Armor core libraries with symbol visibility

[Copilot]

• Reset branch to current main state per reviewer request
• Create PhlexSymbolVisibility.cmake module
• Add phlex_apply_symbol_visibility() calls to all 6 shared library CMakeLists.txt files
• Add export macros to phlex_utilities headers (hashing.hpp, resource_usage.hpp)
• Add export macros to phlex_graph headers (serializer_node.hpp)
• Add export macros to phlex_model headers (9 files)
• Add export macros to phlex_core headers (26 files including concurrency.hpp)
• Add export macros to phlex_configuration_internal headers (configuration.hpp)
• Add export macros to run_phlex headers (load_module.hpp, run.hpp, version.hpp)
• Apply cmake-format
• Centralize export header generation to PROJECT_BINARY_DIR/include
• Install generated export headers for downstream consumers
• Fix operator<< friend/free declaration visibility inconsistency in data_cell_index.hpp
• Code review
• Security scan (8 pre-existing actions alerts, none from this change)

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[greenc-FNAL]

@phlexbot format

[github-actions]

Automatic markdownlint fixes pushed (commit 3299ec5).
⚠️ Note: Some issues may require manual review and fixing.

[github-actions]

No automatic jsonnetfmt fixes were necessary.

[github-actions]

Automatic clang-format fixes pushed (commit 943ef76).
⚠️ Note: Some issues may require manual review and fixing.

[github-actions]

Automatic cmake-format fixes pushed (commit ccb09dd).
⚠️ Note: Some issues may require manual review and fixing.

[Copilot]

Pull request overview

Updates the symbol-visibility feature branch to main and completes hidden-by-default symbol export coverage across Phlex shared libraries, while also modernizing the driver/source plumbing (data-cell indexing, providers, product queries) and refreshing tests/examples accordingly.

Changes:

• Apply GenerateExportHeader + hidden visibility presets and expand export-macro coverage across all shared libraries.
• Replace legacy level-id/label APIs with data_cell_index + product_query (and update tests/configs/plugins accordingly).
• Add/refresh Python/plugin tooling and CI hygiene (ruff/mypy config, SARIF helper, workflow tweaks).

Reviewed changes

Copilot reviewed 287 out of 289 changed files in this pull request and generated 17 comments.

Show a summary per file

File	Description
test/yielding_driver.cpp	Update test to data_cell_index driver model
test/vector_of_abstract_types.cpp	Update graph test to providers + "_in(layer)" queries
test/utilities/CMakeLists.txt	Migrate tests to cet_test
test/specified_label.cpp	Remove tests for deleted specified_label API
test/replicated.cpp	Narrow namespace usage for updated utilities
test/python/verify.py	Add Python observer helper for tests
test/python/test_phlex.py	Update Python import expectations / docs
test/python/sumit.py	Add numpy-based Python algorithm test module
test/python/source.cpp	Add C++ providers for Python tests
test/python/registry.py	Remove old Python registry glue
test/python/reducer.py	Add Python reduction workflow test module
test/python/pyvec.jsonnet	Add Python/numpy config fixture
test/python/pyreduce.jsonnet	Add Python reduction config fixture
test/python/pyfailure.jsonnet	Add intentional Python config failure fixture
test/python/pyconfig.jsonnet	Add “all config types” Python fixture
test/python/pyadd.jsonnet	Update Python add fixture to new driver/sources layout
test/python/phlexpy.py	Update cppyy bootstrap + pythonization docs
test/python/failing_test_wrap.sh	Add wrapper for expected-failure tests
test/python/driver.cpp	Remove legacy C++ driver for Python tests
test/python/all_config.py	Add Python-side configuration consumer
test/python/adder.py	Replace cppyy-defined add with pure Python + registration
test/provider_test.cpp	New provider-focused integration test
test/product_store.cpp	Extend product_store tests for size/empty & id changes
test/product_query.cpp	New tests for product_query + _in literal
test/plugins/source.cpp	Remove legacy plugin source
test/plugins/output.cpp	Update plugin registration macro / namespaces
test/plugins/module.cpp	Update plugin to product_query + new macro
test/plugins/ij_source.cpp	New provider plugin for i/j inputs
test/plugins/add.jsonnet	Update plugin job config to new driver/sources layout
test/plugins/CMakeLists.txt	Add provider plugin + migrate job test to cet_test
test/multiple_function_registration.cpp	Update multi-transform test to provider inputs / new hierarchy
test/mock-workflow/three_tuple_algorithm.cpp	Update workflow module registration + input index type
test/mock-workflow/source.cpp	Remove legacy mock-workflow source
test/mock-workflow/pd_fast_sim.cpp	Update plugin registration macro
test/mock-workflow/mock-workflow.jsonnet	Update workflow config to driver+provider layout
test/mock-workflow/largeant.cpp	Update plugin registration macro
test/mock-workflow/ion_and_scint.cpp	Update plugin registration macro
test/mock-workflow/id_provider.cpp	New provider plugin for “id” product
test/mock-workflow/event_product.libsonnet	Add helper for event-layer product specs
test/mock-workflow/algorithm.hpp	Update algorithm test helper to use product_query inputs
test/mock-workflow/SinglesGen.libsonnet	Update config keys (cpp) + product specs
test/mock-workflow/MC_truth_algorithm.cpp	Update input index type
test/mock-workflow/G4Stage2.libsonnet	Update config keys + product specs
test/mock-workflow/G4Stage1.libsonnet	Update config keys + product specs
test/mock-workflow/CMakeLists.txt	Replace source plugin + migrate test execution to cet_test
test/memory-checks/many_events.cpp	Update memory-check driver/source plumbing
test/memory-checks/CMakeLists.txt	Migrate test to cet_test + link layer_generator
test/max-parallelism/provide_parallelism.cpp	Add provider plugin for parallelism value
test/max-parallelism/check_parallelism_default.jsonnet.in	Update config to driver+provider layout
test/max-parallelism/check_parallelism.cpp	Remove embedded source; update to product_query input
test/function_registration.cpp	Update test inputs to provider registration
test/framework_graph.cpp	Add new graph behavior tests (exceptions, single-thread progress)
test/form/test_helpers.hpp	Add helpers for FORM test type map
test/form/form_test.jsonnet	Add form-module job config
test/form/data_products/CMakeLists.txt	Clean up ROOT dictionary linkage
test/form/CMakeLists.txt	Migrate FORM tests to cet_test + add job test
test/filter_impl.cpp	Add test for data_map completeness behavior
test/demo-giantdata/waveforms.cpp	Remove logging hooks; simplify dtors
test/demo-giantdata/waveform_generator_input.cpp	Remove logging hooks; simplify dtors
test/demo-giantdata/waveform_generator.hpp	Remove unused members/includes
test/demo-giantdata/waveform_generator.cpp	Remove logging hooks; simplify ctor/dtor
test/demo-giantdata/user_algorithms.hpp	Simplify APIs (drop unused id args)
test/demo-giantdata/user_algorithms.cpp	Remove logging hooks; simplify clamp/accumulate
test/demo-giantdata/CMakeLists.txt	Convert demo to cet_test and link generator
test/data_cell_index.cpp	Replace level-id tests with data-cell index hashing test
test/configuration.cpp	Add configuration error and product_query parsing tests
test/class_registration.cpp	Update test inputs to providers + product_query
test/cached_product_stores.cpp	Remove tests for deleted cache helper
test/cached_execution_source.hpp	Remove legacy cached execution source
test/cached_execution.cpp	Update cached execution test to providers + layer generator
