v0.7.0

Summary

Lean installable package for structural biologists: pip install cryoem-halfmap-qc → halfmap-qc CLI.

• Reliability path: windowed smoothness on z-scored half-map average ρ → reliability_score (ranked) and build_zone MRCs
• Package boundary: thesis-only code (ROC/AUC, metric comparison, cohort figures, TV curvature) moved to thesis/ — not shipped on PyPI
• Naming: production metric is reliability_smoothness / windowed_smoothness (legacy reliability_H_repro CSV columns still read)
• Style: style/palette.py + style/figures.py replace nature.py / thesis_palette.py

Install

pip install cryoem-halfmap-qc
halfmap-qc   # interactive: two half-maps → reliability + build-zone MRCs

Breaking changes

• Removed public exports for T/L/H mechanics, placement_utility, tv_curvature, and related thesis modules from cryoem_mrc
• Q-score validation in the package no longer depends on metric_comparison/residue_metrics.csv (uses halfmap reliability bundle instead)

v0.6.0

halfmap-qc (interactive)

• Prompt for auto or manual contour after loading half-maps
• Estimate masked global FSC resolution and warn when outside the model-building band (>4 Å)
• Reuse loaded maps so preflight and pipeline share one read

Thesis validation tooling

• Builder-omission ROC (cryoem_mrc/builder_omission.py, scripts/run_placement_builder_omission_roc.py): classify built Cα vs sequence-gap proxy sites
• Placement Q ROC (scripts/run_placement_q_roc.py)
• Expanded Q-score validation and cross-metric summary scripts
• Placement utility helpers for Q ROC predictors and cohort paths

Install

pip install cryoem-halfmap-qc==0.6.0

Publishing to PyPI is triggered automatically by this GitHub release.

v0.5.3

Summary

• halfmap-qc reliability now writes only two MRC overlays: {label}_reliability.mrc and {label}_build_zones.mrc
• Removed PNG/PDF figures, reliability.npz, run_metadata.json, and the --halfmap-npz requirement from the reliability step
• halfmap-qc analyze no longer writes summary.txt or the default histogram PNG (still produces halfmap_metrics.npz and correlations.csv)
• B-factor validation and metric comparison moved to repo-local thesis/ (not installed from PyPI)

Install

pip install -U cryoem-halfmap-qc

Minimal pipeline

halfmap-qc features map.mrc --out features.npz --float32
halfmap-qc reliability \
  --reference ref.map --half1 half1.map --half2 half2.map \
  --features features.npz --contour CONTOUR --out-dir reliability_out

Analyze is optional if you only need the reliability and build-zone MRCs.

v0.5.1

Fixes

• halfmap-qc features map.mrc — main() now accepts forwarded argv (fixes TypeError: main() takes 0 positional arguments but 1 was given).
• ARC sbatch template — scripts/halfmap_qc_cluster.sbatch.example runs features → analyze → reliability with per-step failure guards.

Docs

• README includes TUI screenshot and sbatch instructions.

pip install -U cryoem-halfmap-qc

v0.5.0

Summary

• Path-based CLI — features, analyze, and reliability require explicit map paths (no thesis defaults or cohort subcommands).
• Rich interactive TUI — colored menu, ASCII banner, guided full pipeline.
• halfmap_metrics — replaces the old half_map_repro module naming; MRC exports use halfmap_ prefix.
• Slim README — PyPI install only.
• CI fix — CLI help test updated for current install text.

Install

pip install cryoem-halfmap-qc
halfmap-qc

Breaking changes

• Removed halfmap-qc cohort / cohort-ids from the installed CLI (thesis batch: python scripts/run_cohort_pipeline.py).
• reliability and analyze require --contour and all map paths explicitly.

v0.3.3

Install

pip install cryoem-halfmap-qc

Changes

• README rewritten for public/PyPI use (no thesis-only sections)
• PyPI/GitHub link metadata: Homepage, Documentation, Issues, Changelog URLs
• Citation metadata updated to v0.3.3

After install, the package should appear in the GitHub repo sidebar under Packages once PyPI indexes the new release (may take a few minutes).

v0.3.2 — halfmap-qc CLI (PyPI)

Install

pip install cryoem-halfmap-qc
halfmap-qc --version

Same as v0.3.1 plus a PyPI metadata fix (removed git URL from optional dependencies).

Highlights

• halfmap-qc CLI — features, analyze, reliability, cohort, cohort-ids, help, interactive TUI
• Cohort drivers packaged for pip install without repo scripts/ paths
• ResMap locres comparison and related cohort exports
• Cluster .sbatch gitignored — use README sbatch --wrap on ARC

See v0.3.1 release notes for the full feature list.

v0.3.1 — halfmap-qc CLI

Install

pip install cryoem-halfmap-qc
# or from git:
pip install "git+https://github.com/sarthaktexas/cryoem-halfmap-qc.git@v0.3.1"

Highlights

• halfmap-qc CLI — features, analyze, reliability, cohort, cohort-ids, help
• Interactive TUI — run halfmap-qc in a terminal for a guided menu
• Packaged drivers — cohort and reliability pipelines work after pip install (no scripts/ path required)
• PyPI publish workflow — this release triggers automated upload if trusted publishing is configured
• ResMap support — locres method comparison and alignment scripts
• Cluster scripts — *.sbatch gitignored; use README sbatch --wrap one-liner on ARC

Quick start

halfmap-qc cohort --pending          # batch from cohort/manifest.csv
halfmap-qc cohort --emd-id 49450     # single map
halfmap-qc help                      # full command reference

Full changelog (since v0.2.3)

• Add halfmap-qc CLI, interactive TUI, and PyPI packaging
• ResMap local-resolution comparison and cohort metric exports
• Placement utility and locres LOO extensions
• Trim README; gitignore cluster .sbatch files
• Thesis figure scripts remain local-only (gitignored)

v0.2.3

Summary

• Add Figma export tooling for thesis figures (Q vs V, cross-metric, placement, conformation pairs, reliability by class)
• Add shared style/thesis_palette.py and cohort summary CSV tables
• Extend conformation-pair analysis (Cα RMSD), placement utility, and half-map reliability export
• Align Zenodo citation to concept DOI 10.5281/zenodo.20618526

Install

pip install "git+https://github.com/sarthaktexas/cryoem-halfmap-qc.git@v0.2.3"

Tests

python -m unittest discover -s tests -v

All 82 tests pass on this release.

v0.2.2 — halfmap reliability, Q-score ablations, thesis figures

Summary

• Rename LH reliability export to halfmap_reliability with density-source support
• Add Q-score constraint V gradient and window ablation runners
• Add metric schematic figure and Figma graphical-abstract export tooling
• Adopt thesis color palette for build zones and domain region annotations
• Add resumable FSC-Q cohort batch runner (run_fscq_cohort_batch.py)
• CI: switch to unittest discover; skip ChimeraX map-shell test when reference maps are absent
• Archive TV decoupling diagnostics runner under scripts/archive/

Install

pip install "git+https://github.com/sarthaktexas/cryoem-halfmap-qc.git@v0.2.2"