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bio-nexus-api

Commit History

Jun 24

09:47
feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update⁠

Samad14

fb8c550

Jun 22

11:21
fix: replace dead embed.rcsb.org iframe with PDBe Mol* viewer

Samad14

7d2b5e1
11:18
Revert "docs: update all .md files to reflect completed Phase 2 features"⁠

Samad14

0a6bfd3
11:16
docs: update all .md files to reflect completed Phase 2 features

Samad14

f5bee9a
11:12
feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

Samad14

305458b
10:59
refactor: enhance dashboard with quick tools, jobs with filter tabs, settings with profile identity

Samad14

32dd681
10:24
feat: download pre-compiled PhyML binary from bioconda instead of source build

Samad14

aad6f8e
10:09
fix: use valid EBI email (example.com), remove PhyML build from Docker

Samad14

87fe374
10:02
fix: remove PhyML source build from Docker (fails on HF), add graceful missing-binary error in phylo.py

Samad14

20cf1ce
09:59
fix: add libtool + ca-certificates to PhyML build, remove -j for low-mem environments

Samad14

e9f3afa
09:58
fix: PhyML build — disable -march=native, split RUN steps, remove -q from wget

Samad14

428cddb
09:35
fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

Samad14

fe5ce87
09:32
feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

Samad14

07e58f6
07:06
fix: accurate phylogenetic tree visualization — proportional branch lengths, scale bar, bootstrap labels, circular layout mode

Samad14

9e11dca

Jun 21

10:18
feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

Samad14

990c867
09:17
chore: move @types /three from dependencies to devDependencies

Samad14

36b2c3d
09:16
fix: make scripts cross-platform (relative paths, no hardcoded cmd.exe interpreter, platform-aware npm)

Samad14

6f8031c
09:15
chore: remove unused celery dependency (worker uses threading, not Celery)

Samad14

794b850
09:15
fix: add logging to init_redis() so Redis failures are visible in server logs

Samad14

3edbe65
09:14
fix: make primer3-py optional (separate install step, router handles missing import gracefully)

Samad14

2572d7f
09:14
fix: convert AlignmentView.tsx light-theme classes to dark void theme tokens

Samad14

312665c
09:11
chore: remove stale bioaiplatform/ directory (duplicate with divergent light-theme AIInterpretation.tsx)

Samad14

d160dc0
08:50
fix: use embed.rcsb.org instead of www.rcsb.org for clean 3D viewer iframe

Samad14

567f164
08:31
feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components⁠

Samad14

342fa92
08:16
fix: use STRING-DB image API for accurate PPI diagram, add PNG/TSV/copy export buttons

Samad14

c1c07f1

Jun 20

11:36
chore: remove temp file

Samad14

f7d1467
11:36
fix: Foldseek alignments are [dict] lists, parse target format

Samad14

5f521f2
11:35
fix: debug alignment structure types

Samad14

19208a9
11:33
fix: debug Foldseek result structure

Samad14

61dd06a
11:30
fix: Foldseek alignments are dicts, parse with .get() correctly

Samad14

7756be4
11:28
fix: debug Foldseek alignment format (list vs dict)

Samad14

758bd07
11:26
fix: add full traceback to Foldseek error

Samad14

106504c
11:24
fix: use aiohttp for Foldseek multipart upload

Samad14

feb3584
11:20
fix: debug Foldseek submit response type

Samad14

2058534
11:18
fix: use sync httpx in thread pool for Foldseek submit

Samad14

8dd7e6b
11:16
fix: restore nested alignments loop, remove debug raw

Samad14

e598246
11:14
fix: return raw Foldseek data for debugging

Samad14

36a7562
11:12
fix: Foldseek returns list directly, no alignments sub-key

Samad14

87455a5
11:10
fix: move fetch inside httpx async with block

Samad14

a55a85f
11:09
fix: manual multipart for Foldseek, add secrets import

Samad14

3b0a62a
11:07
fix: use sync httpx.Client for Foldseek multipart upload

Samad14

6f0c958
11:05
fix: add error detail to Foldseek, use bytes, longer timeout

Samad14

e368884
11:04
fix: simplify Foldseek integration, use full PDB, encode as bytes

Samad14

b4c387f
11:00
fix: primer error handling, interactions scores, structure comparison API⁠

Samad14

3030b52
10:13
fix: handle null name in InterPro domain response⁠

Samad14

76de492
10:00
fix: forward backend error detail in 4 components⁠

Samad14

5b7a343
09:53
fix: handle non-200 responses in domains, interactions, ramachandran, SS components⁠

Samad14

9fc8479
09:48
feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation⁠

Samad14

bac1801

Jun 19

17:42
Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides

Samad14

59495c0
12:17
Fix KEGG search: use find/hsa with symbol matching + parse get/PATHWAY section

Samad14

28de608

Commit History

Jun 24

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update⁠

Jun 22

fix: replace dead embed.rcsb.org iframe with PDBe Mol* viewer

Revert "docs: update all .md files to reflect completed Phase 2 features"⁠

docs: update all .md files to reflect completed Phase 2 features

feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

refactor: enhance dashboard with quick tools, jobs with filter tabs, settings with profile identity

feat: download pre-compiled PhyML binary from bioconda instead of source build

fix: use valid EBI email (example.com), remove PhyML build from Docker

fix: remove PhyML source build from Docker (fails on HF), add graceful missing-binary error in phylo.py

fix: add libtool + ca-certificates to PhyML build, remove -j for low-mem environments

fix: PhyML build — disable -march=native, split RUN steps, remove -q from wget

fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

fix: accurate phylogenetic tree visualization — proportional branch lengths, scale bar, bootstrap labels, circular layout mode

Jun 21

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

chore: move @types /three from dependencies to devDependencies

fix: make scripts cross-platform (relative paths, no hardcoded cmd.exe interpreter, platform-aware npm)

chore: remove unused celery dependency (worker uses threading, not Celery)

fix: add logging to init_redis() so Redis failures are visible in server logs

fix: make primer3-py optional (separate install step, router handles missing import gracefully)

fix: convert AlignmentView.tsx light-theme classes to dark void theme tokens

chore: remove stale bioaiplatform/ directory (duplicate with divergent light-theme AIInterpretation.tsx)

fix: use embed.rcsb.org instead of www.rcsb.org for clean 3D viewer iframe

feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components⁠

fix: use STRING-DB image API for accurate PPI diagram, add PNG/TSV/copy export buttons

Jun 20

chore: remove temp file

fix: Foldseek alignments are [dict] lists, parse target format

fix: debug alignment structure types

fix: debug Foldseek result structure

fix: Foldseek alignments are dicts, parse with .get() correctly

fix: debug Foldseek alignment format (list vs dict)

fix: add full traceback to Foldseek error

fix: use aiohttp for Foldseek multipart upload

fix: debug Foldseek submit response type

fix: use sync httpx in thread pool for Foldseek submit

fix: restore nested alignments loop, remove debug raw

fix: return raw Foldseek data for debugging

fix: Foldseek returns list directly, no alignments sub-key

fix: move fetch inside httpx async with block

fix: manual multipart for Foldseek, add secrets import

fix: use sync httpx.Client for Foldseek multipart upload

fix: add error detail to Foldseek, use bytes, longer timeout

fix: simplify Foldseek integration, use full PDB, encode as bytes

fix: primer error handling, interactions scores, structure comparison API⁠

fix: handle null name in InterPro domain response⁠

fix: forward backend error detail in 4 components⁠

fix: handle non-200 responses in domains, interactions, ramachandran, SS components⁠

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation⁠

Jun 19

Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides

Fix KEGG search: use find/hsa with symbol matching + parse get/PATHWAY section