From cc34c3e0bc3e5f283b3f33f60044370f49513312 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 20 Mar 2026 11:23:30 +0000 Subject: [PATCH 1/9] Bump astro from 5.18.1 to 6.0.6 Bumps [astro](https://github.com/withastro/astro/tree/HEAD/packages/astro) from 5.18.1 to 6.0.6. - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/astro@6.0.6/packages/astro) --- updated-dependencies: - dependency-name: astro dependency-version: 6.0.6 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- package-lock.json | 1350 +++++++++++++++------------------------------ package.json | 2 +- 2 files changed, 436 insertions(+), 916 deletions(-) diff --git a/package-lock.json b/package-lock.json index c92b7c0..b8eff1e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,7 +13,7 @@ "@astrojs/starlight": "^0.37.6", "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", - "astro": "^5.6.1", + "astro": "^6.0.7", "react": "^19.2.4", "react-dom": "^19.2.4", "sharp": "^0.34.2", @@ -24,7 +24,9 @@ } }, "node_modules/@astrojs/compiler": { - "version": "2.13.1", + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/@astrojs/compiler/-/compiler-3.0.1.tgz", + "integrity": "sha512-z97oYbdebO5aoWzuJ/8q5hLK232+17KcLZ7cJ8BCWk6+qNzVxn/gftC0KzMBUTD8WAaBkPpNSQK6PXLnNrZ0CA==", "license": "MIT" }, "node_modules/@astrojs/internal-helpers": { @@ -58,31 +60,6 @@ "vfile": "^6.0.3" } }, - "node_modules/@astrojs/mdx": { - "version": "4.3.14", - "license": "MIT", - "dependencies": { - "@astrojs/markdown-remark": "6.3.11", - "@mdx-js/mdx": "^3.1.1", - "acorn": "^8.15.0", - "es-module-lexer": "^1.7.0", - "estree-util-visit": "^2.0.0", - "hast-util-to-html": "^9.0.5", - "piccolore": "^0.1.3", - "rehype-raw": "^7.0.0", - "remark-gfm": "^4.0.1", - "remark-smartypants": "^3.0.2", - "source-map": "^0.7.6", - "unist-util-visit": "^5.0.0", - "vfile": "^6.0.3" - }, - "engines": { - "node": "18.20.8 || ^20.3.0 || >=22.0.0" - }, - "peerDependencies": { - "astro": "^5.0.0" - } - }, "node_modules/@astrojs/prism": { "version": "3.3.0", "license": "MIT", @@ -124,80 +101,6 @@ "picomatch": "^4.0.3" } }, - "node_modules/@astrojs/react/node_modules/vite": { - "version": "7.3.1", - "resolved": "https://registry.npmjs.org/vite/-/vite-7.3.1.tgz", - "integrity": "sha512-w+N7Hifpc3gRjZ63vYBXA56dvvRlNWRczTdmCBBa+CotUzAPf5b7YMdMR/8CQoeYE5LX3W4wj6RYTgonm1b9DA==", - "license": "MIT", - "dependencies": { - "esbuild": "^0.27.0", - "fdir": "^6.5.0", - "picomatch": 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- }, - "node_modules/zod-to-ts": { - "version": "1.2.0", - "peerDependencies": { - "typescript": "^4.9.4 || ^5.0.2", - "zod": "^3" - } - }, "node_modules/zwitch": { "version": "2.0.4", "license": "MIT", diff --git a/package.json b/package.json index 62f6c7b..0f89a98 100644 --- a/package.json +++ b/package.json @@ -15,7 +15,7 @@ "@astrojs/starlight": "^0.37.6", "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", - "astro": "^5.6.1", + "astro": "^6.0.7", "react": "^19.2.4", "react-dom": "^19.2.4", "sharp": "^0.34.2", From 00cbe82b9647cef2c32f7af5a82c67296730c31e Mon Sep 17 00:00:00 2001 From: lythx Date: Tue, 24 Mar 2026 14:11:19 +0100 Subject: [PATCH 2/9] bump other packages to make them compatible with astro v6 --- package-lock.json | 379 ++++++++++++++++++++++++++-------------------- package.json | 10 +- 2 files changed, 217 insertions(+), 172 deletions(-) diff --git a/package-lock.json b/package-lock.json index b8eff1e..d5aa182 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,14 +9,14 @@ "version": "2.0.0", "dependencies": { "@astrojs/react": "^5.0.1", - "@astrojs/sitemap": "3.2.1", - "@astrojs/starlight": "^0.37.6", + "@astrojs/sitemap": "3.7.1", + "@astrojs/starlight": "^0.38.2", "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", - "astro": "^6.0.7", + "astro": "^6.0.8", "react": "^19.2.4", "react-dom": "^19.2.4", - "sharp": "^0.34.2", + "sharp": "^0.34.5", "swagger-ui-react": "^5.32.1" }, "devDependencies": { @@ -30,19 +30,25 @@ "license": "MIT" }, "node_modules/@astrojs/internal-helpers": { - "version": "0.7.6", - "license": "MIT" + "version": "0.8.0", + "resolved": "https://registry.npmjs.org/@astrojs/internal-helpers/-/internal-helpers-0.8.0.tgz", + "integrity": "sha512-J56GrhEiV+4dmrGLPNOl2pZjpHXAndWVyiVDYGDuw6MWKpBSEMLdFxHzeM/6sqaknw9M+HFfHZAcvi3OfT3D/w==", + "license": "MIT", + "dependencies": { + "picomatch": "^4.0.3" + } }, "node_modules/@astrojs/markdown-remark": { - "version": "6.3.11", + "version": "7.0.1", + 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"sha512-rftlrkhHZOcjDwkGlnUtZZkvaPHCsDATp4pGpuOOMDaTdDDXF91wuVDJoWoPsKX/3YPQ5fHuF3STjcYyKr+Qhg==", "license": "MIT", "funding": { "url": "https://github.com/sponsors/colinhacks" diff --git a/package.json b/package.json index 0f89a98..d33b570 100644 --- a/package.json +++ b/package.json @@ -11,18 +11,18 @@ }, "dependencies": { "@astrojs/react": "^5.0.1", - "@astrojs/sitemap": "3.2.1", - "@astrojs/starlight": "^0.37.6", + "@astrojs/sitemap": "3.7.1", + "@astrojs/starlight": "^0.38.2", "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", - "astro": "^6.0.7", + "astro": "^6.0.8", "react": "^19.2.4", "react-dom": "^19.2.4", - "sharp": "^0.34.2", + "sharp": "^0.34.5", "swagger-ui-react": "^5.32.1" }, "overrides": { - "@astrojs/sitemap": "3.2.1" + "@astrojs/sitemap": "3.7.1" }, "devDependencies": { "@types/swagger-ui-react": "^5.18.0" From 6e27a9ed2a23a231f871c2624a7fd6825cbb53ae Mon Sep 17 00:00:00 2001 From: lythx Date: Tue, 24 Mar 2026 14:11:33 +0100 Subject: [PATCH 3/9] fix new warnings after astro v6 bump --- src/content/docs/local-setup/local-celery.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/docs/local-setup/local-celery.mdx b/src/content/docs/local-setup/local-celery.mdx index 2711acc..1ead17d 100644 --- a/src/content/docs/local-setup/local-celery.mdx +++ b/src/content/docs/local-setup/local-celery.mdx @@ -82,7 +82,7 @@ YAPTIDE stores licensed simulator binaries on S3-compatible object storage. The To use S3 (for the full licensed version), create a `.env` file in the project root with the following variables: -```env +```bash title=".env" S3_ENDPOINT=https://your-s3-endpoint.com S3_ACCESS_KEY=your-access-key S3_SECRET_KEY=your-secret-key From 90964af1f5e3cbba431f65a682a0d867015675d7 Mon Sep 17 00:00:00 2001 From: lythx Date: Sun, 12 Apr 2026 11:37:25 +0200 Subject: [PATCH 4/9] Add orchestration rework documentation structure and templates --- astro.config.mjs | 25 +++++++- .../rework-orchestration/adr/_template.mdx | 64 +++++++++++++++++++ .../docs/rework-orchestration/adr/index.mdx | 19 ++++++ .../rework-orchestration/context/.gitkeep | 0 .../docs/rework-orchestration/design/.gitkeep | 0 .../docs/rework-orchestration/index.mdx | 52 +++++++++++++++ .../rework-orchestration/research/.gitkeep | 0 7 files changed, 159 insertions(+), 1 deletion(-) create mode 100644 src/content/docs/rework-orchestration/adr/_template.mdx create mode 100644 src/content/docs/rework-orchestration/adr/index.mdx create mode 100644 src/content/docs/rework-orchestration/context/.gitkeep create mode 100644 src/content/docs/rework-orchestration/design/.gitkeep create mode 100644 src/content/docs/rework-orchestration/index.mdx create mode 100644 src/content/docs/rework-orchestration/research/.gitkeep diff --git a/astro.config.mjs b/astro.config.mjs index 128abb0..c327036 100644 --- a/astro.config.mjs +++ b/astro.config.mjs @@ -44,7 +44,7 @@ export default defineConfig({ { label: "Full Stack - SLURM", slug: "local-setup/local-slurm", - } + }, ], }, { @@ -76,6 +76,29 @@ export default defineConfig({ { label: "Authentication Model", slug: "architecture/auth-model" }, ], }, + { + label: "Orchestration Rework", + collapsed: false, + items: [ + { label: "Vision", slug: "rework-orchestration" }, + { + label: "Context & Constraints", + autogenerate: { directory: "rework-orchestration/context" }, + }, + { + label: "Architecture Decisions", + autogenerate: { directory: "rework-orchestration/adr" }, + }, + { + label: "Design Documents", + autogenerate: { directory: "rework-orchestration/design" }, + }, + { + label: "Research Sessions", + autogenerate: { directory: "rework-orchestration/research" }, + }, + ], + }, { label: "Contributing", collapsed: false, diff --git a/src/content/docs/rework-orchestration/adr/_template.mdx b/src/content/docs/rework-orchestration/adr/_template.mdx new file mode 100644 index 0000000..af14f09 --- /dev/null +++ b/src/content/docs/rework-orchestration/adr/_template.mdx @@ -0,0 +1,64 @@ +--- +title: ADR Template +description: Copy-paste template for creating orchestration rework ADRs. +draft: true +pagefind: false +sidebar: + hidden: true +--- + +This page is a copy source for new ADRs and is intentionally excluded from production output. + +## Suggested Filename + +adr-NNN-short-title.mdx + +## ADR Template + +```md +--- +title: "ADR-001: Use S3-compatible storage for partial simulation results" +status: proposed +date: 2026-04-15 +authors: [author1, author2] +tags: [storage, partial-results, s3, minio] +related-issues: + - yaptide/yaptide#NNN + - yaptide/deploy#NNN +supersedes: null +superseded-by: null +--- + +## Context + +What is the problem? What forces are at play? + +## Decision Drivers + +- Driver 1 +- Driver 2 + +## Considered Options + +1. Option A +2. Option B +3. Option C + +## Decision Outcome + +Chosen option: "Option X", because ... + +## Consequences + +### Positive + +- ... + +### Negative + +- ... + +### Neutral + +- ... +``` diff --git a/src/content/docs/rework-orchestration/adr/index.mdx b/src/content/docs/rework-orchestration/adr/index.mdx new file mode 100644 index 0000000..0270aa0 --- /dev/null +++ b/src/content/docs/rework-orchestration/adr/index.mdx @@ -0,0 +1,19 @@ +--- +title: ADR Registry +description: Registry of architecture decisions for the orchestration rework. +--- + +## Purpose + +This registry tracks all architecture decision records for the orchestration rework and their lifecycle status. + +## Status Lifecycle + +proposed -> accepted -> superseded -> rejected + +## Registry + +| ADR | Title | Status | Date | Related Issues | +| --- | ----- | ------ | ---- | -------------- | + +No ADRs have been proposed yet. diff --git a/src/content/docs/rework-orchestration/context/.gitkeep b/src/content/docs/rework-orchestration/context/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/src/content/docs/rework-orchestration/design/.gitkeep b/src/content/docs/rework-orchestration/design/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/src/content/docs/rework-orchestration/index.mdx b/src/content/docs/rework-orchestration/index.mdx new file mode 100644 index 0000000..a2a2d4a --- /dev/null +++ b/src/content/docs/rework-orchestration/index.mdx @@ -0,0 +1,52 @@ +--- +title: Orchestration Rework +description: Vision, goals, and scope for redesigning simulation job orchestration. +--- + +## Vision + +This effort defines and documents a new orchestration architecture for simulation jobs that is faster, more observable, and production-ready across both HPC and cloud deployments. + +The design process is intentionally structured so it can be reused for future cross-repository architecture reworks. + +## Goals + +1. Real-time partial results so researchers can inspect intermediate outputs while a simulation is still running. +2. Horizontal