test/benchmarks/verify_even_fibonacci_numbers.cpp	Update plugin macro + product_query input parsing
test/benchmarks/verify_difference.cpp	Update config parsing to product_query inputs
test/benchmarks/read_index.cpp	Update plugin macro + config parsing
test/benchmarks/read_id.cpp	Update id type + input query
test/benchmarks/plus_one.cpp	Update plugin macro + input layer
test/benchmarks/plus_101.cpp	Update plugin macro + input layer
test/benchmarks/last_index.cpp	Update id type + input layer
test/benchmarks/benchmarks_source.cpp	Remove legacy benchmark source
test/benchmarks/benchmarks_provider.cpp	Add provider plugin for benchmark id product
test/benchmarks/benchmark-09.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-08.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-07.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-06.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-05.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-04.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-03.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-02.jsonnet	Update config to driver+provider layout
test/benchmarks/benchmark-01.jsonnet	Update config to driver+provider layout
test/benchmarks/accept_fibonacci_numbers.cpp	Update plugin macro + product_query input parsing
test/benchmarks/accept_even_numbers.cpp	Update plugin macro + product_query input parsing
test/benchmarks/accept_even_ids.cpp	Update id type + config parsing
test/benchmarks/CMakeLists.txt	Replace source plugin with provider + migrate job tests
test/adjust_config.cpp	Add tests for module config normalization (cpp/py)
scripts/sarif-alerts.py	Add SARIF alert printing tool
scripts/export_llvm_lcov.py	Add docstrings for script entrypoints
scripts/create_coverage_symlinks.py	Add docstrings for coverage symlink helper
pyproject.toml	Introduce ruff+mypy configuration
plugins/python/src/wrap.hpp	Add Python registration wrappers + GIL RAII
plugins/python/CMakeLists.txt	Add Python plugin build + optional NumPy support
plugins/generate_layers.cpp	Add configurable layer-generator driver plugin
plugins/CMakeLists.txt	Add core plugins build/install
phlex/utilities/stripped_name.hpp	Remove deleted utility header
phlex/utilities/stripped_name.cpp	Remove deleted utility implementation
phlex/utilities/async_driver.hpp	Switch to std::jthread + propagate driver exceptions
phlex/utilities/CMakeLists.txt	Migrate utilities build/install to cetmodules + visibility
phlex/module.hpp	Replace old registration macro with shared plugin macro helper
phlex/model/qualified_name.hpp	Remove deprecated qualified-name API
phlex/model/qualified_name.cpp	Remove deprecated qualified-name implementation
phlex/model/products.hpp	Switch to product_specification + export + add size/empty
phlex/model/products.cpp	Implement size/empty
phlex/model/product_specification.hpp	Add replacement for qualified-name outputs (with type id)
phlex/model/product_specification.cpp	Implement product_specification + helpers
phlex/model/product_matcher.hpp	Rename level→layer terminology + export
phlex/model/product_matcher.cpp	Update matcher pattern strings for layer terminology
phlex/model/level_id.hpp	Remove legacy level-id API
phlex/model/level_counter.hpp	Remove legacy level-counter API
phlex/model/level_counter.cpp	Remove legacy level-counter implementation
phlex/model/handle.hpp	Update handle to carry data_cell_index
phlex/model/fwd.hpp	Add data-cell index fwd decls + update model fwd set
phlex/model/data_layer_hierarchy.hpp	Rename/replace level hierarchy with data-layer hierarchy
phlex/model/data_cell_index.hpp	Add new data-cell index type
phlex/model/data_cell_counter.hpp	Add new counters for flush accounting
phlex/model/data_cell_counter.cpp	Implement new counters
phlex/model/CMakeLists.txt	Migrate model build/install to cetmodules + visibility
phlex/metaprogramming/type_deduction.hpp	Expand traits/concepts (atomic/container/tuple helpers)
phlex/metaprogramming/CMakeLists.txt	Migrate metaprogramming install/export to cetmodules
phlex/graph/serializer_node.hpp	Include-order tweak for export header
phlex/graph/serial_node.hpp	Include-order tweak for export header
phlex/graph/CMakeLists.txt	Migrate graph build/install to cetmodules + visibility
phlex/driver.hpp	Add unified driver plugin registration + create_next helper
phlex/detail/plugin_macros.hpp	Add shared plugin registration macro machinery
phlex/core/upstream_predicates.hpp	Rename when to experimental_when
phlex/core/store_counters.cpp	Update flush/store accounting to data-cell ids
phlex/core/specified_label.hpp	Remove deprecated specified-label API
phlex/core/specified_label.cpp	Remove deprecated specified-label implementation
phlex/core/registration_api.cpp	Rename when to experimental_when in API
phlex/core/registrar.hpp	Export helper used across shared-library boundary
phlex/core/products_consumer.hpp	Switch inputs to product_query + export
phlex/core/products_consumer.cpp	Switch inputs to product_query
phlex/core/product_query.hpp	Add product_query + _in(layer) literal + type population
phlex/core/product_query.cpp	Implement product_query + literal error handling
phlex/core/node_catalog.hpp	Export node_catalog + add provider catalog
phlex/core/node_catalog.cpp	Add providers to execution_counts + throw on unknown name
phlex/core/multiplexer.hpp	Update multiplexer finalize model for providers
phlex/core/message_sender.hpp	Update sender to use data-layer hierarchy + data-cell ids
phlex/core/message_sender.cpp	Update to new hierarchy constructor
phlex/core/message.hpp	Switch to product_query ports + export required symbols
phlex/core/message.cpp	Update to data_cell_index and new error text
phlex/core/input_arguments.hpp	Switch retrievers to product_query + export duplicate check
phlex/core/input_arguments.cpp	Update duplicate detection types
phlex/core/graph_proxy.hpp	Add provide() to graph proxy + namespace adjustments
phlex/core/glue.hpp	Add provider registration + export name verification
phlex/core/fwd.hpp	Move framework_driver alias to phlex::framework_driver
phlex/core/filter.hpp	Export filter class
phlex/core/end_of_message.hpp	Update to new hierarchy + export
phlex/core/end_of_message.cpp	Update to new hierarchy types
phlex/core/edge_maker.hpp	Add provider edge support + export helper
phlex/core/edge_maker.cpp	Implement provider edge wiring
phlex/core/edge_creation_policy.hpp	Switch producer matching to product_query + include types
phlex/core/edge_creation_policy.cpp	Add type-aware producer matching + better diagnostics
phlex/core/detail/maybe_predicates.hpp	Export predicate extraction + rename config key
phlex/core/detail/maybe_predicates.cpp	Read experimental_when from config
phlex/core/detail/make_algorithm_name.hpp	Export algorithm-name helper
phlex/core/detail/filter_impl.hpp	Export filter maps + switch to product_query
phlex/core/detail/filter_impl.cpp	Fix completeness logic for sparse store vectors
phlex/core/declared_unfold.cpp	Update unfold generator to new data-cell API
phlex/core/declared_transform.cpp	Update ctor arg types + improve cached-store reporting
phlex/core/declared_provider.cpp	Add declared provider implementation
phlex/core/declared_predicate.hpp	Switch to product_query + data-cell hashes + export
phlex/core/declared_predicate.cpp	Switch ctor arg types
phlex/core/declared_output.hpp	Export declared_output
phlex/core/declared_observer.hpp	Switch to product_query + data-cell hashes + export
phlex/core/declared_observer.cpp	Switch cached-hash map key type
phlex/core/declared_fold.cpp	Switch ctor arg types
phlex/core/consumer.hpp	Export consumer base
phlex/core/concurrency.cpp	Move concurrency constants to phlex namespace
phlex/core/concepts.hpp	Add provider concept
phlex/core/cached_product_stores.hpp	Remove deprecated store-cache helper
phlex/configuration.cpp	Add product_query JSON conversion + keys() helper
phlex/concurrency.hpp	Export concurrency + move to phlex namespace
phlex/app/version.hpp	Export version() across shared library boundary
phlex/app/run.hpp	Export run() across shared library boundary
phlex/app/run.cpp	Update config schema (driver/modules/sources) + better errors
phlex/app/phlex.cpp	Catch+print top-level exceptions in CLI
phlex/app/load_module.hpp	Export app API + add adjust_config + new loader functions
phlex/app/CMakeLists.txt	Migrate app build to cetmodules + symbol visibility
phlex/CMakeLists.txt	Register export set + split configuration lib + install headers
form/storage/CMakeLists.txt	Formatting / target definition cleanup
form/root_storage/root_ttree_container.cpp	Fix write semantics on destruction + add guard
form/root_storage/CMakeLists.txt	Formatting / target definition cleanup
form/mock_phlex/phlex_toy_core.hpp	Remove mock-phlex shim (no longer used)
form/mock_phlex/phlex_toy_core.cpp	Remove mock-phlex shim implementation
form/mock_phlex/phlex_toy_config.hpp	Remove mock-phlex config shim
form/mock_phlex/phlex_toy_config.cpp	Remove mock-phlex config shim implementation
form/mock_phlex/CMakeLists.txt	Remove mock-phlex library
form/form/form.hpp	Replace mock-phlex types with FORM-local types
form/README.md	Minor markdown cleanup
form/CMakeLists.txt	Enable PIC + add form_module plugin
codecov.yml	Raise coverage thresholds
README-dev.md	Remove developer notes file
Modules/private/PhlexTargetUtils.cmake	CMake formatting/cleanup
Modules/private/PhlexSymbolVisibility.cmake	CMake formatting/cleanup for visibility helper
.github/workflows/python-fix.yaml	Add workflow to auto-fix Python formatting/lint
.github/workflows/add-issues.yaml	Pin action by SHA + permissions hardening
.github/dependabot.yml	Add Dependabot for GitHub Actions
.github/actions/get-pr-info/action.yaml	Add composite action to resolve PR refs from comments
.github/actions/generate-build-matrix/action.yaml	Add composite action for dynamic build matrix
.github/actions/detect-relevant-changes/action.yaml	Add python file patterns + ref validation
.github/actions/detect-act-env/action.yaml	Add act-environment detection helper
.github/actions/configure-cmake/action.yaml	Refactor CMake configure args + enable color forcing
.github/actions/build-cmake/action.yaml	Force colored output
.github/actionlint.yaml	Add actionlint configuration scaffolding
.github/CodeQL-README.md	Markdown/formatting improvements
.github/CODEOWNERS	Add CODEOWNERS enforcement baseline
.flake8	Remove flake8 config (ruff replaces it)

