From 4a372f3a5248d2a53c258c53b3088716aaa70d88 Mon Sep 17 00:00:00 2001
From: "N. Tessa Pierce-Ward" <ntpierce@gmail.com>
Date: Tue, 3 Jun 2025 09:44:36 -0700
Subject: [PATCH 1/2] add remaining dependencies to pyproject.toml

---
 pyproject.toml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c932b26..399fc16 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,9 +5,16 @@ readme = "README.md"
 requires-python = ">=3.10"
 version = "0.5.0"
 
-dependencies = ["sourmash>=4.8.8,<5", "sourmash_utils>=0.2",
+# note: "legacy_cgi" is currently needed for ete3, but may need to be changed on next ete release, see: https://github.com/etetoolkit/ete/issues/780
+dependencies = ["sourmash>=4.9.2,<5", "sourmash_utils>=0.2",
                 "matplotlib", "numpy", "scipy", "scikit-learn",
-                "seaborn", "upsetplot", "matplotlib_venn", "pandas", "plotly", "biopython", "ete3"]
+                "seaborn", "upsetplot", "matplotlib_venn", "pandas",
+                "plotly", "biopython", "ete3", "kaleido", "pyqt5",
+                "legacy_cgi"]
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
 
 [metadata]
 license = { text = "BSD 3-Clause License" }

From eabb74be3900b259f2944b40281ab7e2fe9e6f5f Mon Sep 17 00:00:00 2001
From: "N. Tessa Pierce-Ward" <ntpierce@gmail.com>
Date: Mon, 9 Jun 2025 10:06:52 -0700
Subject: [PATCH 2/2] update to ete4 to see if pip install issues are sorted

---
 environment.yml | 6 +++---
 pyproject.toml  | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/environment.yml b/environment.yml
index 847e7d4..d12ebde 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,8 +4,8 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - sourmash>=4.8.8,<5
-    - sourmash_plugin_branchwater>=0.9.7
+    - sourmash>=4.9.2,<5
+    - sourmash_plugin_branchwater>=0.9.13,<1
     - pip
     - pytest
     - matplotlib
@@ -17,6 +17,6 @@ dependencies:
     - seaborn
     - plotly
     - biopython
-    - ete3>=3.1.3,<4
+    - ete4>=4.3.0,<5
     - pip:
       - kaleido
diff --git a/pyproject.toml b/pyproject.toml
index 399fc16..ac1998d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ version = "0.5.0"
 dependencies = ["sourmash>=4.9.2,<5", "sourmash_utils>=0.2",
                 "matplotlib", "numpy", "scipy", "scikit-learn",
                 "seaborn", "upsetplot", "matplotlib_venn", "pandas",
-                "plotly", "biopython", "ete3", "kaleido", "pyqt5",
+                "plotly", "biopython", "ete4", "kaleido", "pyqt6",
                 "legacy_cgi"]
 
 [build-system]