csrlite 0.2.1__py3-none-any.whl → 0.3.0__py3-none-any.whl

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Files changed (27) hide show
  1. csrlite/__init__.py +110 -71
  2. csrlite/ae/__init__.py +1 -1
  3. csrlite/ae/ae_listing.py +494 -494
  4. csrlite/ae/ae_specific.py +483 -483
  5. csrlite/ae/ae_summary.py +401 -401
  6. csrlite/ae/ae_utils.py +62 -62
  7. csrlite/cm/cm_listing.py +497 -0
  8. csrlite/cm/cm_summary.py +327 -0
  9. csrlite/common/config.py +34 -34
  10. csrlite/common/count.py +293 -293
  11. csrlite/common/parse.py +308 -308
  12. csrlite/common/plan.py +365 -365
  13. csrlite/common/rtf.py +137 -137
  14. csrlite/common/utils.py +33 -33
  15. csrlite/common/yaml_loader.py +71 -71
  16. csrlite/disposition/__init__.py +2 -2
  17. csrlite/disposition/disposition.py +332 -332
  18. csrlite/ie/ie_listing.py +109 -0
  19. csrlite/ie/{ie.py → ie_summary.py} +292 -405
  20. csrlite/mh/mh_listing.py +209 -0
  21. csrlite/mh/mh_summary.py +333 -0
  22. csrlite/pd/pd_listing.py +461 -0
  23. {csrlite-0.2.1.dist-info → csrlite-0.3.0.dist-info}/METADATA +68 -68
  24. csrlite-0.3.0.dist-info/RECORD +26 -0
  25. csrlite-0.2.1.dist-info/RECORD +0 -20
  26. {csrlite-0.2.1.dist-info → csrlite-0.3.0.dist-info}/WHEEL +0 -0
  27. {csrlite-0.2.1.dist-info → csrlite-0.3.0.dist-info}/top_level.txt +0 -0
csrlite/__init__.py CHANGED
@@ -1,71 +1,110 @@
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- import logging
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- import sys
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-
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- from .ae.ae_listing import ( # AE listing functions
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- ae_listing,
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- study_plan_to_ae_listing,
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- )
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- from .ae.ae_specific import ( # AE specific functions
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- ae_specific,
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- study_plan_to_ae_specific,
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- )
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- from .ae.ae_summary import ( # AE summary functions
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- ae_summary,
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- study_plan_to_ae_summary,
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- )
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- from .common.config import config
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- from .common.count import (
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- count_subject,
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- count_subject_with_observation,
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- )
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- from .common.parse import (
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- StudyPlanParser,
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- parse_filter_to_sql,
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- )
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- from .common.plan import ( # Core classes
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- load_plan,
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- )
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- from .disposition.disposition import study_plan_to_disposition_summary
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- from .ie.ie import (
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- ie_ard,
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- ie_df,
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- ie_rtf,
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- study_plan_to_ie_listing,
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- study_plan_to_ie_summary,
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- )
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-
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- # Configure logging
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- logging.basicConfig(
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- level=config.logging_level,
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- format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
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- stream=sys.stdout,
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- )
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- logger = logging.getLogger("csrlite")
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-
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- # Main exports for common usage
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- __all__ = [
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- # Primary user interface
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- "load_plan",
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- # AE analysis (direct pipeline wrappers)
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- "ae_summary",
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- "ae_specific",
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- "ae_listing",
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- # AE analysis (StudyPlan integration)
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- "study_plan_to_ae_summary",
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- "study_plan_to_ae_specific",
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- "study_plan_to_ae_listing",
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- # