Add cbcflow testing

[transientlunatic]

Description

This PR adds end-to-end testing for CBCFlow and fixes a minor bug which prevented proper CBCFlow running.

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code refactoring
• Performance improvement
• Test coverage improvement

[Copilot]

Pull request overview

This PR introduces end-to-end/CI coverage around CBCFlow usage and broader workflow execution, alongside a bugfix to improve CBCFlow run correctness (notably around analysis directory layout and scheduler/monitor plumbing).

Changes:

• Updates tests, scripts, docs, and configs to use the analyses/ directory instead of C01_offline/.
• Adds new testing modules (monitor helpers/API, optional dependencies, strategies, HTML reporting) plus HTCondor-based CI workflows.
• Introduces/extends infrastructure modules (strategies expansion, scheduler utilities, pydantic-based priors, lazy file logging, plugin command discovery).

Reviewed changes

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

Show a summary per file

File	Description
tests/test_pipelines/test_lalinference.py	Update git-add paths to new analyses/ layout for pipeline test data.
tests/test_pipelines/test_bayeswave.py	Update git-add and DAG path assertions to analyses/ layout.
tests/test_pesummary_subject_analysis.py	Add SubjectAnalysis tests for PESummary combination behavior.
tests/test_optional_dependencies.py	Add tests for optional/required dependency semantics.
tests/test_monitor_helpers.py	Add unit tests for new monitor helper functions.
tests/test_monitor_api.py	Add unit tests for new programmatic monitor API.
tests/test_logging.py	Add tests for lazy/rotating file logging behavior.
tests/test_html_report.py	Add tests for HTML report rendering enhancements.
tests/test_data/test_strategy_single.yaml	Add test blueprint for single-parameter strategy expansion.
tests/test_data/test_strategy_matrix.yaml	Add test blueprint for matrix strategy expansion.
tests/test_data/test_strategy_event.yaml	Add test event blueprint used by strategy tests.
tests/test_data/blueprints/test_analysis_blueprint.yaml	Add minimal analysis blueprint fixture.
tests/test_custom_states.py	Add unit tests for custom monitor states/handlers.
tests/test_cli_manage.py	Update path assertions to match analyses/ directory structure.
tests/test_blueprints/subject_test_pipeline.yaml	Add blueprint for testing SubjectTestPipeline.
tests/test_blueprints/simple_test_pipeline.yaml	Add blueprint for testing SimpleTestPipeline.
tests/test_blueprints/project_test_pipeline.yaml	Add blueprint for testing ProjectTestPipeline.
tests/test_blueprints/lalinference_quick_test.yaml	Add quick LALInference blueprint fixture.
tests/test_blueprints/gwosc_quick_test.yaml	Add quick GWOSC configuration blueprint fixture.
tests/test_blueprints/gwosc_get_data.yaml	Add GW data download analysis blueprint fixture.
tests/test_blueprints/gwosc_event.yaml	Add a GWOSC-style event blueprint fixture.
tests/test_blueprints/bilby_quick_test.yaml	Add quick bilby analysis blueprint fixture.
tests/test_blueprints/bayeswave_quick_test.yaml	Add quick BayesWave analysis blueprint fixture.
tests/test_blueprints.py	Add importability smoke test for blueprints module.
tests/test_asimov.py	Update version-detection tests to use importlib.metadata errors.
tests/test_application.py	Add tests validating strategy blueprint expansion into analyses.
tests/test_analysis.py	Ensure tmp directory is reset before analysis tests run.
tests/mock_gwdatafind_server.py	Add mock GWDataFind HTTP server used for isolated tests.
tests/manual_test_priors.py	Add manual prior-system integration script (non-automated).
tests/integration/test_gwtc2d1.py	Update pipeline category directory from C01_offline to analyses.
tests/integration/GW190426190642.yaml	Update calibration/PSD paths to analyses/.
scripts/find_calibration.py	Update commit destinations to analyses/calibration/.
scripts/check-ifo.py	Update commit destinations to analyses/calibration/.
sandbox/make-nonspin.py	Use repository default branch instead of assuming master.
sandbox/gitlab-issue-tests.py	Update run category paths to analyses/.
pyproject.toml	Add dependencies/entry points incl. pydantic and testing pipelines.
examples/strategy_examples.yaml	Add strategy usage examples.
examples/scheduler_example.py	Add scheduler API example script.
examples/pesummary_subject_analysis.yaml	Add PESummary SubjectAnalysis blueprint examples.
examples/dependency-examples.yaml	Add dependency specification examples (optional/AND/OR/negation).
examples/demo_html_output.py	Add demo script for HTML dependency/stale indicators.
examples/demo_graph_fix.py	Add demo script for dependency graph/modal dependency data.
examples/README.rst	Add examples directory documentation (rst).
examples/README.md	Add examples directory documentation (md).
examples/MODAL_DEPENDENCIES_GUIDE.md	Document new modal dependency display behavior.
docs/source/user-guide/running.rst	Update docs output examples to analyses/ directory naming.
docs/source/test-interface.rst	Update docs path example to analyses/ directory naming.
docs/source/scheduler-integration.rst	Add scheduler integration guide.
docs/source/python-api.rst	Add docs for Python API usage.
docs/source/priors.md	Add documentation for pydantic-based priors/interfaces.
docs/source/index.rst	Wire new docs pages into the Sphinx index.
docs/source/config.rst	Update docs examples to analyses/ directory naming.
docs/source/conf.py	Enable sphinx autodoc for pydantic models.
docs/source/build-process.rst	Update docs examples to analyses/ directory naming.
docs/source/blueprints.rst	Expand docs for new dependency syntax + strategies.
docs/source/api/schedulers.rst	Add API docs entry for scheduler module.
docs/source/api/project.rst	Add API docs entry for Project class.
docs/source/analyses.rst	Document optional dependencies and SubjectAnalysis usage.
conda/environment.yaml	Add conda environment dependency list for CI-like installs.
asimov/strategies.py	Add strategy expansion implementation.
asimov/scheduler_utils.py	Add scheduler configuration helpers/decorator/job mapping.
asimov/priors.py	Add pydantic-based prior specification + interface base classes.
asimov/pipelines/testing/init.py	Add minimal testing pipelines package exports.
asimov/pipelines/testing/README.md	Document testing pipelines and their purpose/usage.
asimov/pipelines/rift.py	Switch DAG submission to scheduler API + analyses/ paths.
asimov/pipelines/lalinference.py	Add LALInference prior interface + switch DAG submission to scheduler API.
asimov/pipelines/bayeswave.py	Switch DAG submission to scheduler API + analyses/ default category.
asimov/olivaw.py	Add plugin command discovery + project-aware click group + entry_points compat.
asimov/monitor_helpers.py	Add reusable monitor helpers for state transitions.
asimov/monitor_context.py	Add context object for monitor state handlers.
asimov/monitor_api.py	Add programmatic monitor API (run_monitor/status/list).
asimov/ledger.py	Make ledger location absolute + improve backward compatibility for project analyses.
asimov/git.py	Add default-branch detection + modernize repo init defaults + update logic.
asimov/configs/subjecttestpipeline.ini	Add template config for SubjectTestPipeline.
asimov/configs/simpletestpipeline.ini	Add template config for SimpleTestPipeline.
asimov/configs/projecttestpipeline.ini	Add template config for ProjectTestPipeline.
asimov/configs/lalinference.ini	Use prior interface in template + update amporder access.
asimov/configs/bilby.ini	Use prior interface + pipeline helpers (sampler kwargs, additional files).
asimov/configs/README.rst	Document scheduler configuration in configs README.
asimov/condor.py	Prefer htcondor2 when available + route submit/delete through scheduler abstraction.
asimov/cli/project.py	Update logging config key + robust python executable detection + set up file logging during init.
asimov/cli/manage.py	Ensure file logging setup for manage commands + adjust submission logic and SubjectAnalysis readiness gating.
asimov/cli/blueprint.py	Add asimov blueprint validate command.
asimov/asimov.conf	Update calibration directory default to analyses.
asimov/init.py	Switch to importlib.metadata/resources + add lazy, rotating, thread-safe file logging setup.
LICENSE	Update license text to MIT-style grant statement.
IMPLEMENTATION.md	Add implementation notes for dependency management + docs pointers.
CHANGELOG.rst	Add extensive 0.7.0-alpha2 changelog entry.
.gitlab-ci.yml	Add HTCondor CI job to exercise project creation/apply steps.
.github/workflows/testing-pipelines.yml	Add HTCondor-based end-to-end workflow for testing pipelines.
.github/workflows/python-app.yml	Expand test matrix + add tag-based publish workflow.
.github/workflows/docs.yml	Add Sphinx multiversion docs build/deploy workflow.
.github/workflows/cbcflow-tests.yml	Add CBCFlow integration workflow (allowed to fail).
.github/actions/wait-for-files/action.yml	Add composite action to wait for output artifacts in HTCondor tests.
.github/actions/setup-htcondor/action.yml	Add composite action to bring up HTCondor in workflow container.
.github/actions/setup-asimov-env/action.yml	Add composite action to provision conda env + install asimov.
.github/actions/run-asimov-command/action.yml	Add composite action to run asimov commands as submituser.
.github/actions/create-submit-user/action.yml	Add composite action to create submituser with permissions.

