Fix ledger io

[transientlunatic]

Description

Brief description of what this PR does.

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

Motivation and Context

Why is this change needed? What problem does it solve?

Fixes #(issue number) (if applicable)

Changes Made

List the main changes:

Testing

How has this been tested?

• Unit tests added/updated
• Integration tests added/updated
• Manual testing performed
• Tested with pipeline: (LALInference / Bilby / BayesWave / RIFT / N/A)

Test configuration:

• Python version(s):
• Operating System:
• Cluster environment (if applicable):

Checklist

• My code follows the project's style guidelines
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published

Documentation

• Documentation updated (if applicable)
• Changelog entry added
• README updated (if applicable)

Breaking Changes

Does this PR introduce any breaking changes? If yes, describe:

Additional Notes

Any additional information, concerns, or considerations for reviewers.

Screenshots (if applicable)

For UI or output changes, include before/after screenshots or terminal output.

---

Reviewer Notes:

• Does this PR need review from specific domain experts?
• Any particular areas that need careful review?

[Copilot]

Pull request overview

This PR modernizes Asimov’s IO and workflow infrastructure by standardizing the analysis directory layout (moving from C01_offline to analyses), introducing scheduler/monitor refactors and APIs, and expanding blueprint capabilities (strategies, dependency logic, prior validation), with substantial updates to tests and documentation.

Changes:

