Genome Forge v0.1.17

Genome Forge v0.1.17

Released: 2026-06-15

Highlights

• Added compatibility audit reports for FASTA, GenBank, SBOL, and portable Genome Forge DNA round trips.
• Added a five-case golden project audit for SnapGene/Geneious-style migration trust.
• Added SBOL conversion support through /api/convert-record.
• Added UI reporting for imported-cleanly, warnings, lost metadata, export-safe, and needs-review outcomes.
• Expanded the training book to 47 cases with a compatibility round-trip trust lesson.

Validation

• 63 unit tests
• 122 smoke checks
• 113 real-world functional workflow steps
• 17 browser E2E tests
• 120 documented /api/* endpoints plus GET /share/<share_id>

Genome Forge v0.1.16

Genome Forge v0.1.16

This release adds the first NGS-lite replacement-phase workflow: FASTQ QC, adapter/quality trimming, lightweight read mapping, simple variant evidence, and a one-click workflow report for small amplicon or construct-verification read sets.

Highlights

• Added POST /api/fastq-qc for read counts, length distribution, GC, Q20/Q30, per-base quality, and adapter detection.
• Added POST /api/fastq-trim for deterministic adapter and quality trimming with retained/dropped read audit rows.
• Added POST /api/ngs-map-reads for local read-to-reference mapping, coverage, consensus, zero-coverage regions, read-level mapping rows, and high-support variant evidence.
• Added POST /api/ngs-workflow-report for QC -> trimming -> mapping -> expected/unexpected variant checks and replacement-phase status.
• Added an NGS Lite browser tab and evidence report panel.
• Expanded the self-study book to 46 cases with Case AT, "NGS-Lite Amplicon Evidence Report."

Validation

• make quality PYTHON=./.venv-docs/bin/python3
• ./.venv-docs/bin/python3 -m unittest discover -s tests -p 'test_*.py'
• ./.venv-docs/bin/python3 smoke_test.py
• ./.venv-docs/bin/python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Baseline

• Unit tests: 57/57
• Smoke checks: 119/119
• Real-world workflow steps: 110/110
• Browser E2E tests: 16/16
• API inventory: 118 documented /api/* endpoints plus GET /share/<share_id>

Genome Forge v0.1.15

Genome Forge v0.1.15

Release date: 2026-06-15

Highlights

• Added Geneious-inspired similarity annotation transfer for known parts in new constructs.
• Added multi-read Sanger consensus with variants, disagreements, expected genotype checks, and final verdicts.
• Updated the tutorial/book, case bundles, API docs, and feature-priority notes around these workflows.
• Hardened audit findings around no-coverage genotype calls and zero-coverage annotation transfer.

Geneious-Inspired Workflows

Genome Forge now covers two high-value bench workflows commonly expected from polished sequence-analysis tools:

• POST /api/annotation-transfer maps annotated reference features onto a target construct by sequence similarity, reporting identity, feature coverage, source record, and target coordinates before optionally adding features.
• POST /api/sanger-consensus combines trace IDs, trace records, or read sequences into a consensus, then separates expected variants from unexpected sequence changes.

Both workflows are available from the browser UI and are covered by deterministic EGFP/pUC19 tests.

Audit Fixes

• Expected Sanger genotype positions with no read coverage now fail the verdict instead of treating an ambiguous N as confirmation.
• Annotation transfer now rejects features with no mapped bases before coordinate projection, including when exploratory thresholds are set to zero.
• The generated training book now points Case R and Case Z to the actual new workflow buttons.

Validation

• make quality PYTHON=./.venv-docs/bin/python3
• ./.venv-docs/bin/python3 -m unittest discover -s tests -p 'test_*.py'
• ./.venv-docs/bin/python3 smoke_test.py
• ./.venv-docs/bin/python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Validation Snapshot

• Unit tests: 53/53
• Smoke checks: 115/115
• Real-world functional checks: 106/106
• Browser E2E tests: 15/15

Notes

• This release expands the current API inventory to 114 documented /api/* endpoints plus GET /share/<share_id>.
• Historical release archives under dist/ remain local artifacts unless explicitly published.

Genome Forge v0.1.14

Genome Forge v0.1.14

Release date: 2026-05-15

Highlights

• Added a configurable JSON POST body limit to the local web server.
• Oversized requests now fail before body reads with HTTP 413 and a clear configured-limit error.
• Added --max-post-mb for trusted local workflows that intentionally need larger records or bundles.
• Updated security, install, architecture, API, developer, README, and handoff docs to describe the request-size boundary.

Request-Size Safety

Genome Forge remains a local-first workstation app, but local tools can still be asked to process malformed or accidentally huge payloads. The server now validates Content-Length before reading the request body.

Default cap:

64 MiB

Override for trusted local workloads:

python3 web_ui.py --port 8080 --max-post-mb 128

Invalid Content-Length values return HTTP 400; oversized bodies return HTTP 413.

