
 - prompt-toolkit=3.0.42
 - prompt_toolkit=3.0.42
@@ -212,11 +212,11 @@ dependencies:
 - pygments=2.17.2
 - pyjwt=2.8.0
 - pynacl=1.5.0
-- pyparsing=3.1.1
+- pyparsing=3.1.2
 - pysocks=1.7.1
-- pytest=8.0.0
+- pytest=8.1.1
 - python=3.8.18
-- python-dateutil=2.8.2
+- python-dateutil=2.9.0
 - python-fastjsonschema=2.19.1
 - python-json-logger=2.0.7
 - python-slugify=8.0.4
@@ -224,13 +224,13 @@ dependencies:
 - pytz=2024.1
 - pyyaml=6.0.1
 - pyzmq=24.0.1
-- q2-fmt=2024.2.0
-- q2-mystery-stew=2024.2.0
-- q2-stats=2024.2.0
-- q2-types=2024.2.0
-- q2-vizard=2024.2.0
-- q2cli=2024.2.0
-- qiime2=2024.2.0
+- q2-fmt=2024.5.0.dev0
+- q2-mystery-stew=2024.5.0.dev0
+- q2-stats=2024.5.0.dev0
+- q2-types=2024.5.0.dev0+4.g823b5a4
+- q2-vizard=2024.5.0.dev0
+- q2cli=2024.5.0.dev0
+- qiime2=2024.5.0.dev0+1.g6306962
 - r-base=4.2.3
 - readline=8.2
 - referencing=0.33.0
@@ -238,7 +238,7 @@ dependencies:
 - rfc3339-validator=0.1.4
 - rfc3986=2.0.0
 - rfc3986-validator=0.1.1
-- rich=13.7.0
+- rich=13.7.1
 - rpds-py=0.18.0
 - samtools=1.6
 - scikit-bio=0.5.8
@@ -247,39 +247,39 @@ dependencies:
 - sed=4.8
 - send2trash=1.8.2
 - setproctitle=1.3.3
-- setuptools=69.0.3
+- setuptools=69.2.0
 - shellingham=1.5.4
 - simpleeval=0.9.13
 - six=1.16.0
-- sniffio=1.3.0
+- sniffio=1.3.1
 - soupsieve=2.5
 - stack_data=0.6.2
 - stringcase=1.2.0
 - sysroot_linux-64=2.12
 - tabulate=0.9.0
 - tblib=3.0.0
-- terminado=0.18.0
+- terminado=0.18.1
 - text-unidecode=1.3
 - threadpoolctl=3.3.0
 - tinycss2=1.2.1
 - tk=8.6.13
 - tktable=2.10
 - tomli=2.0.1
-- tomlkit=0.12.3
-- tornado=6.3.3
+- tomlkit=0.12.4
+- tornado=6.4
 - traitlets=5.9.0
 - typeguard=2.13.3
 - typer=0.9.0
-- types-python-dateutil=2.8.19.20240106
-- typing-extensions=4.9.0
-- typing_extensions=4.9.0
+- types-python-dateutil=2.9.0.20240315
+- typing-extensions=4.10.0
+- typing_extensions=4.10.0
 - typing_utils=0.1.0
 - tzlocal=2.1
 - unicodedata2=15.1.0
 - unifrac=1.3
 - unifrac-binaries=1.3.2
 - uri-template=1.3.0
-- urllib3=2.2.0
+- urllib3=2.2.1
 - validators=0.22.0
 - wcwidth=0.2.13
 - webcolors=1.13
diff --git a/2024.5/fmt/passed/seed-environment-conda.yml b/2024.5/fmt/passed/seed-environment-conda.yml
index fedfacb9..59f14c9c 100644
--- a/2024.5/fmt/passed/seed-environment-conda.yml
+++ b/2024.5/fmt/passed/seed-environment-conda.yml
@@ -12,13 +12,13 @@ dependencies:
 - pandas=1.5.3
 - parsl=2023.12.04
 - python=3.8
-- q2-fmt=2024.2.0
-- q2-mystery-stew=2024.2.0
-- q2-stats=2024.2.0
-- q2-types=2024.2.0
-- q2-vizard=2024.2.0
-- q2cli=2024.2.0
-- qiime2=2024.2.0
+- q2-fmt=2024.5.0.dev0
+- q2-mystery-stew=2024.5.0.dev0
+- q2-stats=2024.5.0.dev0
+- q2-types=2024.5.0.dev0+4.g823b5a4
+- q2-vizard=2024.5.0.dev0
+- q2cli=2024.5.0.dev0
+- qiime2=2024.5.0.dev0+1.g6306962
 - r-base=4.2.2
 - scikit-bio=0.5.8
 - scikit-learn=0.24.1
@@ -27,4 +27,4 @@ dependencies:
 - unifrac=1.3
 extras:
   variant_override:
-    qiime2_epoch: '2024.2'
+    qiime2_epoch: '2024.5'
diff --git a/2024.5/fmt/staged/seed-environment-conda.yml b/2024.5/fmt/staged/seed-environment-conda.yml
index 96b7abd6..ed19a007 100644
--- a/2024.5/fmt/staged/seed-environment-conda.yml
+++ b/2024.5/fmt/staged/seed-environment-conda.yml
@@ -12,13 +12,13 @@ dependencies:
 - pandas=1.5.3
 - parsl=2023.12.04
 - python=3.8
-- q2-fmt=2024.2.0
-- q2-mystery-stew=2024.2.0
-- q2-stats=2024.2.0
-- q2-types=2024.2.0
-- q2-vizard=2024.2.0
-- q2cli=2024.2.0
-- qiime2=2024.2.0
+- q2-fmt=2024.5.0.dev0
+- q2-mystery-stew=2024.5.0.dev0
+- q2-stats=2024.5.0.dev0
+- q2-types=2024.5.0.dev0+4.g823b5a4
+- q2-vizard=2024.5.0.dev0
+- q2cli=2024.5.0.dev0
+- qiime2=2024.5.0.dev0+1.g6306962
 - r-base=4.2.2
 - scikit-bio=0.5.8
 - scikit-learn=0.24.1