chore(staging): release 0.1.0

[sbp-release-please]

🤖 I have created a release beep boop

0.1.0 (2026-09-14)

Features

• add 'download all' endpoint for results (SBP-388) (#87) (4f6d516)
• add admin-only endpoint to show GADI PBS queue status (dc98f4d)
• add admin-only endpoint to show GADI PBS queue status (054eb32)
• add chmod +x bin in prerunscipt (835bd36)
• add compute_env checks for seqera tower aliveness (8ad7193)
• add credit metadata for users (8e5d5f7)
• add DataTransfer model and migration (1c52e24)
• add DataTransfer model and migration (e93f313)
• add dropdown for queue selection (183a428)
• add easy way to generate migrations (4bea6ca)
• add endpoint for workflow credit calculation (aaad9bb)
• add endpoint to serve result files (71a56fb)
• add endpoint to serve result files (SBP-196) (9dcec6e)
• add export all and enable owner search in workflow runs (4fd1c38)
• add export all and enable owner search in workflow runs (eb3fafd)
• add form validation for single prediction based on sequence length and number of entities (SBP-483) (536f9ce)
• add health status route in backend for users (5c2c50c)
• add health status route in backend for users (4c1a228)
• add health system api for admins (0abf6ce)
• add health system api for admins (18706e7)
• add jitter and more attempts to submit jobs (3041105)
• add merge alembic heads (58939e9)
• add migration (bb01dfd)
• add more tooltip for admin dashboard health status (ef6ba18)
• add more tooltip for admin dashboard health status (a1a0e21)
• add nxf_assets (e74a72c)
• add OwnerEmailField in workflow run table (b15888e)
• Add PDB file upload with S3 integration and workflow support (#4) (a632de8)
• add profile in workflows table (eee717b)
• add profile in workflows table (545b742)
• add ProteinDjFromData (8a6881d)
• add QueuedJob to db admin dashboard (#85) (de08174)
• add repo assets (cc79f14)
• add required fields to ProteinDJ form data (76c6f1b)
• add rfd_length params (1e3ccd0)
• add sbp credits, rename service unit to NCI (965e848)
• add single-prediction entity validation and related tests (0b7a2a6)
• add specs and functions for proteinfold outputs (538355f)
• add structured settings management (SBP-531) (#132) (80d9529)
• add submission_timestamp to WorkflowRun table and admin dashboard (1f1a9a2)
• add submission_timestamp to WorkflowRun table and admin dashboard (b51b846)
• add target input folder to fasta (#46) (b7f9374)
• add test sequences (dd57252)
• add tool, force repo-url, revision and (ffd4b89)
• add types/dataclasses to define outputs (e5f6069)
• add user credit to db and route (377605f)
• add user decrease-only update credit (290725c)
• add user decrease-only update credit (c81902f)
• add workflow credit information (dc0ceff)
• add workflow credit information (351deb2)
• add workflows name and tool constraint (0b6442d)
• additional proteindj form data validation (22d1a12)
• AGENTS.md with guidelines (#141) (5e375e2)
• automatically generate UUIDs for DB models (69d0892)
• automatically grant new sbp bundle users credits (e8db882)
• automatically grant new sbp bundle users credits (9d5675f)
• base64 encode utils (c1a7cc9)
• bootstrap script for auto-migrations and switch to shared ECR (c4a0bf0)
• bootstrap script for auto-migrations and switch to shared ECR (fdd225c)
• check for SBP bundle roles when running a workflow (225379c)
• CI workflow to check migrations after merge (#70) (79775be)
• collect bulk prediction outputs (9624571)
• collect bulk prediction outputs (5f33003)
• collect pae and allow report render (0a7808c)
• collect PAE, remove confidence in wisps (4b52648)
• collect wisps output (ae010ba)
• delete, cancel jobs (#14) (83cc339)
• derive final_designs from max_traj (1a470f3)
• detect time zone in system status (65023ec)
• display data transfer on admin dashboard (378ce34)
• display historic health status (379a7f9)
• display SBP credit cost in admin dashboard (a4efe1f)
