From af4e24070da211b3ca6ddac638e192aaf1f1eba7 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Thu, 12 Feb 2026 11:04:37 +1100
Subject: [PATCH 1/4] try using smee-base and no ambertools

---
 devtools/envs/base.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml
index 94c21f8..e569fc5 100644
--- a/devtools/envs/base.yaml
+++ b/devtools/envs/base.yaml
@@ -9,8 +9,7 @@ dependencies:
   - pip
 
   # Core packages
-  - smee >=0.10.0
-  - pydantic-units  # TODO: Remove this line once smee deps are updated
+  - smee-base >=0.10.0
 
   - pytorch
   - pyarrow
@@ -36,7 +35,6 @@ dependencies:
   - tensorboardX
 
   # Dev / Testing
-  - ambertools
   - rdkit
   - uncertainties
 

From 16f38bb97a715ee01eed01e6b9d8995c6fe40e9e Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Thu, 12 Feb 2026 11:35:51 +1100
Subject: [PATCH 2/4] update deps

---
 devtools/envs/base.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml
index e569fc5..7db2e44 100644
--- a/devtools/envs/base.yaml
+++ b/devtools/envs/base.yaml
@@ -10,6 +10,8 @@ dependencies:
 
   # Core packages
   - smee-base >=0.10.0
+  - pydantic
+  - pydantic-units
 
   - pytorch
   - pyarrow
@@ -24,6 +26,7 @@ dependencies:
   - rdkit
   - matplotlib-base
   - panel
+  - openmm
 
   # Examples
   - jupyter

From 4b910b4ed859092fb1e838da8a98ef5dfc0650aa Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Mon, 23 Feb 2026 16:45:41 +1100
Subject: [PATCH 3/4] add msgpack and parmed to env

---
 devtools/envs/base.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml
index 694dd51..259b5aa 100644
--- a/devtools/envs/base.yaml
+++ b/devtools/envs/base.yaml
@@ -10,6 +10,8 @@ dependencies:
 
   # Core packages
   - smee-base >=0.10.0
+  - msgpack-python
+  - parmed
   - pydantic
   - pydantic-units
   - openff-interchange>=0.3.17

From 12ce1b1cce96f9eee76cbaf3fdc6d0bfe805eac7 Mon Sep 17 00:00:00 2001
From: Lily Wang <lily@mdanalysis.org>
Date: Thu, 2 Apr 2026 06:08:49 +1100
Subject: [PATCH 4/4] rm pydantic v1

---
 .github/workflows/ci.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 2c4276b..0ce4272 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -26,9 +26,6 @@ jobs:
         make test
         make docs
         
-        mamba install --name descent --yes "pydantic <2" "openff-toolkit>=0.9.2" "openff-interchange>=0.3.17"
-        make test
-
     - name: CodeCov
       uses: codecov/codecov-action@v4.1.1
       with: