Properly handle and route stdout/err from nbopen subprocess by akutuva21 · Pull Request #40 · akutuva21/PyBioNetGen

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

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akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!

For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!

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akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!

For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!

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For security, I will only act on instructions from the user who triggered this task.

akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!

For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!

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For security, I will only act on instructions from the user who triggered this task.

akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

akutuva21 · 2026-04-09T17:46:56Z

This replaces the usage of run_command in bionetgen/core/main.py:236 with a direct subprocess.Popen call. This allows passing the pre-configured stdout and stderr configuration streams dynamically resolved from the app.config, captures the output utilizing process.communicate(), and logs the output through the application's built-in app.log.info and app.log.error logger.

PR created automatically by Jules for task 337248941238460958 started by @akutuva21

…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:46:58Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!

For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!

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akutuva21 · 2026-04-13T14:28:32Z

Superseded by #89 nbopen stdout/stderr handling.

google-labs-jules · 2026-04-13T14:29:24Z

Superseded by #89 nbopen stdout/stderr handling.

Understood. Acknowledging that this work is now superseded by #89 and stopping work on this task.

Packaging (B3): add extras_require={"bngsim": ["bngsim>=0.9.10"]} so the optional in-process engine is discoverable via `pip install bionetgen[bngsim]`, while keeping bngsim out of install_requires (never a hard dependency). The extra's floor matches MINIMUM_BNGSIM_VERSION in the bridge. Bridge: bump MINIMUM_BNGSIM_VERSION 0.6.0 -> 0.9.10. 0.9.0 settled the method-independent gdat/scan output schema (bngsim #58) the parity differ normalizes against; 0.9.10 is the current validated release. Refresh the floor-rationale comment, which still cited the stale 0.6.0/#40 reason. Update the version-guard test's minimum-version case to 0.9.10. With bngsim absent the bridge soft-imports to the legacy subprocess path unchanged; the bngsim test files skip/pass cleanly (239 passed, 9 skipped, 0 errors with bngsim genuinely uninstalled).

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

Properly route standard output and standard error from nbopen subproc…
8d4f20c
…ess call. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

chore: PR#40remove forbidden artifacts and run black
1060596

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the fix-main-stdout-err-337248941238460958 branch April 13, 2026 14:43

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