From 866cdb58da851b0c7e635e5f68dc8b33c5c7fe6e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 12 Feb 2024 21:28:19 +0000
Subject: [PATCH 01/43] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.1.1 → 24.2.0](https://github.com/psf/black/compare/24.1.1...24.2.0)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9035f09..8366b81 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 24.1.1
+  rev: 24.2.0
   hooks:
     - id: black
       args: [--line-length=80]

From c791c351663e69e8e38721ef2881c49040cc5edb Mon Sep 17 00:00:00 2001
From: Marjan Albooyeh <marjan.albouye73@gmail.com>
Date: Tue, 27 Feb 2024 12:12:21 -0700
Subject: [PATCH 02/43] pin freud version

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 8973c9e..0f2a500 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,7 +5,7 @@ dependencies:
   - python=3.10
   - numpy
   - ele
-  - freud>=2.13.1
+  - freud =2.13.2
   - gsd>=3.0
   - jupyterlab
   - mbuild

From 48b6006085a2d982e623d0a38b373b53190439ae Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Mar 2024 19:22:09 +0000
Subject: [PATCH 03/43] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8366b81..8907bd1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 24.2.0
+  rev: 24.3.0
   hooks:
     - id: black
       args: [--line-length=80]

From 8034d736e4d01cb0c94215e799fd2d78e2fdba2e Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 27 Mar 2024 12:27:47 -0600
Subject: [PATCH 04/43] change param name for showing ports

---
 grits/coarsegrain.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/grits/coarsegrain.py b/grits/coarsegrain.py
index 28e3d72..8ff2847 100644
--- a/grits/coarsegrain.py
+++ b/grits/coarsegrain.py
@@ -362,7 +362,7 @@ def visualize(
         if atom_names:
             atomistic.save(
                 os.path.join(tmp_dir, "atomistic_tmp.mol2"),
-                show_ports=show_ports,
+                include_ports=show_ports,
                 overwrite=True,
             )
 
@@ -397,7 +397,7 @@ def visualize(
                 simplefilter("ignore")
                 coarse.save(
                     os.path.join(tmp_dir, "coarse_tmp.mol2"),
-                    show_ports=show_ports,
+                    include_ports=show_ports,
                     overwrite=True,
                 )
             with open(os.path.join(tmp_dir, "coarse_tmp.mol2"), "r") as f:

From 8f1a9c58d02b1b2de36461b8cc2c08c2c441372b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 8 Apr 2024 19:33:02 +0000
Subject: [PATCH 05/43] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8907bd1..b2b4258 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer

From c8d57aac5178faaa9483611ca7b6acc92862f21b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 15 Apr 2024 19:28:12 +0000
Subject: [PATCH 06/43] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b2b4258..db2ad02 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 24.3.0
+  rev: 24.4.0
   hooks:
     - id: black
       args: [--line-length=80]

From 0b0cd0ff796c7da73a5d84affb7d1ca2510e07f6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 19:32:07 +0000
Subject: [PATCH 07/43] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index db2ad02..f9c9a32 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 24.4.0
+  rev: 24.4.2
   hooks:
     - id: black
       args: [--line-length=80]

From 552fdc9563c63d9ca672ca984f2390da4f2f26dc Mon Sep 17 00:00:00 2001
From: chrisjonesbsu <chrisjones4@u.boisestate.edu>
Date: Wed, 1 May 2024 09:31:12 -0600
Subject: [PATCH 08/43] add stride parameter when saving a CG trajectory

---
 grits/coarsegrain.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/grits/coarsegrain.py b/grits/coarsegrain.py
index 8ff2847..d43718e 100644
--- a/grits/coarsegrain.py
+++ b/grits/coarsegrain.py
@@ -667,7 +667,7 @@ def save_mapping(self, filename):
             json.dump(self.mapping, f, cls=NumpyEncoder)
         print(f"Mapping saved to {filename}")
 
-    def save(self, cg_gsdfile, start=0, stop=None):
+    def save(self, cg_gsdfile, start=0, stop=None, stride=1):
         """Save the coarse-grain system to a gsd file.
 