[greenc-FNAL]

@copilot I think for maximum clarity, it would be better to reset this branch to upstream/main and then re-do the work following the current philosophy, library names, etc. Otherwise this looks like a huge body of work that would be way to much for a human to review.

[Copilot]

@copilot I think for maximum clarity, it would be better to reset this branch to upstream/main and then re-do the work following the current philosophy, library names, etc. Otherwise this looks like a...

Done. In commit aeae5d2 I reset the branch to current main, then in c4cb573 I re-implemented the symbol visibility changes cleanly on top. The diff is now purely the visibility work — 51 files changed (1 new CMake module, 7 CMakeLists.txt edits, 43 header files with export macros). No merge noise.

[Copilot]

Pull request overview

Copilot reviewed 51 out of 51 changed files in this pull request and generated 3 comments.

[greenc-FNAL]

@copilot apply changes based on the comments in this thread

[Copilot]

@copilot apply changes based on the comments in this thread

All three review comments addressed in 017903d:

• Export headers now generate into ${PROJECT_BINARY_DIR}/include (centralized)
• Export headers are installed via install(FILES ...)
• operator<< friend/free declaration inconsistency fixed in data_cell_index.hpp

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

@@           Coverage Diff           @@
##             main     #322   +/-   ##
=======================================
  Coverage   82.26%   82.26%           
=======================================
  Files         127      127           
  Lines        3102     3102           
  Branches      547      547           
=======================================
  Hits         2552     2552           
  Misses        333      333           
  Partials      217      217           

Flag	Coverage Δ
unittests	82.26% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
phlex/configuration.hpp	95.23% <ø> (ø)
phlex/core/declared_fold.hpp	94.82% <ø> (ø)
phlex/core/declared_observer.hpp	100.00% <ø> (ø)
phlex/core/declared_output.hpp	100.00% <ø> (ø)
phlex/core/declared_predicate.hpp	89.65% <ø> (ø)
phlex/core/declared_provider.hpp	100.00% <ø> (ø)
phlex/core/declared_transform.hpp	91.30% <ø> (ø)
phlex/core/declared_unfold.hpp	94.73% <ø> (ø)
phlex/core/detail/filter_impl.hpp	100.00% <ø> (ø)
phlex/core/edge_creation_policy.hpp	81.81% <ø> (ø)
... and 22 more

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[greenc-FNAL]

@phlexbot clang-fix

[github-actions]

Automatic clang-format fixes pushed (commit 47f34ae).
⚠️ Note: Some issues may require manual review and fixing.

[greenc-FNAL]

@phlexbot format

[github-actions]

No automatic markdownlint fixes were necessary.

[github-actions]

Automatic cmake-format fixes pushed (commit 8ba091a).
⚠️ Note: Some issues may require manual review and fixing.

[github-actions]

No automatic jsonnetfmt fixes were necessary.

[github-actions]

No automatic clang-format fixes were necessary.