Changelog

Author:

Rohit Goswami

1.9.22

Surface-fit knobs (auto_thin) are TOML-only; see tools/eon/plot_config.org.

rgpycrumbs 1.10.10 (2026-07-18)

Fixed

• Align save_plot tests with always-tight bbox (chemparseplot 1.9.17).

• Pure CI: accept in-env or uv run dispatcher modes; skip plot/ase/eon/ scipy tests when optional stacks are absent; floor assert 1.9.15; cache-dir ensure_import test isolation.

• Surfaces collection: probe ovito lightly (not full ptmdisp) so missing libEGL does not abort the suite.

• prek/ruff 0.15.2: expand per-file ignores for deferred imports / PEP 723 dual-import scripts (TID252, PLC0415, E402).

• Lazy rgpycrumbs.geom exports so PEP 723 collection works without ase.

• Stop shipping tests/ in the wheel; hatch copies were shadowing source probes and broke surfaces collection (libEGL / missing tblite).

• CI: install scipy/ase via uv run --with after feature extras were dropped.

• ensure_import: failed AUTO_DEPS installs fall through to ImportError (no bare RuntimeError) so optional probes do not abort collection.

rgpycrumbs 1.10.9 (2026-07-18)

Fixed

• Floor chemparseplot to >=1.9.17 (lazy frame_series, SurfaceFitConfig).

• Pure-env collection: plot CLI tests marked fragments (need matplotlib), not pure; importorskip matplotlib so pure jobs no longer ERROR.

rgpycrumbs 1.10.8 (2026-07-17)

Fixed

• Floor chemparseplot to >=1.9.15 (xyzrender Python API strips).

• Map xyzrender in ensure_import; plot modules ensure_import chemparseplot before hard imports (lazy stack, no host pins for plot heavies).

rgpycrumbs 1.10.7 (2026-07-17)

Fixed

• Library plot_* / run_plot / plot() call enable_library_auto_deps() so RGPYCRUMBS_AUTO_DEPS defaults on (same as CLI). No host jax / adjustText pin for gallery plot_neb landscapes.

• Defer adjustText until label adjustment in plt_neb.

rgpycrumbs 1.10.6 (2026-07-17)

Fixed

• Library plot_* / run_plot / plot() call enable_library_auto_deps() so RGPYCRUMBS_AUTO_DEPS defaults on (same as CLI). Gallery imports no longer need a hard jax / adjustText pin for grad_imq landscapes.

• Defer adjustText until label adjustment in plt_neb (not at import).

• Drop mistaken [plot] optional extra if present; floors stay in _aux AUTO_DEPS and PEP 723 only.

rgpycrumbs 1.10.5 (2026-07-17)

Fixed

• Pure test collection no longer imports plt_neb (avoid adjustText hard fail when [plot] extra is installed).

• Refresh pixi.lock after transient [plot] extra experiment.

rgpycrumbs 1.10.4 (2026-07-17)

Added

• from rgpycrumbs.eon import plot: type-dispatch on pyeonclient objects (path_frames / movie_frames / climb_frames) and ConFrame sequences (kind= required). Shares run_plot + existing runners.

Changed

• DRY eOn plot wiring: run_plot / run_from_click / library_plot in plot_config; plot_{neb,min,saddle} are factory products; Click main is run_from_click(..., **params).

• plot_*_from_settings are plain callables again (Click decorators sit on main only), so library callers are not handed a Click Command.

• plot_min_from_settings / plot_saddle_from_settings accept trajectory=; plot_neb_from_settings accepts frames= / in-memory atoms (ConFrame object-plot path).

• Floor chemparseplot[neb,plot] to >=1.9.14 (frame_series) in _aux AUTO_DEPS and PEP 723 headers (lazy; no plot feature extra).

rgpycrumbs 1.10.3 (2026-07-17)

Added

• Library APIs plot_min / plot_saddle (and *_from_settings) alongside plot_neb — same pipelines as the Click CLIs, no argv.

Changed

• seed_dimers writes a minimal explicit INI (eon-schema write_ini + L0 validation), not a full L1 default dump.

• NEB plot failures raise informative RuntimeError messages instead of generic exit 1 strings.

