From 1aa4202ba7a91e59576a98f85c62c9b252452807 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Wed, 8 Nov 2023 14:51:45 -0500
Subject: [PATCH 1/4] Cleaning imports and adding dependencies

---
 devtools/conda-envs/test_env.yaml          | 4 ++++
 feflow/protocols/nonequilibrium_cycling.py | 2 --
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 5456c86..cb0a8c8 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -5,7 +5,11 @@ channels:
 dependencies:
     # Base depends
   - gufe
+  - numpy
   - openfe  # TODO: Remove once we don't depend on openfe
+  - openff-units
+  - openmm
+  - pymbar
   - python
   - pip
 
diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
index a906df0..4d8e377 100644
--- a/feflow/protocols/nonequilibrium_cycling.py
+++ b/feflow/protocols/nonequilibrium_cycling.py
@@ -118,9 +118,7 @@ def _execute(self, ctx, *, state_a, state_b, mapping, settings, **inputs):
             trajectory coordinates for systems A and B.
         """
         # needed imports
-        import numpy as np
         import openmm
-        import openmm.unit as openmm_unit
         from openff.units.openmm import ensure_quantity
         from openmmtools.integrators import PeriodicNonequilibriumIntegrator
         from gufe.components import SmallMoleculeComponent

From 0180d13458d3daccb8d560f278c34ed8cba277b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 7 Dec 2023 16:26:00 -0500
Subject: [PATCH 2/4] Removing unneeded channel

---
 devtools/conda-envs/test_env.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 88e5c17..e653eb7 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -1,7 +1,6 @@
 name: feflow-test
 channels:
   - conda-forge
-  - defaults
 dependencies:
     # Base depends
   - gufe

From 2e93f48322d71279e4ce9667e91543adc6cdc4e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 7 Dec 2023 16:52:45 -0500
Subject: [PATCH 3/4] Update devtools/conda-envs/test_env.yaml

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index e653eb7..0d9573b 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -8,7 +8,7 @@ dependencies:
   - openfe  # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
-  - pymbar
+  - pymbar <4
   - pydantic=1  # TODO: Modify when we support pydantic 2
   - python
 

From 05ab4bcf008955bc95f13135c3fa136d2cb88340 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 7 Dec 2023 16:53:58 -0500
Subject: [PATCH 4/4] minimum supported gufe

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 0d9573b..7682b0c 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
     # Base depends
-  - gufe
+  - gufe >=0.9.5
   - numpy
   - openfe  # TODO: Remove once we don't depend on openfe
   - openff-units