         Does not calculate the image of the coarse-grain bead.
@@ -688,6 +688,8 @@ def save(self, cg_gsdfile, start=0, stop=None):
         stop : int, default None
             Where to stop reading the gsd trajectory the system was created
             with. If None, will stop at the last frame.
+        stride : int, default 1
+            The step size to use when iterating through start:stop
         """
         typeid = []
         types = [i.split("...")[0] for i in self.mapping]
@@ -722,7 +724,7 @@ def save(self, cg_gsdfile, start=0, stop=None):
         ) as old:
             # stop being None is fine; slicing [0:None] gives whole array,
             # even in edge case where there's only one or two frames
-            for s in old[start:stop]:
+            for s in old[start:stop:stride]:
                 new_snap = gsd.hoomd.Frame()
                 position = []
                 mass = []

From c3ba3cc99b3de30b00bf700561815e0a7916f0f7 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 1 May 2024 10:37:02 -0600
Subject: [PATCH 09/43] add test for stride

---
 grits/tests/test_coarsegrain.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/grits/tests/test_coarsegrain.py b/grits/tests/test_coarsegrain.py
index cfd34b6..bfaad63 100644
--- a/grits/tests/test_coarsegrain.py
+++ b/grits/tests/test_coarsegrain.py
@@ -213,6 +213,22 @@ def test_benzene(self, tmp_path):
         cg_json = tmp_path / "cg-benzene.json"
         system.save_mapping(cg_json)
 
+    def test_stride(self, tmp_path):
+        gsdfile = path.join(asset_dir, "benzene-aa.gsd")
+        system = CG_System(
+            gsdfile,
+            beads={"_B": "c1ccccc1"},
+            conversion_dict=amber_dict,
+            mass_scale=12.011,
+        )
+        assert isinstance(system.mapping, dict)
+        assert len(system.mapping["_B...c1ccccc1"]) == 20
+
+        cg_gsd = tmp_path / "cg-benzene.gsd"
+        system.save(cg_gsdfile=cg_gsd, start=0, stop=-1, stride=2)
+        with gsd.hoomd.open(cg_gsd) as f:
+            assert len(f) == 3
+
     def test_anisobenzene(self, tmp_path):
         gsdfile = path.join(asset_dir, "benzene-aa.gsd")
         system = CG_System(

From 95b1fc34209def527122b7208b94211ae495bf30 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 1 May 2024 10:44:08 -0600
Subject: [PATCH 10/43] remove copied over stuff from another unit test

---
 grits/tests/test_coarsegrain.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/grits/tests/test_coarsegrain.py b/grits/tests/test_coarsegrain.py
index bfaad63..534f471 100644
--- a/grits/tests/test_coarsegrain.py
+++ b/grits/tests/test_coarsegrain.py
@@ -221,9 +221,6 @@ def test_stride(self, tmp_path):
             conversion_dict=amber_dict,
             mass_scale=12.011,
         )
-        assert isinstance(system.mapping, dict)
-        assert len(system.mapping["_B...c1ccccc1"]) == 20
-
         cg_gsd = tmp_path / "cg-benzene.gsd"
         system.save(cg_gsdfile=cg_gsd, start=0, stop=-1, stride=2)
         with gsd.hoomd.open(cg_gsd) as f:

From 374a1debce2c07bb9b040b73b80f806ce5ef4b85 Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Wed, 1 May 2024 11:30:30 -0600
Subject: [PATCH 11/43] Add cmeutils to docs env

---
 docs/environment-docs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/environment-docs.yml b/docs/environment-docs.yml
index 6659b67..9348d11 100644
--- a/docs/environment-docs.yml
+++ b/docs/environment-docs.yml
@@ -7,6 +7,7 @@ dependencies:
   - numpydoc
   - sphinx
   - sphinx_rtd_theme
+  - cmeutils
   - ele
   - freud
   - gsd

From 9e536512001d844d233da37501ebbb0e913d2cd5 Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Wed, 1 May 2024 11:43:41 -0600
Subject: [PATCH 12/43] Pin mbuild version

---
 docs/environment-docs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/environment-docs.yml b/docs/environment-docs.yml
index 9348d11..4cb83ae 100644
--- a/docs/environment-docs.yml
+++ b/docs/environment-docs.yml
@@ -11,6 +11,6 @@ dependencies:
   - ele
   - freud
   - gsd
-  - mbuild
+  - mbuild>=0.17
   - numpy
   - openbabel

From d0c581691f93e77d2831228527ca82738d42ef0b Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Wed, 1 May 2024 11:56:57 -0600
Subject: [PATCH 13/43] Add docs badge

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 75a7e30..4669fa6 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@
 [![Docker Repository on Quay](https://quay.io/repository/cmelab/grits/status "Docker Repository on Quay")](https://quay.io/repository/cmelab/grits)
 [![pytest](https://github.com/cmelab/grits/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/cmelab/grits/branch/main/graph/badge.svg?token=lGG8Zf65HP)](https://codecov.io/gh/cmelab/grits)
+[![Documentation Status](https://readthedocs.org/projects/grits/badge/?version=latest)](https://grits.readthedocs.io/en/latest/?badge=latest)
 
 ![GRiTS workflow](/.github/grits.png)
 

From dbb141bb1daae182b415028fd2520e327ab6d02f Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Fri, 3 May 2024 11:14:02 -0600
Subject: [PATCH 14/43] Add docker builder

shoutout to @mikemhenry and using https://github.com/OpenFreeEnergy/openfe/blob/main/.github/workflows/docker.yaml as example
---
 .github/workflows/build.yml | 78 +++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 .github/workflows/build.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..88f9775
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,78 @@
+name: build
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: cmelab/grits
+  DOCKERFILE: containers/dockerfile_cpu
+
+on:
+  push:
+    branches: [ main ]
+    # Run when container or environment is changed
+    paths:
+        - ${{ env.DOCKERFILE }}
+  # Allows workflow to be manually triggered
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+        with:
+          fetch-depth: 0
+
+      - name: Get Latest Version
+        id: latest-version
+        run: |
+          LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
+          echo $LATEST_TAG
+          echo "LATEST_TAG=$LATEST_TAG" >> $GITHUB_OUTPUT
+          # slice off the v, ie v0.7.2 -> 0.7.2
+          VERSION=${LATEST_TAG:1}
+          echo $VERSION
+          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Print Latest Version
+        run: echo ${{ steps.latest-version.outputs.VERSION }}
+
+      - name: Create fully qualified image registry path
+        id: fqirp
+        run: |
+          FQIRP=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}
+          echo "FQIRP=$FQIRP" >> $GITHUB_OUTPUT
+
+      - name: Print FQIRP
+        run: echo ${{ steps.fqirp.outputs.FQIRP  }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and export to Docker
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: production/Dockerfile
+          load: true
+          push: false
+          build-args: |
+            VERSION=${{ steps.latest-version.outputs.VERSION }}
+
+      - name: Test image
+        run: |
+          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
+
+      - name: Push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE }}
+          push: true
+          build-args: |
+            VERSION=${{ steps.latest-version.outputs.VERSION }}

From a9a381e3e4f68ed8c1d3d1ee2e9785d03669cb03 Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Fri, 3 May 2024 11:16:50 -0600
Subject: [PATCH 15/43] Remove quay badge

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 75a7e30..358ff14 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,5 @@
 # GRiTS : Grits Reduces/Restores Topology with SMILES
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/grits/badges/version.svg)](https://anaconda.org/conda-forge/grits)
-[![Docker Repository on Quay](https://quay.io/repository/cmelab/grits/status "Docker Repository on Quay")](https://quay.io/repository/cmelab/grits)
 [![pytest](https://github.com/cmelab/grits/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/cmelab/grits/branch/main/graph/badge.svg?token=lGG8Zf65HP)](https://codecov.io/gh/cmelab/grits)
 

From 7ee4915b4556772e6720df5bd17019d119a8fdd5 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:24:52 -0600
Subject: [PATCH 16/43] Move env later

---
 .github/workflows/build.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 88f9775..c0c76c3 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -1,19 +1,19 @@
 name: build
 
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: cmelab/grits
-  DOCKERFILE: containers/dockerfile_cpu
-
 on:
   push:
     branches: [ main ]
     # Run when container or environment is changed
     paths:
-        - ${{ env.DOCKERFILE }}
+        - containers/dockerfile_cpu
   # Allows workflow to be manually triggered
   workflow_dispatch:
 
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: cmelab/grits
+  DOCKERFILE: containers/dockerfile_cpu
+
 jobs:
   build:
     runs-on: ubuntu-latest

From 948255158f2ccf87824684bd54ad806bb0c4e18c Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:27:39 -0600
Subject: [PATCH 17/43] Update dockerfile

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

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index c0c76c3..fcdd06c 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -58,7 +58,7 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           context: .
-          file: production/Dockerfile
+          file: ${{ env.DOCKERFILE }}
           load: true
           push: false
           build-args: |

From e592026b81b3aeaf7a3688883cb4b63d7a2ad158 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:33:19 -0600
Subject: [PATCH 18/43] Update dockerfile_cpu

---
 containers/dockerfile_cpu | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/containers/dockerfile_cpu b/containers/dockerfile_cpu
index c54c092..e07c06c 100644
--- a/containers/dockerfile_cpu
+++ b/containers/dockerfile_cpu
@@ -7,11 +7,9 @@ RUN micromamba install -y -n base -f /tmp/env.yml && \
 
 COPY grits/ /tmp/grits/
 
-COPY setup.py /tmp/
-
 RUN ls -la /tmp
 
-RUN python -m pip install /tmp
+RUN python -m pip install /tmp/grits
 
 RUN pytest -vx
 

From 717730a62b1bc5122c9d17212a9405d2e9ab15a1 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:35:16 -0600
Subject: [PATCH 19/43] Remove testing

tests are done during the docker build
---
 .github/workflows/build.yml | 16 +---------------
 1 file changed, 1 insertion(+), 15 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index fcdd06c..b269ce1 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -54,22 +54,8 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build and export to Docker
+      - name: Build and Push to Docker
         uses: docker/build-push-action@v4
-        with:
-          context: .
-          file: ${{ env.DOCKERFILE }}
-          load: true
-          push: false
-          build-args: |
-            VERSION=${{ steps.latest-version.outputs.VERSION }}
-
-      - name: Test image
-        run: |
-          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
-
-      - name: Push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
         with:
           context: .
           file: ${{ env.DOCKERFILE }}

From 642bb6201b018ed55a899fafd207803aafa39a8e Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:41:36 -0600
Subject: [PATCH 20/43] Update dockerfile_cpu

---
 containers/dockerfile_cpu | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/containers/dockerfile_cpu b/containers/dockerfile_cpu
index e07c06c..9d0210e 100644
--- a/containers/dockerfile_cpu
+++ b/containers/dockerfile_cpu
@@ -5,11 +5,11 @@ COPY --chown=micromamba:micromamba environment.yml /tmp/env.yml
 RUN micromamba install -y -n base -f /tmp/env.yml && \
     micromamba clean --all --yes
 
-COPY grits/ /tmp/grits/
+COPY grits setup.py README /tmp/
 
 RUN ls -la /tmp
 
-RUN python -m pip install /tmp/grits
+RUN python -m pip install /tmp/
 
 RUN pytest -vx
 

From db6eda2c16de1471f000325f647bc888166b14e9 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:46:04 -0600
Subject: [PATCH 21/43] Update build.yml

---
 .github/workflows/build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index b269ce1..286a50e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -60,5 +60,6 @@ jobs:
           context: .
           file: ${{ env.DOCKERFILE }}
           push: true
+          tags: ${{ steps.latest-version.outputs.VERSION }}
           build-args: |
             VERSION=${{ steps.latest-version.outputs.VERSION }}

From 5c1c7bad670455e1c9365576df5af7e66a7a5c9d Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:47:19 -0600
Subject: [PATCH 22/43] Update dockerfile_cpu

---
 containers/dockerfile_cpu | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/containers/dockerfile_cpu b/containers/dockerfile_cpu
index 9d0210e..b88d3cf 100644
--- a/containers/dockerfile_cpu
+++ b/containers/dockerfile_cpu
@@ -5,7 +5,7 @@ COPY --chown=micromamba:micromamba environment.yml /tmp/env.yml
 RUN micromamba install -y -n base -f /tmp/env.yml && \
     micromamba clean --all --yes
 
-COPY grits setup.py README /tmp/
+COPY grits setup.py README.md /tmp/
 
 RUN ls -la /tmp
 

From ab99ed59001b8202c4901325a854bb774570181a Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 11:58:31 -0600
Subject: [PATCH 23/43] Update build.yml

---
 .github/workflows/build.yml | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 286a50e..c783d49 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -6,6 +6,7 @@ on:
     # Run when container or environment is changed
     paths:
         - containers/dockerfile_cpu
+        - environment.yml
   # Allows workflow to be manually triggered
   workflow_dispatch:
 
@@ -56,6 +57,21 @@ jobs:
 
       - name: Build and Push to Docker
         uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE }}
+          load: true
+          push: false
+          tags: ${{ steps.latest-version.outputs.VERSION }}
+          build-args: |
+            VERSION=${{ steps.latest-version.outputs.VERSION }}
+            
+      - name: Test image
+        run: |
+          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
+      
+      - name: Push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
         with:
           context: .
           file: ${{ env.DOCKERFILE }}

From a28c825a0cad0811b394538d8d76f58961021eba Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 12:00:57 -0600
Subject: [PATCH 24/43] Update dockerfile_cpu

---
 containers/dockerfile_cpu | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/containers/dockerfile_cpu b/containers/dockerfile_cpu
index b88d3cf..8f98301 100644
--- a/containers/dockerfile_cpu
+++ b/containers/dockerfile_cpu
@@ -3,18 +3,5 @@ FROM mambaorg/micromamba:0.15.2
 COPY --chown=micromamba:micromamba environment.yml /tmp/env.yml
 
 RUN micromamba install -y -n base -f /tmp/env.yml && \
+    micromamba install -y -n base -c conda-forge grits && \
     micromamba clean --all --yes
-
-COPY grits setup.py README.md /tmp/
-
-RUN ls -la /tmp
-
-RUN python -m pip install /tmp/
-
-RUN pytest -vx
-
-USER root
-
-RUN rm -r /tmp/*
-
-RUN python -c "import grits"

From 34c572b78295540e25537255050107326a4b5951 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 12:07:29 -0600
Subject: [PATCH 25/43] Update build.yml

---
 .github/workflows/build.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index c783d49..63f35de 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -55,7 +55,7 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build and Push to Docker
+      - name: Build Docker Image
         uses: docker/build-push-action@v4
         with:
           context: .
@@ -63,6 +63,7 @@ jobs:
           load: true
           push: false
           tags: ${{ steps.latest-version.outputs.VERSION }}
+          labels: ${{ steps.latest-version.outputs.VERSION }}
           build-args: |
             VERSION=${{ steps.latest-version.outputs.VERSION }}
             
@@ -77,5 +78,6 @@ jobs:
           file: ${{ env.DOCKERFILE }}
           push: true
           tags: ${{ steps.latest-version.outputs.VERSION }}
+          labels: ${{ steps.latest-version.outputs.VERSION }}
           build-args: |
             VERSION=${{ steps.latest-version.outputs.VERSION }}

From 8c29526cf796907fa3564c276a50acb151765efd Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 12:53:31 -0600
Subject: [PATCH 26/43] Update build.yml

---
 .github/workflows/build.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 63f35de..362e129 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -10,6 +10,10 @@ on:
   # Allows workflow to be manually triggered
   workflow_dispatch:
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 env:
   REGISTRY: ghcr.io
   IMAGE_NAME: cmelab/grits
@@ -18,6 +22,9 @@ env:
 jobs:
   build:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
 
     steps:
       - name: Checkout
@@ -69,6 +76,7 @@ jobs:
             
       - name: Test image
         run: |
+          docker ls
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
       
       - name: Push Docker image

From 11aa31b1b838a97b92adab73e19ae3d766b16750 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 12:55:54 -0600
Subject: [PATCH 27/43] Update dockerfile_cpu

---
 containers/dockerfile_cpu | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/containers/dockerfile_cpu b/containers/dockerfile_cpu
index 8f98301..5cb63ef 100644
--- a/containers/dockerfile_cpu
+++ b/containers/dockerfile_cpu
@@ -1,7 +1,12 @@
-FROM mambaorg/micromamba:0.15.2
+FROM mambaorg/micromamba:1.4.1
 
-COPY --chown=micromamba:micromamba environment.yml /tmp/env.yml
+ARG VERSION
 
-RUN micromamba install -y -n base -f /tmp/env.yml && \
-    micromamba install -y -n base -c conda-forge grits && \
+ENV PYTHONUNBUFFERED=1
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yml
+
+RUN micromamba install -y -n base "grits==$VERSION" -f /tmp/env.yml && \
     micromamba clean --all --yes
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1

From c93305dcc16ce8d686ed643ab1103b1e5c4139ce Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 13:13:25 -0600
Subject: [PATCH 28/43] Update build.yml

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

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 362e129..bc9a21f 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -76,7 +76,7 @@ jobs:
             
       - name: Test image
         run: |
-          docker ls
+          docker ps
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
       
       - name: Push Docker image

From e436f858c974daab07b2c34e416727cc5ffeeda3 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 13:37:11 -0600
Subject: [PATCH 29/43] Update build.yml

---
 .github/workflows/build.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index bc9a21f..cb11556 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -62,6 +62,14 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            ${{ steps.latest-version.outputs.VERSION }}
+
       - name: Build Docker Image
         uses: docker/build-push-action@v4
         with:

From c872fb71d135098e4d1a355e84a67b07ff61ab58 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 13:41:46 -0600
Subject: [PATCH 30/43] Update build.yml

---
 .github/workflows/build.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index cb11556..3579591 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -77,8 +77,8 @@ jobs:
           file: ${{ env.DOCKERFILE }}
           load: true
           push: false
-          tags: ${{ steps.latest-version.outputs.VERSION }}
-          labels: ${{ steps.latest-version.outputs.VERSION }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             VERSION=${{ steps.latest-version.outputs.VERSION }}
             
@@ -93,7 +93,7 @@ jobs:
           context: .
           file: ${{ env.DOCKERFILE }}
           push: true
-          tags: ${{ steps.latest-version.outputs.VERSION }}
-          labels: ${{ steps.latest-version.outputs.VERSION }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             VERSION=${{ steps.latest-version.outputs.VERSION }}

From 44f6a02cf2482d1af274ab5041e1a109b6dedd10 Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Fri, 3 May 2024 13:53:45 -0600
Subject: [PATCH 31/43] Fix precommit

---
 .github/workflows/build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 3579591..78c71c4 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -81,12 +81,12 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             VERSION=${{ steps.latest-version.outputs.VERSION }}
-            
+
       - name: Test image
         run: |
           docker ps
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
-      
+
       - name: Push Docker image
         uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
         with:

From 4de362634716daf091e0db8a04d16f7a0bdde1a7 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 14:00:41 -0600
Subject: [PATCH 32/43] Update README.md