• PEP 723 script headers require rgpycrumbs>=1.10.2.

rgpycrumbs 1.10.2 (2026-07-17)

Added

• Library API plot_neb / plot_neb_from_settings (from rgpycrumbs.eon import plot_neb) — same pipeline as rgpycrumbs eon plt-neb without Click argv. CLI now calls the shared settings-driven implementation.

rgpycrumbs 1.10.1 (2026-07-17)

Changed

• Floor chemparseplot[neb,plot] to >=1.9.13 (fixes SurfaceFitConfig NameError on 1.9.10–1.9.12).

rgpycrumbs 1.10.0 (2026-07-17)

Changed

• eOn job-config tooling uses eon-schema>=0.2 (write_eon_config, seed_dimers, MLflow hydrate) instead of eon-akmc ConfigClass. Install with pip install 'rgpycrumbs[eon]' (Python >= 3.11).

• CLI no longer treats site-packages wheels as monorepo editables when resolving uv --with-editable peers (avoids eon-akmc false positives).

rgpycrumbs 1.9.24 (2026-07-15)

Documentation

• Sphinx: enable sphinx-design and sphinxcontrib-mermaid alongside Shibuya; richer theme options (toctree collapse, maxdepth).

• Mermaid + cards/tabs on plot config, plt-min, surfaces, and quickstart pages.

rgpycrumbs 1.9.23 (2026-07-15)

Documentation

• Full orgmode pass: new tools/eon/plot_config.org; plt-min / plt-neb / minimization tutorial / FAQ / troubleshooting / glossary document TOML-only auto_thin (default off) and --config workflow.

• --config help text lists surface-fit keys and min/neb examples.

rgpycrumbs 1.9.22 (2026-07-15)

Changed

• Surface-fit knobs auto_thin / max_surface_points are TOML-only ([shared] or [min] / [neb] via --config), not CLI flags. Defaults remain off / 64. Example in eon/examples/plot_config.example.toml.

• plt-neb and plt-min forward those keys to chemparseplot>=1.9.10 SurfaceFitConfig / plot_landscape_surface.

rgpycrumbs 1.9.21 (2026-07-15)

Changed

• Floor chemparseplot[neb,plot] to >=1.9.9 in PEP 723 scripts and ensure_import pins.

• Plot TOML keys for surface fit (defaults off); see 1.9.22 for TOML-only policy.

rgpycrumbs 1.9.20 (2026-07-10)

Fixed

• Profile panels with crit_points use a content-sized structure strip under the axes (re-rendered after layout) instead of crushed insets on the energy curve. (plt-neb-profile-strip)

rgpycrumbs 1.9.19 (2026-07-09)

Added

• Docs: consumer path documents chemparseplot.api.extract_orca_geomscan_energy as the stable parse→typed library path (with rgpycrumbs.api for config/pins).

rgpycrumbs 1.9.18 (2026-07-09)

Added

• Stable public suite surface rgpycrumbs.api (config, locks, ensure_import) for consumers (chemparseplot, pychum, wailord). Documented in docs/orgmode/explanation/public_api.org.

rgpycrumbs 1.9.17 (2026-07-09)

Added

• rgpycrumbs config show prints merged suite config (sources, lock path, force_uv, package pins). Suite architecture notes under docs/orgmode/explanation/suite_architecture.org.

rgpycrumbs 1.9.16 (2026-07-09)

Changed

• Config identity is ecosystem-wide ``rgpkgs``, not package-private: ~/.config/rgpkgs/config.toml and project rgpkgs.toml (shared with chemparseplot and other suite tools). Legacy rgpycrumbs.toml / ~/.config/rgpycrumbs/ still load as fallbacks. Env aliases: RGPKGS_LOCK, RGPKGS_CONFIG, RGPKGS_FORCE_UV, RGPKGS_AUTO_DEPS (RGPYCRUMBS_* kept).

rgpycrumbs 1.9.15 (2026-07-09)

Added

• Layered TOML config for pins and dispatch defaults: ~/.config/rgpycrumbs/config.toml (global), project rgpycrumbs.toml / .rgpycrumbs.toml (walk-up from CWD), optional RGPYCRUMBS_CONFIG. Sections: [dispatch] (auto_deps, force_uv), [pins] (lock), [pins.packages] (explicit overrides). Precedence: CLI > env > project > global. Example: docs/examples/rgpycrumbs.config.toml.

rgpycrumbs 1.9.14 (2026-07-09)

Added

• Optional lock consume is not SBOM-only: --lock / RGPYCRUMBS_LOCK accepts uv.lock, PEP 751 pylock.toml / pylock.*.toml, and CycloneDX JSON. Pins feed uv run --constraints / UV_CONSTRAINT and ensure_import (RGPYCRUMBS_LOCK_PINS). --sbom / RGPYCRUMBS_SBOM remain aliases. Auto-detect by path/content; non-PyPI CDX rows still skipped.

rgpycrumbs 1.9.13 (2026-07-08)

Added

• Optional CycloneDX SBOM consume on the CLI: --sbom PATH or RGPYCRUMBS_SBOM. PyPI components (pkg:pypi/...) become install pins for uv run --constraints and ensure_import / AUTO_DEPS. Non-PyPI entries (e.g. eb-stack pkg:generic/...) are skipped. Missing path fails clearly; unset SBOM leaves default floating resolution.

• PEP 723 headers declare rgpycrumbs>=1.9.13 so standalone uv run of a plot script can resolve the package (dispatcher remains preferred entry).

rgpycrumbs 1.9.12 (2026-07-08)

Removed

• Runtime feature extras [analysis], [surfaces], [interpolation], and [all]. They diluted the real design: CLI deps via PEP 723 + uv, library deps via ensure_import + RGPYCRUMBS_AUTO_DEPS=1. Dev extras (test / lint / release) remain.

• _DEPENDENCY_MAP no longer stores fake extra names; values are pip specs only, and error messages say pip install "<spec>" or enable AUTO_DEPS.

rgpycrumbs 1.9.11 (2026-07-08)

Fixed

• Restore auto-deps design: [analysis] does not hard-depend on jax / adjustText. Those stay optional and resolve via uv PEP 723 (isolated dispatch) or ensure_import (in-env).

• CLI dispatch now defaults RGPYCRUMBS_AUTO_DEPS=1 so in-env plt-* can cache-install heavies without host env pins. Set =0 to disable.

• plt-neb loads adjustText via ensure_import (not a bare import).

rgpycrumbs 1.9.10 (2026-07-08)

Changed

• PEP 723 pins for plot scripts: readcon>=0.13.1, chemparseplot[neb,plot].

• (Yanked design) briefly hard-pinned jax/adjustText on [analysis]; corrected in 1.9.11 — use auto-deps / uv instead.

rgpycrumbs 1.9.9 (2026-07-07)

Fixed

• plt-min landscapes: title from job label (e.g. Reactant minimization), initial / minimized endpoint and strip labels, relative-energy colorbar, and readable axis labels (via chemparseplot 1.9.7 single-ended pipeline).

rgpycrumbs 1.9.8 (2026-07-07)

Fixed

• Landscape structure strip uses two rows (max_cols=6) with a taller strip panel and higher zoom so molecules are larger and readable.

• Keep square 1:1 (s, d) panel: Δs = Δd (e.g. both 1.34 Å); d ticks show ±half while s shows 0→span — same physical length on both axes.

rgpycrumbs 1.9.7 (2026-07-07)

Fixed

• plt-neb projected landscapes use a square equal-aspect panel with Δd = Δs so 1 Å of progress matches 1 Å of orthogonal deviation (true 1:1 RMSD metric). Figure is still sized to map+strip (no left void); structure strip is re-rendered after layout.

rgpycrumbs 1.9.6 (2026-07-07)

Fixed

• plt-neb projected landscape layout: size the figure to map+strip (no left void in a leftover 12×8 cell), re-render the structure strip after layout so molecules use the final large axes, keep equal aspect for (s, d).

rgpycrumbs 1.9.5 (2026-07-07)

Fixed

• plt-neb projected landscapes always use equal aspect (s and d are both Å from the same RMSD metric). Figure size follows the data aspect so the map is not stretched; colorbar/strip are placed against that box. Never use aspect='auto' for (s, d).

rgpycrumbs 1.9.4 (2026-07-07)

Fixed

• First pass at equal-aspect (s, d) landscapes (superseded by 1.9.5 layout).

rgpycrumbs 1.9.3 (2026-07-07)

Fixed

• plt-neb 1D profiles mark the saddle with a gold star, SP label box, and a vertical guide line (was a small white star easy to miss).

• plt-neb 2D landscapes use path-driven d limits and tighter save padding so GP-masked margins no longer dominate the frame.

rgpycrumbs 1.9.0 (2026-07-07)

Added

• Prefer the active interpreter for PEP 723 script dispatch when the readcon/plot stack is already importable (avoids broken isolated uv run Python ABIs when plotting eOn 2.16 con_spec_version=2 outputs). Override with RGPYCRUMBS_FORCE_UV=1; force in-env with RGPYCRUMBS_DEV=1 or --dev.

