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AtomisticSkills 2.0.0: portable uv runtime, containers, and scientific fixes - #47

Merged

bowen-bd merged 106 commits into

learningmatter-mit:mainfrom

bowen-bd:refactor/skills-at-repo-root

Oct 6, 2026

Commits on Sep 1, 2026

refactor(skills)!: move skills to repo root so the repo is importable

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9151b69

Commits on Sep 2, 2026

fix(mat-elasticity): default to relaxed-ion, split the two force thresholds

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test(mat-elasticity): pin the relax_deformed no-op bug and the Voigt shear factor

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6ca8899

Commits on Sep 3, 2026

feat(docker): ship the MCP servers as container images

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45daaa6
fix(docker): make the image registry configurable, not hardcoded

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bc2d414

Commits on Sep 13, 2026

fix(docker): install cmake for the packages with no aarch64 wheel

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1cb5075
fix(docker): hold stdin open in the smoke test until the server replies

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f955b41
fix(envs): pin mcp<2 -- every server uses the 1.x FastMCP API

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Merge fork/main into refactor/skills-at-repo-root

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e6ea91b
fix(docker): unbreak the three GPU image builds

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975b1c4

Commits on Sep 14, 2026

fix(docker): wait for the smoke-test reply instead of sleeping a fixed time

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f126c28
docs: correct the plugin install identifier

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7872fd4
feat(docker): support Apptainer so the plugin works on HPC

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f5052ae
fix(docker): make the Apptainer path survive a real HPC node

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0080f6e
fix(docker): repair the four bugs the HPC retest exposed

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ad0d3e1
fix(release): sync the default image tag with VERSION

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b199f18
fix(docker): find the pre-built SIF instead of predicting its path

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fix(docker): let the pre-build reuse a SIF it already has

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22308a0
feat(docker): build mace and fairchem for amd64 as well as arm64

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Merge origin/main into refactor/skills-at-repo-root
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50598fa

Commits on Sep 18, 2026

fix(docker): recover from the mksquashfs thread limit, and let the image be inspected

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8edac08
feat(venv): add dual-arch uv projects to replace the conda environments

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feat(venv): place every remaining environment in a uv project

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feat(skills): run every skill script through a uv project

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324709e

Commits on Sep 19, 2026

feat(mat-elasticity): shear-modulus extrema, acoustic branches, moduli under load

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c0fbc05

Commits on Sep 28, 2026

fix: resolve DiffCSP++ and example paths instead of hardcoding one machine

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595323c
fix: drop machine-specific paths from skills, envs and examples

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840248f

Commits on Oct 5, 2026

feat(venv): three uv projects on latest releases, repository as a package

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feat(venv): one launcher for skill commands and MCP servers

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feat(mcp): call any MCP tool from the shell

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f9886c4
feat(docker): images from the uv locks, plugin servers through venv/run

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feat(skills): self-locating commands, uv environments, MCP fallback

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feat(mlips): matgl 4.1 CHGNet by default, backend-agnostic MD observer

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fix(nvalchemi): stream race in batch relax/MD, cell-aware convergence

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Merge origin/main (publisher-access-guard location)

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chore(release): 1.5.0, registry packages name the uv images

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docs: setup guide for the uv runtime, 1.5.0 change log and plan

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docs(changes): answers for the Gemini agent (G4 failure strings)

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docs(changes): second verification round, plugin findings, task G6

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ci(images): build the uv images, smoke-test the cpu image

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[G1] docs(rules): describe the uv runtime in agent instructions
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[G2] docs: update user-facing documentation for the uv launcher runtime
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[G4] feat(tools): classify known platform limits in check_skill_commands
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[G3] ci: add uv-envs workflow and update build-images for uv runtime
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[G5] docs(skill): update ml-mlip-nvalchemi for stream fix, inflight accuracy, and cell convergence
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docs: finalize 1.5.0 gemini progress log
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Merge release/1.5.0-gemini: docs, rules, CI, sweep classification (G1-G5)

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fix(skills): example scripts answer --help instead of querying MP

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ci(uv-envs): skip docs-only changes; record the first green CI run

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docs(changes): verification matrix, tester runs, upstream PR plan

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c5500af
[G7] fix(skills): resolve undefined names across skill scripts and smol_utils
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[G8] fix(skills): audit and protect skill scripts for safe --help handling
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Merge release/1.5.0-gemini: undefined names and --help audit (G7, G8)

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fix(venv): RHEL 8 and CentOS 7 hosts, old NVIDIA drivers (Engaging, desta)

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docs(changes): desta and Engaging results in the verification matrix

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docs: no local paths, host names or personal projects in shipped files

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chore(release)!: 2.0.0 -- not backward compatible with 1.x

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feat(venv): CUDA 12.6 torch for NVIDIA drivers older than 580

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fix(venv): torchvision from the same CUDA index as torch

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[G9] fix: remove local environment and personal details from shipped files
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Merge release/1.5.0-gemini: no local information in shipped files (G9)

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fix: GPU selection under CUDA_VISIBLE_DEVICES, doctor on multi-GPU hosts, libGL for PyMOL

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docs(changes): retest results on the A100 workstation and the HPC cluster

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docs(changes): A100 workstation round 3 results

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docs(changes): 2.0.0 images built and published

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docs: HPC notes from the cluster run (Apptainer for extras, SIF cleanup, GPU nodes); round 3 results

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docs(changes): ready for upstream -- drop internal planning docs

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chore(conda-envs): keep only the stacks still in use

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feat(venv): uv projects for the generative stacks and React-OT

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feat(venv): ICEBERG on its own uv project, ported to ms-pred 2.1

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fix(chem-msms-predict): load ICEBERG checkpoints under torch 2.6

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fix(chem-msms-predict): sum same-m/z fragment peaks in the plot; real example output

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feat(venv): SelfConditionedDenoisingAtoms on its own uv project

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fix(ml-property-predict-scd): load checkpoints from the SCD checkout

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fix(generative): find the ADiT checkout without PYTHONPATH; mount source checkouts into containers

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refactor(configure_mcp): every server starts through venv/run

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docs: every stack on uv; conda only for LAMMPS and the arm64 image

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docs(verification): ICEBERG and SCD results on x86_64

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fix(mattergen): run MatterGen from a source checkout

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feat(images): build the generative image from the uv locks

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feat(mat-lammps-md): build and run LAMMPS on the uv environments

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docs: no conda anywhere

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fix(tests): run the MCP server tests in their uv environments

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docs(tests): troubleshooting and CI notes for the uv environments

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docs(changes): no conda in 2.0.0; MatterGen checkout, generative image, test fixes

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docs(skills): name the uv environments, not the 1.x conda ones

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ci: run the MCP servers' unit tests in their environments

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docs(changes): AmberTools is an external install

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fix(tests): skip the local VASP run without VASP; SCINE lowercases option values

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fix(images): RDKit drawing in every image; CUDA libraries of each torch at run time

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docs(mat-lammps-md): Kokkos targets for Blackwell; MatGL build verified on GB10

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fix(generative): fresh checkouts generate; ADiT gets OpenBabel; pytest for the stacks

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docs(verification): x86-A100 round 4 results

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Commits on Oct 6, 2026

fix: review and EL8 findings: OpenFF, Sella, MatGL device, container GPUs, measured glibc floors

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docs: research-stack glibc floors, amd64 generative image, review and EL8 results

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fix(openmm): python-constraint from its git tag; the sweep shows why an env failed

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fix(run): a stack with no image says how to run it natively anyway

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fix: correct batch relaxation convergence and cell optimization

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fix: guard NValchemi 0.2 neighbor geometry allocations

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fix: require explicit opt-in for experimental NValchemi batching

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docs(migration): batched NValchemi is opt-in

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docs(verification): the draft NValchemi upstream issue

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fix(images): unrelated venv/ changes no longer recompile the generative image

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fix(run): preserve CA bundles across Apptainer launches
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docs: record successful Round 5 follow-up validation
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fix(runtime): serialize setup and gate image releases
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