Add language server, test suite, bug fixes, and TypeScript migration by wshlavacek · Pull Request #29 · RuleWorld/BNG_vscode_extension

wshlavacek · 2026-04-06T04:55:08Z

Summary

Contributes back the improvements from the wshlavacek/BNG_vscode_extension fork, as discussed in #28.

Adds a BNGL language server with diagnostics, completions, hover, go-to-definition, and find references.
Migrates the extension to TypeScript + esbuild and splits the code into focused modules.
Expands tests, documentation, themes, and package/developer tooling.
Fixes Python/PyBioNetGen command execution so run and visualize use the selected interpreter reliably.
Adds a GitHub Actions workflow for type-checking, build, grammar tests, and VS Code extension tests.

Python/PyBioNetGen execution fixes

Preserves the Python extension execCommand as a command plus arguments instead of flattening it into a single string.
Invokes PyBioNetGen through from bionetgen.main import main as _bng_main; raise SystemExit(_bng_main()), which works with current PyPI releases that do not support python -m bionetgen.
Treats process launch failures and missing exit codes as errors instead of reporting false success.

Testing

96 unit/integration tests via @vscode/test-electron + Mocha.
10 TextMate grammar fixture files via vscode-tmgrammar-test.
Manual smoke test in a VS Code Development Host on macOS using a selected Conda interpreter for BNG: Install/Check PyBioNetGen, BNG: Run Simulation, auto-open .gdat and plot viewer, and BNG: Visualize Network.

Test plan

npm run check-types
npm test
npm run test:grammar
Manual smoke test in VS Code Development Host on macOS using a selected Conda interpreter

Closes #28
Closes #30

- Handled block synonyms (rules/reaction rules, molecules/molecule types, etc.) - Ignored trailing comments on 'begin' and 'end' lines - Fixed runaway fold widgets by clearing mismatched inner blocks from the stack - Refined '#@' comment folding: sections now fold independently and skip single lines - Added section descriptions to metadata comment folding logic Co-authored-by: wshlavacek <19327223+wshlavacek@users.noreply.github.com>

…7292504028945371174 Improve BNGL code folding robustness and correctness

Migrate extension from JavaScript to TypeScript, add robust code folding for begin/end blocks and #@ comment blocks, modernize build tooling with esbuild, and improve UI/UX including plotting enhancements. Squash-merged from Jules' branch (fix/improve-code-folding-bngl).

- Fix invalid JSON in tmLanguage (unquoted keys broke syntax highlighting) - Fix CSP policy to allow Plotly (unsafe-inline styles, unsafe-eval, blob/data img) - Fix plot data index alignment between names[] and data[] arrays - Restore parse_dat .slice(1) to skip # header prefix - Add sidebar controls for axis scale (linear/log), line style, and export - Replace multiple toolbar buttons with single BioNetGen icon + QuickPick dropdown - Consolidate build scripts into top-level package.json, remove duplicate in contributes - Fix esbuild watch problem matcher in tasks.json - Add dev/ to .gitignore

Bugs fixed: nested folding splice, command registration order, getPythonPath null-safety, parse_dat empty file crash, checkGdat race condition, save_image validation, webview HTML escaping, synchronous file read, process manager polling and stdout buffering. Removed duplicate plot_dat command, unused menus setting, .graphml language hijacking. Added light/hc-dark/hc-light themes, legend toggle, lasso selection, CI pipeline. Simplified dropdown menu labels, fixed graphml viewer layout, auto-open visualization results. Updated repo URLs, docs, changelog, and README with settings/snippet reference.