• Declarative TOML plot config for NEB/min/saddle CLIs; CON trajectory splitter via readcon.

Changed

• Analysis extras require readcon>=0.13.1 and chemparseplot[neb,plot]>=1.8.0.

rgpycrumbs 1.8.0 (2026-06-27)

Added

• plt-neb-stitch CLI for full-path 1D strip and 2D landscape plots stitched from NEB segments. (#1800)

• gen-dimer seeds dimer saddle searches from all NEB peaks; plt-kmc plots N2-ejection KMC timelines. (#1801)

• Profile strip rendering for NEB plots via chemparseplot/xyzrender overlays. (#1802)

• Energy unit selection for NEB (plt-neb) and single-ended (plt-min / plt-saddle) landscape tools. (#1803)

• plt-min --energy-cap / --energy-cap-window options to limit landscape energy scale. (#1804)

Developer

• Cocogitto (cog) release tooling and contributor release docs; CI creates GitHub Release for Zenodo on publish. (#1813)

• Tests fail loudly on broken optional imports; pytest-pep723 required in test env; tighter CLI plotting gates. (#1814)

Changed

• eOn plot scripts consume typed chemparseplot NEB/single-ended helpers and shared renderer option bundles. (#1812)

• CLI warns when PEP 723 scripts are imported directly instead of through the dispatcher. (#1815)

Fixed

• NEB xyzrender strip layout budgets, clearance, and sizing for readable profile overlays. (#1805)

• Single-ended landscape overlays stay on the shared projection basis; plt-min default prefix aligned. (#1806)

• Dispatcher preserves parent site-packages paths; PEP 723 plot scripts execute when invoked via the CLI. (#1807)

• Lazy imports for xts / cuh2 so optional plotting stacks do not break base imports. (#1808)

• ira_kmax default 14, Init/Min label boxes, larger SP star; NEB viewport includes trajectory d-range. (#1809)

• Require chemparseplot eOn APIs for NEB overlays; simplify OCI overlays and local dispatch. (#1810)

• PLUMED direct reconstruction script metadata aligned with dispatcher expectations. (#1811)

rgpycrumbs 1.7.0 (2026-04-07)

Added

• Integrated pytest-pep723 plugin for static validation of PEP 723 inline script dependencies in CI.

Developer

• Added OIDC trusted publishing workflow for PyPI releases, gated on tests, lints, and docs.

• Migrated documentation deployment from GitHub Pages to Cloudflare Pages.

Fixed

• Added missing numpy and rich to PEP 723 inline script dependencies in plot_gp.py.

• Added readcon to PEP 723 inline script dependencies in plt_neb.py and plt_saddle.py, fixing dispatch failures.

rgpycrumbs 1.5.0 (2026-03-23)

Added

• New plt-saddle CLI tool for dimer/saddle search trajectory visualization with profile, landscape, convergence, and mode-evolution plot types. Supports --ref-product for (initial, product) reference pairs.

• New plt-min CLI tool for minimization trajectory visualization with profile, landscape, and convergence plot types.

• Extended plt-neb with OCI-NEB/RONEB options: --mmf-peaks for MMF peak overlay (auto-detected), --peak-dir for explicit peak file directory, --show-evolution for band evolution across iterations.

• Four rendering backends for structure galleries: xyzrender (default, ball-and-stick), ase (space-filling), solvis (PyVista, transparent background), ovito (OVITO off-screen). All via --strip-renderer.

• --rotation flag (renamed from --ase-rotation) applies viewing angle uniformly to all rendering backends via pre-rotation of atom coordinates.

• --perspective-tilt flag for Rodrigues off-axis rotation to reveal atoms hidden by orthographic projection overlap. 5-10 degrees typical.

• --strip-spacing and --strip-dividers for wider gaps and vertical separator lines between structure images.

• NEB visualization tutorial with real Diels-Alder [4+2] cycloaddition data, covering all plot types and rendering backends.

• Multi-environment coverage CI workflow (ci_coverage.yml) combining test, surfaces, fragments, and eonmlflow pixi environments with --fail-under=89.

Changed

• Default rendering backend changed from ase to xyzrender for ball-and-stick visualization with bonds visible.

Fixed

• Fixed infinite recursion in __init__.py lazy imports (replaced from rgpycrumbs import X with importlib.import_module).

• Fixed chemgp/__init__.py re-export names after migration (plot_convergence -> plot_convergence_curve, etc.).

• Fixed plot_gp.py batch parallel I/O bug (CliRunner in threads).

• Fixed parsers/bless.py datetime.UTC for Python 3.10 compat.

• Fixed plt_neb.py dangling inline projection variables after refactor.

• Fixed plt_neb.py compute_profile_rmsd keyword-only args.

rgpycrumbs 1.4.0 (2026-03-15)

Removed

• Moved ChemGP plotting (chemgp/plotting.py, chemgp/plot_gp.py, chemgp/hdf5_io.py), NEB CLI (eon/plt_neb.py), ChemGP JSONL parsers (parsers/chemgp.py), and PLUMED parsing (plumed/fes_calculation.py) to chemparseplot. Use chemparseplot.parse and chemparseplot.scripts for these modules going forward. (scope_migration)

Added

• Updated plt-neb documentation with comprehensive usage examples, options table, and troubleshooting guide for landscape plotting. (docs_plt_neb)

• Tutorial documentation following Diataxis structure: quickstart, first-project tutorial, how-to guides (install, troubleshooting, FAQ), reference (glossary), and developer guides (testing, lazy imports, best practices). (docs_tutorials)

• Added 2D landscape plotting capabilities to plt-neb with gradient-enhanced surface methods (grad_imq, grad_matern), structure strip rendering, and colorbar legend support. (feat_plt_neb_landscape)

Developer

• Added batch command with --parallel/-j flag for concurrent plot generation using ThreadPoolExecutor. Provides 3-5x speedup for batch operations with 4-8 workers. Pattern adopted from nebmmf_repro project. (perf_batch)

• Added safe_plot() decorator and validate_hdf5_structure() function for robust error handling. Better error messages for missing files and invalid structures. (perf_errorhandling)

• Added complete type hints to chemgp modules (hdf5_io.py, plotting.py) reaching 90%+ coverage. Improves IDE support and code documentation. (perf_typehints)

Changed

• Changed default surface method in plt-neb from rbf to grad_imq for higher-quality gradient-enhanced interpolation. (feat_plt_neb_defaults)

rgpycrumbs v1.3.0 (2026-03-09)

Added

• [all] optional dependency extra combining plot, eon, and other extras. (all-extra)

• ASV benchmark infrastructure with asv-perch CI integration. (asv-benchmarks)

• ChemGP JSONL parsers for optimization logs, convergence data, and GP diagnostics (rgpycrumbs.parsers.chemgp). (chemgp-parsers)

• Dynamic dependency resolution via ensure_import for optional packages. (ensure-import)

• plt-gp PEP 723 CLI script for ChemGP figure generation with batch mode and landscape subcommand. (plt-gp-cli)

Developer

• ASV benchmark infrastructure, prek linting, taplo formatting, codespell configuration. (dev-infra)

Changed

• Documentation overhaul: Shibuya theme, quickstart page, Google-style docstrings, CI/PyPI badges, and README generation from Org source. (docs-overhaul)

Fixed

• Skip missing H5 inputs in batch mode instead of failing. (batch-skip)

• Fix plt-neb keyword arguments for compute_profile_rmsd call. (plt-neb-kwargs)

• CI formatting and py3.10 compatibility fixes. (ci-py310)

rgpycrumbs v1.2.0 (2026-02-24)

Added

• Added –strip-renderer CLI option for selecting structure rendering backend. (#1)

• Export Nystrom threshold, default inducing count, and nystrom_paths_needed from rgpycrumbs.surfaces so callers can trim data before expensive RMSD/IRA aggregation. (#2)

• Added –source traj support to plt_neb for loading NEB paths from ASE-readable trajectory files (extxyz, .traj, etc.). (#3)

• Added –source hdf5 support to plt_neb for loading NEB paths from ChemGP HDF5 output files. (#4)

• Added –n-inducing flag to eON surface-fitting CLI for controlling the Nystrom approximation inducing-point count. (#5)

Developer

• Added versionadded directives to all public API docstrings. (#7)

Changed

• Per-image RMSD alignment in rgpycrumbs.geom now runs in parallel over threads for improved performance on large NEB paths. (#6)

rgpycrumbs v1.1.0 (2026-02-21)

Added

• Comprehensive pytest suite for surface models, covering fit, prediction, variance, and optimization.

Developer

• Added detailed API docstrings and Org-mode documentation for surfaces, including uncertainty and variance windowing.