Validation

• python3 docs/validate_docs.py
• python3 -m py_compile web_ui.py tests/test_web_ui_security.py docs/validate_docs.py
• python3 -m unittest tests.test_web_ui_security -v
• python3 -m unittest discover -s tests -p 'test_*.py'
• ./.venv-docs/bin/python -m pytest
• python3 smoke_test.py
• python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Validation Snapshot

• Unit tests: 48/48
• Smoke checks: 115/115
• Real-world functional checks: 104/104
• Browser E2E tests: 15/15

Notes

• This is a focused local-server resilience release following v0.1.13.
• Genome Forge still does not claim hosted SaaS isolation, authenticated browser sessions, or regulated electronic-records compliance.

Genome Forge v0.1.13

Genome Forge v0.1.13

Release date: 2026-05-15

Highlights

• Added an explicit safety gate for non-loopback web UI binding.
• Kept normal workstation use unchanged: python3 web_ui.py --port 8080 still binds to 127.0.0.1.
• Required --allow-remote before accepting hosts such as 0.0.0.0.
• Updated security, install, architecture, API, developer, and README docs to explain the local-first bind model.
• Stabilized browser workflow tests so repeated UI actions wait for fresh output instead of accepting stale responses.

Bind Safety

Genome Forge is a local-first workstation app. Starting the server on a network-facing address now requires an explicit acknowledgement:

python3 web_ui.py --host 0.0.0.0 --port 8080 --allow-remote

Without --allow-remote, non-loopback hosts fail fast with a clear error. This reduces accidental exposure on lab or public networks while preserving an intentional opt-in path for trusted environments.

Validation

• python3 docs/validate_docs.py
• python3 -m py_compile web_ui.py tests/test_web_ui_security.py docs/validate_docs.py
• python3 -m unittest tests.test_web_ui_security -v
• python3 -m unittest discover -s tests -p 'test_*.py'
• ./.venv-docs/bin/python -m pytest
• python3 smoke_test.py
• python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Validation Snapshot

• Unit tests: 44/44
• Smoke checks: 115/115
• Real-world functional checks: 104/104
• Browser E2E tests: 15/15

Notes

• This is a focused local-server safety release following v0.1.12.
• Genome Forge still does not claim hosted SaaS isolation, authenticated browser sessions, or regulated electronic-records compliance.

Genome Forge v0.1.12

Genome Forge v0.1.12

Release date: 2026-05-15

Highlights

• Added defense-in-depth security headers to the local HTTP server.
• Added a documented local-first security model for workstation/lab usage.
• Added integration tests that verify root-page and API responses emit the expected browser security boundary.

Security Headers

The local server now sends:

• Content-Security-Policy
• X-Content-Type-Options: nosniff
• X-Frame-Options: DENY
• Referrer-Policy: no-referrer
• Cross-Origin-Opener-Policy: same-origin
• Permissions-Policy

The CSP keeps scripts local with script-src 'self', blocks object/frame embedding, and keeps network calls local with connect-src 'self'.

Validation

• python3 docs/validate_docs.py
• python3 -m py_compile web_ui.py tests/test_web_ui_security.py docs/validate_docs.py
• for f in webui/js/*.js; do node --check "$f" || exit 1; done
• ./.venv-docs/bin/python -m pytest
• python3 -m unittest discover -s tests -p 'test_*.py'
• python3 smoke_test.py
• python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Validation Snapshot

• Unit tests: 41/41
• Smoke checks: 115/115
• Real-world functional checks: 104/104
• Browser E2E tests: 15/15

Notes

• This is a focused local-server hardening release following v0.1.11.
• Genome Forge remains a local-first workstation app, not a production multi-tenant hosted service.

Genome Forge v0.1.11

Genome Forge v0.1.11

Release date: 2026-05-15

Highlights

• Added a browser-side SVG allowlist sanitizer for server-generated visual panels before DOM insertion.
• Routed map, sequence track, MSA heatmap, sequence analytics, comparison lens, trace chromatogram, and project history SVG rendering through the sanitizer.
• Escaped the remaining enzyme labels in server-rendered map SVG attributes and text.
• Added browser regression coverage that verifies active SVG content, event attributes, unsafe links, and unsafe URL paint values are stripped before rendering.

Validation

• python3 docs/validate_docs.py
• python3 -m py_compile genomeforge_toolkit.py
• for f in webui/js/*.js; do node --check "$f" || exit 1; done
• ./.venv-docs/bin/python -m pytest
• python3 -m unittest discover -s tests -p 'test_*.py'
• python3 smoke_test.py
• python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Validation Snapshot

• Unit tests: 39/39
• Smoke checks: 115/115
• Real-world functional checks: 104/104
• Browser E2E tests: 15/15

Notes

• This is a focused hardening release following v0.1.10.
• Local source archives and SHA-256 checksums are included for reproducible handoff.