scalability so a single simulation job can span multiple machines in parallel. +3. Optimized result transport using S3-compatible object storage and efficient binary formats instead of large JSON payloads through the message broker. +4. Optimized result merge by replacing pure-Python averaging with high-performance numerical libraries. +5. Enhanced stability and control through production-grade retry logic, centralized logging, and robust error handling. + +## Scope + +Primary repositories in scope: + +- [yaptide/yaptide](https://github.com/yaptide/yaptide) +- [yaptide/for_developers](https://github.com/yaptide/for_developers) + +Possible secondary changes: + +- [yaptide/deploy](https://github.com/yaptide/deploy) +- [yaptide/ui](https://github.com/yaptide/ui) + +## Process Structure + +This section follows a reusable pattern: + +- context: as-is architecture, bottlenecks, constraints, and user requirements +- adr: decision records with explicit status changes +- design: implementation-ready design documents +- research: AI-assisted investigation logs for auditability + +## Phase 0 Deliverables + +- Bootstrap the documentation structure under this section. +- Add the ADR registry and template. +- Wire sidebar navigation for the full process structure. +- Create cross-repository tracking artifacts for implementation planning. + +## Related Issues + +- [for_developers#45](https://github.com/yaptide/for_developers/issues/45) +- [for_developers#48](https://github.com/yaptide/for_developers/issues/48) +- [for_developers#8](https://github.com/yaptide/for_developers/issues/8) diff --git a/src/content/docs/rework-orchestration/research/.gitkeep b/src/content/docs/rework-orchestration/research/.gitkeep new file mode 100644 index 0000000..e69de29 From 9f1c6ac4a87bfdd177134a21e8018a58ad481809 Mon Sep 17 00:00:00 2001 From: lythx Date: Sun, 12 Apr 2026 12:21:22 +0200 Subject: [PATCH 5/9] add initial documentation for current architecture and bottlenecks in orchestration --- .../context/current-architecture.mdx | 216 ++++++++++++++++++ .../context/current-bottlenecks.mdx | 186 +++++++++++++++ 2 files changed, 402 insertions(+) create mode 100644 src/content/docs/rework-orchestration/context/current-architecture.mdx create mode 100644 src/content/docs/rework-orchestration/context/current-bottlenecks.mdx diff --git a/src/content/docs/rework-orchestration/context/current-architecture.mdx b/src/content/docs/rework-orchestration/context/current-architecture.mdx new file mode 100644 index 0000000..a28d13f --- /dev/null +++ b/src/content/docs/rework-orchestration/context/current-architecture.mdx @@ -0,0 +1,216 @@ +--- +title: Current Architecture +description: As-is orchestration architecture traced from backend and UI code. +--- + +This document describes what the code does today for simulation orchestration. + +It is based on direct inspection of the current implementations in: + +- backend: https://github.com/yaptide/yaptide/tree/master/yaptide +- UI: https://github.com/yaptide/ui/tree/master/src +- existing docs for cross-checking: [System Overview](/for_developers/architecture/overview/) and [Data Flow](/for_developers/architecture/data-flow/) + +## Scope + +In-scope execution paths: + +- Direct execution via Celery workers (`/jobs/direct`) +- Batch execution via SLURM over SSH (`/jobs/batch`) + +Not in scope here: + +- Geant4 local browser execution internals +- Future architecture proposals (covered by ADRs and design docs) + +## Runtime Components + +| Component | Current role | +| ------------------------------------ | ------------------------------------------------------------------------------ | +| UI (`ui`) | Submits jobs, polls statuses, fetches final results | +| Flask API (`yaptide/application.py`) | Accepts submissions, validates update tokens, stores state/results | +| Celery simulation worker | Runs simulator tasks and merge task for direct jobs | +| Celery helper worker | Submits SLURM jobs and performs helper operations | +| Redis | Celery broker + result backend | +| PostgreSQL | Persistent storage for simulations, tasks, inputs, estimators, pages, logfiles | +| Remote cluster (SLURM) | Executes array jobs and collect jobs for batch mode | + +## Direct Path (Celery) + +```mermaid +sequenceDiagram + participant U as UI + participant F as Flask API + participant DB as PostgreSQL + participant C as Celery Broker/Backend (Redis) + participant W as Simulation Worker + + U->>F: POST /jobs/direct + F->>DB: Create Simulation + Task rows + Input + F->>W: run_job() -> group(run_single_simulation) + chord merge + U->>F: Poll GET /jobs/direct + W->>F: POST /tasks (progress updates) + F->>DB: Update Task/Job states + W->>W: merge_results() after all tasks complete + W->>F: POST /results (averaged estimator payload) + F->>DB: Store Estimator/Page rows, set COMPLETED + U->>F: GET /results (after completion) +``` + +### Submission and orchestration + +Current behavior in code: + +1. UI submits to `/jobs/direct` (run type in `RemoteWorkerSimulationService`). +2. `JobsDirect.post` validates payload, clamps `ntasks`, creates: + - `CelerySimulationModel` + - `CeleryTaskModel` rows + - `InputModel` +3. Backend creates per-task UUIDs and dispatches workflow through `run_job`: + - `group(run_single_simulation.s(...).set(task_id=...))