From b076b5f9c3b4b29f20f3b400debe62096fef7fd7 Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Tue, 11 Aug 2026 16:07:50 +0200
Subject: [PATCH 1/4] =?UTF-8?q?=E2=9E=95=20Add=20ParallelTestRunner?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 test/Project.toml | 90 ++++++++++++++++++++++-------------------------
 1 file changed, 42 insertions(+), 48 deletions(-)

diff --git a/test/Project.toml b/test/Project.toml
index f259a849d..924add655 100644
--- a/test/Project.toml
+++ b/test/Project.toml
@@ -1,93 +1,96 @@
 [deps]
-# These are the additional test dependencies
+AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
+AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d"
 DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
+FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
+MKL_jll = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
+MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 NQCBase = "78c76ebc-5665-4934-b512-82d81b5cbfb7"
 NQCCalculators = "ddd1f41d-9621-41e2-91a4-6b87cc8989f3"
+NQCDInterfASE = "4606675f-2246-4a0b-99d5-75b910de637b"
 NQCDistributions = "657014a1-bd25-4aa2-92cb-cbcede0310ad"
 NQCDynamics = "36248dfb-79eb-4f4d-ab9c-e29ea5f33e14"
 NQCModels = "c814dc9f-a51f-4eaf-877f-82eda4edad48"
-NQCDInterfASE = "4606675f-2246-4a0b-99d5-75b910de637b"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
-RingPolymerArrays = "81cd853e-d334-476c-b156-f95acc8a32dc"
-SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-# These are NQCDynamics deps copied over from the main Project.toml
-AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
-ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
-Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
-DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
-Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
-FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
-HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-MKL_jll = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
+ParallelTestRunner = "d3525ed8-44d0-4b2c-a655-542cee43accc"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+RingPolymerArrays = "81cd853e-d334-476c-b156-f95acc8a32dc"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLOperators = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
+[sources]
+NQCBase = {rev = "main", url = "https://github.com/NQCD/NQCBase.jl.git"}
+NQCCalculators = {rev = "main", url = "https://github.com/NQCD/NQCCalculators.jl.git"}
+NQCDInterfASE = {rev = "main", url = "https://github.com/NQCD/NQCDInterfASE.jl.git"}
+NQCDistributions = {rev = "main", url = "https://github.com/NQCD/NQCDistributions.jl.git"}
+NQCDynamics = {path = ".."}
+NQCModels = {rev = "main", url = "https://github.com/NQCD/NQCModels.jl.git"}
+RingPolymerArrays = {rev = "main", url = "https://github.com/NQCD/RingPolymerArrays.jl.git"}
+
 [compat]
-# This compat information covers the additional testing packages. 
-CSV = "0.10"
-DataFrames = "1"
-DiffEqDevTools = "2"
-DiffEqNoiseProcess = "5"
-FiniteDiff = "2"
-JLD2 = "0.6"
-JSON = "0.21"
-MKL = "0.5, 0.6, 0.7, 0.8, 0.9"
-NQCDInterfASE = "1"
-Plots = "1"
-PythonCall = "=0.9.0, =0.9.1, =0.9.2, =0.9.3, =0.9.4, =0.9.5, =0.9.6, =0.9.7, =0.9.8, =0.9.9, =0.9.10, =0.9.11, =0.9.12, =0.9.13, =0.9.14, =0.9.15, =0.9.16, =0.9.17, =0.9.18, =0.9.19, =0.9.20, =0.9.21, =0.9.22, =0.9.23, =0.9.24, =0.9.25, =0.9.26"
-SafeTestsets = "0.1"
-# This compat information should mirror the main Project.toml. 
 AdvancedHMC = "0.5, 0.6"
 AdvancedMH = "0.8"
+CSV = "0.10"
 ComponentArrays = "0.11, 0.12, 0.13, 0.14, 0.15"
+DataFrames = "1"
 Dictionaries = "0.3, 0.4"
 DiffEqBase = "6"
+DiffEqDevTools = "2"
+DiffEqNoiseProcess = "5"
 Distributions = "0.25"
 FastBroadcast = "0.1, 0.2, 0.3"
 FastLapackInterface = "1, 2"
+FiniteDiff = "2"
 HDF5 = "0.15, 0.16, 0.17"
 Interpolations = "0.13, 0.14, 0.15, 0.16"
+JLD2 = "0.6"
+JSON = "0.21"
+MKL = "0.5, 0.6, 0.7, 0.8, 0.9"
 MuladdMacro = "0.2"
 NQCBase = "1"
 NQCCalculators = "1.0.10"
+NQCDInterfASE = "1"
 NQCDistributions = "1"
 NQCModels = "1"
 Optim = "1"
@@ -95,7 +98,9 @@ OrdinaryDiffEq = "6.103"
 OrdinaryDiffEqCore = "1.32, 2, 3"
 Parameters = "0.12"
 PeriodicTable = "1"
+Plots = "1"
 ProgressMeter = "1"
+PythonCall = "=0.9.0, =0.9.1, =0.9.2, =0.9.3, =0.9.4, =0.9.5, =0.9.6, =0.9.7, =0.9.8, =0.9.9, =0.9.10, =0.9.11, =0.9.12, =0.9.13, =0.9.14, =0.9.15, =0.9.16, =0.9.17, =0.9.18, =0.9.19, =0.9.20, =0.9.21, =0.9.22, =0.9.23, =0.9.24, =0.9.25, =0.9.26"
 QuadGK = "2"
 RecipesBase = "1"
 RecursiveArrayTools = "2, 3"
@@ -103,6 +108,7 @@ Reexport = "1"
 RingPolymerArrays = "0.1, 1"
 Roots = "1, 2"
 Rotations = "1"
+SafeTestsets = "0.1"
 SciMLBase = "1, 2"
 SciMLOperators = "0.3, 1"
 StaticArrays = "1"
@@ -116,15 +122,3 @@ UnicodePlots = "2, 3"
 Unitful = "1"
 UnitfulAtomic = "1"
 julia = "1"
-
-# For testing, we should be using the most recent dev versions of our packages by default. 
-# Override this by manually installing e.g. custom branches first. 
-[sources]
-NQCBase = {rev = "main", url = "https://github.com/NQCD/NQCBase.jl.git"}
-NQCCalculators = {rev = "main", url = "https://github.com/NQCD/NQCCalculators.jl.git"}
-NQCDistributions = {rev = "main", url = "https://github.com/NQCD/NQCDistributions.jl.git"}
-NQCDynamics = {path="../"}
-NQCDInterfASE = {rev = "main", url = "https://github.com/NQCD/NQCDInterfASE.jl.git"}
-NQCModels = {rev = "main", url = "https://github.com/NQCD/NQCModels.jl.git"}
-RingPolymerArrays = {rev = "main", url = "https://github.com/NQCD/RingPolymerArrays.jl.git"}
-

From 72c1d92b8c43c945e576a3665b8434d7adbed4f4 Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Tue, 11 Aug 2026 16:08:19 +0200
Subject: [PATCH 2/4] =?UTF-8?q?=F0=9F=91=B7=20Use=20ParallelTestRunner=20i?=
 =?UTF-8?q?nstead=20of=20test=20sets?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 test/runtests.jl | 155 +----------------------------------------------
 1 file changed, 2 insertions(+), 153 deletions(-)

diff --git a/test/runtests.jl b/test/runtests.jl
index cd57444e5..871ebafcb 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -1,157 +1,6 @@
 using Test
-using SafeTestsets
+using ParallelTestRunner
 using NQCDynamics
 using JSON
 
-const GROUP = get(ENV, "GROUP", "All")
-
-if GROUP == "All" || GROUP == "Core"
-    @safetestset "FastDeterminant Tests" begin
-        include("Core/FastDeterminant.jl")
-    end
-    @safetestset "Simulation Tests" begin
-        include("Core/simulations.jl")
-    end
-    @safetestset "Ring Polymer Tests" begin
-        include("Core/ring_polymers.jl")
-    end
-
-end
-
-if GROUP == "All" || GROUP == "Analysis"
-    @safetestset "Estimator tests" begin
-        include("Core/estimators.jl")
-    end
-    @safetestset "Structure Manipulation" begin
-        include("Structure/structure.jl")
-    end
-    @safetestset "Diatomic Analysis" begin
-        include("Analysis/diatomic.jl")
-    end
-end
-
-if GROUP == "All" || GROUP == "InitialConditions"
-    @safetestset "Monte Carlo Tests" begin
-        include("InitialConditions/monte_carlo.jl")
-    end
-    @safetestset "AdvancedMH Sampling Tests" begin
-        include("InitialConditions/advancedmh_sampling.jl")
-    end
-    @safetestset "QuantisedDiatomic Tests" begin
-        include("InitialConditions/quantised_diatomic.jl")
-    end
-end
-
-if GROUP == "All" || GROUP == "dynamics_classical"
-    @safetestset "DynamicsUtils Tests" begin
-        include("Dynamics/DynamicsUtils.jl")
-    end
-    @safetestset "Classical Tests" begin
-        include("Dynamics/classical.jl")
-    end
-    @safetestset "BCB Tests" begin
-        include("Dynamics/algorithms/bcb.jl")
-    end
-    @safetestset "Langevin Tests" begin
-        include("Dynamics/langevin.jl")
-    end
-end
-
-if GROUP == "All" || GROUP == "dynamics_mdef"
-    @safetestset "MDEF BAOAB Tests" begin
-        include("Dynamics/mdef_baoab.jl")
-    end
-    @safetestset "MDEF Tests" begin
-        include("Dynamics/mdef.jl")
-    end
-     @safetestset "DiabaticMDEF Tests" begin
-        include("Dynamics/diabatic_mdef.jl")
-    end 
-    @safetestset "RPMDEF Tests" begin
-        include("Dynamics/rpmdef.jl")
-    end
-end
-
-if GROUP == "All" || GROUP == "dynamics_surface_hopping"
-    @safetestset "BCBwithTsit5 Tests" begin
-        include("Dynamics/bcbwithtsit5.jl")
-    end
-    @safetestset "FSSH Tests" begin
-        include("Dynamics/fssh.jl")
-    end
-     @safetestset "IESH Tests" begin
-        include("Dynamics/iesh.jl")
-    end
-    @safetestset "Decoherence Tests" begin
-        include("Dynamics/test_decoherence_corrections.jl")
-    end
-    @safetestset "RPIESH Tests" begin
-        include("Dynamics/rpiesh.jl")
-    end
-end
-
-if GROUP == "All" || GROUP == "dynamics_cme"
-    @safetestset "CME Tests" begin
-        include("Dynamics/cme.jl")
-    end
-    @safetestset "BCME Tests" begin
-        include("Dynamics/bcme.jl")
-    end
-    @safetestset "RPCME Tests" begin
-        include("Dynamics/rpcme.jl")
-    end
-    @safetestset "RPBCME Tests" begin
-        include("Dynamics/rpbcme.jl")
-    end
-end
-
-
-if GROUP == "All" || GROUP == "dynamics_mapping"
-    @safetestset "Electronic dynamics Tests" begin
-        include("Dynamics/electronic_dynamics.jl")
-    end
-    @safetestset "NRPMD Tests" begin
-        include("Dynamics/nrpmd.jl")
-    end
-    @safetestset "CMM Tests" begin
-        include("Dynamics/cmm.jl")
-    end
-    @safetestset "RPeCMM Tests" begin
-        include("Dynamics/rpecmm.jl")
-    end
-    @safetestset "SpinMapping Tests" begin
-        include("Dynamics/spin_mapping.jl")
-    end
-end
-
-if GROUP == "All" || GROUP == "dynamics_ehrenfest"
-    @safetestset "Ehrenfest Tests" begin
-        include("Dynamics/ehrenfest.jl")
-    end
-    @safetestset "NA Ehrenfest Tests" begin
-        include("Dynamics/ehrenfest_na.jl")
-    end
-    @safetestset "NA RPEhrenfest Tests" begin
-        include("Dynamics/rp_ehrenfest_na.jl")
-    end
-end
-
-
-if GROUP == "All" || GROUP == "dynamics_ensembles"
-    @safetestset "Ensemble Tests" begin
-        include("Ensembles/ensembles.jl")
-    end
-    @safetestset "Ensemble Selection Tests" begin
-        include("Ensembles/selections.jl")
-    end
-    @safetestset "Ensemble Reduction Tests" begin
-        include("Ensembles/reductions.jl")
-    end
-    @safetestset "Ensemble Output Tests" begin
-        include("Ensembles/outputs.jl")
-    end
-    @safetestset "Cell Boundary Callback Tests" begin
-        include("Dynamics/cell_boundary_callback.jl")
-    end
-end
-
+runtests(NQCDynamics, ARGS)

