From 850e868a271e19f3be4701303c60f7b6b0d3f283 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 19 Jun 2024 13:12:12 -0600
Subject: [PATCH 1/7] update versions of dependancies

---
 environment-dev.yml | 12 ++++++------
 environment.yml     | 10 +++++-----
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/environment-dev.yml b/environment-dev.yml
index 473c87a2..54bee1cc 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -4,11 +4,11 @@ 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
   - openbabel >=3
@@ -18,6 +18,6 @@ dependencies:
   - pytest
   - pytest-cov
   - nbmake
-  - python >=3.10, <3.12
+  - 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..8d84ad2c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,10 +4,10 @@ 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
-  - hoomd=4.3
+  - hoomd >=4.5
   - mbuild >=0.17.0
   - numpy
   - openbabel >=3
@@ -15,5 +15,5 @@ dependencies:
   - py3Dmol
   - python >=3.10, <3.12
   - fresnel >=0.13.5
-  - cmeutils >=1.1.1
-  - grits =0.4.1
+  - cmeutils >=1.3
+  - grits >=0.5.0

From be3a8ddde93be52ef3ddf044c8b83915f2a16a34 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 19 Jun 2024 14:38:40 -0600
Subject: [PATCH 2/7] update env

---
 environment.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 8d84ad2c..74d11288 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,4 @@
-name: flowermd
+name: flowermd-dev
 channels:
   - conda-forge
 dependencies:
@@ -7,13 +7,13 @@ dependencies:
   - freud >=3.0
   - gmso >=0.12.0
   - gsd >=3.0
+  - grits >=0.5.0
   - hoomd >=4.5
   - mbuild >=0.17.0
   - numpy
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10, <3.12
+  - python >=3.10, <=3.12
   - fresnel >=0.13.5
   - cmeutils >=1.3
-  - grits >=0.5.0

From dce7caa142205432cb4df7b2f47460e68d6788cf Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Wed, 19 Jun 2024 17:43:41 -0600
Subject: [PATCH 3/7] change labels used in tests

---
 flowermd/tests/base/test_molecule.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

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):

From 39bfb7edbb1350b9027bda8bcc8c9c53b7aae94c Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Wed, 19 Jun 2024 17:54:49 -0600
Subject: [PATCH 4/7] pin numpy, 2.0 is coming soon

---
 environment-dev.yml | 2 +-
 environment.yml     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment-dev.yml b/environment-dev.yml
index 54bee1cc..3287ad43 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -10,7 +10,7 @@ dependencies:
   - grits >=0.5.0
   - hoomd >=4.5
   - mbuild >=0.17.0
-  - numpy
+  - numpy <2.0
   - openbabel >=3
   - pip
   - pre-commit
diff --git a/environment.yml b/environment.yml
index 74d11288..5b25b479 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,7 +10,7 @@ dependencies:
   - grits >=0.5.0
   - hoomd >=4.5
   - mbuild >=0.17.0
-  - numpy
+  - numpy <2.0
   - openbabel >=3
   - pip
   - py3Dmol

From bbaa7c4731815a56753a91ef9153241b63f14914 Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Wed, 19 Jun 2024 17:57:16 -0600
Subject: [PATCH 5/7] update up version in __version__.py

---
 flowermd/__version__.py | 2 +-
 setup.py                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

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/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 0704cee03ef046c21360da7db7d520363238c94e Mon Sep 17 00:00:00 2001
From: Chris Jones <50423140+chrisjonesBSU@users.noreply.github.com>
Date: Wed, 19 Jun 2024 18:04:08 -0600
Subject: [PATCH 6/7] add python 3.12 to test matrix

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 284423a0..41dd0657 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, macOS-13, ubuntu-latest]
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
 
     runs-on: ${{ matrix.os }}
 

From e55b2071d3370a9cd53a22a7f1a690d26f6369d5 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 19 Jun 2024 22:09:11 -0600
Subject: [PATCH 7/7] remove python 3.12, not supported by latest gmso release

---
 .github/workflows/pytest.yml | 2 +-
 environment-dev.yml          | 2 +-
 environment.yml              | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 41dd0657..284423a0 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, macOS-13, ubuntu-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11']
 
     runs-on: ${{ matrix.os }}
 
diff --git a/environment-dev.yml b/environment-dev.yml
index 3287ad43..3285b1f1 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -18,6 +18,6 @@ dependencies:
   - pytest
   - pytest-cov
   - nbmake
-  - python >=3.10, <=3.12
+  - python >=3.10, <3.12
   - fresnel >=0.13.5
   - cmeutils >=1.3
diff --git a/environment.yml b/environment.yml
index 5b25b479..3bd46996 100644
--- a/environment.yml
+++ b/environment.yml
@@ -14,6 +14,6 @@ dependencies:
   - openbabel >=3
   - pip
   - py3Dmol
-  - python >=3.10, <=3.12
+  - python >=3.10, <3.12
   - fresnel >=0.13.5
   - cmeutils >=1.3