` + - `chord(..., chain(set_merging_queued_state, merge_results))` +4. Merge task id is stored as `simulation.merge_id`. + +Key files: + +- `yaptide/routes/celery_routes.py` +- `yaptide/celery/utils/manage_tasks.py` + +### Task execution and progress updates + +Each `run_single_simulation` task: + +1. Writes input files to a temporary working directory. +2. Runs simulator subprocess (`shieldhit` or `fluka`). +3. Starts monitor thread (`read_shieldhit_file` or `read_fluka_file`) to parse log progress. +4. Sends task updates to Flask `/tasks` with `simulation_id`, `task_id`, `update_key`, and `update_dict`. +5. Converts estimator objects to JSON-like dictionaries via `estimators_to_list`. + +Key files: + +- `yaptide/celery/tasks.py` +- `yaptide/celery/utils/pymc.py` +- `yaptide/celery/utils/requests.py` +- `yaptide/routes/task_routes.py` + +### Merge and persistence + +After all direct tasks complete, `merge_results`: + +1. Sets job state to `MERGING_RUNNING`. +2. Averages per-task estimator pages in Python (`average_estimators`). +3. Sends merged payload to Flask `/results`. +4. `ResultsResource.post` upserts estimators/pages into DB and marks simulation `COMPLETED`. + +Result retrieval path: + +- UI fetches from `/results`. +- Backend serves from DB (`EstimatorModel` + `PageModel`), with optional estimator/page filtering. + +Key files: + +- `yaptide/celery/tasks.py` +- `yaptide/routes/common_sim_routes.py` +- `yaptide/persistence/models.py` + +## Batch Path (SLURM) + +```mermaid +sequenceDiagram + participant U as UI + participant F as Flask API + participant DB as PostgreSQL + participant H as Helper Worker + participant S as SLURM Cluster + + U->>F: POST /jobs/batch + F->>DB: Create BatchSimulation + BatchTask + Input rows + F->>H: submit_job.delay(...) + H->>S: Upload scripts/input and submit array+collect jobs + S->>F: POST /tasks (watcher updates) + F->>DB: Update task/job states + S->>F: POST /results (simulation_data_sender after collect) + F->>DB: Store Estimator/Page rows, set COMPLETED + U->>F: Poll GET /jobs/batch and GET /results +``` + +### Submission and remote execution + +`JobsBatch.post` enqueues `submit_job` on helper worker. + +`submit_job` currently: + +1. Opens SSH connection using user certificate/private key. +2. Creates remote working directory in `$SCRATCH/yaptide_runs/`. +3. Uploads zipped inputs, `watcher.py`, and `simulation_data_sender.py`. +4. Generates scripts from templates and runs `sbatch` for: + - array job (N simulations) + - collect job (merge/convert/send) +5. Posts `/jobs` updates with `array_id`, `collect_id`, and `job_dir`. + +Key files: + +- `yaptide/routes/batch_routes.py` +- `yaptide/batch/batch_methods.py` +- `yaptide/batch/shieldhit_string_templates.py` +- `yaptide/batch/fluka_string_templates.py` + +### Batch progress and result delivery + +- Per-task progress: `watcher.py` parses logs and POSTs `/tasks`. +- Final results: collect script runs `convertmc json --many` on output files and then posts `/results` using `simulation_data_sender.py`. + +## Current State Model + +Current states in `EntityState`: + +- `UNKNOWN` +- `PENDING` +- `RUNNING` +- `MERGING_QUEUED` +- `MERGING_RUNNING` +- `CANCELED` +- `COMPLETED` +- `FAILED` + +State transitions are distributed across: + +- `/jobs/direct` and `/jobs/batch` submission handlers +- monitor updates through `/tasks` +- merge stage (`set_merging_queued_state`, `merge_results`) +- `/results` persistence handler + +## Storage Model (Current) + +Current persistence model in PostgreSQL: + +- `Simulation` (+ `CelerySimulation` / `BatchSimulation`) +- `Task` (+ `CeleryTask` / `BatchTask`) +- `Input` (gzip-compressed JSON blob) +- `Estimator` (gzip-compressed metadata) +- `Page` (gzip-compressed page JSON) +- `Logfiles` (gzip-compressed JSON) + +Compression/decompression is performed in model property getters/setters using JSON serialize + gzip. + +## UI Behavior Today + +Current UI orchestration behavior: + +- Polls simulation statuses periodically (fast interval while active). +- Fetches full numerical results only when simulation state is `COMPLETED`. +- Uses `/results` and estimator/page filtering endpoints after completion. + +Key files: + +- `ui/src/services/RemoteWorkerSimulationService.ts` +- `ui/src/WrapperApp/components/Simulation/SimulationsGrid/SimulationsGridHelpers.ts` +- `ui/src/WrapperApp/components/Simulation/RecentSimulations.tsx` + +## What This Means For Phase 1+ + +As-is architecture is functional and supports two production paths, but it combines control-plane and data-plane concerns tightly: + +- state updates and large result payload transport both flow through the same backend APIs and Celery/Redis stack +- merge is centralized in one Python task +- numerical result delivery is effectively end-of-job, not true incremental partial-result streaming diff --git a/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx b/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx new file mode 100644 index 0000000..9c3f504 --- /dev/null +++ b/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx @@ -0,0 +1,186 @@ +--- +title: Current Bottlenecks +description: Evidence-backed bottlenecks in transport, merge, visibility, and operational control. +--- + +This page documents current bottlenecks from code-level analysis and local fixture measurements. + +## Evidence Base + +Primary evidence sources: + +- backend orchestration and merge code in `yaptide` +- UI polling/result-fetch behavior in `ui` +- representative result fixture: `yaptide/tests/res/json_with_results.json` + +Measured fixture snapshot (`json_with_results.json`): + +- file size: `2,564,199` bytes +- estimators: `4` +- pages: `21` +- total numeric values across pages: `98,892` +- largest page value array length: `32,000` + +These numbers are not production maxima, but they are large enough to expose current scaling pressure points. + +## 1. JSON-Centric Result Transport and Serialization + +### Current behavior + +Direct path and batch path both convert estimator outputs into JSON structures before transport/persistence: + +- direct: `estimators_to_list` writes estimator JSON to disk, then reads it back into Python dicts +- batch: collect scripts run `convertmc json --many` and sender script reads all `*.json` files and posts them as one JSON payload +- backend `/results` receives nested JSON and re-serializes page/metadata data into compressed DB blobs + +### Why this is a bottleneck + +- multiple JSON encode/decode cycles occur in one workflow +- direct path has extra temp-file round-trips in `estimators_to_list` +- large nested numeric arrays are moved in-memory as Python lists and JSON strings repeatedly + +### Code references + +- `yaptide/utils/sim_utils.py` (`estimators_to_list`) +- `yaptide/batch/fluka_string_templates.py` and `yaptide/batch/shieldhit_string_templates.py` +- `yaptide/batch/simulation_data_sender.py` +- `yaptide/routes/common_sim_routes.py` (`ResultsResource.post`) + +## 2. Broker/Backend Data Plane Pressure (Redis + Celery Results) + +### Current behavior + +- Redis is configured as both Celery broker and Celery result backend in deployment compose. +- Direct tasks return full estimator payloads to Celery chord body (`merge_results`). +- If `/results` POST fails during merge, merged estimators are left in Celery task result payload (`final_result`). +- `ResultsDirect.get` can fallback to Celery `AsyncResult.info` if DB has no results yet. + +### Why this is a bottleneck + +- control messages and heavy data share the same broker/backend infrastructure +- large result payloads can amplify Redis memory/network pressure +- fallback behavior keeps heavy payload coupling between compute and broker state + +### Code references + +- `docker-compose.yml` (`CELERY_BROKER_URL`, `CELERY_RESULT_BACKEND`) +- `yaptide/celery/tasks.py` (`run_single_simulation`, `merge_results`) +- `yaptide/celery/utils/manage_tasks.py` (`get_job_results`) +- `yaptide/routes/celery_routes.py` (`ResultsDirect.get`) + +## 3. Merge Pipeline in Pure Python Loops + +### Current behavior + +`average_estimators` performs page-value averaging in Python loops over list structures. + +Pseudo-complexity: + +- $O(T \times P \times V)$ where: +- $T$ is number of completed tasks, +- $P$ is number of pages, +- $V$ is values per page. + +With the measured fixture shape (`98,892` values) and many tasks, per-value Python loop overhead becomes significant. + +### Why this is a bottleneck + +- Python-level numeric loops are slower than vectorized kernels +- merge task is single-task chokepoint in the chord callback +- all merged payloads are materialized in memory as nested Python objects + +### Code references + +- `yaptide/celery/utils/pymc.py` (`average_values`, `average_estimators`) +- `yaptide/celery/tasks.py` (`merge_results`) + +## 4. No True Partial Numerical Results During RUNNING + +### Current behavior + +Progress updates are streamed, numerical estimators are not. + +- monitors send task progress (`simulated_primaries`, `estimated_time`, states) via `/tasks` +- merged estimator payload is sent at end of workflow via `/results` +- UI fetches/loads result datasets when status becomes `COMPLETED` + +Batch mode similarly sends final results in collect stage after array completion. + +### Why this is a bottleneck + +- users can see progress bars but not intermediate dosimetry/fluence data +- misconfiguration detection is delayed until after full run completion +- long runs provide limited actionable feedback + +### Code references + +- `yaptide/celery/utils/pymc.py` (`read_shieldhit_file`, `read_fluka_file`) +- `yaptide/routes/task_routes.py` +- `ui/src/WrapperApp/components/Simulation/SimulationsGrid/SimulationsGridHelpers.ts` +- `ui/src/services/RemoteWorkerSimulationService.ts` +- `yaptide/batch/simulation_data_sender.py` + +## 5. Reliability and Operational Control Gaps + +### Current behavior + +- no explicit Celery task retry policies (`autoretry_for`, `max_retries`, etc.) in task definitions +- HTTP update/result posts are single-attempt requests with no backoff strategy +- known log handling issue is documented in code comments and partially disabled behavior +- helper task process inspection uses hardcoded worker name (`celery@yaptide-simulation-worker`) + +### Why this is a bottleneck + +- transient network/backend failures can drop updates or results +- operational behavior depends on implicit defaults rather than explicit policy +- brittle assumptions reduce portability across deployment topologies + +### Code references + +- `yaptide/celery/tasks.py` (comments around logfile overwrite handling) +- `yaptide/celery/utils/requests.py` +- `yaptide/utils/helper_tasks.py` +- `yaptide/celery/simulation_worker.py` + +## 6. Scaling Model Limits in Current Topology + +### Current behavior + +- default compose topology runs a single simulation worker service container +- merge is serialized in one callback task per job +- no object-storage-based result fan-in; final payloads are moved through backend API and DB writes + +### Why this is a bottleneck + +- single-job fan-in stage can dominate latency as task count grows +- throughput scales less predictably for large payloads and high parallelism +- architecture is not yet optimized for multi-node distributed result transport/merge + +### Code references + +- `docker-compose.yml` +- `yaptide/celery/utils/manage_tasks.py` +- `yaptide/celery/tasks.py` + +## Impact Summary + +| Bottleneck | Current behavior | Main impact | +| ------------------------------ | ----------------------------------------------------------------- | -------------------------------------------- | +| JSON-heavy