0.7.1

[0.7.1] - 2026-07-31

CLI

• Added cax auto --export-commands PATH to write the final Mash-selected, resource-limited command list without executing or cleaning the plan output.
• Added cax --version to report the installed CAX package version.

0.7.0

[0.7.0] - 2026-07-28

Resource limits

• CAX now detects one effective CPU/memory budget from the local process, cgroup/container limits, and an active Slurm allocation, then applies the smallest known limits consistently.
• cactus-prepare receives automatic --defaultCores/--defaultMemory values, while generated, loaded, edited, exported, and executed commands are capped with --maxCores, --maxMemory, and RaMAx --threads.
• Run Settings displays the detected resource source and allows lower CPU/memory limits while rejecting values above the runtime budget. The CLI accepts --memory-limit alongside --threads.

0.6.1

[0.6.1] - 2026-01-26

Parser

• Added support for the latest cactus-prepare output format, including cactus-hal2fasta and cactus-halAppendSubtrees, while preserving legacy parsing.
• Improved halmerge root inference from log filenames to keep RaMAx hal-merge skipping behavior consistent.

Tests

• Added coverage for parsing the 9.1.2-style cactus-prepare output sample.

0.6.0

[0.6.0] - 2026-01-26

CLI

• Added cax auto to run Mash-based auto-selection and execute without launching the UI; supports --seqfile for a short-form input and enforces Mash presence in auto mode.
• Auto mode now refreshes the cached preprocess seq file before Mash so cached local inputs are honored when URLs were downloaded.

0.5.0

[0.5.0] - 2026-01-24

Mash auto-selection

• Added tree-aware pairwise Mash distance evaluation with early-stop pruning ("prove > threshold") and persistent caching under <out_dir>/logs/ to avoid recomputation across repeated runs.
• PlanUI: threshold modal (T) recomputes and reselects rounds; tree labels show Mash:…@source when the displayed distance originates from a descendant witness/max to avoid misinterpretation.
• CLI: optional prompt before computing Mash distances (includes leaf / max-pairs estimate) and stronger warning when mash is missing; supports caching remote sequences up front so Mash can run locally.

0.4.0

[0.4.0] - 2025-12-14

UI

• Run Settings now has a dual-view toggle (F6): switch between the classic plan overview and a new flow view that renders the execution dependency tree as ASCII, so you can see round ordering and ancestry while editing thread/verbose options.
• When an existing logs/run_state.json is detected and you keep the output directories, PlanUI opens directly into a dedicated resume view (inside Run Settings) that shows completed/pending steps and the next command to run.
• Added an explicit Subtree Mode toggle (CAX-only sentinel, not passed to ramax): enabling it on a node forces RaMAx for that subtree and automatically disables RaMAx on descendants; switching back to node mode removes the sentinel. Child-level edits now auto-cancel an ancestor’s subtree mode to avoid conflicts (with safe handling when no Textual app is active).

Fixes

• Safeguard subtree-mode reversion when no Textual app context exists (tests/CLI), preventing NoActiveAppError during node-level toggles.

0.3.0

[0.3.0] - 2025-11-25

UI

• Rebuilt the alignment browser as an ASCII phylogenetic canvas with proportional branch spacing, inline RaMAx/cactus colouring, and in-place repainting without the old Textual tree widget.
• Added scope switching between subtree and single-node toggles (key b), plus bulk-revert safeguards with modal hints so mixed cactus/RaMAx edits stay consistent.
• Added search (/, n / Shift+N), dotted branch-length annotations, ASCII glyph fallback, and a detail buffer/info modal so large trees stay navigable and summaries remain visible even on narrow terminals.
• Introduced a bottom Dashboard HUD that mirrors the current node, subtree/total RaMAx coverage, and live CPU/GPU/memory/disk metrics; keeps summaries readable on narrow terminals.
• Display a short welcome/quick-start overlay after mount to highlight navigation, toggles, and run flow for new users.

Planner

• Skip RaMAx rounds whose ancestors already run with RaMAx, while still honoring cactus overrides inside those subtrees so users can mix modes intentionally.
• Suppress halAppendSubtree merges when the parent round output was produced by RaMAx, preventing redundant HAL writes.

Tree parsing

• Alignment nodes now retain branch lengths, support values, and parent links, enabling proportional layouts and state colouring while tolerating unlabeled or missing edges.
• Newick parsing accepts numeric internal labels as support scores and ignores malformed branch lengths instead of failing the entire parse.

CLI & plumbing

• Moved the plan overview/environment rendering helpers into cax.ui (retiring cax.render) and pointed CLI previews at the shared UI renderer for consistent output and script exports.

Tests

• Added coverage for RaMAx ancestor/descendant overrides in the planner and for bulk RaMAx subtree reversion when toggling individual nodes in the UI.

0.2.2

[0.2.2] - 2025-11-08

UI

• The cactus-prepare wizard now lives inside a full-height scroll container with a dedicated footer so form fields remain focusable while actions stay pinned, even in narrow or short terminals.
• Instructions switch between compact and detailed copy, and resize-driven layout classes collapse spacing and stack buttons when needed to keep the wizard readable at any screen size.
• Pressing R now switches to a dedicated Run Settings screen that gathers verbose/log streaming and the shared cactus/RaMAx thread count in one place before execution, removing the in-plan toggles.
• The Run Settings screen shows a live plan summary next to the form, updates instantly as you toggle verbose or edit the thread count, and exposes keyboard hints (Tab, Ctrl+Enter, V) so the entire flow can be driven without the mouse. All instructional text has been converted to English for consistency.

CLI & Planner

• cax ui still accepts --threads N, but the value now seeds the Run Settings dialog (or the post-UI prompt when --run-after is used) instead of bloating the plan definition; the planner applies --maxCores/--threads overrides only at execution time.
• Plan serialization drops the verbose/thread_count fields, keeping plan files focused on cactus/RaMAx steps while run-only options live alongside the executor.

Runner

• Enhanced the quiet-mode progress bar with wait time, CPU utilization, memory usage, and peak memory columns, while printing the full command in a separate line so the bar stays readable on narrow terminals.
• Added a psutil-backed telemetry thread that periodically aggregates CPU and memory stats from the running command and its descendants, synchronizing the metrics on dry-run skips, failures, and successful completions.

0.2.1

[0.2.1] - 2025-11-07

Highlights

• The Textual cactus-prepare prompt now features an argument wizard (F2 / :wizard), template chooser (F3 / :template), and history window (F4 / !N), guiding newcomers through common flags, bundling Evolver examples, and reusing the 20 most recent commands to shorten onboarding.
• The CLI persists each command, infers the real output directory from --outDir or --outSeqFile, and writes cax_prepare_debug.txt into that directory so logs travel alongside their artifacts.

CLI & Prompt

• Added inline shortcut hints plus !N history recall and the :wizard/:template quick commands, reducing re-typing and accidental edits.
• The wizard separates the species tree, outputs, HAL target, job store, and extra arguments; the extra field honors shlex parsing, and defaults are inferred from the current command or a chosen template.
• Before running cactus-prepare, the CLI records the exact command in ~/.cax/history.json and emits debug output next to the inferred outputs (defaulting to steps-output/), keeping history, logs, and artifacts aligned.

Templates & Examples

• Introduced a template manager that scans the packaged Evolver Newick samples together with user entries in ~/.cax/templates.json, deduplicates them, and points defaults to ~/.cax/outputs/<stem> so repeated runs do not collide.
• Wheel builds now ship the Evolver example files, so templates work immediately after installation without manual copies.

History

• Added a lightweight history store (max 20 entries) in ~/.cax/history.json, including the ability to delete entries from the history window and reuse them across projects.

UI

• Plan Overview supports a compact mode below 110 columns, hiding the environment card and tightening columns to avoid overflow, while environment summaries and RaMAx option dialogs now use English copy.
• The command editor switched to a multi-line TextArea with Ctrl+S save support, making long commands easier to edit and presenting modal text in English for clarity.
• The environment summary card condenses multi-line paths and versions into single-line snippets, uses English labels, and stays readable at any terminal width.

0.2.0

[0.2.0] - 2025-10-28

Highlights

• Added interactive confirmation before running cactus-prepare, allowing users to remove stale --outDir/--jobStore directories in advance.
• Enhanced execution feedback with Rich-based progress indicators, end-of-run summaries, and optional verbose streaming of all command output.
• Surfaced plan-level verbose state in the UI (toggle with V) and overview rendering, keeping the terminal quiet by default while filtering RaMAx graph verification noise.

UI

• Added Environment Summary card to the top of the details pane, showing RaMAx/cactus paths and versions, GPU, CPU, memory, and disk. The card is now rendered as a Rich Panel and adapts to terminal width to avoid overflow and misalignment.
• Replaced fixed-width string rendering with Rich renderables (Panel, Table) for both the Environment Summary and Plan Overview, ensuring responsive layout from narrow to full-screen terminals.
• Introduced RaMAx options editor: global plan.global_ramax_opts and per-round round.ramax_opts editable via a new modal with add/remove controls. Options are reflected in command previews automatically.
• Removed unsupported gap CSS usage and adjusted spacing with margins to fix Textual CSS errors.

Detection & Tooling

• Environment detection now reports cactus (not cactus-prepare) path and version. Cactus version is obtained via pip show cactus | grep -i ^Version with a fallback to python -m pip show cactus parsing; noisy NVML messages are filtered out.
• Minor CLI polish: removed echoing of the full cactus-prepare command to reduce console noise.

Documentation & Tooling

• Updated README with the new verbose shortcut and pre-run cleanup behaviour.
• Expanded PlanRunner logging to emphasise failures and log locations.