Deduplicate block setattr logging helpers by wshlavacek · Pull Request #100 · RuleWorld/PyBioNetGen

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

wshlavacek · 2026-05-12T16:34:20Z

Summary

factor repeated block __setattr__ logging paths into shared helpers in the model and network block modules
unify logger-backed warnings for invalid non-coercible assignments across the remaining block subclasses
route duplicate action-argument warnings through BNGLogger and fold the duplicate OrderedDict import-guard cleanup into the same refactor
add focused upstream-safe regression tests for the setattr/logging paths

Testing

uv run pytest tests/test_block_setattr_logging.py -q
uv run pytest tests/test_bionetgen.py::test_bionetgen_model tests/test_bionetgen.py::test_action_loading tests/test_bng_parsing.py::test_network_parse -q
uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py bionetgen/modelapi/structs.py tests/test_block_setattr_logging.py

jrfaeder · 2026-05-12T18:22:36Z

@wshlavacek Please check the conficts

wshlavacek · 2026-05-12T18:45:25Z

@jrfaeder conflicts resolved and the branch has been rebased onto current main. The focused block setattr logging tests pass locally, so it should be ready for another look.

wshlavacek · 2026-05-12T21:32:44Z

CI root cause looks narrower than the PR UI suggests: I do not currently see a live merge conflict, but I do see a reproducible warning-message regression causing the full deploy matrix to fail.

The helper dedup changed parameter and compartment warning text from the existing field-specific wording ("keeping existing value" / "keeping existing size") to generic wording ("keeping existing parameter" / "keeping existing compartment"). Upstream tests in tests/test_block_warning_paths.py still assert the older wording, so we now fail the same four assertions across every platform. I reproduced those four failures locally as well.

Tentative fix plan:

Preserve the existing field-specific warning wording for parameter and compartment numeric-assignment failures in both model and network block helpers.
Update tests/test_block_setattr_logging.py so the new focused tests match the established upstream warning contract instead of the regressed generic wording.
Re-run the focused warning-path and block-setattr tests locally, then force-push the repair branch.

I am keeping this PR in draft until that repair is in.

…edup The deduplicated `_set_item_attribute` helper rewrote the numeric-coercion failure warning to "keeping existing {kind}", which regressed the "keeping existing value"/"keeping existing size" wording that PR RuleWorld#97 (now in main) standardized on. The merged `tests/test_block_warning_paths.py` asserts the original wording, so all CI matrix jobs failed after rebase. Restore "keeping existing {num_field} <existing>" (informative trailer from PR RuleWorld#97 included) and align the new `test_block_setattr_logging.py` parameter/compartment fixtures with the canonical messages.

wshlavacek · 2026-05-19T02:47:04Z

These edits have grown stale.

…rsing rules (#100) * fix: Handle zero arguments in pyparsing rules Wrapped `pp.delimitedList` inside `pp.Optional()` for `arg_type_curly`, `list_arg`, and `arg_type_list` in `bionetgen/core/utils/utils.py`. This ensures zero-argument scenarios such as `{}` and `[]` are parsed properly and resolves the TODO statements around zero arguments. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #100 remove forbidden artifacts and run black --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

Deduplicate block setattr logging helpers
319d926

wshlavacek force-pushed the block-setattr-logging-dedup branch from bf84943 to 319d926Compare May 12, 2026 18:45

wshlavacek marked this pull request as draft May 12, 2026 21:32

wshlavacek marked this pull request as ready for review May 13, 2026 05:23

wshlavacek marked this pull request as draft May 13, 2026 05:25

wshlavacek marked this pull request as ready for review May 13, 2026 13:17

wshlavacek closed this May 19, 2026

wshlavacek mentioned this pull request Jun 10, 2026
Deduplicate block __setattr__ logging paths and add regression tests #106
Open

wshlavacek deleted the block-setattr-logging-dedup branch June 10, 2026 16:49

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wshlavacek commented May 12, 2026

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wshlavacek commented May 19, 2026

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wshlavacek commented May 12, 2026

Summary

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jrfaeder commented May 12, 2026

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wshlavacek commented May 12, 2026

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wshlavacek commented May 12, 2026

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wshlavacek commented May 19, 2026

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wshlavacek commented May 12, 2026

Summary

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jrfaeder commented May 12, 2026

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wshlavacek commented May 12, 2026

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wshlavacek commented May 12, 2026

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wshlavacek commented May 19, 2026

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