transport | Multiple JSON conversions and full-payload posts | CPU, memory, and I/O overhead | +| Redis data-plane coupling | Broker and result backend share Redis with large payload exposure | Throughput and reliability risk under load | +| Pure-Python merge loops | Single-task Python list averaging | Longer merge time and higher memory pressure | +| No partial estimator streaming | Only progress updates during run | Delayed scientific feedback | +| Limited retry/control policy | Mostly single-attempt update/result posting | Fragility on transient failures | +| Fan-in merge topology | One callback merge step per job | Scaling bottleneck as tasks/data grow | + +## Immediate Profiling Tasks (Phase 1 input) + +To replace assumptions with hard numbers, run these measurements next: + +1. End-to-end timings per stage: run, merge, `/results` persistence. +2. Payload size telemetry: per-task estimator JSON size, merged JSON size, response times. +3. Merge CPU and memory profiling for realistic task counts (for example 4, 8, 16, 32). +4. Redis memory/network telemetry under concurrent workloads. +5. Failure-injection tests for `/tasks` and `/results` posting resilience. + +These measurements will feed ADR option comparisons and benchmark-based design choices in Phase 2 and Phase 3. From f53ccf9298ce8166cf60f8ba4225a1fd338e89e3 Mon Sep 17 00:00:00 2001 From: lythx Date: Sun, 12 Apr 2026 12:26:29 +0200 Subject: [PATCH 6/9] add mermaid plugin --- astro.config.mjs | 2 + package-lock.json | 1683 ++++++++++++++++++++++++++++++++++++++++++--- package.json | 1 + 3 files changed, 1575 insertions(+), 111 deletions(-) diff --git a/astro.config.mjs b/astro.config.mjs index c327036..47c1b77 100644 --- a/astro.config.mjs +++ b/astro.config.mjs @@ -2,6 +2,7 @@ import { defineConfig } from "astro/config"; import starlight from "@astrojs/starlight"; import react from "@astrojs/react"; +import starlightClientMermaid from "@pasqal-io/starlight-client-mermaid"; // https://astro.build/config export default defineConfig({ @@ -25,6 +26,7 @@ export default defineConfig({ editLink: { baseUrl: "https://github.com/yaptide/for_developers/edit/main/", }, + plugins: [starlightClientMermaid()], sidebar: [ { label: "Home", diff --git a/package-lock.json b/package-lock.json index d5aa182..8defe8a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,6 +11,7 @@ "@astrojs/react": "^5.0.1", "@astrojs/sitemap": "3.7.1", "@astrojs/starlight": "^0.38.2", + "@pasqal-io/starlight-client-mermaid": "^0.1.0", "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", "astro": "^6.0.8", @@ -23,6 +24,19 @@ "@types/swagger-ui-react": "^5.18.0" } }, + "node_modules/@antfu/install-pkg": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-1.1.0.tgz", + "integrity": "sha512-MGQsmw10ZyI+EJo45CdSER4zEb+p31LpDAFp2Z3gkSd1yqVZGi0Ebx++YTEMonJy4oChEMLsxZ64j8FH6sSqtQ==", + "license": "MIT", + "dependencies": { + "package-manager-detector": "^1.3.0", + "tinyexec": "^1.0.1" + }, + "funding": { + "url": "https://github.com/sponsors/antfu" + } + }, "node_modules/@astrojs/compiler": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/@astrojs/compiler/-/compiler-3.0.1.tgz", @@ -39,6 +53,68 @@ } }, "node_modules/@astrojs/markdown-remark": { + "version": "6.3.11", + "resolved": "https://registry.npmjs.org/@astrojs/markdown-remark/-/markdown-remark-6.3.11.tgz", + "integrity": "sha512-hcaxX/5aC6lQgHeGh1i+aauvSwIT6cfyFjKWvExYSxUhZZBBdvCliOtu06gbQyhbe0pGJNoNmqNlQZ5zYUuIyQ==", + "license": "MIT", + "dependencies": { + "@astrojs/internal-helpers": "0.7.6", + "@astrojs/prism": "3.3.0", + "github-slugger": "^2.0.0", + "hast-util-from-html": "^2.0.3", + "hast-util-to-text": "^4.0.2", + "import-meta-resolve": "^4.2.0", + "js-yaml": "^4.1.1", + "mdast-util-definitions": "^6.0.0", + "rehype-raw": "^7.0.0", + "rehype-stringify": "^10.0.1", + "remark-gfm": "^4.0.1", + "remark-parse": "^11.0.0", + "remark-rehype": "^11.1.2", + "remark-smartypants": "^3.0.2", + "shiki": "^3.21.0", + "smol-toml": "^1.6.0", + "unified": "^11.0.5", + "unist-util-remove-position": "^5.0.0", + "unist-util-visit": "^5.0.0", + "unist-util-visit-parents": "^6.0.2", + "vfile": "^6.0.3" + } + }, + "node_modules/@astrojs/markdown-remark/node_modules/@astrojs/internal-helpers": { + "version": "0.7.6", + "resolved": "https://registry.npmjs.org/@astrojs/internal-helpers/-/internal-helpers-0.7.6.tgz", + "integrity": "sha512-GOle7smBWKfMSP8osUIGOlB5kaHdQLV3foCsf+5Q9Wsuu+C6Fs3Ez/ttXmhjZ1HkSgsogcM1RXSjjOVieHq16Q==", + "license": "MIT" + }, + "node_modules/@astrojs/mdx": { + "version": "5.0.2", + "resolved": "https://registry.npmjs.org/@astrojs/mdx/-/mdx-5.0.2.tgz", + "integrity": "sha512-0as6odPH9ZQhS3pdH9dWmVOwgXuDtytJiE4VvYgR0lSFBvF4PSTyE0HdODHm/d7dBghvWTPc2bQaBm4y4nTBNw==", + "license": "MIT", + "dependencies": { + "@astrojs/markdown-remark": "7.0.1", + "@mdx-js/mdx": "^3.1.1", + "acorn": "^8.16.0", + "es-module-lexer": "^2.0.0", + "estree-util-visit": "^2.0.0", + "hast-util-to-html": "^9.0.5", + "piccolore": "^0.1.3", + "rehype-raw": "^7.0.0", + "remark-gfm": "^4.0.1", + "remark-smartypants": "^3.0.2", + "source-map": "^0.7.6", + "unist-util-visit": "^5.1.0", + "vfile": "^6.0.3" + }, + "engines": { + "node": ">=22.12.0" + }, + "peerDependencies": { + "astro": "^6.0.0" + } + }, + "node_modules/@astrojs/mdx/node_modules/@astrojs/markdown-remark": { "version": "7.0.1", "resolved": "https://registry.npmjs.org/@astrojs/markdown-remark/-/markdown-remark-7.0.1.tgz", "integrity": "sha512-zAfLJmn07u9SlDNNHTpjv0RT4F8D4k54NR7ReRas8CO4OeGoqSvOuKwqCFg2/cqN3wHwdWlK/7Yv/lMXlhVIaw==", @@ -66,7 +142,19 @@ "vfile": "^6.0.3" } }, - "node_modules/@astrojs/markdown-remark/node_modules/@shikijs/core": { + "node_modules/@astrojs/mdx/node_modules/@astrojs/prism": { + "version": "4.0.1", + "resolved": "https://registry.npmjs.org/@astrojs/prism/-/prism-4.0.1.tgz", + "integrity": "sha512-nksZQVjlferuWzhPsBpQ1JE5XuKAf1id1/9Hj4a9KG4+ofrlzxUUwX4YGQF/SuDiuiGKEnzopGOt38F3AnVWsQ==", + "license": "MIT", + "dependencies": { + "prismjs": "^1.30.0" + }, + "engines": { + "node": ">=22.12.0" + } + }, + "node_modules/@astrojs/mdx/node_modules/@shikijs/core": { "version": "4.0.2", "resolved": 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"https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.1.0.tgz", + "integrity": "sha512-/BpdSx+yCQGnCvecbyXdxHDkuk55/G3xwnC0GqY4gmQ3j+A+g8kzzgB4Nk/SINjqn6+waqw3EgbVF2QKExkRxQ==", + "license": "MIT" + }, "node_modules/web-namespaces": { "version": "2.0.1", "license": "MIT", diff --git a/package.json b/package.json index d33b570..967d6e0 100644 --- a/package.json +++ b/package.json @@ -13,6 +13,7 @@ "@astrojs/react": "^5.0.1", "@astrojs/sitemap": "3.7.1", "@astrojs/starlight": "^0.38.2", + "@pasqal-io/starlight-client-mermaid": "^0.1.0", "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", "astro": "^6.0.8", From d95a4ed97e68e7febd0728857111ad17454fe113 Mon Sep 17 00:00:00 2001 From: lythx Date: Sun, 12 Apr 2026 12:26:41 +0200 Subject: [PATCH 7/9] fix formatting issues in current-bottlenecks.mdx --- .../rework-orchestration/context/current-bottlenecks.mdx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx b/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx index 9c3f504..5ce4642 100644 --- a/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx +++ b/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx @@ -76,10 +76,10 @@ Direct path and batch path both convert estimator outputs into JSON structures b Pseudo-complexity: -- $O(T \times P \times V)$ where: -- $T$ is number of completed tasks, -- $P$ is number of pages, -- $V$ is values per page. +- O(T _ P _ V), where: +- T is number of completed tasks, +- P is number of pages, +- V is values per page. With the measured fixture shape (`98,892` values) and many tasks, per-value Python loop overhead becomes significant. From 04d33372929437ceaa22a4bf421a64a807c4d8b4 Mon Sep 17 00:00:00 2001 From: lythx Date: Sun, 12 Apr 2026 12:36:31 +0200 Subject: [PATCH 8/9] add profiling plan --- .../context/current-bottlenecks.mdx | 11 ++ .../rework-orchestration/research/.gitkeep | 0 .../research/phase-1-profiling-plan.mdx | 177 ++++++++++++++++++ 3 files changed, 188 insertions(+) delete mode 100644 src/content/docs/rework-orchestration/research/.gitkeep create mode 100644 src/content/docs/rework-orchestration/research/phase-1-profiling-plan.mdx diff --git a/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx b/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx index 5ce4642..61b7f5f 100644 --- a/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx +++ b/src/content/docs/rework-orchestration/context/current-bottlenecks.mdx @@ -184,3 +184,14 @@ To replace assumptions with hard numbers, run these measurements next: 5. Failure-injection tests for `/tasks` and `/results` posting resilience. These measurements will feed ADR option comparisons and benchmark-based design choices in Phase 2 and Phase 3. + +Detailed execution plan: [Phase 1 Profiling Plan](/for_developers/rework-orchestration/research/phase-1-profiling-plan/) + +Recommended default tooling: + +- OpenTelemetry + Prometheus + Grafana for stage timing and trace correlation +- Locust for concurrent workload generation +- py-spy for merge CPU profiling +- Memray for merge memory profiling +- redis_exporter + Prometheus for Redis memory/network telemetry +- Toxiproxy for deterministic `/tasks` and `/results` failure injection diff --git a/src/content/docs/rework-orchestration/research/.gitkeep b/src/content/docs/rework-orchestration/research/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/src/content/docs/rework-orchestration/research/phase-1-profiling-plan.mdx b/src/content/docs/rework-orchestration/research/phase-1-profiling-plan.mdx new file mode 100644 index 0000000..f214bf1 --- /dev/null +++ b/src/content/docs/rework-orchestration/research/phase-1-profiling-plan.mdx @@ -0,0 +1,177 @@ +--- +title: Phase 1 Profiling Plan +description: Reproducible measurement runbook for orchestration timing, payload, merge, Redis, and resilience benchmarks. +--- + +This runbook turns Phase 1 profiling goals into a repeatable protocol that can be reused for ADR comparisons in Phase 2 and design validation in Phase 3. + +Related context: [Current Bottlenecks](/for_developers/rework-orchestration/context/current-bottlenecks/) + +## Required Outputs + +Produce these artifacts from the same test matrix: + +1. End-to-end timing percentiles for run, merge, and `/results` persistence. +2. Payload size distributions for per-task and merged estimator JSON. +3. Merge CPU hotspot evidence and memory peak measurements for task counts 4, 8, 16, and 32. +4. Redis memory and network telemetry under concurrent workloads. +5. Failure-injection resilience results for `/tasks` and `/results` posting. + +## Recommended Tool Stack + +| Measurement goal | Recommended tool(s) | Why this is a good fit | +| -------------------------------------- | ------------------------------------- | --------------------------------------------------------------------- | +| Stage timings and service latency | OpenTelemetry + Prometheus + Grafana | One source for traces plus percentile metrics and historical trends | +| Concurrent workload generation | Locust | Scriptable and repeatable load patterns for matrix testing | +| Merge CPU profiling | py-spy | Low overhead sampling and flamegraph output for live worker processes | +| Merge memory profiling | Memray | Detailed allocation and peak usage visibility | +| Redis memory/network/command telemetry | redis_exporter + Prometheus + Grafana | Standard metrics pipeline for broker/backend behavior | +| Network/transport failure injection | Toxiproxy | Deterministic latency, loss, and disconnect scenarios | + +## Baseline Test Matrix + +Start with one representative simulation input and vary only orchestration pressure. + +| Scenario | Concurrent jobs | Tasks per job | Fault mode | Repetitions | +| -------- | --------------- | ------------- | ---------- | ----------- | +| S1 | 1 | 4 | none | 10 | +| S2 | 1 | 8 | none | 10 | +| S3 | 1 | 16 | none | 10 | +| S4 | 1 | 32 | none | 10 | +| S5 | 5 | 8 | none | 10 | +| S6 | 10 | 8 | none | 10 | +| S7 | 10 | 8 | latency | 10 | +| S8 | 10 | 8 | drop/retry | 10 | + +Use S1-S6 for throughput/latency characterization and S7-S8 for resilience behavior. + +## Instrumentation Plan + +### 1) End-to-End Timings per Stage + +Instrument three stage boundaries in backend orchestration: + +- run stage: task execution start to completion +- merge stage: merge callback start to completion +- persistence stage: `/results` receive to durable DB write completion + +Recommended metrics: + +- `yaptide_stage_duration_seconds` (histogram) + - labels: `stage=run|merge|persist`, `success=true|false`, `task_count_bucket` +- `yaptide_job_duration_seconds` (histogram) +- `yaptide_stage_events_total` (counter) + +Guidance: + +- keep labels low-cardinality; do not attach unique `job_id` as metric label +- attach `job_id` in tracing spans, not in Prometheus labels + +### 2) Payload Size Telemetry + +Capture payload bytes at key boundaries: + +- per-task estimator JSON before transport +- merged estimator JSON before `/results` POST +- `/tasks` and `/results` request and response body sizes + +Recommended metrics: + +- `yaptide_payload_bytes` (histogram) + - labels: `kind=task_estimator|merged_estimator|tasks_request|results_request|results_response` +- `yaptide_http_request_duration_seconds` (histogram) + - labels: `route=/tasks|/results`, `method=POST`, `status_code` + +Expected output: + +- percentiles and max sizes by scenario +- scatter: payload size vs endpoint latency + +### 3) Merge CPU and Memory Profiling + +For each task count (4, 8, 16, 32), execute merge repeatedly with realistic fixtures. + +Suggested commands: + +```bash +py-spy record -o profiles/merge-16.svg --pid "$SIMULATION_WORKER_PID" --duration 60 +python -m memray run -o profiles/merge-16.bin scripts/profile_merge.py --tasks 16 +python -m memray summary profiles/merge-16.bin +``` + +Track per scenario: + +- merge wall time: p50/p95 +- CPU: top hotspots and cumulative percentage +- memory: peak RSS and top allocation sources + +### 4) Redis Memory and Network Telemetry + +Monitor Redis while running S1-S8: + +- memory usage (`used_memory`, `used_memory_rss`) +- network throughput (`instantaneous_input_kbps`, `instantaneous_output_kbps`) +- pressure indicators (`blocked_clients`, `evicted_keys`) +- command rates and latency where available + +Required correlation: + +- overlay Redis telemetry with stage latency panels for the same run window +- identify inflection points when increasing concurrency or task counts + +### 5) Failure-Injection Tests for `/tasks` and `/results` + +Inject deterministic failures between workers and backend endpoints: + +- added latency (for example +250 ms, +1 s) +- packet loss (for example 2%, 5%) +- temporary disconnects + +Validate resilience behavior: + +- retries occur as expected +- no duplicated final writes +- eventual consistency of terminal simulation status +- bounded recovery time after link restoration + +Record per test: + +- success/failure +- retries attempted +- recovery latency +- final state correctness + +## Execution Protocol + +Use this run protocol for reproducibility: + +1. Freeze code revision (record git SHAs for backend, UI, docs notes). +2. Use fixed dataset and simulator settings for all scenarios. +3. Warm up services once before recording metrics. +4. Run scenario matrix in randomized order to reduce temporal bias. +5. Export dashboards/traces/raw CSV after each scenario group. +6. Store artifacts under a date-stamped directory. + +Suggested artifact structure: + +```text +rework-orchestration/research/phase-1-results/YYYY-MM-DD/ + timings/ + payloads/ + merge-profiles/ + redis/ + resilience/ + summary.md +``` + +## Phase 1 Exit Criteria + +Phase 1 can be considered complete when all are true: + +1. Timing percentiles are available for run, merge, and persistence across S1-S8. +2. Payload-size and endpoint-latency relationship is quantified. +3. Merge CPU and memory hotspots are evidenced for 4, 8, 16, and 32 tasks. +4. Redis saturation behavior is visible under concurrent load. +5. Failure-injection results show current retry/idempotency limits and recovery characteristics. + +The output of this runbook becomes input evidence for ADR option scoring in Phase 2. From c2a9edd4a67569b83dacd46142024d6c9fe7f76d Mon Sep 17 00:00:00 2001 From: lythx Date: Sun, 12 Apr 2026 12:36:58 +0200 Subject: [PATCH 9/9] remove /rework-orchestration/context/.gitkeep --- src/content/docs/rework-orchestration/context/.gitkeep | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 src/content/docs/rework-orchestration/context/.gitkeep diff --git a/src/content/docs/rework-orchestration/context/.gitkeep b/src/content/docs/rework-orchestration/context/.gitkeep deleted file mode 100644 index e69de29..0000000