From 23932e9283a4d045abc5a79637ba741d83bb332d Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Wed, 19 Jun 2024 22:47:43 -0600
Subject: [PATCH 1/2] Update dependancies (#144)

* update versions of dependancies

* update env

* change labels used in tests

* pin numpy, 2.0 is coming soon

* update up version in __version__.py

* add python 3.12 to test matrix

* remove python 3.12, not supported by latest gmso release
---
 environment-dev.yml                  | 12 ++++++------
 environment.yml                      | 14 +++++++-------
 flowermd/__version__.py              |  2 +-
 flowermd/tests/base/test_molecule.py | 10 +++++-----
 setup.py                             |  2 +-
 5 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/environment-dev.yml b/environment-dev.yml
index 473c87a2..3285b1f1 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -4,13 +4,13 @@ channels:
 dependencies:
   - foyer >=0.12.0
   - fresnel
-  - freud >=2.13.1
-  - gmso >=0.11.2
+  - freud >=3.0
+  - gmso >=0.12.0
   - gsd >=3.0
-  - grits=0.4.1
-  - hoomd=4.3
+  - grits >=0.5.0
+  - hoomd >=4.5
   - mbuild >=0.17.0
-  - numpy
+  - numpy <2.0
   - openbabel >=3
   - pip
   - pre-commit
@@ -20,4 +20,4 @@ dependencies:
   - nbmake
   - python >=3.10, <3.12
   - fresnel >=0.13.5
-  - cmeutils >=1.1.1
+  - cmeutils >=1.3
diff --git a/environment.yml b/environment.yml
index 52d62117..3bd46996 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,19 +1,19 @@
-name: flowermd
+name: flowermd-dev
 channels:
   - conda-forge
 dependencies:
   - foyer >=0.12.0
   - fresnel
-  - freud >=2.13.1
-  - gmso >=0.11.2
+  - freud >=3.0
+  - gmso >=0.12.0
   - gsd >=3.0
-  - hoomd=4.3
+  - grits >=0.5.0
+  - hoomd >=4.5
   - mbuild >=0.17.0
-  - numpy
+  - numpy <2.0
   - openbabel >=3
   - pip
   - py3Dmol
   - python >=3.10, <3.12
   - fresnel >=0.13.5
-  - cmeutils >=1.1.1
-  - grits =0.4.1
+  - cmeutils >=1.3
diff --git a/flowermd/__version__.py b/flowermd/__version__.py
index 553ce3ca..6fbb7f6c 100644
--- a/flowermd/__version__.py
+++ b/flowermd/__version__.py
@@ -1,3 +1,3 @@
-VERSION = (1, 3, 0)
+VERSION = (1, 4, 0)
 
 __version__ = ".".join(map(str, VERSION))
diff --git a/flowermd/tests/base/test_molecule.py b/flowermd/tests/base/test_molecule.py
index 38c3b015..a78ccbc6 100644
--- a/flowermd/tests/base/test_molecule.py
+++ b/flowermd/tests/base/test_molecule.py
@@ -207,8 +207,8 @@ def test_polymer_different_chain_lengths(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 53
-        assert len(polymer.molecules[0].labels["monomer"]) == 3
-        assert len(polymer.molecules[1].labels["monomer"]) == 4
+        assert len(polymer.molecules[0].labels["Compound"]) == 3
+        assert len(polymer.molecules[1].labels["Compound"]) == 4
 
     def test_polymer_different_num_mol(self, dimethylether_smiles):
         polymer = Polymer(
@@ -220,9 +220,9 @@ def test_polymer_different_num_mol(self, dimethylether_smiles):
             bond_orientation=[None, None],
         )
         assert polymer.n_particles == 55
-        assert len(polymer.molecules[0].labels["monomer"]) == 3
-        assert len(polymer.molecules[1].labels["monomer"]) == 2
-        assert len(polymer.molecules[2].labels["monomer"]) == 2
+        assert len(polymer.molecules[0].labels["Compound"]) == 3
+        assert len(polymer.molecules[1].labels["Compound"]) == 2
+        assert len(polymer.molecules[2].labels["Compound"]) == 2
 
     def test_polymer_unequal_num_mol_length(self, dimethylether_smiles):
         with pytest.raises(ValueError):
diff --git a/setup.py b/setup.py
index cd3f223a..7369f8ab 100644
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,7 @@
 URL = "https://github.com/cmelab/flowerMD"
 EMAIL = "chrisjones4@u.boisestate.edu"
 AUTHOR = "CME Lab"
-REQUIRES_PYTHON = ">=3.9.0"
+REQUIRES_PYTHON = ">=3.10.0"
 VERSION = None
 
 # What packages are required for this module to be executed?

From dfa5881a2dfcf10bb721357271d23a0953c4bfc2 Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Thu, 20 Jun 2024 09:09:28 -0600
Subject: [PATCH 2/2] Fix name in `environment.yml` file. (#145)

* update versions of dependancies

* update env

* change labels used in tests

* pin numpy, 2.0 is coming soon

* update up version in __version__.py

* add python 3.12 to test matrix

* remove python 3.12, not supported by latest gmso release

* fix name in non-dev env file