@pikaa-ai/pikaa 0.3.22 → 0.3.24

package/skills/pylabrobot/SKILL.md

@@ -1,216 +0,0 @@
----
-name: pylabrobot
-description: Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protocols or API questions; keep physical execution behind an explicit operator safety gate.
-license: MIT
-compatibility: Verified against PyLabRobot 0.2.1 on Python 3.9+. Bundled planning CLIs require only Python 3.11+ and make no serial, USB, or network connections. Physical devices need model-specific extras, configuration, calibration, and trained operator approval.
-allowed-tools: Read Write Edit Bash
-metadata:
-  version: "1.2"
-  skill-author: "K-Dense Inc."
-  pylabrobot-version: "0.2.1"
-  researched: "2026-07-23"
----
-
-# PyLabRobot
-
-Use PyLabRobot's hardware-agnostic frontends, resource tree, trackers, and
-device-specific backends to develop laboratory automation. Default to local
-manifest validation, bookkeeping, and the software-only chatterbox backend.
-
-## Verified snapshot
-
-- PyPI stable: **`PyLabRobot==0.2.1`**, released **2026-03-23**.
-- Upstream requirement: **Python >=3.9**. This skill uses Python 3.11 for its
-  reproducible smoke tests.
-- `/stable/` documentation identifies itself as 0.2.1. `/dev/` and repository
-  `main` describe unreleased work and must not be assumed available in 0.2.1.
-- Stable liquid-handler backends include `STARBackend`, `VantageBackend`,
-  `EVOBackend`, `OpentronsOT2Backend`, and the offline
-  `LiquidHandlerChatterboxBackend`.
-- PyLabRobot's GitHub Releases page has no 0.2.x software release entry; use
-  the PyPI history, `v0.2.1` tag, and changelog as release evidence.
-
-## Non-negotiable hardware boundary
-
-Never connect to, initialize, home, move, heat, shake, spin, pump, open/close,
-or otherwise command physical equipment automatically. Do not turn a simulation
-plan into a live backend merely by changing an environment variable, config
-value, or import.
-
-Before any separately authorized live run, require a trained human to:
-
-1. Explicitly confirm the exact backend, device identity, firmware, transport,
-   deck, and protocol revision.
-2. Reconcile the physical deck against the resource tree, including carriers,
-   adapters, lids, plates, tip racks, waste, labware orientation, barcodes, and
-   every occupied coordinate.
-3. Verify calibration, teaching, motion envelopes, collision risks, gripper or
-   channel clearances, and all aspiration/dispense coordinates.
-4. Review source identity and actual fill volume, dead volume, destination
-   capacity, tip type/capacity/filter compatibility, channel mapping, units,
-   heights, rates, liquid class, blowout/mixing, and contamination boundaries.
-5. Confirm guards, doors, waste capacity, containment, emergency stop readiness,
-   PPE, biosafety/chemical controls, and a safe abort/recovery procedure.
-6. Approve a slow dry run or nonhazardous commissioning run when anything is
-   new or changed.
-
-Tracker state is **bookkeeping**, not sensing. It cannot prove that liquid or a
-tip is physically present. The Visualizer renders resource/tracker events; it
-does not model physics. Chatterbox prints planned operations; it does not prove
-calibration, reachability, collision freedom, liquid behavior, or device state.
-
-## Required intake
-
-Do not guess any of these:
-
-- Exact device model, installed options, firmware, computer/OS, and transport.
-- Stable PyLabRobot version and required extras.
-- Deck/deck origin, carriers, adapters, resource definitions, dimensions,
-  coordinates, orientations, and motion clearances.
-- Plate/tube/reservoir capacities and dead volumes; initial physical volumes.
-- Tip model, filter, fitting, capacity, rack state, channel count, and channel
-  mapping.
-- Transfer units (`uL`, `mm`, `uL/s`, `s`), heights, rates, mixing, air gaps,
-  blowout, liquid properties, and validated vendor liquid class.
-- Contamination policy, controls, waste handling, operator interventions,
-  acceptance criteria, and recovery procedure.
-
-If information is missing, produce an assumptions/blockers list and an offline
-draft only.
-
-## Reproducible install
-
-For offline API inspection and chatterbox simulation:
-
-```bash
-uv venv --python 3.11 .venv-pylabrobot
-uv pip install --python .venv-pylabrobot/bin/python "PyLabRobot==0.2.1"
-```
-
-On Windows, use `.venv-pylabrobot\Scripts\python.exe`. Do not install hardware
-extras until the user names the device and explicitly approves its transport
-dependencies. Then inspect the matching stable device page before considering a
-pin such as `"PyLabRobot[serial]==0.2.1"` or `"PyLabRobot[usb]==0.2.1"`.