From 164ac314bb72e15e7cad822cb70428f89aba32e4 Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Tue, 11 Aug 2026 16:11:40 +0200
Subject: [PATCH 3/4] =?UTF-8?q?=F0=9F=91=B7=20CI=20modified=20for=20parall?=
 =?UTF-8?q?el=20testing?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/CI.yml | 25 +++----------------------
 1 file changed, 3 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index b7f80266e..0afc976b0 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -8,20 +8,6 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        group:
-          - Core
-          - Analysis
-          - InitialConditions
-          - dynamics_classical
-          - dynamics_mdef
-          - dynamics_surface_hopping
-          - dynamics_cme
-          - dynamics_mapping
-          - dynamics_ehrenfest
-          - dynamics_ensembles
-      fail-fast: false
 
     steps:
       - id: workspace
@@ -47,9 +33,6 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
 
-      - name: Add JuliaMolSim registry
-        run: julia -e 'using Pkg; Pkg.Registry.add(RegistrySpec(url="https://github.com/JuliaMolSim/MolSim"))'
-        shell: bash
       - name: Add ACEregistry
         run: julia -e 'using Pkg; Pkg.Registry.add(RegistrySpec(url="https://github.com/ACEsuit/ACEregistry"))'
         shell: bash
@@ -60,7 +43,7 @@ jobs:
 
       - name: Install ase for IO tests
         id: install-python
-        run: | 
+        run: |
           pip3 install ase
           echo "python="$(which python) >> $GITHUB_OUTPUT
       - uses: julia-actions/julia-buildpkg@v1
@@ -69,7 +52,6 @@ jobs:
           JULIA_CONDAPKG_BACKEND: "Null"
       - uses: julia-actions/julia-runtest@v1
         env:
-          GROUP: ${{ matrix.group }}
           BENCHMARK_OUTPUT_DIR: /home/runner/NQCDynamics.jl/NQCDynamics.jl/benchmarks
           JULIA_PYTHONCALL_EXE: ${{ steps.install-python.outputs.python }}
           JULIA_CONDAPKG_BACKEND: "Null"
@@ -80,7 +62,7 @@ jobs:
       - name: 'Upload Artifact'
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ matrix.group }}-timings
+          name: test-timings
           path: /home/runner/NQCDynamics.jl/NQCDynamics.jl/benchmarks/*.json
           retention-days: 21
   upload_benchmarks:
@@ -90,7 +72,7 @@ jobs:
     outputs:
       newest_release_version: ${{ steps.save_tag.current_version }}
       previous_release_version: ${{ steps.save_tag.last_version }}
-    steps: 
+    steps:
       # Now we're in /home/runner/NQCDynamics.jl/NQCDynamics.jl
       - uses: actions/checkout@v4
         with:
@@ -165,4 +147,3 @@ jobs:
           echo "### Unit test benchmark :rocket:" >> "$GITHUB_STEP_SUMMARY"
           echo "Compared dynamics test timings between ${{ steps.save_tag.outputs.newest_release_version }} and ${{ github.sha }}." >> "$GITHUB_STEP_SUMMARY"
           echo "Download the results [here](${{ steps.upload-artifact.outputs.artifact-url }})" >> "$GITHUB_STEP_SUMMARY"
-

From 923848a04aee1cafcc88f03a0addfcf6518c1057 Mon Sep 17 00:00:00 2001
From: Alexander Spears <39826690+Alexsp32@users.noreply.github.com>
Date: Tue, 11 Aug 2026 16:21:27 +0200
Subject: [PATCH 4/4] Add instructions for developers and AI agents

---
 AGENTS.md | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 AGENTS.md

diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 000000000..bad39e935
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,11 @@
+# Information for developers
+
+Really these should just be called developer documentation, but hey ho, AI and all that.  
+I thought I'd hide these instructions in a separate file which LLMs will hopefully find.
+
+If you're making changes to dynamics propagation, adding new models or new methods, make sure to read the files in `docs/src/devdocs` for guidelines on how to do those things. 
+
+When adding unit tests, make sure to add any new package dependencies to `test/Project.toml`, not the main `Project.toml`. 
+Unit tests should be as small as practical, as they will be run in parallel automatically. 
+This means no `include()` statements in test sets. 
+Any files in `test/` will be read automatically, no need to add anything more to `test/runtests.jl`.