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[Copilot]

pipe.submit_dag() is not consistently a scalar across pipelines (e.g., BayesWave returns a tuple like (int(cluster_id),)). Casting a tuple to int will raise TypeError and break submissions for those pipelines. Normalize cluster_id the same way you already do later in this file (treat list/tuple as sequence and take the first element) before assigning analysis.job_id.

Suggested change

	cluster_id = pipe.submit_dag(dryrun=dryrun)
	# Normalize cluster_id in case some pipelines return a sequence
	if isinstance(cluster_id, (list, tuple)):
	cluster_id = cluster_id[0]

[Copilot]

self.event is not defined anywhere in the shown GitRepo class, so this warning path can raise AttributeError while already handling an exception, masking the original failure and breaking get_default_branch(). Log a stable attribute like self.directory (or the remote URL if you have it) instead of self.event.

[Copilot]

This file is named like a conda environment YAML, but it is not a valid environment.yaml format (it lacks name: and dependencies: keys). If CI/scripts run conda env create -f conda/environment.yaml, it will fail to parse. Convert it to a standard conda env spec (or rename it to something like conda/requirements.txt / conda/spec.txt if it’s intended to be used with conda install --file).

Suggested change

	name: bayeswave-env
	channels:
	- conda-forge
	dependencies:
	- bayeswave
	- bayeswaveutils
	- bilby_pipe
	- asimov-gwdata
	- pip

[transientlunatic]

@copilot open a new pull request to apply changes based on the comments in this thread