• Standardize run/checkouts paths to use analyses/ instead of C01_offline/ across code, tests, scripts, and docs.
• Add/extend monitoring architecture (state handlers, helpers, programmatic API) and scheduler integration utilities.
• Introduce/extend blueprint functionality (strategy expansion, optional dependencies, pydantic-based priors) plus new examples/docs and test coverage.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
tests/test_pipelines/test_lalinference.py	Update test repo paths to analyses/
tests/test_pipelines/test_bayeswave.py	Update test repo paths / DAG path assertions
tests/test_pesummary_subject_analysis.py	Add SubjectAnalysis tests for PESummary
tests/test_optional_dependencies.py	Add tests for optional/required dependency behavior
tests/test_monitor_helpers.py	Add unit tests for monitor helper functions
tests/test_monitor_api.py	Add unit tests for programmatic monitor API
tests/test_logging.py	Add tests ensuring lazy file logging behavior
tests/test_html_report.py	Add tests for enhanced HTML rendering
tests/test_data/test_strategy_single.yaml	Add single-parameter strategy blueprint fixture
tests/test_data/test_strategy_matrix.yaml	Add matrix strategy blueprint fixture
tests/test_data/test_strategy_event.yaml	Add strategy event blueprint fixture
tests/test_data/blueprints/test_analysis_blueprint.yaml	Add analysis blueprint fixture
tests/test_custom_states.py	Add unit tests for custom monitor states
tests/test_cli_manage.py	Update expected checkout path to analyses/
tests/test_blueprints/subject_test_pipeline.yaml	Add SubjectTestPipeline blueprint fixture
tests/test_blueprints/simple_test_pipeline.yaml	Add SimpleTestPipeline blueprint fixture
tests/test_blueprints/project_test_pipeline.yaml	Add ProjectTestPipeline blueprint fixture
tests/test_blueprints/lalinference_quick_test.yaml	Add quick lalinference blueprint example/fixture
tests/test_blueprints/gwosc_quick_test.yaml	Add quick GWOSC config fixture
tests/test_blueprints/gwosc_get_data.yaml	Add gwdata pipeline blueprint fixture
tests/test_blueprints/gwosc_event.yaml	Add GWOSC event blueprint fixture
tests/test_blueprints/bilby_quick_test.yaml	Add quick bilby blueprint fixture
tests/test_blueprints/bayeswave_quick_test.yaml	Add quick bayeswave blueprint fixture
tests/test_blueprints.py	Add minimal importability test for blueprints module
tests/test_asimov.py	Replace pkg_resources version probing in tests
tests/test_application.py	Add strategy expansion tests
tests/test_analysis.py	Improve tmp cleanup in test setup
tests/mock_gwdatafind_server.py	Add mock gwdatafind HTTP server for tests
tests/manual_test_priors.py	Add manual prior system test script
tests/integration/test_gwtc2d1.py	Update pipeline category to analyses
tests/integration/GW190426190642.yaml	Update calibration/PSD paths to analyses/
scripts/find_calibration.py	Update calibration destination to analyses/
scripts/check-ifo.py	Update calibration destination to analyses/
sandbox/make-nonspin.py	Use detected default branch instead of hardcoded master
sandbox/gitlab-issue-tests.py	Update category paths to analyses/
pyproject.toml	Add deps/extras, packaging metadata, entry points
examples/strategy_examples.yaml	Add blueprint strategy examples
examples/scheduler_example.py	Add scheduler module usage example script
examples/pesummary_subject_analysis.yaml	Add PESummary subject analysis example blueprint
examples/dependency-examples.yaml	Add dependency syntax examples
examples/demo_html_output.py	Add HTML output demo script
examples/demo_graph_fix.py	Add demo for graph dependency fixes
examples/README.rst	Add examples directory documentation
examples/README.md	Add dependency management examples README
examples/MODAL_DEPENDENCIES_GUIDE.md	Document modal dependencies UI feature
docs/source/user-guide/running.rst	Update CLI output examples to analyses/
docs/source/test-interface.rst	Update prior file path to analyses/
docs/source/scheduler-integration.rst	Add scheduler integration guide
docs/source/python-api.rst	Add Python API documentation
docs/source/priors.md	Add priors system documentation
docs/source/monitor-api.rst	Add programmatic monitor API documentation
docs/source/index.rst	Add new docs to TOC, update API links
docs/source/config.rst	Update example paths to analyses/
docs/source/conf.py	Enable autodoc_pydantic extension
docs/source/build-process.rst	Update example paths to analyses/
docs/source/blueprints.rst	Expand dependency docs; add strategy docs
docs/source/api/schedulers.rst	Add scheduler API page
docs/source/api/project.rst	Add project API page
docs/source/analyses.rst	Document optional dependencies + subject analyses usage
conda/environment.yaml	Add conda environment dependency list
asimov/strategies.py	Add blueprint strategy expansion implementation
asimov/scheduler_utils.py	Add scheduler helper functions and decorator
asimov/priors.py	Add pydantic-based prior models + interface base
asimov/pipelines/testing/init.py	Add minimal testing pipelines package
asimov/pipelines/testing/README.md	Document testing pipelines
asimov/pipelines/rift.py	Switch to scheduler API and analyses/ defaults
asimov/pipelines/lalinference.py	Add prior interface + scheduler DAG submission
asimov/pipelines/bayeswave.py	Switch to scheduler API + logging config key change
asimov/olivaw.py	Add project-aware Click group + plugin command discovery
asimov/monitor_helpers.py	Add reusable monitor helper functions
asimov/monitor_context.py	Add monitor context object for state handlers
asimov/monitor_api.py	Add programmatic monitor API
asimov/ledger.py	Fix ledger path handling + backward compatible project analyses
asimov/git.py	Add default-branch detection; update update() default
asimov/configs/subjecttestpipeline.ini	Add subject test pipeline template
asimov/configs/simpletestpipeline.ini	Add simple test pipeline template
asimov/configs/projecttestpipeline.ini	Add project test pipeline template
asimov/configs/lalinference.ini	Switch to LALInference prior interface in template
asimov/configs/bilby.ini	Switch to bilby prior interface helpers in template
asimov/configs/README.rst	Document scheduler configuration for templates
asimov/condor.py	Use scheduler abstraction internally; htcondor2 support
asimov/cli/project.py	Logging config key rename; init logging setup changes
asimov/cli/manage.py	Ensure file logging setup; job_id handling changes
asimov/cli/blueprint.py	Add CLI blueprint validation command
asimov/asimov.conf	Change calibration_directory default to analyses
asimov/init.py	Replace pkg_resources; implement lazy rotating file logging
LICENSE	Update license text formatting/content
IMPLEMENTATION.md	Add dependency system implementation notes
CHANGELOG.rst	Add 0.7.0-alpha2 changelog entry
.gitlab-ci.yml	Add HTCondor job integration test job
.github/workflows/testing-pipelines.yml	Add HTCondor-based testing pipelines workflow
.github/workflows/python-app.yml	Expand Python CI matrix and add publish job
.github/workflows/docs.yml	Add docs build/deploy workflow
.github/actions/wait-for-files/action.yml	Add composite action to wait for job outputs
.github/actions/setup-htcondor/action.yml	Add composite HTCondor startup action
.github/actions/setup-asimov-env/action.yml	Add composite action for conda env setup
.github/actions/run-asimov-command/action.yml	Add composite runner for Asimov CLI under submituser
.github/actions/create-submit-user/action.yml	Add composite action to create submituser