• enable admins to manuallly update user credits (3aa63d3)
• enable admins to manuallly update user credits (5741047)
• enable download structures.zip for bindcraft (61dbcb7)
• encode email and IP address in cluster options (cc4b121)
• encode email and ip for cluster options (18b2699)
• ensure sample_id is generated if not received from form data (591f162)
• fetch prerun scripts from prerun_script_path (9cd91a3)
• fix remote url (0d1bf43)
• fix summary time min width (a26dd97)
• fix workflow staging, add nxf_assets in prerunscript (b894515)
• for not null in data transfer and backfill (ae0a03d)
• get max score (#16) (e2800c7)
• get max score from results (#5) (2f21da3)
• handle structure files for wisps (541310d)
• improve admin view + add for all models (5289d9d)
• improve GADI dashboard status (656dc16)
• improve GADI dashboard status (8f58fc6)
• improvements for database admin (1f9a4db)
• jobs listing api (#13) (aa7417a)
• limit the number of jobs submitted (c89a070)
• limit the number of jobs submitted (e66870e)
• machine-only health component (a2d6a85)
• machine-only health component (136d131)
• maintain jobs list while seqera api is off (2e050ef)
• max score, archive pdb file for rfdiffusion (a07b068)
• molecular sequence validation (9544296)
• only refresh credits for approved users (f2acc81)
• proteindj config and executor (ccf7489)
• proteinfold output collection (and refactor of existing output) (543d76c)
• publish versioned image tag (e8057cb)
• publish versioned image tag (092f3ba)
• push job list sort/filter/pagination into SQL (9fda9ae)
• query tool if workflows.tool is not null (42cea4d)
• queued jobs table in database (#81) (98cde17)
• record input and output in data transfer (c858a11)
• record system status incidents in the db (c2b59c9)
• refresh user credits to 1000 every month (34ded08)
• removal of boltzgen (f240bb0)
• removal of boltzgen (4f7065f)
• remove afd_length, update related tests (eb22765)
• remove gadi config in bindflow (0f1682e)
• remove gadi config in bindflow (75e5734)
• remove profile, add ref_database support (6653b88)
• replace seqera dataset by s3 upload (7d58bf9)
• reports and download links (#27) (bf2dd7c)
• results logs (#24) (414e467)
• rfdiffusion results (cea3758)
• RFDiffusion workflow (ebcb54c)
• scheduler improvements for prod (SBP-609) (#162) (f745247)
• score extraction for single prediction workflows (#72) (477d455)
• select wisps outputs based on tool used (e145fa8)
• smiles ligand validation (65cb0f3)
• smiles ligand validation (2edd1d0)
• split bootstrap into migrate/serve modes (fa07132)
• split bootstrap into migrate/serve modes (e9bdc0a)
• staging workflow url (30d10b0)
• submit single prediction fasta and form (#36) (679a4ae)
• sync workflow status/results in job scheduler (SBP-523) (#118) (8796607)
• track service unit cost of runs in database (SBP-445) (#113) (896ee39)
• update cluster options (b3d3717)
• update database diagram (dc1941d)
• update diagram (4a0dc56)
• update new schema diagram (cd483ef)
• update nextflow module version (57ac01a)
• update nextflow module version (a3536fb)
• Update proteinfold output files to capture structures in cif format (SBP-451) (6a17515)
• update schema diagram (af16c33)
• update schema diagram (2bf7487)
• update shared workflow import (46ef414)
• update tool in admin dashboard (43e5ad2)
• use a job scheduler to launch workflows when the system is healthy (SBP-421) (#96) (43cc676)
• use Globus data transfers for results/output (SBP-535) (#139) (a5fa2e7)
• wire proteindj workflow to de-novo-design (82604b5)
• wisps bulk prediction launch (945d711)
• wisps bulk prediction launch (c26778a)
• wisps confidence scores (510974b)
• wisps output (0bc1ce2)
• wisps workflow executor and config (fb0a036)
• wisps workflow executor and config (a3a6e78)
• workflow staging (c586418)
• workflow staging, resolve bindflow settings (37e5c8a)
• workflow submit (#15) (8aa5a28)

Bug Fixes

• fix: (ec65571)
• _CONFIGS_BY_CATEGORY keys typed as WorkflowName (00fa995)
• _parse_snapshot now raises ValueError (2c09e4e)
• add back the scripts (e950ac5)
• add interaction-screening dataset upload (64442e4)
• add load dotenv to run_scheduler.py (b25f78f)
• add missing 1 credit for boltzgen (bc8e54c)
• add missing 1 credit for boltzgen (779ab7b)
• add pdb to zip category (1906098)
• add submissions workflow timestamp for admin view (e720d2a)
• add submissions workflow timestamp for admin view (675d2d2)
• add timezone info in admin database UI (c58e543)
• add timezone info in admin database UI (25a9839)
• add workflow revision in staging path (b374359)
• add workflow revision in staging path (f3c2c79)
• add workflow revision in staging path (b7da63c)
• add workflow_runs tool for admin view (#60) (72ef9cd)
• admin dashboard title (19c361c)
• admin dashboard title (0918492)
• allow syncing to be marked complete with missing outputs (#150) (b709db2)
• backfill sbp bundle credit grant for (894e5fd)
• black (c989aba)
• check cached health status (840000c)
• comments (074f665)
• consolidate credits components to credits.py (8dba4ce)
• count active workflows via totalSize (dca5839)
• decode account name for gadi status (8736e86)
• decode account name for gadi status (d7763ff)
• decouple Seqera health checks from job submission to stop timeou… (b7a80c4)
• decouple Seqera health checks from job submission to stop timeout stalls (d3e0a31)
• Dockerfile for uv run command (0e53194)
• Dockerfile for uv run command (d48f4a1)
• don't write prerun scripts to the database, add them at launch time (#89) (20337c3)
• drop stale name-only unique index (00c0514)
• drop stale name-only unique index (359988d)
• enable proxy headers for admin assets behind ALB (#21) (ad4ce2c)
• errors in fetching max score shouldn't block jobs list (#75) (b0b4477)
• exclude sbp_credit from order_by (b96748f)
• fix comment string (255606c)
• fix Docker build (4d4c432)
• fix null values in workflows on admin views (464beb9)
• fix out_dir in proteindj workflow (32eaf54)
• format (11afe67)
• grant (fda31d5)
• hardcode max concurrent workflows from now (555f9a6)
• import (41f8503)
• imports (e6542e4)
• improved data transfer sync logic (SBP-535) (#149) (984ec28)
• include tool name in job search (f9439e0)
• include tool name in job search (9386da8)
• job scheduler database sessions (#136) (b8ee3b5)
• lint (cf31110)
• lint (bb6bdb0)
• lint (c4d6bc2)
• lint (ee8dc98)
• lint (35c9ef8)
• lint (7393430)
• lint (ebae901)
• lint (c41d1de)
• lint (55d34dd)
• lint (e71a3a1)
• lint (8e60f62)
• lint (0d8b5a3)
• lint (0449229)
• lint (291b354)
• lint (bdd973b)
• lint (d31a0a8)
• lint - black (cc113d2)
• lint black (ab7d405)
• log admin user email when updating user credits (7b734cd)
• make and use right migration file (b70d964)
• make CreditBasis flow end-to-end (2873c5a)
• max traj only applies to de-novo designs (fe41f68)
• merge dev (3488313)
• merge workflow repo staging cache and (daab56f)
• merge workflow repo staging cache and (af62926)
• migration for submission timestamp (e1f1623)
• minor admin improvements (#151) (d259e5b)
• move SBP_USER_CREDIT_ALLOWANCE and (c921402)
• normalise full_name using unidecode (3bd77e0)
• nxf_assets and gadi path for workflow (83a107f)
• optional data_transfer_id and rmeove backfill (66b220c)
• out_dir params (2def2a2)
• out_dir params (5691624)
• prefer email first (faf15b2)
• profile format (5565e18)
• proper validation for getting credetials (60f10c6)
• qstats job command (52dbfcb)
• qstats job command (e5a0788)
• refactor bindcraft max score function (50cb0c1)
• refactor error handling (36846ce)
• refactor migration head (bfa1aa5)
• remove _has_column() for admin.py (87d6529)
• remove auth configs fallback (25c2b88)
• remove CIF format support from AlphaFold and ColabFold (aa81cf6)
• remove confusing user_admin_routers (0846610)
• remove cost estimates in backend (b375faf)
• remove default values in dependancy.py (2c3c66a)
• remove demo code (b3bbc29)
• remove formulas (6db83c8)
• remove group in bulk prediction dataset (5251a8f)
• remove limit and offset (f685e06)
• remove not needed comments (7f46a7b)