-
-## Offline-first workflow
-
-Run from the repository root. Every bundled CLI uses strict, bounded UTF-8
-JSON/CSV, local non-symlink paths, fixed allowlists, and JSON output. None can
-select a live backend.
-
-```bash
-python3 skills/pylabrobot/scripts/validate_manifest.py \
-  --input tests/pylabrobot/fixtures/protocol_manifest.json
-
-python3 skills/pylabrobot/scripts/check_deck_geometry.py \
-  --input tests/pylabrobot/fixtures/protocol_manifest.json
-
-python3 skills/pylabrobot/scripts/plan_transfers.py \
-  --manifest tests/pylabrobot/fixtures/protocol_manifest.json \
-  --transfers tests/pylabrobot/fixtures/transfers.csv
-
-python3 skills/pylabrobot/scripts/generate_simulation_plan.py \
-  --manifest tests/pylabrobot/fixtures/protocol_manifest.json \
-  --transfers tests/pylabrobot/fixtures/transfers.csv
-
-python3 skills/pylabrobot/scripts/inspect_backends.py \
-  --expected-version 0.2.1 --strict
-```
-
-The geometry checker uses conservative static axis-aligned boxes; it is not a
-motion planner. The transfer planner requires one new tip per row and checks
-source/dead/destination volumes, tip capacity, wells, channels, heights, rates,
-units, and allowlists. Review
-`assets/protocol-manifest.schema.json` and the synthetic fixtures before making
-a project-specific manifest.
-
-## Verified software-only example
-
-The exact backend below is software-only. Do not substitute a hardware backend.
-
-```python
-from pylabrobot.liquid_handling import LiquidHandler
-from pylabrobot.liquid_handling.backends import LiquidHandlerChatterboxBackend
-from pylabrobot.resources import (
-    Cor_96_wellplate_360ul_Fb,
-    PLT_CAR_L5AC_A00,
-    TIP_CAR_480_A00,
-    hamilton_96_tiprack_1000uL_filter,
-    set_tip_tracking,
-    set_volume_tracking,
-)
-from pylabrobot.resources.hamilton import STARLetDeck
-
-set_tip_tracking(True)
-set_volume_tracking(True)
-
-deck = STARLetDeck()
-tip_carrier = TIP_CAR_480_A00(name="tip_carrier")
-tips = hamilton_96_tiprack_1000uL_filter(name="tips")
-tip_carrier[0] = tips
-plate_carrier = PLT_CAR_L5AC_A00(name="plate_carrier")
-source = Cor_96_wellplate_360ul_Fb(name="source")
-destination = Cor_96_wellplate_360ul_Fb(name="destination")
-plate_carrier[0] = source
-plate_carrier[1] = destination
-deck.assign_child_resource(tip_carrier, rails=3)
-deck.assign_child_resource(plate_carrier, rails=15)
-source.get_well("A1").tracker.set_volume(100.0)  # planned state, not sensing
-
-lh = LiquidHandler(backend=LiquidHandlerChatterboxBackend(), deck=deck)
-await lh.setup()  # safe here only because the backend above is software-only
-try:
-    await lh.pick_up_tips(tips["A1"])
-    await lh.aspirate(source["A1"], vols=[10.0])
-    await lh.dispense(destination["A1"], vols=[10.0])
-    await lh.return_tips()
-finally:
-    await lh.stop()
-```
-
-## API rules that prevent stale code
-
-- Current names are `STARBackend`, `VantageBackend`, `EVOBackend`, and
-  `OpentronsOT2Backend`; do not use stale `STAR`, `TecanBackend`,
-  `OpentronsBackend`, or `ChatterboxBackend` imports.
-- Use `LiquidHandlerChatterboxBackend` for generic offline liquid-handler
-  testing. `ChatterBoxBackend` is a separate legacy-named export; do not
-  conflate the two.
-- `Visualizer(resource=...)` is valid, followed by `await vis.setup()` and
-  `await vis.stop()`; it starts localhost HTTP/WebSocket servers and may open a
-  browser.
-- There is no generic `from pylabrobot.liquid_handling import LiquidClass` in
-  0.2.1. Stable liquid classes are vendor-specific, for example
-  `pylabrobot.liquid_handling.liquid_classes.hamilton.HamiltonLiquidClass`.
-- Most frontend methods are async. Backend kwargs and capabilities are
-  vendor/model specific; a shared frontend does not imply identical behavior.
-
-## References
-
-- [Liquid handling](references/liquid-handling.md) — operations, tips, tracking,
-  liquid classes, units, and validation.
-- [Resources](references/resources.md) — decks, coordinates, plates, tip racks,
-  collisions, state, and serialization.
-- [Hardware backends](references/hardware-backends.md) — verified names,
-  support levels, capabilities, and live-run gate.
-- [Analytical equipment](references/analytical-equipment.md) — plate readers
-  and scales.
-- [Material handling](references/material-handling.md) — pumps, heaters,
-  shakers, temperature control, storage, and centrifuges.
-- [Visualization](references/visualization.md) — chatterbox, Visualizer,
-  localhost services, and simulation limits.
-
-## Dated upstream sources
-
-Checked **2026-07-23**:
-
-- [PyPI 0.2.1](https://pypi.org/project/PyLabRobot/) — released 2026-03-23;
-  Python >=3.9; extras and artifacts.
-- [Stable installation guide](https://docs.pylabrobot.org/stable/user_guide/_getting-started/installation.html)
-  — stable versus source/dev install and optional transport groups.
-- [Stable API](https://docs.pylabrobot.org/stable/api/pylabrobot.html) and
-  [supported machines](https://docs.pylabrobot.org/stable/user_guide/machines.html)
-  — 0.2.1 API and model-specific support labels.
-- [`v0.2.1` source tag](https://github.com/PyLabRobot/pylabrobot/tree/v0.2.1)
-  and [changelog](https://github.com/PyLabRobot/pylabrobot/blob/main/CHANGELOG.md)
-  — tag dated 2026-03-23; `Unreleased` is development-only.

package/skills/pymatgen/SKILL.md

@@ -1,404 +0,0 @@
----
-name: pymatgen
-description: Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symmetry sensitivity, electronic-structure I/O, and explicitly bounded Materials Project queries.
-license: MIT
-compatibility: Python 3.11+ with uv. The verified snapshot uses pymatgen 2026.5.4, pymatgen-core 2026.7.16, and mp-api 0.46.4. Bundled help and planning CLIs use only the standard library; local scientific execution lazily requires the pinned pymatgen packages. Materials Project access additionally requires explicit network approval and the single named secret MP_API_KEY.
-allowed-tools: Read Write Bash Glob Python
-metadata:
-  version: "1.2"
-  skill-author: "K-Dense Inc."
-  last-reviewed: "2026-07-23"
----
-
-# pymatgen
-
-Use pymatgen for explicit, provenance-preserving work with compositions,
-molecules, periodic structures, computed entries, symmetry, phase diagrams,
-electronic structures, and electronic-structure-code files. Treat every parse,
-conversion, symmetry assignment, transformation, and database result as
-method- and parameter-dependent.
-
-The MIT frontmatter license covers this skill. `pymatgen` and
-`pymatgen-core` are MIT; `mp-api` declares BSD-3-Clause-LBNL. Materials Project
-data is generally CC BY 4.0, while contributed data remains owned by its
-contributors. Check the exact artifact and data terms before redistribution.
-
-## Verified snapshot (2026-07-23)
-
-- `pymatgen==2026.5.4` is the latest stable wrapper release (2026-05-04).
-  Package metadata requires Python 3.11+ and directly requires
-  `pymatgen-core>=2026.4.16`.
-- `pymatgen-core==2026.7.16` is the latest stable core release (2026-07-16).
-  It now contains core objects, symmetry/lattice operations, and the I/O layer,
-  all under the existing `pymatgen.*` namespace.
-- `mp-api==0.46.4` is the latest stable Materials Project client
-  (2026-06-15), requires Python 3.11+, and depends on
-  `pymatgen>2024.2.20`.
-- The current API site is built from 2026.7.16 core documentation. Pinning both
-  distributions prevents `pymatgen==2026.5.4` from silently resolving to a
-  different future core.
-- Pymatgen uses date-based versions. PyPI renders the date with dots; do not
-  infer semantic-version compatibility from the numbers.
-
-Create a project lock for reproducibility:
-
-```bash
-uv init --python 3.11
-uv add "pymatgen==2026.5.4" "pymatgen-core==2026.7.16" "mp-api==0.46.4"
-uv lock
-uv sync --frozen
-```
-
-For a disposable reviewed environment:
-
-```bash
-uv venv --python 3.11 .venv-pymatgen
-uv pip install --python .venv-pymatgen/bin/python \
-  "pymatgen==2026.5.4" "pymatgen-core==2026.7.16" "mp-api==0.46.4"
-```
-
-Direct pins do not freeze all transitive wheels. Preserve `uv.lock`, platform,
-Python version, package versions, and artifact hashes.
-
-## Required workflow
-
-1. State whether the object is a non-periodic `Molecule` or periodic
-   `Structure`; record lattice and periodic boundary conditions.
-2. State units. Pymatgen commonly uses Å, degrees, eV, eV/atom, amu, and
-   g/cm³, but each API's documented contract is authoritative.
-3. State coordinate mode. `Structure` coordinates are fractional unless
-   `coords_are_cartesian=True`; `Molecule` coordinates are Cartesian.
-4. Inspect every parser warning. For CIF, preserve occupancy, site-merging,
-   stoichiometry, and correction warnings; do not silently accept fixes.
-5. Report disorder/partial occupancies and oxidation-state decoration. Never
-   guess oxidation states implicitly.
-6. Run validation before symmetry, neighbor, transformation, conversion, or
-   thermodynamic analysis.
-7. Sweep symmetry tolerances and report `symprec` in Å and
-   `angle_tolerance` in degrees with every assignment.
-8. Treat transformations as new artifacts. Preserve the input, parameters,
-   software versions, warnings, and parent/child checksums.
-9. Before conversion, identify representation loss. Write only to a new path
-   and round-trip-check scientifically relevant properties.
-10. Build phase diagrams only from compatible total energies and correction
-    schemes. A computed hull is conditional on the supplied entry set.
-11. Keep all database access off by default. Disclose endpoint, filters,
-    fields, result limit, cache behavior, output, license, and citation before
-    an explicit execution step.
-12. Preserve an artifact manifest. Never use pickle or load an untrusted
-    general object graph; use schema-validated JSON and explicit constructors.
-
-## Core objects
-
-Use the public convenience imports:
-
-```python
-from pymatgen.core import Composition, Element, Lattice, Molecule, Structure
-
-composition = Composition("LiFePO4", strict=True)
-iron = Element("Fe")
-
-lattice = Lattice.cubic(5.64)  # Å
-structure = Structure(
-    lattice,
-    ["Na", "Cl"],
-    [[0, 0, 0], [0.5, 0.5, 0.5]],
-    coords_are_cartesian=False,
-    validate_proximity=True,
-)
-
-molecule = Molecule(
-    ["O", "H", "H"],
-    [[0.0, 0.0, 0.0], [0.758, 0.0, 0.504], [-0.758, 0.0, 0.504]],
-    charge=0,
-    spin_multiplicity=1,
-)
-```
-
-`Structure` and `Molecule` are mutable; use `IStructure`/`IMolecule` or an
-explicit copy when mutation would compromise provenance. See
-[core classes](references/core_classes.md).
-
-## Safe local structure intake
-
-Prefer the bundled validator, which captures CIF and Python warnings and
-reports units, occupancy, disorder, oxidation states, periodicity, coordinate
-mode, and minimum distances:
-
-```bash
-python scripts/composition_structure_validator.py composition "Fe2O3"
-python scripts/composition_structure_validator.py structure structure.cif
-python scripts/structure_analyzer.py structure.cif --symmetry
-```
-
-For direct CIF work, use the current parser method and inspect both warning
-channels:
-
-```python
-import warnings
-from pymatgen.io.cif import CifParser
-
-with warnings.catch_warnings(record=True) as caught:
-    warnings.simplefilter("always")
-    parser = CifParser("input.cif", check_cif=True)
-    structures = parser.parse_structures(
-        primitive=False,
-        check_occu=True,
-        on_error="raise",
-    )
-
-parser_messages = list(parser.warnings)
-python_messages = [str(item.message) for item in caught]
-```
-
-Do not parse untrusted files in a privileged process. A critical malicious-CIF
-code-execution flaw affected pymatgen through 2024.2.8 and was fixed in
-2024.2.20; the pinned release is newer, but parsers still process attacker
-controlled input. Use isolation and CPU/RAM/disk/time limits.
-
-## Symmetry
-
-Space-group assignment depends on tolerances and structure quality:
-
-```python
-from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-
-analyzer = SpacegroupAnalyzer(
-    structure,
-    symprec=0.01,          # Å
-    angle_tolerance=5.0,   # degrees
-)
-symbol = analyzer.get_space_group_symbol()
-number = analyzer.get_space_group_number()
-```
-
-The Materials Project pipeline commonly uses `symprec=0.1 Å`, while pymatgen's
-documented default is `0.01 Å`; these can produce different assignments.
-Generate a sensitivity report instead of changing tolerance until a preferred
-answer appears:
-
-```bash
-python scripts/symmetry_sensitivity_report.py structure.cif \
-  --symprec 0.001,0.01,0.1 --angle-tolerance 1,5
-```
-
-See [analysis modules](references/analysis_modules.md).
-
-## Conversion and parser/writer I/O
-
-Plan first; the planner does not open files or import pymatgen:
-
-```bash
-python scripts/io_conversion_plan.py \
-  --input input.cif --input-format cif \
-  --output POSCAR.new --output-format poscar \
-  --periodic --coordinate-mode direct
-```
-
-Then convert to a new path with explicit loss acknowledgement:
-
-```bash
-python scripts/structure_converter.py input.cif POSCAR.new \
-  --output-format poscar --coordinate-mode direct --allow-lossy \
-  --acknowledge-parser-warnings
-```
-
-CIF, POSCAR, XYZ, and JSON do not preserve the same semantics. Check lattice,
-periodicity, coordinate mode, species ordering, selective dynamics, site
-properties, oxidation states, labels, and disorder after every conversion.
-See [I/O formats](references/io_formats.md).
-
-## Transformations and provenance
-
-Transform a copy and preserve history:
-
-```python
-from pymatgen.alchemy.materials import TransformedStructure
-from pymatgen.transformations.standard_transformations import (
-    SubstitutionTransformation,
-    SupercellTransformation,
-)
-
-tracked = TransformedStructure(structure.copy(), [])
-tracked.append_transformation(SupercellTransformation([2, 2, 2]))
-tracked.append_transformation(SubstitutionTransformation({"Na": "K"}))
-derived = tracked.final_structure
-history = tracked.history
-```
-
-One-to-many ordering, doping, slab, and magnetic transformations can expand
-combinatorially or invoke optional executables. Bound candidates, sites,
-supercell size, runtime, and output count. See
-[transformations and workflows](references/transformations_workflows.md).
-
-## Local phase diagrams
-
-The bundled generator is offline and accepts only a strict JSON schema with
-total eV per entry and provenance:
-
-```json
-{
-  "schema_version": "1.0",
-  "energy_unit": "eV",
-  "energy_basis": "total_per_entry",
-  "provenance": {
-    "source": "reviewed local calculations",
-    "method": "one compatible energy/correction scheme"
-  },
-  "entries": [
-    {
-      "entry_id": "local-Li",
-      "composition": "Li",
-      "energy_eV": -1.0,
-      "provenance": {"source": "calculation manifest sha256:..."}
-    }
-  ]
-}
-```
-
-```bash
-python scripts/phase_diagram_generator.py entries.json --analyze Li2O
-```
-
-Elemental endpoints and all competing phases must be present. Do not mix raw
-energies from different functionals, pseudopotentials, magnetic states, or
-correction conventions. Computed on-hull status is not experimental stability.
-
-## Band structures, DOS, VASP, and Q-Chem
-
-Parse only the data needed:
-
-```python
-from pymatgen.io.vasp import Vasprun
-
-run = Vasprun(
-    "vasprun.xml",
-    parse_dos=True,
-    parse_eigen=True,
-    parse_projected_eigen=False,
-    parse_potcar_file=False,
-)
-band_structure = run.get_band_structure(line_mode=True)
-band_gap = band_structure.get_band_gap()
-complete_dos = run.complete_dos
-```
-
-Projected eigenvalues can require extreme memory. Verify convergence, k-path,
-spin/SOC settings, Fermi-level conventions, smearing, and projection basis
-before interpreting gaps or DOS. A parser success is not a converged
-calculation.
-
-Current Q-Chem interfaces are `pymatgen.io.qchem.inputs.QCInput` and
-`pymatgen.io.qchem.outputs.QCOutput`:
-
-```python
-from pymatgen.io.qchem.inputs import QCInput
-
-job = QCInput(
-    molecule,
-    rem={"job_type": "sp", "method": "wb97x-v", "basis": "def2-svpd"},
-)
-text = str(job)
-```
-
-Pymatgen writes inputs and parses outputs; it does not grant a VASP or Q-Chem
-license or establish method validity. POTCAR files are VASP-licensed and are
-not distributed by pymatgen. Never redistribute them or scan unrelated
-directories for them. Optional tools such as enumlib, Bader, packmol, ffmpeg,
-and Zeo++ are native/external executables: review provenance, licenses, argv,
-working directory, and resource limits before a separate explicit invocation.
