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Clean up block warning paths - #97

Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom
wshlavacek:block-warning-cleanup
May 12, 2026
Merged

Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom
wshlavacek:block-warning-cleanup

Conversation

@wshlavacek

@wshlavacekwshlavacek commented May 12, 2026

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Summary

  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths

Testing

  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py

@jrfaeder
jrfaeder merged commit 7dddd22 into RuleWorld:mainMay 12, 2026
17 checks passed
wshlavacek added a commit to wshlavacek/PyBioNetGen that referenced this pull request May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek deleted the block-warning-cleanup branch May 15, 2026 15:13
wshlavacek added a commit to wshlavacek/PyBioNetGen that referenced this pull request May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit that referenced this pull request Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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@wshlavacek@jrfaeder
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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


Copy Markdown

Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


Copy Markdown

Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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@wshlavacek@jrfaeder

, 'i');
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var __re = new RegExp('^' + ".*" + '
Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


Copy Markdown

Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


Copy Markdown

Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


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Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


Copy Markdown

Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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2 participants

@wshlavacek@jrfaeder

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Clean up block warning paths by wshlavacek · Pull Request #97 · RuleWorld/PyBioNetGen · GitHub
Skip to content
Clean up block warning paths - #97
Merged
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
May 12, 2026
Merged
Clean up block warning paths#97
jrfaeder merged 1 commit into
RuleWorld:mainfrom 
wshlavacek:block-warning-cleanup
Conversation
@wshlavacek
@wshlavacekwshlavacek
commented
May 12, 2026

Copy link


Copy Markdown

Contributor
Summary
  • clean up warning-only block setattr paths in the model and network block modules
  • keep existing items unchanged when warning-only assignments receive unsupported values
  • add focused upstream-safe regression tests for those warning paths
Testing
  • uv run pytest tests/test_block_warning_paths.py -q
  • uv run pytest tests/test_bng_parsing.py::test_network_parse -q
  • uvx black --check bionetgen/modelapi/blocks.py bionetgen/network/blocks.py tests/test_block_warning_paths.py
@jrfaeder
jrfaeder
merged commit 7dddd22
into
RuleWorld:mainMay 12, 2026

17 checks passed

wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 13, 2026
@wshlavacek
Preserve PRRuleWorld#97numeric-failure warning text after setattr d…
dd283f4
…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
wshlavacek
deleted the

block-warning-cleanup

branch
May 15, 2026 15:13
wshlavacek added a commit
to wshlavacek/PyBioNetGen
that referenced
this pull request
May 19, 2026
@wshlavacek@claude
Fix block __setattr__ warning-text assertions (5 stale tests)
b557ceb
Five tests asserted the pre-PR-RuleWorld#97 warning wording. When a numeric block
field is assigned a non-coercible value, the shared _set_item_attribute
helper (commit 8de992a) emits "...; keeping existing {num_field}" — the
field that was preserved ("size" for compartments, "value" for
parameters) — which PR RuleWorld#97 standardized on. The tests still expected the
older "keeping existing {kind}" wording ("compartment"/"parameter"), so
they had failed on main ever since.
The current message is correct and more informative (it names the field
kept, not the block kind); the non-numeric branch still says "keeping
existing {kind}" and those tests already pass. Update the five numeric-
assignment assertions to the canonical wording. No product code change.
Full suite: 1311 passed, 0 failed, 4 skipped — clears the long-standing
5-failure caveat.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
jrfaeder pushed a commit
that referenced
this pull request
Jul 20, 2026
@akutuva21@google-labs-jules
🧹 [code health improvement] Resolve FIXME by adding interaction sourc…
ce62863
…e information (#97)
* refactor: resolve FIXME in pathwaycommons warning messages
Extracted 'BIOGRID_INTERACTION_ID' and 'PUBMED_ID' from the BioGrid API JSON response to append exact source information to the logger warning messages. Removed the unresolved FIXME comment concerning an interactive interaction selection mode, as blocking the execution pipeline with user prompts is an anti-pattern for PyBioNetGen.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
* chore: PR #97 remove forbidden artifacts and run black
---------
Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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2 participants

@wshlavacek@jrfaeder