Accept trailing whitespace between `\` and newline in line continuations by wshlavacek · Pull Request #85 · RuleWorld/PyBioNetGen

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-10T23:17:39Z

Summary

`BNGFile.strip_actions` collapses `\` continuations before stripping action lines, but the regex `r"\\n"` rejects shapes like:

```
method=>"ode",<space>
```

which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too.

Fix

Loosen the regex to `r"\[ \t]*\n"`.

Note on conflict with #79

This PR and #79 ("Don't collapse `\` continuations inside commented BNGL lines") both modify the same line. Logically the two fixes compose — the combined regex would be `r"^([^#\n])\[ \t]\n"` with MULTILINE — but I've kept them as separate PRs per the audit's split guidance. Whichever lands first, the other can rebase trivially.

Test plan

Existing CI passes
A model with `...,\...` no longer drops the continuation line on the floor

`BNGFile.strip_actions` collapses `\<newline>` continuations before stripping action lines, but the regex `r"\\\n"` rejects shapes like method=>"ode",\<space><newline> which appear in real-world BNGL. BNG2.pl tolerates trailing whitespace between the `\` and the newline; the modelapi parser should too. Fix: loosen the regex to `r"\\[ \t]*\n"`.

Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR

…es and warnings (#85) * Refactor multi-compartment volume correction warning - Replace simple flag break with logic that dynamically collects all unique compartment names from a rule's reactants. - Replace `FIXME: what do we do if we have more than one compartment?` with proper runtime checking that logs a specific `WARNING:ATOMIZATION` via `logMess` when a reaction's reactants span multiple compartments. - Preserve backward-compatible default behavior (using the first found compartment's volume) but improve code readability and maintainability. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #85 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacekand others added 4 commits May 10, 2026 17:17

Merge branch 'main' into modelapi-b4-trailing-whitespace-continuation
65e8af4

Trigger GitHub PR status refresh
cb1df61

Merge main into modelapi-b4-trailing-whitespace-continuation
df0e6fc
Resolved conflict by combining: - Comment-aware continuation handling from main (don't collapse backslashes in comments) - Trailing whitespace tolerance from this PR