Genome Forge v0.1.10

Genome Forge v0.1.10

Release date: 2026-05-15

Highlights

• Added in-app Learning Mode for guided flagship workflows.
• Added evidence-to-decision cards that translate workflow outputs into biological inference, confidence limits, and next bench actions.
• Expanded the tutorial into a 45-case self-study textbook with exact UI walkthroughs, glossary cards, evidence/inference checkpoints, bench decision cards, common wrong interpretations, and lab-chief prompts.
• Hardened SVG interaction handling so minimap and pan/zoom gestures use scoped pointer-event listeners instead of brittle global handler assignment.
• Added an embedded favicon to remove browser console noise during local UI testing.
• Tightened documentation validation so README, npm package metadata, Python package metadata, tutorial structure, and release markers stay synchronized.

Validation

• python3 docs/tutorial/generate_tutorial.py
• ./.venv-docs/bin/python docs/build_tutorial_pdf.py
• python3 docs/validate_docs.py
• python3 -m py_compile backend/project_api.py collab/store.py docs/tutorial/generate_tutorial.py docs/validate_docs.py docs/tutorial/datasets/extract_case_bundle.py docs/build_tutorial_pdf.py
• node --check webui/js/ui-core.js && node --check webui/js/workflows-core.js && node --check webui/js/workflows-analysis.js && node --check webui/js/workflows-search.js && node --check webui/js/workflows-projects.js && node --check webui/js/app.js
• python3 -m unittest discover -s tests -p 'test_*.py'
• python3 smoke_test.py
• python3 real_world_functional_test.py
• npm run test:e2e
• git diff --check

Validation Snapshot

• Unit tests: 37/37
• Smoke checks: 115/115
• Real-world functional checks: 104/104
• Browser E2E tests: 14/14

Notes

• Tutorial PDF remains a US Letter print-oriented edition.
• This release supersedes the already-published v0.1.9 tag rather than force-moving it.

Genome Forge v0.1.9

Genome Forge v0.1.9

Release date: 2026-04-29

Highlights

• Retitled the tutorial to Teach Yourself DNA Bioinformatics with Genome Forge to match the DNA-centered scope of the course.
• Expanded the tutorial to 45 lessons with ApE-inspired DNA workflows:
  • diagnostic cutter selection between related constructs
  • custom DNA ladder-centric digest planning
  • dense text-map sequence inspection
  • silent restriction-site engineering
  • linked trace-to-reference navigation
  • selected-sequence external BLAST launch
• Added publication-quality concept illustrations for diagnostic digests, silent-site engineering, and trace evidence review.
• Rebuilt the tutorial PDF as a US Letter, duplex-oriented print edition with a designed front cover, inside front cover, mirrored gutters, and an even-page back cover.
• Regenerated tutorial HTML, PDF, dataset metadata, playbook, and per-case bundles.

Validation

• python3 docs/tutorial/generate_tutorial.py
• ./.venv-docs/bin/python docs/build_tutorial_pdf.py
• python3 docs/validate_docs.py
• python3 -m py_compile docs/tutorial/generate_tutorial.py docs/validate_docs.py docs/tutorial/datasets/extract_case_bundle.py docs/build_tutorial_pdf.py
• pdfinfo docs/tutorial/user_training_tutorial.pdf
• git diff --check

Notes

• The PDF reports US Letter geometry: 612 x 792 pts.
• The release includes source archives and SHA-256 checksums for reproducible handoff.
• The older untracked local dist/genomeforge-v0.1.4 through v0.1.8 artifacts were left untouched.

Genome Forge v0.1.8

Genome Forge v0.1.8

Release date: 2026-04-27

Highlights

• Hardened collaboration trust boundaries around project permissions, review approval, and audit history.
• Escaped public share-page metadata so stored project names cannot inject HTML into shared views.
• Preserved minimap interactivity while avoiding global mouse-handler clobbering during rerenders.
• Refined the tutorial into a more polished textbook-style edition and regenerated both HTML and PDF artifacts.

Validation

• python3 -m py_compile backend/project_api.py collab/store.py docs/tutorial/generate_tutorial.py docs/build_tutorial_pdf.py
• python3 -m unittest discover -s tests -p 'test_*.py'
• python3 smoke_test.py
• python3 real_world_functional_test.py
• python3 docs/tutorial/generate_tutorial.py
• python3 docs/validate_docs.py
• ./.venv-docs/bin/python docs/build_tutorial_pdf.py
• npm run test:e2e
• git diff --check

Notes

• The release includes source archives and SHA-256 checksums for reproducible handoff.
• The local PDF build may emit non-fatal fontconfig cache warnings on this workstation; the generated PDF artifact is still written successfully.