---
 README.md | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 0c06a77..6be2c41 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@
 [![pytest](https://github.com/cmelab/grits/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/cmelab/grits/branch/main/graph/badge.svg?token=lGG8Zf65HP)](https://codecov.io/gh/cmelab/grits)
 [![Documentation Status](https://readthedocs.org/projects/grits/badge/?version=latest)](https://grits.readthedocs.io/en/latest/?badge=latest)
+[![Docker build](https://github.com/cmelab/grits/actions/workflows/build.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/build.yml)
 
 ![GRiTS workflow](/.github/grits.png)
 
@@ -13,21 +14,21 @@ GRiTS is a toolkit for working with coarse-grain systems. It uses [mBuild](https
 
 To use GRiTS in a prebuilt container (using [Singularity](https://singularity.lbl.gov/)), run:
 ```bash
-singularity pull docker://quay.io/cmelab/grits:latest
-singularity exec grits_latest.sif bash
+singularity pull docker://ghcr.io/cmelab/grits:0.4.1
+singularity exec grits_0.4.1.sif bash
 ```
 
 **Or** using [Docker](https://docs.docker.com/), run:
 ```bash
-docker pull quay.io/cmelab/grits:latest
-docker run -it cmelab/grits:latest
+docker pull ghcr.io/cmelab/grits:0.4.1
+docker run -it cmelab/grits:0.4.1
 ```
 
 #### Custom install
-To create a local environment with [conda](https://docs.conda.io/en/latest/miniconda.html), run:
+To create a local environment with [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html)), run:
 ```bash
-conda env create -f environment.yml
-conda activate grits
+micromamba create -f environment.yml
+micromamba activate grits
 ```
 With the `grits` environment active, install the package with pip:
 ```

From 81827a3593e016bf9256d7167642bf7455ba70a4 Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Fri, 3 May 2024 15:41:47 -0600
Subject: [PATCH 33/43] Switch to pyproject exclusively

trying to fix versioning on conda-forge
---
 pyproject.toml | 42 +++++++++++++++++++++++++++++++++---
 setup.py       | 58 --------------------------------------------------
 2 files changed, 39 insertions(+), 61 deletions(-)
 delete mode 100644 setup.py

diff --git a/pyproject.toml b/pyproject.toml
index 2758df1..c19b306 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,42 @@
 [build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=61.2", "versioningit"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools_scm]
-write_to = "grits/__version__.py"
+[project]
+name = "grits"
+description = "A toolkit for working with coarse-grained systems"
+readme = "README.md"
+authors = [{name = "Jenny Fothergill", email = "jennyfothergill@boisestate.edu"}]
+license= {text = "GPLv3"}
+classifiers=[
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+urls = {Homepage = "https://github.com/cmelab/grits"}
+requires-python = ">=3.8"
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages]
+find = {namespaces = false}
+
+[tool.setuptools.package-data]
+grits = ['"./compounds/*"']
+
+[tool.versioningit]
+default-version = "1+unknown"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.vcs]
+method = "git"
+match = ["*"]
+default-tag = "0.0.0"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index a762818..0000000
--- a/setup.py
+++ /dev/null
@@ -1,58 +0,0 @@
-from codecs import open
-from os import path
-
-from setuptools import find_packages, setup
-
-# Package meta-data.
-NAME = "grits"
-DESCRIPTION = "A toolkit for working with coarse-grained systems"
-URL = "https://github.com/cmelab/grits"
-EMAIL = "jennyfothergill@boisestate.edu"
-AUTHOR = "Jenny Fothergill"
-REQUIRES_PYTHON = ">=3.8"
-
-# What packages are required for this module to be executed?
-REQUIRED = []
-
-here = path.abspath(path.dirname(__file__))
-
-with open("README.md", "r", encoding="utf-8") as f:
-    long_description = f.read()
-
-
-def myversion():
-    from setuptools_scm.version import get_local_dirty_tag
-
-    def clean_scheme(version):
-        return get_local_dirty_tag(version) if version.dirty else "+clean"
-
-    return {"local_scheme": clean_scheme}
-
-
-setup(
-    name=NAME,
-    use_scm_version=myversion,
-    author=AUTHOR,
-    author_email=EMAIL,
-    description=DESCRIPTION,
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url=URL,
-    license="GPLv3",
-    project_urls={
-        "Bug Tracker": f"{URL}/issues",