-
-## Materials Project: plan before network
-
-Use only:
-
-```python
-from mp_api.client import MPRester
-```
-
-The client reads `MP_API_KEY` when constructed. Supply only that named
-environment variable through the user's shell or secret manager. Do not accept
-the key as a CLI argument, traverse `.env` files, dump environment variables,
-or print exception data without redaction.
-
-Dry-run planning is the default:
-
-```bash
-python scripts/mp_query.py \
-  --chemsys Li-Fe-O \
-  --energy-above-hull 0 0.05 \
-  --fields formula_pretty,energy_above_hull,band_gap,origins \
-  --limit 25
-```
-
-Only `--execute` permits one bounded summary query and requires a new output:
-
-```bash
-python scripts/mp_query.py \
-  --material-id mp-149 \
-  --fields formula_pretty,structure,origins,last_updated \
-  --limit 1 --output mp-149.json --execute
-```
-
-The CLI sets `num_chunks=1`, requires explicit fields and filters, caps results,
-does not implement an implicit result cache, and never overwrites output.
-`MPRester` initialization also performs compatibility/heartbeat metadata
-requests; the plan discloses these, disables the platform-detail user agent and
-local database-version notification log, and records the returned database
-version. The summary workflow does not request full-dataset cache downloads.
-`mp-api` 0.46.4 retries HTTP 429/502/504 according to its own configured policy
-and respects `Retry-After`; do not invent a numeric service quota or add an
-unbounded retry loop.
-
-Materials Project core values are computed, method-dependent data—not
-experimental truth. PBE commonly overestimates lattice parameters and
-systematically underestimates band gaps; aggregated values can change across
-database releases. Preserve retrieval time, query, fields, material/task
-origins, database release when available, client versions, CC BY attribution,
-and the canonical plus property-specific citations. See
-[Materials Project API](references/materials_project_api.md).
-
-## Bundled CLIs
-
-All CLIs have dependency-free `--help`, lazy scientific imports, bounded JSON,
-and no implicit network:
-
-- `scripts/composition_structure_validator.py` — strict composition/structure
-  checks; optional oxidation-state guessing is explicit and bounded.
-- `scripts/structure_analyzer.py` — bounded lattice, sites, symmetry, distance,
-  and optional CrystalNN report.
-- `scripts/symmetry_sensitivity_report.py` — tolerance-grid space groups.
-- `scripts/io_conversion_plan.py` — dependency-free representation-loss plan.
-- `scripts/structure_converter.py` — one-file conversion to a new path.
-- `scripts/phase_diagram_generator.py` — strict local computed-entry hull.
-- `scripts/mp_query.py` — dry-run MP query plan and opt-in bounded client.
-- `scripts/artifact_manifest.py` — checksums, versions, sources, and provenance.
-
-Use:
-
-```bash
-python scripts/artifact_manifest.py \
-  --artifact input.cif --artifact analysis.json \
-  --workflow "local symmetry sensitivity" --output manifest.json
-```
-
-## References
-
-- [Core classes](references/core_classes.md)
-- [I/O formats, VASP, and Q-Chem](references/io_formats.md)
-- [Analysis, symmetry, phase diagrams, bands, and DOS](references/analysis_modules.md)
-- [Transformations and workflows](references/transformations_workflows.md)
-- [Materials Project API, provenance, license, and limits](references/materials_project_api.md)
-
-## Sources (verified 2026-07-23)
-
-- [pymatgen 2026.5.4 on PyPI](https://pypi.org/project/pymatgen/)
-- [pymatgen-core 2026.7.16 on PyPI](https://pypi.org/project/pymatgen-core/)
-- [pymatgen API documentation](https://pymatgen.org/)
-- [pymatgen changelog](https://pymatgen.org/CHANGES.html)
-- [mp-api 0.46.4 on PyPI](https://pypi.org/project/mp-api/)
-- [Materials Project API getting started](https://docs.materialsproject.org/downloading-data/using-the-api/getting-started)
-- [Materials Project query guide](https://docs.materialsproject.org/downloading-data/using-the-api/querying-data)
-- [Materials Project FAQ and computed-data caveats](https://docs.materialsproject.org/frequently-asked-questions)
-- [Materials Project citation page](https://materialsproject.org/about/cite)
-- [Official tutorial series endorsed by pymatgen](https://github.com/computron/pymatgen_tutorials)