From af55f97124279d1e2f96a6cf4eabd8712a6fa557 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Fri, 10 Jan 2025 12:45:34 -0700
Subject: [PATCH 1/2] PREP: bump skbio to 0.6.2 (tiny)

---
 2025.4/tiny/passed/seed-environment-conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/2025.4/tiny/passed/seed-environment-conda.yml b/2025.4/tiny/passed/seed-environment-conda.yml
index a75ca658..50882c3c 100644
--- a/2025.4/tiny/passed/seed-environment-conda.yml
+++ b/2025.4/tiny/passed/seed-environment-conda.yml
@@ -19,7 +19,7 @@ dependencies:
 - qiime2=2025.4.0.dev0+11.g85975ad
 - r-base=4.3.3
 - r-reticulate=1.36.0
-- scikit-bio=0.6.0
+- scikit-bio=0.6.2
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - unifrac-binaries=1.4

From e9844b50199709db20c4e61191546848001794e0 Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Fri, 10 Jan 2025 22:33:16 +0000
Subject: [PATCH 2/2] Update conda environments (Prepare-bump-skbio/tiny)

---
 2025.4/tiny/passed/qiime2-tiny-macos-latest-conda.yml | 11 ++++++-----
 .../tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml   | 11 ++++++-----
 2025.4/tiny/passed/seed-environment-conda.yml         |  2 +-
 2025.4/tiny/staged/seed-environment-conda.yml         |  4 ++--
 4 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/2025.4/tiny/passed/qiime2-tiny-macos-latest-conda.yml b/2025.4/tiny/passed/qiime2-tiny-macos-latest-conda.yml
index b1154247..5afdfd38 100644
--- a/2025.4/tiny/passed/qiime2-tiny-macos-latest-conda.yml
+++ b/2025.4/tiny/passed/qiime2-tiny-macos-latest-conda.yml
@@ -75,7 +75,6 @@ dependencies:
 - h5py=3.11.0
 - harfbuzz=9.0.0
 - hdf5=1.14.3
-- hdmedians=0.14.2
 - hpack=4.0.0
 - htslib=1.21
 - hyperframe=6.0.1
@@ -175,6 +174,7 @@ dependencies:
 - paramiko=3.5.0
 - parsl=2024.4.15
 - parso=0.8.4
+- patsy=1.0.1
 - pcre2=10.43
 - pexpect=4.9.0
 - pickleshare=0.7.5
@@ -190,7 +190,7 @@ dependencies:
 - pure_eval=0.2.3
 - pycparser=2.22
 - pygments=2.19.1
-- pyhmmer=0.10.15
+- pyhmmer=0.11.0
 - pyjwt=2.10.1
 - pynacl=1.5.0
 - pyobjc-core=10.3.2
@@ -209,7 +209,7 @@ dependencies:
 - pyzmq=24.0.1
 - q2-metadata=2025.4.0.dev0+5.g7af916f
 - q2-mystery-stew=2025.4.0.dev0+5.g51996ef
-- q2-types=2025.4.0.dev0+5.gea31a99
+- q2-types=2025.4.0.dev0+6.g11e14d8
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
@@ -233,17 +233,18 @@ dependencies:
 - rfc3986-validator=0.1.1
 - rpds-py=0.22.3
 - samtools=1.21
-- scikit-bio=0.6.0
+- scikit-bio=0.6.2
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - send2trash=1.8.3
 - setproctitle=1.3.4
-- setuptools=75.6.0
+- setuptools=75.8.0
 - sigtool=0.1.3
 - six=1.17.0
 - sniffio=1.3.1
 - soupsieve=2.5
 - stack_data=0.6.3
+- statsmodels=0.14.4
 - tapi=1100.0.11
 - tblib=3.0.0
 - terminado=0.18.1
diff --git a/2025.4/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml b/2025.4/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
index b2e227fe..053e4afb 100644
--- a/2025.4/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
+++ b/2025.4/tiny/passed/qiime2-tiny-ubuntu-latest-conda.yml
@@ -67,7 +67,6 @@ dependencies:
 - h5py=3.11.0
 - harfbuzz=10.1.0
 - hdf5=1.14.3
-- hdmedians=0.14.2
 - hpack=4.0.0
 - htslib=1.21
 - hyperframe=6.0.1
@@ -165,10 +164,11 @@ dependencies:
 - packaging=24.2
 - pandas=2.2.2
 - pandocfilters=1.5.0
-- pango=1.54.0
+- pango=1.56.0
 - paramiko=3.5.0
 - parsl=2024.4.15
 - parso=0.8.4
+- patsy=1.0.1
 - pcre2=10.44
 - pexpect=4.9.0
 - pickleshare=0.7.5
@@ -202,7 +202,7 @@ dependencies:
 - pyzmq=24.0.1
 - q2-metadata=2025.4.0.dev0+5.g7af916f
 - q2-mystery-stew=2025.4.0.dev0+5.g51996ef
-- q2-types=2025.4.0.dev0+5.gea31a99
+- q2-types=2025.4.0.dev0+6.g11e14d8
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
@@ -226,17 +226,18 @@ dependencies:
 - rfc3986-validator=0.1.1
 - rpds-py=0.22.3
 - samtools=1.21
-- scikit-bio=0.6.0
+- scikit-bio=0.6.2
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - sed=4.8
 - send2trash=1.8.3
 - setproctitle=1.3.4
-- setuptools=75.6.0
+- setuptools=75.8.0
 - six=1.17.0
 - sniffio=1.3.1
 - soupsieve=2.5
 - stack_data=0.6.3
+- statsmodels=0.14.4
 - sysroot_linux-64=2.17
 - tblib=3.0.0
 - terminado=0.18.1
diff --git a/2025.4/tiny/passed/seed-environment-conda.yml b/2025.4/tiny/passed/seed-environment-conda.yml
index 50882c3c..ef4e1bc7 100644
--- a/2025.4/tiny/passed/seed-environment-conda.yml
+++ b/2025.4/tiny/passed/seed-environment-conda.yml
@@ -13,7 +13,7 @@ dependencies:
 - python=3.10
 - q2-metadata=2025.4.0.dev0+5.g7af916f
 - q2-mystery-stew=2025.4.0.dev0+5.g51996ef
-- q2-types=2025.4.0.dev0+5.gea31a99
+- q2-types=2025.4.0.dev0+6.g11e14d8
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
diff --git a/2025.4/tiny/staged/seed-environment-conda.yml b/2025.4/tiny/staged/seed-environment-conda.yml
index 904e9efa..bad669ab 100644
--- a/2025.4/tiny/staged/seed-environment-conda.yml
+++ b/2025.4/tiny/staged/seed-environment-conda.yml
@@ -14,13 +14,13 @@ dependencies:
 - python_abi=3.9
 - q2-metadata=2025.4.0.dev0+5.g7af916f
 - q2-mystery-stew=2025.4.0.dev0+5.g51996ef
-- q2-types=2025.4.0.dev0+5.gea31a99
+- q2-types=2025.4.0.dev0+6.g11e14d8
 - q2cli=2025.4.0.dev0+8.g63d82cb
 - q2templates=2025.4.0.dev0+5.gfcd2c55
 - qiime2=2025.4.0.dev0+11.g85975ad
 - r-base=4.3.3
 - r-reticulate=1.36.0
-- scikit-bio=0.6.0
+- scikit-bio=0.6.2
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - unifrac-binaries=1.4