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← NGS Analysis WorkbenchCONTENT HISTORY

Update to NGS Analysis Workbench

Snapshot Oct 8, 2026 · 00:04 UTC · version 0.2.18

WHAT CHANGED · RULE-BASED ANALYSIS

Package or technical metadata updated

Package contents changed in 50 files: .codex-plugin/plugin.json, .mcp.json, README.md, …. Open the file diff to inspect the edits.

Observed in package metadata. These changes alone do not establish a new customer-facing feature.

Package file

Before

a32ecaede3ce6d04098191997359900169259682e2b4909200a624fafe2e0ea1

After

5d7af566ffe23ab2d9495c6c7f6cfea3d14156ca2acce06b2ef8f404ed068eef

Package file

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Package file

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Compare saved observations

Download comparison JSON

Changed files

.codex-plugin/plugin.json →

.mcp.json →

README.md →

integrity.json →

mcp/PLUGIN_VENV_VERSION →

mcp/mcp-app.html →

mcp/mcp-inline.html →

mcp/ngs_app_mcp/__main__.py →

mcp/ngs_app_mcp/app.py →

mcp/ngs_compute_mcp/__main__.py →

mcp/ngs_workbench_daemon/persistence/database.py →

mcp/ngs_workbench_daemon/runs.py →

mcp/ngs_workbench_daemon/server.py →

mcp/ngs_workbench_daemon/ssh.py →

mcp/ngs_workbench_mcp/__main__.py →

mcp/ngs_workbench_mcp/app.py →

mcp/ngs_workbench_mcp/approved_execution.py →

mcp/requirements.in →

mcp/requirements.txt →

mcp/rosalind_logging/__init__.py →

mcp/rosalind_logging/mcp.py →

mcp/start_server →

mcp/start_server.cmd →

package-lock.json →

package.json →

scripts/check-release-ci.sh →

src/App.stories.tsx →

src/App.tsx →

src/components/RunHistory.module.css →

src/components/RunHistory.stories.tsx →

src/components/RunHistory.tsx →

src/components/RunHistorySidebar.tsx →

src/design-system/Icon.tsx →

src/design-system/icons/chat-plus.svg →

src/hooks/useNgsWorkbench.ts →

src/inline/RunReviewApp.tsx →

src/inline/client.ts →

src/mcp/client.ts →

src/mcp/ngs.ts →

tests/daemon_test_case.py →

tests/test_daemon_lifecycle.py →

tests/test_mcp_ui.py →

tests/test_nextflow_mcp.py →

tests/test_run_persistence.py →

tests/test_sentry_logging.py →

tests_js/client-logging.test.ts →

tests_js/workflow-catalog.test.ts →

tsconfig.json →

vite.config.ts →

vite.inline.config.ts →

README.md

--- before
+++ after
@@ -85,6 +85,10 @@
 execution; the Codex host authorizes the exact tool call; the MCP server
 revalidates it and submits the approved work to the local Workbench daemon.
 
+On the Runs page, **New pipeline run** opens an editable Codex draft with the
+Workbench plugin mentioned. Describe the pipeline and inputs before sending;
+opening the draft does not select a pipeline or start execution.
+
 SQLite under the local plugin state root owns run lifecycle and history. Public `target + run_dir` identifies execution, with scientific outputs under `<run_dir>/results`. Approval records, source staging, and submitted analyses live in internal local state.
 
 Workbench provides controller log tails and structured execution evidence for local and SSH runs. Codex inspects workflow outputs, writes a local Markdown analysis, and submits it with `update_ngs_run_analysis_summary(registry_run_id, summary_path)`. The daemon saves the summary in the run record; detail and history display it on refresh or reopen.
@@ -103,6 +107,19 @@
 test -s mcp/mcp-inline.html
 ```
 
+For a development or internal distribution, set `VITE_NGS_WORKBENCH_PLUGIN_ID`
+to its installed `plugin-name@marketplace-name` when building. For example:
+
+```bash
+VITE_NGS_WORKBENCH_PLUGIN_ID=ngs-analysis-workbench-dev@plugin-development npm run build
+```
+
+This binds **New pipeline run** to that distribution. Without the override,
+release builds mention `ngs-analysis-workbench@openai-curated-remote`. Set it
+in the packager before building, including when renaming the plugin for local
+testing; copying a production bundle into another marketplace does not retarget
+its mention.
+
 If the same development version is already installed, remove and re-add that
 exact marketplace entry so Codex rebuilds its versioned cache:
 
@@ -145,6 +162,17 @@
 input, reference, runtime, and result provenance, and do not treat successful
 execution as support for a biological claim.
 
+## Server telemetry
+
+The three MCP servers and detached workflow daemon send explicit startup and
+failure records to the Rosalind Sentry Logs project. `ROSALIND_SENTRY_DSN`
+overrides the bundled public ingestion DSN; an empty or invalid override, or
+`ROSALIND_SENTRY_ENABLED=0`, disables logging. Records use fixed messages and
+approved scalar metadata only. Workflow failure details, pipeline logs,
+paths, inputs, scientific content, user identity, and hostname stay local.
+Telemetry is best effort and cannot change execution or approval behavior.
+See [shared logging documentation](../rosalind-logging/README.md).
+
 ## Development
 
 Start the Workbench MCP server from `mcp/`:
@@ -163,12 +191,21 @@
 version creates `$CODEX_HOME/cache/ngs-analysis-workbench/venvs/<version>`;
 later launches reuse that environment. Update `mcp/PLUGIN_VENV_VERSION`
 whenever `mcp/requirements.txt` changes. A shared installation lock protects
-concurrent first launches.
+concurrent first launches. Both launchers enforce `--require-hashes` and
+`--only-binary=:all:` before marking the environment ready or running a server.
+The committed `requirements.txt` includes pinned transitive dependencies and
+SHA-256 artifact hashes for macOS, Linux, and Windows. Edit direct dependencies
+in `mcp/requirements.in`, then regenerate the lock from `mcp/`:
+
+```bash
+uv pip compile --universal --python-version 3.10 --generate-hashes \
+  --only-binary :all: --no-header --output-file requirements.txt requirements.in
+```
 
 Run Python tests from the same directory:
 
 ```bash
-PYTHONPATH=. uv run --no-project --isolated \
+PYTHONPATH=. ROSALIND_SENTRY_ENABLED=0 uv run --no-project --isolated \
   --with-requirements ./requirements.txt \
   python -m unittest discover -s ../tests -p 'test_*.py'
 ```
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