• remove path ref to GADI push script (88823e6)
• remove project in proteinfold config (745805f)
• remove refresh param from user-facing endpoints (3f4014b)
• remove seqera dataset (4b443c9)
• remove timestamp, username, jobid (ab7bd65)
• remove unsued params in bindflow (95f1714)
• remove unused animations (70d233c)
• remove unused details in executor and config (90693ed)
• remove unused user details (62a07bf)
• removed unintended added changes (ee2a57e)
• replace before_save by before_update and (70b83fd)
• replace before_save by before_update and (e964cee)
• replace tar by pdb in rfdiffusion regex (317e299)
• replace tar by pdb in rfdiffusion regex (a2a4df0)
• require repo url and config path (351a28c)
• required params (fdd9b66)
• restore Dockerfile (ec0d408)
• restore Dockerfile (9be34bc)
• rounded NCI service units field (ec62f35)
• run metrics path for max scores (68f542c)
• s3 access with attached role (#7) (bcdd9ee)
• sample ID handling (#68) (5cc7409)
• set and use proper variables for roles (6e1f875)
• set de-novo-design run name from form job name (#48) (f56ab56)
• set default port (#135) (9a33aae)
• set skip_source_errors for Globus transfers (#157) (2439c48)
• simplify round and sort fields (5bf1bc1)
• simply to hardcode to SYD/MEL timezone (2218284)
• skip orphaned Seqera runs and enforce auth at router level (#37) (15e357b)
• skip score for workflows unexpected situations (79d5a9b)
• skip score for workflows unexpected situations (eea69d5)
• slow health-check interval to 5 minutes per review feedback (3d65f32)
• small fixes for workflow run syncing (#122) (0161a6a)
• sort jobs by score server-side (6d98905)
• sort jobs by score server-side (3e6b79e)
• split routes to admin-facing and user-facing (c5c4ee5)
• split to admins.py new file (96f416c)
• switch the list endpoint to accept page and per_page (fbca3a3)
• test (538cbf7)
• tests (e1b40e4)
• tests (81fb124)
• tests (bc9e885)
• tests (cf4bea4)
• tests (506480f)
• tests (9f32174)
• tests (6476a69)
• tests (28fece8)
• tests (9d82347)
• tests (27d1203)
• timezone for monthly trigger to avoid DST (59eed77)
• toolMultipliers is now typed as dict[WorkflowTool, int] (d9362f6)
• unmask email and auth0_id (7d26538)
• update .env example (26c5925)
• update auth variable names (ab7d65a)
• update auth variable names (adf23f8)
• update config path (6bdf269)
• update credit cost (885d8a9)
• update credit cost (eaebb65)
• update datasets service tests (8878a0b)
• update job completed if score is valid (351c61f)
• update lock file so rdkit installs (68e71ba)
• update lock file so rdkit installs (bf93619)
• update output to support cif file formats (6fb4f57)
• update related tests (429f489)
• update schema diagram (f8df2cc)
• update tests (d5138c6)
• update tests (035546d)
• update tests for admin view (41c2007)
• update to nextflow 25.10.4 (4a1f521)
• use --no-sync in uv run to prevent dev dep sync at container startup (8f8e761)
• use --no-sync in uv run to skip dev dep sync at container startup (9aeff25)
• use --no-sync in uv run to skip dev dep sync at container startup (fb8e0eb)
• use internal run ids for job/result endpoints (SBP-421) (#97) (4b7b17b)
• use latest action versions (03686bd)
• use replace_existing so we don't try to insert duplicates in the DB (#98) (9590040)
• use right auth related configs (d6268b1)
• use same submission_timestamp (346a528)
• workflow and dataset update (a17bb2d)
• workflow staging and nxf_asset (8fcb2ee)
• workflow staging and nxf_asset comments (ed659e5)
• wrong identity name for linked objects (#153) (7a12b3e)

Performance Improvements

• parallelize Seqera calls and batch DB query (ca8ba6d)
• parallelize Seqera calls and batch DB query (170852c)

Reverts

• drop unrelated workflows.py credit-cost change from this PR (f3e4162)

Documentation

• add comments (6264fac)
• add credit calculation reference (695a4bb)
• add GADI_PROJECT in .env.example (12fa0c2)
• add health check flags (3613da3)
• add load env docs in app scheduler (3706861)
• update GET /api/health/agent (6bebbc8)
• update MAX_CONCURRENT_WORKFLOWS docs string (14b382c)

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