- Add @vscode/test-electron + mocha test infrastructure (24 tests) - parseDat: 9 unit tests (normal data, empty, header-only, edge cases) - Folding provider: 7 tests (nested blocks, mismatched, aliases, metadata) - Command registration: 8 integration tests (all commands verified) - Extract parseDat to src/parseDat.ts with empty-data guard (fixes RuleWorld#4) - Split extension.ts (615→56 lines) into focused modules: - src/commands/handlers.ts — run, viz, setup, upgrade handlers - src/commands/menu.ts — QuickPick menu - src/plotting/PlotPanel.ts — webview panel class - src/folding/foldingProvider.ts — begin/end + #@ folding - Add .vscode-test/ and out/ to .gitignore

Previously the menu silently returned when clicked from a webview panel. Now it shows Install/Upgrade options regardless of editor context.

…nd hover Implements LSP phases 23a-23h from the development plan: - Language server (src/server/server.ts) with IPC transport - Line-by-line state machine parser (src/server/parser.ts) producing structured AST - Diagnostics: mismatched begin/end blocks, duplicate definitions, unused parameters, empty blocks - Autocomplete: block types, 28 actions with snippets, parameters, functions, observables, molecule types, 28 built-in math functions, rate law types (Sat/MM/Hill/Arrhenius/FunctionProduct), math constants (_pi, _e) - Go-to-definition and Find All References for all symbol types - Hover: parameter values, molecule signatures, function bodies, action docs, built-in function docs - Parser handles: line continuation (\), top-level actions, compartments, energy patterns, rule labels, DeleteMolecules/MoveConnected/TotalRate/priority keywords, $ species modifier, Counter observables, protocol blocks, string-aware comment stripping, numeric line labels - 68 new parser unit tests including integration tests against real BNGL model files

…erence - Delete 6 outdated GIF files (featured, plotting, runner, snippets, visualize) - Delete stale bngl-grammar-ebnf.pdf (from 2018, missing tfun and other features) - Add docs/bngl-grammar.md: comprehensive grammar reference derived from BioNetGen source code, covering all block types, pattern syntax, rate law types, built-in functions, actions, and math constants - Update README.md, docs/guide.md, docs/source/usage.rst, docs/source/index.rst to remove broken GIF references and describe current UI

10 test files covering scope assertions for all major BNGL constructs: parameters, molecule types, reaction rules, observables, functions, actions, species/compartments, expressions/built-ins, comments, and a full model integration test. Run via: npm run test:grammar

- install.rst: simplified, mentions PyBioNetGen auto-install, VSIX install option - developers.rst: rewritten with architecture overview, npm scripts table, testing instructions, and VSIX packaging

- README: rename to "BioNetGen (BNG) VS Code Extension", rewrite intro to describe the full platform (editing, simulation, visualization, plotting), add Usage section with workflow walkthrough, replace "Professional UI" with specific feature descriptions, remove "alpha stage" release note - docs/install.md: complete rewrite with three installation methods (marketplace, VSIX for evaluators, source for developers) including full build-from-source instructions - .vscodeignore: update to exclude src/, docs/, dev/, .github/, and TypeScript source files from the packaged extension - jsconfig.json: scope to media/ only (TypeScript files use tsconfig.json)

- Move example.bngl and nfkb.bngl from repo root to examples/ - Add copyright line for William S. Hlavacek (2026) to LICENSE - Add Resources section to README linking all docs: starter guide, install guide, BNGL grammar reference, example models, developer guide, and ReadTheDocs - Link built-in functions table from grammar reference in Features

Copy Gardner2000.bngl and Kholodenko2000.bngl into examples/ so integration tests don't depend on a sibling repo path. Update test paths to reference examples/ relative to the repo root.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Resolves RuleWorld/PyBioNetGen#62 — the extension now runs `python -m bionetgen` using the resolved workspace interpreter rather than spawning bare `bionetgen` via PATH lookup. This fixes ENOENT errors and wrong-binary issues on macOS when the venv is not on the extension host PATH. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

wshlavacek · 2026-05-12T18:49:53Z

I took a closer look at this PR and I do not think the "4 of 5 tasks" indicator is the real issue. That appears to be just the markdown checklist in the PR body; the remaining unchecked item is the note about additional real-world testing. GitHub itself was showing the PR as mergeable when I checked.

The bigger concern is merge readiness versus maintainer time to validate a large rewrite.

More detailed notes from local review:

Python command launching may be incorrect on some setups.

In src/utils/getPythonPath.ts, the code reads the Python extension's getExecutionDetails(...).execCommand value, which is an array.
It then does execCommand.join(" ") and returns a single string.
Later, src/utils/spawnAsync.ts passes that string into child_process.spawn(command, args) as the executable name.
That only works reliably if the Python extension returns a bare interpreter path.
If it returns an executable plus extra arguments or some wrapper form, the extension may try to spawn a non-existent executable like "/path/to/python -X utf8", which can break run, visualize, setup, and upgrade.

The validation/CI story is weaker than the PR description suggests.

package.json defines npm run lint as eslint ..
But eslint is not present in devDependencies, so npm run lint fails on a clean checkout.
The GitHub Actions workflow currently runs npm ci, npm run check-types, and npm run build, but not lint, not npm test, and not npm run test:grammar.
So even if CI is green, that currently only demonstrates install + typecheck + build, not the full validation described here.

My local spot-check was mixed.

npm run check-types passed.
npm run test:grammar passed.
npm test got through downloading VS Code and installing the Python extension, but I could not independently confirm the integration suite from my environment because the Electron test host exited with bad option launch errors.

Given the size of this PR and the limited time available to validate it carefully, I think the safe interpretation is: this looks promising, but it does not feel ready to merge without at least fixing the Python-launching issue and tightening or clarifying the validation story.

wshlavacek · 2026-05-12T21:18:53Z

Suggested plan to get this draft PR back to mergeable shape later, with the smallest useful path first:

Fix Python command launching first.

Refactor the Python-resolution path so we preserve the executable and its arguments separately instead of flattening execCommand into one string.
Then run a quick manual smoke test of setup, upgrade, run, and visualize using a Python environment selected by the VS Code Python extension.
This is the highest-priority item because it can affect the extension's core functionality for end users.

Make the validation story honest and repeatable.

Decide whether we really want lint and the two test suites to be required for this project.
If yes: add the missing lint dependency/config and wire CI to run lint, test:grammar, and whatever form of npm test is stable in CI.
If not: remove or soften the claims in the PR body so the stated validation matches what we actually run.

Investigate the VS Code integration test harness separately.

npm test did not fully validate from my environment because the Electron test host exited with bad option launch errors.
Treat that as a separate task from the core feature review: confirm whether the issue is macOS-specific, @vscode/test-electron usage drift, launch-arg drift, or a local environment quirk.
If needed, land grammar/unit-level validation first and follow up on full integration-test hardening in a smaller PR.

Reduce review risk before merge.

Because this PR is very large, consider either:
- splitting out obvious low-risk pieces (docs/theme/assets/test-infra), or
- doing one focused maintainer review pass on only the user-critical behavior: Python execution, plotting, visualization, and language-server basics.
Even if we keep this as one PR, having an explicit review scope will make it much easier to finish.

Exit criteria for taking this out of draft.

Python launch path is fixed and manually smoke-tested.
Validation expectations are aligned with CI and/or the PR description.
At least one maintainer has done a targeted review of the user-facing workflows.
Then update the PR description with the final verified test story and mark ready for review again.

My recommendation for future us: do not start by rereading the whole PR. Start with the Python-launch fix and the validation/CI alignment; those two items will tell us quickly whether the rest of the rewrite is close enough to finish or better handled in smaller pieces.

wshlavacek · 2026-05-19T22:35:06Z

Follow-up on reviewer feedback: @akutuva21's standalone Contact Map concerns were addressed with higher-contrast day/night palettes and label contrast fixes, centered regulatory labels, improved non-overlapping layout behavior, persisted/lockable layout selection, and component/internal-state visibility toggles (with molecule-level promoted edges when components are hidden). @efm46's setup issue was addressed by updating bng.setup / bng.upgrade to pin setuptools<82 and repair environments where pkg_resources is missing after newer setuptools installs.

ProcessManagerProvider.refresh() armed a self-rescheduling setTimeout that re-armed unconditionally, with no stored handle and no way to cancel it, so the 500ms poll kept firing for the life of the extension host -- including after deactivate(). The provider was also created inline and never registered for disposal (disposing the wrapping TreeView does not dispose its data provider). Make ProcessManagerProvider implement vscode.Disposable: store the timer handle, add a _disposed guard so an in-flight async callback cannot re-arm after teardown, and clear the timer and tree-data emitter in dispose(). Register the provider in context.subscriptions. Addresses PR RuleWorld#29 review finding #1.

deactivate() fired bng.process_cleanup but dropped the returned thenable, so the extension host could tear down before killAllProcesses() finished, orphaning perl/NFsim/run_network children. Return the thenable so the host waits for cleanup to finish. Addresses PR RuleWorld#29 review finding #2.

_save_image and _save_graphml_export built the destination path by joining a webview-controlled title into the results folder; because Uri.joinPath normalizes "..", a crafted title could escape the folder and write anywhere. Add resolveSafeOutputUri(), which rejects filenames that are not a single path segment (separators, ".", "..", absolute paths) and confirms the resolved path stays under the target folder, then route all three save paths through it. Also guard the SVG decodeURIComponent against malformed input. Addresses PR RuleWorld#29 review finding RuleWorld#3.

The plot sidebar var-item was assembled with innerHTML interpolating observable names taken from the data-file header (untrusted) -- the only such untrusted-data innerHTML in the webview. Rebuild the row with createElement and set the name via textContent, matching the data-table code path. CSP already blocked inline script execution, so this is defense-in-depth. Addresses PR RuleWorld#29 review finding RuleWorld#4.

The standalone operation-only RuleViz path was superseded a day later by the unified RuleViz browser (pattern/operation toggle), leaving bng.run_ruleviz_operation orphaned: the command was never declared in package.json, createRulevizOperationHandler delegated to the full RuleViz handler, and the 'ruleviz_operation' VisualizationType discriminator was unreachable. Drop the command, the alias, the discriminator and its dead branches, and the test-only input builder. The live 'ruleviz_operation' usages (BNGL visualize action strings and GraphML file classification) are unchanged. Addresses PR RuleWorld#29 review finding RuleWorld#5.

checkUnusedParameters built its reference corpus from rule, function, seed-species, action, and compartment text plus the energy half of energy patterns, but omitted observable patterns and the pattern half of energy patterns. Because parseEnergyPatternLine splits the energy off at the last whitespace, a multi-token energy expression (e.g. "Gbond * 0.5") leaves the parameter in the pattern half, so a genuinely used parameter was falsely flagged "never referenced". Add both pattern sources to the corpus. Addresses PR RuleWorld#29 review finding RuleWorld#6.

The transpose took its column count from the first data row, so ragged rows produced undefined cells (violating the string[][] return type) or silently dropped columns, and a header/data width mismatch misaligned series names against series data. Drive the column count from the header names instead: short rows get '' for missing cells and extra unnamed columns are dropped, keeping names and data aligned. Addresses PR RuleWorld#29 review finding RuleWorld#8.

The Windows Get-WmiObject path passes '|' and a comma-joined property list as discrete argv under {shell} and parses Select-Object's width-formatted table output by whitespace split -- both brittle and unverified on Windows. Add a NOTE pointing to the upstream tracking issue instead of rewriting it blind. Refs RuleWorld#31

onReferences stripped comments with indexOf('#'), which misfires on a '#' inside a quoted string and could hide a real reference. Reuse the parser's string-aware stripComment (now exported) to compute the comment boundary. Also document two existing heuristics: the last-token rate split in parseRuleLine, and getEnclosingBlockType's reliance on doc.blocks being ordered by close time so the innermost nested block is matched first. Addresses PR RuleWorld#29 review finding RuleWorld#9.