-    },
-    python_requires=REQUIRES_PYTHON,
-    packages=find_packages(exclude=("tests", "docs", "examples")),
-    package_data={"grits": ["compounds/*"]},
-    install_requires=REQUIRED,
-    include_package_data=True,
-    classifiers=[
-        # Trove classifiers
-        # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
-        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-    ],
-)

From 969ff02dcf1eef3c4b59ddd967f9112ea20bc1c7 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 15:51:09 -0600
Subject: [PATCH 34/43] Update build.yml

---
 .github/workflows/build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 78c71c4..fb4b8cc 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -68,6 +68,7 @@ jobs:
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
+            type=raw,value=latest,enable={{ is_default_branch }}
             ${{ steps.latest-version.outputs.VERSION }}
 
       - name: Build Docker Image

From b428541d97a7cc4ced3912d15cfcadd796c8960c Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Fri, 3 May 2024 15:57:05 -0600
Subject: [PATCH 35/43] Update install instructions

---
 README.md | 22 +++++++---------------
 1 file changed, 7 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index 6be2c41..94f006e 100644
--- a/README.md
+++ b/README.md
@@ -12,29 +12,21 @@ GRiTS is a toolkit for working with coarse-grain systems. It uses [mBuild](https
 ### Installation
 #### Using a container
 
-To use GRiTS in a prebuilt container (using [Singularity](https://singularity.lbl.gov/)), run:
+To use GRiTS in a prebuilt container (using [Apptainer](https://apptainer.org/)), run:
 ```bash
-singularity pull docker://ghcr.io/cmelab/grits:0.4.1
-singularity exec grits_0.4.1.sif bash
+apptainer pull docker://ghcr.io/cmelab/grits:latest
+apptainer run grits_latest.sif python
 ```
 
 **Or** using [Docker](https://docs.docker.com/), run:
 ```bash
-docker pull ghcr.io/cmelab/grits:0.4.1
-docker run -it cmelab/grits:0.4.1
+docker pull ghcr.io/cmelab/grits:latest
+docker run -it cmelab/grits:latest
 ```
 
-#### Custom install
+#### Micromamba install
 To create a local environment with [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html)), run:
 ```bash
-micromamba create -f environment.yml
+micromamba create grits -f environment.yml
 micromamba activate grits
 ```
-With the `grits` environment active, install the package with pip:
-```
-pip install .
-```
-And to test your installation, run:
-```
-pytest
-```

From 304d9e4437c59de19a0a6352ad521de4d552cd1b Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 16:02:58 -0600
Subject: [PATCH 36/43] Update build.yml

---
 .github/workflows/build.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index fb4b8cc..e66421c 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -68,7 +68,7 @@ jobs:
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
-            type=raw,value=latest,enable={{ is_default_branch }}
+            type=ref,enable=true,priority=600,event=tag
             ${{ steps.latest-version.outputs.VERSION }}
 
       - name: Build Docker Image
@@ -85,7 +85,6 @@ jobs:
 
       - name: Test image
         run: |
-          docker ps
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import grits; print(grits.__version__)"
 
       - name: Push Docker image

From aa0605601a3e4264f6604f4d8d457dbee39c453c Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 16:27:56 -0600
Subject: [PATCH 37/43] Update build.yml

---
 .github/workflows/build.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e66421c..bf3afd5 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -68,7 +68,10 @@ jobs:
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
-            type=ref,enable=true,priority=600,event=tag
+            type=ref,event=tag,enable=true,priority=600
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{version}}
+            type=sha
             ${{ steps.latest-version.outputs.VERSION }}
 
       - name: Build Docker Image

From ae22a57955cc40ce2dd61c5213583de7b3774a29 Mon Sep 17 00:00:00 2001
From: Jenny <39961845+jennyfothergill@users.noreply.github.com>
Date: Fri, 3 May 2024 16:49:15 -0600
Subject: [PATCH 38/43] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 94f006e..ead8e37 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ docker run -it cmelab/grits:latest
 ```
 