Changed

• Refactored rgpycrumbs.surfaces into a structured package with BaseSurface and BaseGradientSurface abstractions.

rgpycrumbs v1.0.1 (2026-02-17)

Added

• CI workflow to auto-generate README.md from readme_src.org on push to main.

• Downstream users page (used_by.org) listing public projects that depend on rgpycrumbs.

Changed

• Updated readme_src.org with current uv + hatch-vcs + twine development and release workflow.

rgpycrumbs v1.0.0 (2026-02-17)

Removed

• ira_mod from pip-installable optional dependencies (conda-only; managed exclusively via pixi). (#37)

• pdm and pip from pixi base dependencies. (#37)

Added

• Library modules extracted from chemparseplot: basetypes (NEB, dimer, saddle point data types), surfaces (JAX-based GP surface fitting with gradient-enhanced kernels), interpolation (spline helpers), and parsers (common parsing patterns). (#36)

• Public API with lazy loading via __getattr__ for surfaces, basetypes, and interpolation modules. (#36)

• Click-based CLI dispatcher with rgpycrumbs entry point. (#36)

• Optional dependency groups for surfaces (JAX), analysis (ASE, scipy), and interpolation (scipy). (#36)

• test and lint optional dependency groups in pyproject.toml. (#37)

• rich as a core dependency (used across CLI modules). (#37)

Changed

• uv-first development workflow; pixi now only needed for conda-gated features (IRA, fragments). (#37)

• CI split into uv job (pure, interpolation, align tests on Python 3.10-3.12) and pixi job (fragments, surfaces tests requiring conda packages). (#37)

Fixed

• Interpolation tests correctly marked as interpolation (needs scipy), not pure. (#37)

rgpycrumbs v0.1.2 (2026-01-28)

Fixed

• Additional imports

rgpycrumbs v0.1.1 (2026-01-28)

Fixed

• Add an __init__ for modules

• Rework documentation

Changelog

v0.1.0 - 2026-01-28

• feat(eon): add dictionary support (#28ac681.eon)

• feat(jup): add subprocess run helpers for atomistic-cookbook (#a60da70.jup)

• Added alignment using IRA for splitting con files.

• Added robust alignment API using Isomorphic Robust Alignment (IRA) with ASE fallback.

• Fallback to using ase minimize_rotations_and_translations if IRA fails.

• Generate hydrated logging configurations for MLFlow.

• feat(pltneb): Add a strip to handle sub-figures uniformly

• feat(pltneb): Add multiple structures and labels

• feat(pltneb): Automatically determine the smoothing factor from the global median RMSD step distance

• Refactored alignment internals into structured dataclasses for improved API clarity.

v0.0.6 - 2025-12-23

• Added a new fragment detection tool () supporting both Geometric (covalent radii) and Bond Order (GFN2-xTB) methodologies.

• feat(cli): drop dependency on click

• feat(pltneb): Add ‘ira-kmax’ to tweak settings for IRA

• Refactored internal import helper to use , fixing support for nested module imports (e.g., ).

v0.0.5 - 2025-12-06

• feat(pltneb): Add ‘index’ rc-mode to plot against image number

• Use white as a default background for plots

• feat(cache1D): Add disk caching for 1D profiles with rmsd using Parquet

• feat(cache2D): Add disk caching for 2D landscape plots using Parquet

• fix(plt_neb): Use standard spline for RMSD profiles to fix artifacts

v0.0.4 - 2025-12-01

• Added _import_from_parent_env helper to enable fallback imports from the parent python environment.

• Updated con_splitter to handle multi-path trajectories via --images-per-path and --path-index arguments.

• Migrated linting configuration to tool.ruff.lint and applied global formatting fixes.

• Refactored CLI architecture to support dynamic command dispatch and environment propagation for isolated scripts.

• Updated plt_neb to use the new import helper for optional ira_mod loading.

• Added conditional skipping for ptmdisp tests when ase is not present in the environment.

• Fixed variable name typo in plt_neb when falling back to globbed overlay data.

v0.0.3 - 2025-10-27

• Add a FES direct reconstruction helper

• Add a version picker for the prefix package deleter

• Add an eigenvalue plotter

• Add more options for NEB visualization

• Add the PES estimated NEB plot

• Add the ruhi colorscheme

• Use hermite interpolation for NEB plots

v0.0.2 - 2025-09-06

• Helper to delete prefix packages

• Helper to generate initial paths for EON’s NEB

• EON helpers using OVITO

• Enable image insets for the NEB