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

self.event is referenced in the exception handler, but GitRepo does not appear to define an event attribute in this diff. If get_default_branch() hits this path, the warning call itself can raise AttributeError, masking the original failure. Use a safe identifier (e.g., self.directory or getattr(self, 'event', None)), or log without referencing potentially-missing attributes.

[Copilot]

pipe.submit_dag() returns different shapes across pipelines (e.g., BayesWave returns a 1-tuple (cluster_id,) in this PR). Calling int(cluster_id) will fail for tuple/list returns. Normalize cluster_id the same way you do later in the function (handle scalar vs sequence) before casting/storing.

Suggested change

	cluster_id = pipe.submit_dag(dryrun=dryrun)
	# Normalize cluster_id in case some pipelines return a 1-tuple/list
	if isinstance(cluster_id, (list, tuple)):
	cluster_id = cluster_id[0]

[Copilot]

This file is not a valid Conda environment YAML (it’s missing keys like name:, channels:, and dependencies:). If referenced by CI or docs, conda env create -f conda/environment.yaml will fail. Convert it to standard environment format (or rename it to something like requirements-conda.txt and adjust consumers accordingly).

Suggested change

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

[Copilot]

This BayesWave test previously staged Prod1_test.ini but now stages Prod0_test.ini. In the same file, test_dag asserts a DAG under .../Prod1/..., so staging Prod0_test.ini looks inconsistent and may cause the test repo setup to miss required inputs. Stage the correct INI for the production under test (likely analyses/Prod1_test.ini) or update the test expectations to match the staged file.

Suggested change

	os.system("git add analyses/Prod1_test.ini analyses/s000000xx_gpsTime.txt")

[Copilot]

The return type/docstring for get_prior() is inconsistent with the implementation: the annotation says Optional[PriorSpecification], but the docstring mentions dict, and the function can return arbitrary non-dict values via return value. Consider either (a) tightening behavior to only return PriorSpecification | None (and raising on unsupported types), or (b) updating the type annotation/docstring to match the actual return possibilities.

[Copilot]

The return type/docstring for get_prior() is inconsistent with the implementation: the annotation says Optional[PriorSpecification], but the docstring mentions dict, and the function can return arbitrary non-dict values via return value. Consider either (a) tightening behavior to only return PriorSpecification | None (and raising on unsupported types), or (b) updating the type annotation/docstring to match the actual return possibilities.

[Copilot]

The return type/docstring for get_prior() is inconsistent with the implementation: the annotation says Optional[PriorSpecification], but the docstring mentions dict, and the function can return arbitrary non-dict values via return value. Consider either (a) tightening behavior to only return PriorSpecification | None (and raising on unsupported types), or (b) updating the type annotation/docstring to match the actual return possibilities.

[Copilot]

Checking hasattr(self, 'scheduler') is fragile if scheduler exists but is None (or is defined as a property on the base class). In that case, this decorator won’t initialize a configured scheduler and downstream calls like self.scheduler.submit_dag(...) can fail. Prefer initializing when getattr(self, 'scheduler', None) is None.

Suggested change

	# Add scheduler instance to the pipeline object if not already present or is None
	if getattr(self, "scheduler", None) is None: