From 44ceae18db9dfc2779e111dde1091d537321f780 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 08:45:07 -0500
Subject: [PATCH 1/8] Try switching back to Mambaforge

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index f890236..58c189a 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: "ubuntu-24.04"
   tools:
-    python: "latest"
+    python: "mambaforge-latest"
   jobs:
     create_environment:
       - asdf plugin add pixi

From 7ed039aaeab4742b8d44b3ce0329006f0416d305 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 08:46:37 -0500
Subject: [PATCH 2/8] Drop CI

---
 .github/workflows/ci-dev-main.yaml           |  65 -----------
 .github/workflows/ci.yaml                    |  84 --------------
 .github/workflows/cpu-vslow-tests.yaml       | 109 -------------------
 .github/workflows/gpu-integration-tests.yaml | 109 -------------------
 .github/workflows/mypy.yaml                  |  47 --------
 5 files changed, 414 deletions(-)
 delete mode 100644 .github/workflows/ci-dev-main.yaml
 delete mode 100644 .github/workflows/ci.yaml
 delete mode 100644 .github/workflows/cpu-vslow-tests.yaml
 delete mode 100644 .github/workflows/gpu-integration-tests.yaml
 delete mode 100644 .github/workflows/mypy.yaml

diff --git a/.github/workflows/ci-dev-main.yaml b/.github/workflows/ci-dev-main.yaml
deleted file mode 100644
index 3e2aa39..0000000
--- a/.github/workflows/ci-dev-main.yaml
+++ /dev/null
@@ -1,65 +0,0 @@
-name: "CI - main branch of deps"
-on:
-  push:
-    branches:
-      - main
-  schedule:
-    # At 07:00 UTC on Monday (weekly)
-    - cron: "0 7 * * 1"
-  workflow_dispatch:
-
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -l {0}
-
-jobs:
-  tests:
-    runs-on: ${{ matrix.os }}
-    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest"]
-        python-version:
-          - "3.12"
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: devtools/environment_dev.yml
-          environment-name: pontibus-dev
-          create-args: >-
-            python=${{ matrix.python-version }}
-          init-shell: bash
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          PONTIBUS_SLOW_TESTS: TRUE
-          PONTIBUS_CPUVSLOW_TESTS: FALSE
-          PONTIBUS_GPU_TESTS: FALSE
-          DUECREDIT_ENABLE: 'yes'
-        run: |
-          pytest -n logical -v --durations=10
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
deleted file mode 100644
index 15f7f5c..0000000
--- a/.github/workflows/ci.yaml
+++ /dev/null
@@ -1,84 +0,0 @@
-name: "CI"
-on:
-  pull_request:
-    branches:
-      - main
-    paths-ignore:
-      - "docs/*"
-  push:
-    branches:
-      - main
-  schedule:
-    # At 07:00 UTC on Monday and Thursday
-    - cron: "0 7 * * *"
-  workflow_dispatch:
-
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -l {0}
-
-jobs:
-  tests:
-    runs-on: ${{ matrix.os }}
-    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest"]
-        python-version:
-          - "3.11"
-          - "3.12"
-          - "3.13"
-        include:
-          - os: "macos-latest"
-            python-version: "3.13"
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          create-args: >-
-            python=${{ matrix.python-version }}
-          init-shell: bash
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          # For now, disable these as they are too slow to run on gh ci
-          PONTIBUS_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
-          DUECREDIT_ENABLE: 'yes'
-        run: |
-          pytest -n logical -v --cov=pontibus --cov-report=xml --durations=10
-
-      - name: codecov-pr
-        if: ${{ github.repository == 'OpenFreeEnergy/pontibus'
-                && github.event_name != 'schedule' }}
-        uses: codecov/codecov-action@v5
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          file: coverage.xml
-          fail_ci_if_error: False
-          verbose: True
diff --git a/.github/workflows/cpu-vslow-tests.yaml b/.github/workflows/cpu-vslow-tests.yaml
deleted file mode 100644
index 78984bb..0000000
--- a/.github/workflows/cpu-vslow-tests.yaml
+++ /dev/null
@@ -1,109 +0,0 @@
-name: CPU Very Slow Tests (manual dispatch)
-on:
-  workflow_dispatch:
-
-jobs:
-  start-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    outputs:
-      mapping: ${{ steps.aws-start.outputs.mapping }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Create cloud runner
-        id: aws-start
-        uses: omsf/start-aws-gha-runner@v1.0.0
-        with:
-          aws_image_id: ami-0b7f661c228e6a4bb
-          aws_instance_type: c8i.2xlarge
-          aws_home_dir: /home/ubuntu
-          aws_root_device_size: 125
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-
-  self-hosted-test:
-    runs-on: self-hosted
-    timeout-minutes: 720  # 12 hours
-    defaults:
-      run:
-        shell: bash -leo pipefail {0}
-
-    needs:
-      - start-aws-runner
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Schedule auto-shutdown after 24 hours
-        # This is the failsafe if timeout-minutes above fails
-        # More info https://github.com/openforcefield/openff-evaluator/issues/740
-        run: nohup bash -c 'sleep 86400 && sudo shutdown -h now' > /tmp/auto-shutdown.log 2>&1 &
-
-      - name: Print disk usage
-        run: "df -h"
-
-      - name: Print Docker details
-        run: "docker version || true"
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          condarc: |
-            channels:
-              - conda-forge
-          create-args: >-
-            python=3.13
-
-      - name: "Check if OpenMM can get a GPU"
-        run: python -m openmm.testInstallation
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          DUECREDIT_ENABLE: 'yes'
-          PONTIBUS_CPUVSLOW_TESTS: TRUE
-          PONTIBUS_GPU_TESTS: FALSE
-        run: |
-          # The -m flag will only run tests with @pytest.mark.cpuvslow
-          pytest -n logical -vv --durations=10 -m cpuvslow
-
-  stop-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-        id-token: write
-        contents: read
-    needs:
-      - start-aws-runner
-      - self-hosted-test
-    if: ${{ always() }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Stop instances
-        uses: omsf/stop-aws-gha-runner@v1.0.0
-        with:
-          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/gpu-integration-tests.yaml b/.github/workflows/gpu-integration-tests.yaml
deleted file mode 100644
index d5939b8..0000000
--- a/.github/workflows/gpu-integration-tests.yaml
+++ /dev/null
@@ -1,109 +0,0 @@
-name: GPU Integration Tests (manual dispatch)
-on:
-  workflow_dispatch:
-
-jobs:
-  start-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    outputs:
-      mapping: ${{ steps.aws-start.outputs.mapping }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Create cloud runner
-        id: aws-start
-        uses: omsf/start-aws-gha-runner@v1.0.0
-        with:
-          aws_image_id: ami-076a54ed41e67782d
-          aws_instance_type: g4dn.xlarge
-          aws_home_dir: /home/ubuntu
-          aws_root_device_size: 125
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-
-  self-hosted-test:
-    runs-on: self-hosted
-    timeout-minutes: 720  # 12 hours
-    defaults:
-      run:
-        shell: bash -leo pipefail {0}
-
-    needs:
-      - start-aws-runner
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Print disk usage
-        run: "df -h"
-
-      - name: Print Docker details
-        run: "docker version || true"
-
-      - name: Check for nvidia-smi
-        run: "nvidia-smi"
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          condarc: |
-            channels:
-              - conda-forge
-          create-args: >-
-            python=3.13
-            cuda-version=12.8
-
-      - name: "Check if OpenMM can get a GPU"
-        run: python -m openmm.testInstallation
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          DUECREDIT_ENABLE: 'yes'
-          PONTIBUS_CPUVSLOW_TESTS: FALSE
-          PONTIBUS_GPU_TESTS: TRUE
-        run: |
-          # The -m flag will only run tests with @pytest.mark.gpu
-          pytest -n logical -vv --durations=10 -m gpu
-
-  stop-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-        id-token: write
-        contents: read
-    needs:
-      - start-aws-runner
-      - self-hosted-test
-    if: ${{ always() }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Stop instances
-        uses: omsf/stop-aws-gha-runner@v1.0.0
-        with:
-          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/mypy.yaml b/.github/workflows/mypy.yaml
deleted file mode 100644
index 5f622af..0000000
--- a/.github/workflows/mypy.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-name: "mypy"
-on:
-  pull_request:
-    branches:
-      - main
-  push:
-    branches:
-      - main
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -leo pipefail {0}
-
-jobs:
-  mypy:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          cache-environment: true
-          cache-downloads: true
-          create-args: >-
-            python=3.11
-          init-shell: bash
-
-      - name: "Install steps"
-        run: |
-          python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
-          python -m pip install mypy
-          python -m pip install --no-deps -e .
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-
-      - name: "Lint with mypy"
-        run: mypy

From a9894a8e4c4862b32ae67c99a61757d2958de5f5 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 08:46:42 -0500
Subject: [PATCH 3/8] Force 3.11

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 58c189a..e8e0baf 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-latest"
+    python: "3.11"
   jobs:
     create_environment:
       - asdf plugin add pixi

From a49b957c2e0537b7b43b60d9754e798b901b2c29 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 09:11:03 -0500
Subject: [PATCH 4/8] Revert "Drop CI"

This reverts commit 7ed039aaeab4742b8d44b3ce0329006f0416d305.
---
 .github/workflows/ci-dev-main.yaml           |  65 +++++++++++
 .github/workflows/ci.yaml                    |  84 ++++++++++++++
 .github/workflows/cpu-vslow-tests.yaml       | 109 +++++++++++++++++++
 .github/workflows/gpu-integration-tests.yaml | 109 +++++++++++++++++++
 .github/workflows/mypy.yaml                  |  47 ++++++++
 5 files changed, 414 insertions(+)
 create mode 100644 .github/workflows/ci-dev-main.yaml
 create mode 100644 .github/workflows/ci.yaml
 create mode 100644 .github/workflows/cpu-vslow-tests.yaml
 create mode 100644 .github/workflows/gpu-integration-tests.yaml
 create mode 100644 .github/workflows/mypy.yaml

diff --git a/.github/workflows/ci-dev-main.yaml b/.github/workflows/ci-dev-main.yaml
new file mode 100644
index 0000000..3e2aa39
--- /dev/null
+++ b/.github/workflows/ci-dev-main.yaml
@@ -0,0 +1,65 @@
+name: "CI - main branch of deps"
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    # At 07:00 UTC on Monday (weekly)
+    - cron: "0 7 * * 1"
+  workflow_dispatch:
+
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version:
+          - "3.12"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: devtools/environment_dev.yml
+          environment-name: pontibus-dev
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          PONTIBUS_SLOW_TESTS: TRUE
+          PONTIBUS_CPUVSLOW_TESTS: FALSE
+          PONTIBUS_GPU_TESTS: FALSE
+          DUECREDIT_ENABLE: 'yes'
+        run: |
+          pytest -n logical -v --durations=10
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..15f7f5c
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,84 @@
+name: "CI"
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - "docs/*"
+  push:
+    branches:
+      - main
+  schedule:
+    # At 07:00 UTC on Monday and Thursday
+    - cron: "0 7 * * *"
+  workflow_dispatch:
+
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version:
+          - "3.11"
+          - "3.12"
+          - "3.13"
+        include:
+          - os: "macos-latest"
+            python-version: "3.13"
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          # For now, disable these as they are too slow to run on gh ci
+          PONTIBUS_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
+          DUECREDIT_ENABLE: 'yes'
+        run: |
+          pytest -n logical -v --cov=pontibus --cov-report=xml --durations=10
+
+      - name: codecov-pr
+        if: ${{ github.repository == 'OpenFreeEnergy/pontibus'
+                && github.event_name != 'schedule' }}
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: False
+          verbose: True
diff --git a/.github/workflows/cpu-vslow-tests.yaml b/.github/workflows/cpu-vslow-tests.yaml
new file mode 100644
index 0000000..78984bb
--- /dev/null
+++ b/.github/workflows/cpu-vslow-tests.yaml
@@ -0,0 +1,109 @@
+name: CPU Very Slow Tests (manual dispatch)
+on:
+  workflow_dispatch:
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf/start-aws-gha-runner@v1.0.0
+        with:
+          aws_image_id: ami-0b7f661c228e6a4bb
+          aws_instance_type: c8i.2xlarge
+          aws_home_dir: /home/ubuntu
+          aws_root_device_size: 125
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  self-hosted-test:
+    runs-on: self-hosted
+    timeout-minutes: 720  # 12 hours
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+
+    needs:
+      - start-aws-runner
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Schedule auto-shutdown after 24 hours
+        # This is the failsafe if timeout-minutes above fails
+        # More info https://github.com/openforcefield/openff-evaluator/issues/740
+        run: nohup bash -c 'sleep 86400 && sudo shutdown -h now' > /tmp/auto-shutdown.log 2>&1 &
+
+      - name: Print disk usage
+        run: "df -h"
+
+      - name: Print Docker details
+        run: "docker version || true"
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: >-
+            python=3.13
+
+      - name: "Check if OpenMM can get a GPU"
+        run: python -m openmm.testInstallation
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          DUECREDIT_ENABLE: 'yes'
+          PONTIBUS_CPUVSLOW_TESTS: TRUE
+          PONTIBUS_GPU_TESTS: FALSE
+        run: |
+          # The -m flag will only run tests with @pytest.mark.cpuvslow
+          pytest -n logical -vv --durations=10 -m cpuvslow
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - self-hosted-test
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Stop instances
+        uses: omsf/stop-aws-gha-runner@v1.0.0
+        with:
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/gpu-integration-tests.yaml b/.github/workflows/gpu-integration-tests.yaml
new file mode 100644
index 0000000..d5939b8
--- /dev/null
+++ b/.github/workflows/gpu-integration-tests.yaml
@@ -0,0 +1,109 @@
+name: GPU Integration Tests (manual dispatch)
+on:
+  workflow_dispatch:
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf/start-aws-gha-runner@v1.0.0
+        with:
+          aws_image_id: ami-076a54ed41e67782d
+          aws_instance_type: g4dn.xlarge
+          aws_home_dir: /home/ubuntu
+          aws_root_device_size: 125
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  self-hosted-test:
+    runs-on: self-hosted
+    timeout-minutes: 720  # 12 hours
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+
+    needs:
+      - start-aws-runner
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Print disk usage
+        run: "df -h"
+
+      - name: Print Docker details
+        run: "docker version || true"
+
+      - name: Check for nvidia-smi
+        run: "nvidia-smi"
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: >-
+            python=3.13
+            cuda-version=12.8
+
+      - name: "Check if OpenMM can get a GPU"
+        run: python -m openmm.testInstallation
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          DUECREDIT_ENABLE: 'yes'
+          PONTIBUS_CPUVSLOW_TESTS: FALSE
+          PONTIBUS_GPU_TESTS: TRUE
+        run: |
+          # The -m flag will only run tests with @pytest.mark.gpu
+          pytest -n logical -vv --durations=10 -m gpu
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - self-hosted-test
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Stop instances
+        uses: omsf/stop-aws-gha-runner@v1.0.0
+        with:
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/mypy.yaml b/.github/workflows/mypy.yaml
new file mode 100644
index 0000000..5f622af
--- /dev/null
+++ b/.github/workflows/mypy.yaml
@@ -0,0 +1,47 @@
+name: "mypy"
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=3.11
+          init-shell: bash
+
+      - name: "Install steps"
+        run: |
+          python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
+          python -m pip install mypy
+          python -m pip install --no-deps -e .
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: "Lint with mypy"
+        run: mypy

From ff3d0869a54947a0b3ac6b3be9b62072c8179d1b Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 09:23:01 -0500
Subject: [PATCH 5/8] Revert "Force 3.11"

This reverts commit a9894a8e4c4862b32ae67c99a61757d2958de5f5.
---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index e8e0baf..58c189a 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: "ubuntu-24.04"
   tools:
-    python: "3.11"
+    python: "mambaforge-latest"
   jobs:
     create_environment:
       - asdf plugin add pixi

From 6a10e6b4f53f4019220ade96ba5a183aa0c025c5 Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 09:23:16 -0500
Subject: [PATCH 6/8] Revert "Try switching back to Mambaforge"

This reverts commit 44ceae18db9dfc2779e111dde1091d537321f780.
---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 58c189a..f890236 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-latest"
+    python: "latest"
   jobs:
     create_environment:
       - asdf plugin add pixi

From 8a709853d845d107a471b79cba39db7dcc3c06ee Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 09:23:28 -0500
Subject: [PATCH 7/8] Reapply "Drop CI"

This reverts commit a49b957c2e0537b7b43b60d9754e798b901b2c29.
---
 .github/workflows/ci-dev-main.yaml           |  65 -----------
 .github/workflows/ci.yaml                    |  84 --------------
 .github/workflows/cpu-vslow-tests.yaml       | 109 -------------------
 .github/workflows/gpu-integration-tests.yaml | 109 -------------------
 .github/workflows/mypy.yaml                  |  47 --------
 5 files changed, 414 deletions(-)
 delete mode 100644 .github/workflows/ci-dev-main.yaml
 delete mode 100644 .github/workflows/ci.yaml
 delete mode 100644 .github/workflows/cpu-vslow-tests.yaml
 delete mode 100644 .github/workflows/gpu-integration-tests.yaml
 delete mode 100644 .github/workflows/mypy.yaml

diff --git a/.github/workflows/ci-dev-main.yaml b/.github/workflows/ci-dev-main.yaml
deleted file mode 100644
index 3e2aa39..0000000
--- a/.github/workflows/ci-dev-main.yaml
+++ /dev/null
@@ -1,65 +0,0 @@
-name: "CI - main branch of deps"
-on:
-  push:
-    branches:
-      - main
-  schedule:
-    # At 07:00 UTC on Monday (weekly)
-    - cron: "0 7 * * 1"
-  workflow_dispatch:
-
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -l {0}
-
-jobs:
-  tests:
-    runs-on: ${{ matrix.os }}
-    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest"]
-        python-version:
-          - "3.12"
-    steps:
-      - uses: actions/checkout@v6
-        with:
-          fetch-depth: 0
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: devtools/environment_dev.yml
-          environment-name: pontibus-dev
-          create-args: >-
-            python=${{ matrix.python-version }}
-          init-shell: bash
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          PONTIBUS_SLOW_TESTS: TRUE
-          PONTIBUS_CPUVSLOW_TESTS: FALSE
-          PONTIBUS_GPU_TESTS: FALSE
-          DUECREDIT_ENABLE: 'yes'
-        run: |
-          pytest -n logical -v --durations=10
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
deleted file mode 100644
index 15f7f5c..0000000
--- a/.github/workflows/ci.yaml
+++ /dev/null
@@ -1,84 +0,0 @@
-name: "CI"
-on:
-  pull_request:
-    branches:
-      - main
-    paths-ignore:
-      - "docs/*"
-  push:
-    branches:
-      - main
-  schedule:
-    # At 07:00 UTC on Monday and Thursday
-    - cron: "0 7 * * *"
-  workflow_dispatch:
-
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -l {0}
-
-jobs:
-  tests:
-    runs-on: ${{ matrix.os }}
-    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest"]
-        python-version:
-          - "3.11"
-          - "3.12"
-          - "3.13"
-        include:
-          - os: "macos-latest"
-            python-version: "3.13"
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          create-args: >-
-            python=${{ matrix.python-version }}
-          init-shell: bash
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          # For now, disable these as they are too slow to run on gh ci
-          PONTIBUS_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
-          DUECREDIT_ENABLE: 'yes'
-        run: |
-          pytest -n logical -v --cov=pontibus --cov-report=xml --durations=10
-
-      - name: codecov-pr
-        if: ${{ github.repository == 'OpenFreeEnergy/pontibus'
-                && github.event_name != 'schedule' }}
-        uses: codecov/codecov-action@v5
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          file: coverage.xml
-          fail_ci_if_error: False
-          verbose: True
diff --git a/.github/workflows/cpu-vslow-tests.yaml b/.github/workflows/cpu-vslow-tests.yaml
deleted file mode 100644
index 78984bb..0000000
--- a/.github/workflows/cpu-vslow-tests.yaml
+++ /dev/null
@@ -1,109 +0,0 @@
-name: CPU Very Slow Tests (manual dispatch)
-on:
-  workflow_dispatch:
-
-jobs:
-  start-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    outputs:
-      mapping: ${{ steps.aws-start.outputs.mapping }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Create cloud runner
-        id: aws-start
-        uses: omsf/start-aws-gha-runner@v1.0.0
-        with:
-          aws_image_id: ami-0b7f661c228e6a4bb
-          aws_instance_type: c8i.2xlarge
-          aws_home_dir: /home/ubuntu
-          aws_root_device_size: 125
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-
-  self-hosted-test:
-    runs-on: self-hosted
-    timeout-minutes: 720  # 12 hours
-    defaults:
-      run:
-        shell: bash -leo pipefail {0}
-
-    needs:
-      - start-aws-runner
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Schedule auto-shutdown after 24 hours
-        # This is the failsafe if timeout-minutes above fails
-        # More info https://github.com/openforcefield/openff-evaluator/issues/740
-        run: nohup bash -c 'sleep 86400 && sudo shutdown -h now' > /tmp/auto-shutdown.log 2>&1 &
-
-      - name: Print disk usage
-        run: "df -h"
-
-      - name: Print Docker details
-        run: "docker version || true"
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          condarc: |
-            channels:
-              - conda-forge
-          create-args: >-
-            python=3.13
-
-      - name: "Check if OpenMM can get a GPU"
-        run: python -m openmm.testInstallation
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          DUECREDIT_ENABLE: 'yes'
-          PONTIBUS_CPUVSLOW_TESTS: TRUE
-          PONTIBUS_GPU_TESTS: FALSE
-        run: |
-          # The -m flag will only run tests with @pytest.mark.cpuvslow
-          pytest -n logical -vv --durations=10 -m cpuvslow
-
-  stop-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-        id-token: write
-        contents: read
-    needs:
-      - start-aws-runner
-      - self-hosted-test
-    if: ${{ always() }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Stop instances
-        uses: omsf/stop-aws-gha-runner@v1.0.0
-        with:
-          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/gpu-integration-tests.yaml b/.github/workflows/gpu-integration-tests.yaml
deleted file mode 100644
index d5939b8..0000000
--- a/.github/workflows/gpu-integration-tests.yaml
+++ /dev/null
@@ -1,109 +0,0 @@
-name: GPU Integration Tests (manual dispatch)
-on:
-  workflow_dispatch:
-
-jobs:
-  start-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    outputs:
-      mapping: ${{ steps.aws-start.outputs.mapping }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Create cloud runner
-        id: aws-start
-        uses: omsf/start-aws-gha-runner@v1.0.0
-        with:
-          aws_image_id: ami-076a54ed41e67782d
-          aws_instance_type: g4dn.xlarge
-          aws_home_dir: /home/ubuntu
-          aws_root_device_size: 125
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-
-  self-hosted-test:
-    runs-on: self-hosted
-    timeout-minutes: 720  # 12 hours
-    defaults:
-      run:
-        shell: bash -leo pipefail {0}
-
-    needs:
-      - start-aws-runner
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Print disk usage
-        run: "df -h"
-
-      - name: Print Docker details
-        run: "docker version || true"
-
-      - name: Check for nvidia-smi
-        run: "nvidia-smi"
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          condarc: |
-            channels:
-              - conda-forge
-          create-args: >-
-            python=3.13
-            cuda-version=12.8
-
-      - name: "Check if OpenMM can get a GPU"
-        run: python -m openmm.testInstallation
-
-      - name: "Install"
-        run: python -m pip install --no-deps -e .
-
-      - name: "Test imports"
-        run: |
-          # if we add more to this, consider changing to for + env vars
-          python -Ic "import pontibus; print(pontibus.__version__)"
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-          pip list
-
-      - name: "Run tests"
-        env:
-          DUECREDIT_ENABLE: 'yes'
-          PONTIBUS_CPUVSLOW_TESTS: FALSE
-          PONTIBUS_GPU_TESTS: TRUE
-        run: |
-          # The -m flag will only run tests with @pytest.mark.gpu
-          pytest -n logical -vv --durations=10 -m gpu
-
-  stop-aws-runner:
-    runs-on: ubuntu-latest
-    permissions:
-        id-token: write
-        contents: read
-    needs:
-      - start-aws-runner
-      - self-hosted-test
-    if: ${{ always() }}
-    steps:
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
-          aws-region: us-east-2
-      - name: Stop instances
-        uses: omsf/stop-aws-gha-runner@v1.0.0
-        with:
-          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/mypy.yaml b/.github/workflows/mypy.yaml
deleted file mode 100644
index 5f622af..0000000
--- a/.github/workflows/mypy.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-name: "mypy"
-on:
-  pull_request:
-    branches:
-      - main
-  push:
-    branches:
-      - main
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
-
-defaults:
-  run:
-    shell: bash -leo pipefail {0}
-
-jobs:
-  mypy:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: "Setup Micromamba"
-        uses: mamba-org/setup-micromamba@v2
-        with:
-          environment-file: environment.yml
-          environment-name: pontibus
-          cache-environment: true
-          cache-downloads: true
-          create-args: >-
-            python=3.11
-          init-shell: bash
-
-      - name: "Install steps"
-        run: |
-          python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
-          python -m pip install mypy
-          python -m pip install --no-deps -e .
-
-      - name: "Environment Information"
-        run: |
-          micromamba info
-          micromamba list
-
-      - name: "Lint with mypy"
-        run: mypy

From 3220d4e1cc3163fe2b1815a2e0dc9a3d3d078d1e Mon Sep 17 00:00:00 2001
From: "Matthew W. Thompson" <mattwthompson@protonmail.com>
Date: Mon, 31 Aug 2026 09:26:53 -0500
Subject: [PATCH 8/8] Revert "Reapply "Drop CI""

This reverts commit 8a709853d845d107a471b79cba39db7dcc3c06ee.
---
 .github/workflows/ci-dev-main.yaml           |  65 +++++++++++
 .github/workflows/ci.yaml                    |  84 ++++++++++++++
 .github/workflows/cpu-vslow-tests.yaml       | 109 +++++++++++++++++++
 .github/workflows/gpu-integration-tests.yaml | 109 +++++++++++++++++++
 .github/workflows/mypy.yaml                  |  47 ++++++++
 5 files changed, 414 insertions(+)
 create mode 100644 .github/workflows/ci-dev-main.yaml
 create mode 100644 .github/workflows/ci.yaml
 create mode 100644 .github/workflows/cpu-vslow-tests.yaml
 create mode 100644 .github/workflows/gpu-integration-tests.yaml
 create mode 100644 .github/workflows/mypy.yaml

diff --git a/.github/workflows/ci-dev-main.yaml b/.github/workflows/ci-dev-main.yaml
new file mode 100644
index 0000000..3e2aa39
--- /dev/null
+++ b/.github/workflows/ci-dev-main.yaml
@@ -0,0 +1,65 @@
+name: "CI - main branch of deps"
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    # At 07:00 UTC on Monday (weekly)
+    - cron: "0 7 * * 1"
+  workflow_dispatch:
+
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version:
+          - "3.12"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: devtools/environment_dev.yml
+          environment-name: pontibus-dev
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          PONTIBUS_SLOW_TESTS: TRUE
+          PONTIBUS_CPUVSLOW_TESTS: FALSE
+          PONTIBUS_GPU_TESTS: FALSE
+          DUECREDIT_ENABLE: 'yes'
+        run: |
+          pytest -n logical -v --durations=10
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..15f7f5c
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,84 @@
+name: "CI"
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - "docs/*"
+  push:
+    branches:
+      - main
+  schedule:
+    # At 07:00 UTC on Monday and Thursday
+    - cron: "0 7 * * *"
+  workflow_dispatch:
+
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version:
+          - "3.11"
+          - "3.12"
+          - "3.13"
+        include:
+          - os: "macos-latest"
+            python-version: "3.13"
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          # For now, disable these as they are too slow to run on gh ci
+          PONTIBUS_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
+          DUECREDIT_ENABLE: 'yes'
+        run: |
+          pytest -n logical -v --cov=pontibus --cov-report=xml --durations=10
+
+      - name: codecov-pr
+        if: ${{ github.repository == 'OpenFreeEnergy/pontibus'
+                && github.event_name != 'schedule' }}
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: coverage.xml
+          fail_ci_if_error: False
+          verbose: True
diff --git a/.github/workflows/cpu-vslow-tests.yaml b/.github/workflows/cpu-vslow-tests.yaml
new file mode 100644
index 0000000..78984bb
--- /dev/null
+++ b/.github/workflows/cpu-vslow-tests.yaml
@@ -0,0 +1,109 @@
+name: CPU Very Slow Tests (manual dispatch)
+on:
+  workflow_dispatch:
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf/start-aws-gha-runner@v1.0.0
+        with:
+          aws_image_id: ami-0b7f661c228e6a4bb
+          aws_instance_type: c8i.2xlarge
+          aws_home_dir: /home/ubuntu
+          aws_root_device_size: 125
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  self-hosted-test:
+    runs-on: self-hosted
+    timeout-minutes: 720  # 12 hours
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+
+    needs:
+      - start-aws-runner
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Schedule auto-shutdown after 24 hours
+        # This is the failsafe if timeout-minutes above fails
+        # More info https://github.com/openforcefield/openff-evaluator/issues/740
+        run: nohup bash -c 'sleep 86400 && sudo shutdown -h now' > /tmp/auto-shutdown.log 2>&1 &
+
+      - name: Print disk usage
+        run: "df -h"
+
+      - name: Print Docker details
+        run: "docker version || true"
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: >-
+            python=3.13
+
+      - name: "Check if OpenMM can get a GPU"
+        run: python -m openmm.testInstallation
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          DUECREDIT_ENABLE: 'yes'
+          PONTIBUS_CPUVSLOW_TESTS: TRUE
+          PONTIBUS_GPU_TESTS: FALSE
+        run: |
+          # The -m flag will only run tests with @pytest.mark.cpuvslow
+          pytest -n logical -vv --durations=10 -m cpuvslow
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - self-hosted-test
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Stop instances
+        uses: omsf/stop-aws-gha-runner@v1.0.0
+        with:
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/gpu-integration-tests.yaml b/.github/workflows/gpu-integration-tests.yaml
new file mode 100644
index 0000000..d5939b8
--- /dev/null
+++ b/.github/workflows/gpu-integration-tests.yaml
@@ -0,0 +1,109 @@
+name: GPU Integration Tests (manual dispatch)
+on:
+  workflow_dispatch:
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf/start-aws-gha-runner@v1.0.0
+        with:
+          aws_image_id: ami-076a54ed41e67782d
+          aws_instance_type: g4dn.xlarge
+          aws_home_dir: /home/ubuntu
+          aws_root_device_size: 125
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  self-hosted-test:
+    runs-on: self-hosted
+    timeout-minutes: 720  # 12 hours
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+
+    needs:
+      - start-aws-runner
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Print disk usage
+        run: "df -h"
+
+      - name: Print Docker details
+        run: "docker version || true"
+
+      - name: Check for nvidia-smi
+        run: "nvidia-smi"
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: >-
+            python=3.13
+            cuda-version=12.8
+
+      - name: "Check if OpenMM can get a GPU"
+        run: python -m openmm.testInstallation
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          DUECREDIT_ENABLE: 'yes'
+          PONTIBUS_CPUVSLOW_TESTS: FALSE
+          PONTIBUS_GPU_TESTS: TRUE
+        run: |
+          # The -m flag will only run tests with @pytest.mark.gpu
+          pytest -n logical -vv --durations=10 -m gpu
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - self-hosted-test
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::010438489691:role/GHARunnerAWS
+          aws-region: us-east-2
+      - name: Stop instances
+        uses: omsf/stop-aws-gha-runner@v1.0.0
+        with:
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/mypy.yaml b/.github/workflows/mypy.yaml
new file mode 100644
index 0000000..5f622af
--- /dev/null
+++ b/.github/workflows/mypy.yaml
@@ -0,0 +1,47 @@
+name: "mypy"
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: pontibus
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=3.11
+          init-shell: bash
+
+      - name: "Install steps"
+        run: |
+          python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
+          python -m pip install mypy
+          python -m pip install --no-deps -e .
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: "Lint with mypy"
+        run: mypy