 #### Micromamba install
-To create a local environment with [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html)), run:
+To create a local environment with [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html), run:
 ```bash
 micromamba create grits -f environment.yml
 micromamba activate grits

From 8a181002f9e74e691735ac48e0ff111c682b666b Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Mon, 6 May 2024 11:32:54 -0600
Subject: [PATCH 39/43] Remove rdkit, sort dependencies

---
 environment.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/environment.yml b/environment.yml
index 0f2a500..37c34a1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,20 +2,19 @@ name: grits
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
-  - numpy
+  - cmeutils >= 1.2.0
   - ele
-  - freud =2.13.2
-  - gsd>=3.0
+  - freud = 2.13.2
+  - gsd >= 3.0
   - jupyterlab
   - mbuild
   - ele
   - freud
+  - numpy
   - openbabel
   - pip
   - pre-commit
   - py3Dmol
   - pytest
   - pytest-cov
-  - rdkit
-  - cmeutils >= 1.2.0
+  - python = 3.10

From ff72e3e5af36c105325dc2310ca46fb820ee842e Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Mon, 6 May 2024 15:19:48 -0600
Subject: [PATCH 40/43] Only push on manual trigger

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

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index bf3afd5..0a0a4ec 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -95,7 +95,7 @@ jobs:
         with:
           context: .
           file: ${{ env.DOCKERFILE }}
-          push: true
+          push: ${{ github.event_name == 'workflow_dispatch' }}
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           build-args: |

From d5d5bffa0e87a9a1158f763cd1b63c42b998189c Mon Sep 17 00:00:00 2001
From: Jenny Fothergill <jennyfothergill@boisestate.edu>
Date: Mon, 6 May 2024 15:25:59 -0600
Subject: [PATCH 41/43] Add v prefix to tags

Hopefully this will trigger latest?
---
 .github/workflows/build.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 0a0a4ec..15f1299 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -68,10 +68,7 @@ jobs:
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
-            type=ref,event=tag,enable=true,priority=600
-            type=semver,pattern={{major}}.{{minor}}
-            type=semver,pattern={{version}}
-            type=sha
+            type=semver,pattern={{version}},prefix=v
             ${{ steps.latest-version.outputs.VERSION }}
 
       - name: Build Docker Image

From 5ee91d6aef38bc1a8ec2cb9111fa6b6c475ef200 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Tue, 18 Jun 2024 23:46:47 -0600
Subject: [PATCH 42/43] update env file, use snap mol cluster func from
 cmeutils instead of internal one

---
 environment.yml      | 11 +++++------
 grits/coarsegrain.py |  5 ++---
 grits/utils.py       | 17 -----------------
 3 files changed, 7 insertions(+), 26 deletions(-)

diff --git a/environment.yml b/environment.yml
index 37c34a1..9bb7ef1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,14 +2,13 @@ name: grits
 channels:
   - conda-forge
 dependencies:
-  - cmeutils >= 1.2.0
+  - cmeutils >=1.2.0
   - ele
-  - freud = 2.13.2
-  - gsd >= 3.0
+  - freud >=3.0
+  - gsd >=3.0
   - jupyterlab
-  - mbuild
+  - mbuild >=0.17.1
   - ele
-  - freud
   - numpy
   - openbabel
   - pip
@@ -17,4 +16,4 @@ dependencies:
   - py3Dmol
   - pytest
   - pytest-cov
-  - python = 3.10
+  - python >=3.10
diff --git a/grits/coarsegrain.py b/grits/coarsegrain.py
index d43718e..7d7fd2f 100644
--- a/grits/coarsegrain.py
+++ b/grits/coarsegrain.py
@@ -10,7 +10,7 @@
 import freud
 import gsd.hoomd
 import numpy as np
-from cmeutils.gsd_utils import identify_snapshot_connections
+from cmeutils.gsd_utils import get_molecule_cluster, identify_snapshot_connections
 from ele import element_from_symbol
 from mbuild import Compound, clone
 from mbuild.utils.io import run_from_ipython
@@ -24,7 +24,6 @@
     get_quaternion,
     has_common_member,
     has_number,
-    snap_molecules,
 )
 
 __all__ = ["CG_Compound", "CG_System", "Bead"]
@@ -574,7 +573,7 @@ def _get_compounds(
                 conversion_dict[i].symbol for i in snap.particles.types
             ]
         # Break apart the snapshot into separate molecules
-        molecules = snap_molecules(snap)
+        molecules = get_molecule_cluster(snap=snap)
         mol_inds = []
         for i in range(max(molecules) + 1):
             mol_inds.append(np.where(molecules == i)[0])
diff --git a/grits/utils.py b/grits/utils.py
index ce3487b..e5898ce 100644
--- a/grits/utils.py
+++ b/grits/utils.py
@@ -82,23 +82,6 @@ def comp_from_snapshot(snapshot, indices, length_scale=1.0, mass_scale=1.0):
     return comp
 
 
-def snap_molecules(snap):
-    """Get the molecule indices based on bonding in a gsd.hoomd.Frame."""
-    system = freud.AABBQuery.from_system(snap)
-    n_query_points = n_points = snap.particles.N
-    query_point_indices = snap.bonds.group[:, 0]
-    point_indices = snap.bonds.group[:, 1]
-    distances = system.box.compute_distances(
-        system.points[query_point_indices], system.points[point_indices]
-    )
-    nlist = freud.NeighborList.from_arrays(
-        n_query_points, n_points, query_point_indices, point_indices, distances
-    )
-    cluster = freud.cluster.Cluster()
-    cluster.compute(system=system, neighbors=nlist)
-    return cluster.cluster_idx
-
-
 def align(compound, particle, towards_compound, around=None):
     """Spin a compound such that particle points at towards_compound.
 

From f40c005f9c230e2b6a4dbff5cb984f83e236a2e5 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Wed, 19 Jun 2024 07:53:52 -0600
Subject: [PATCH 43/43] use latest cmeutils version

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 9bb7ef1..ef7f34f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: grits
 channels:
   - conda-forge
 dependencies:
-  - cmeutils >=1.2.0
+  - cmeutils >=1.3.0
   - ele
   - freud >=3.0
   - gsd >=3.0