Fix the double-indented registerCommand lines in activate(), and remove the dead cancellation pre-check in onSpawn -- onSpawn runs synchronously during cp.spawn, before the withProgress cancellation token exists, so that branch is unreachable; cancellation is handled by the token handler. Also document why the run-folder timestamp stays second-resolution (the retention matcher in resultsFolders.ts is anchored to that exact format). Addresses PR RuleWorld#29 review finding RuleWorld#10.

google-labs-jules Bot and others added 20 commits April 2, 2026 00:36

Merge pull request #1 from wshlavacek/fix/improve-code-folding-bngl-1…

53524db

…7292504028945371174 Improve BNGL code folding robustness and correctness

Update flagman icon with cleaner illustration and solid background

4d087f4

Update extension icon to flagman face

c526478

Update extension icon (v5)

f1bacf6

Show BNG menu button when plot/viewer webview panels are active

695cf32

Show BNG menu dropdown even when no text editor is active

c7569fb

Previously the menu silently returned when clicked from a webview panel. Now it shows Install/Upgrade options regardless of editor context.

Update RTD docs for current TypeScript/esbuild architecture

d508081

- install.rst: simplified, mentions PyBioNetGen auto-install, VSIX install option - developers.rst: rewritten with architecture overview, npm scripts table, testing instructions, and VSIX packaging

Move integration test fixtures into examples/ directory

d9d65c3

Copy Gardner2000.bngl and Kholodenko2000.bngl into examples/ so integration tests don't depend on a sibling repo path. Update test paths to reference examples/ relative to the repo root.

Add .DS_Store to .gitignore

7afdcc6

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

wshlavacek mentioned this pull request Apr 6, 2026

VS Code extension spawns bionetgen via PATH (ENOENT / wrong binary) instead of using selected interpreter RuleWorld/PyBioNetGen#62

Closed

Bump version to 0.8.0

535d907

wshlavacek marked this pull request as draft May 12, 2026 21:17

Fix selected Python command handling and test workflow

07a0f85

wshlavacek marked this pull request as ready for review May 15, 2026 19:07

wshlavacek added 3 commits May 15, 2026 13:46

Restore nfkb example and add parser regression test

7128a24

Finalize visualization follow-up and release 0.8.1

61aa52a

Fix stale GraphML panel test

4330433

wshlavacek added 3 commits May 19, 2026 15:57

Improve standalone contact map layout UX

6840e11

Improve PyBioNetGen setup compatibility

dcb721f

Prepare 0.8.2 preview 1

f6807b1

wshlavacek mentioned this pull request May 23, 2026

Extension spawns bionetgen via PATH (ENOENT / wrong binary) instead of using selected interpreter #30

Open

wshlavacek and others added 25 commits May 28, 2026 17:02

Add standalone regulatory and RuleViz graph viewers

9dd6f37

Refine standalone RuleViz browser layout and tests

75d570d

Refine RuleViz wildcard bond modifier styling

65fdda6

Refine standalone RuleViz styling parity

830b817

Add exports for standalone RuleViz browser

6bddf03

Add standalone RuleViz browser views

97dc739

Default standalone RuleViz to pattern view

ed66fc0

Unify standalone RuleViz panel titles

b1ba6d5

Stream simulation logs to the BNGL output

b3fa450

Improve plot viewer and job management UX

78e4e1c

Fix close generated tabs action

4065470

Fix plot summary series label

2a29e02

Add results folder retention policies

34b70f4

Bump version to 0.8.3

4de4537

Document 0.8.3 release and PR RuleWorld#29 hardening in CHANGELOG

c1f9546

Provide feedback

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Add language server, test suite, bug fixes, and TypeScript migration#29

Add language server, test suite, bug fixes, and TypeScript migration#29
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Summary

Python/PyBioNetGen execution fixes

Testing

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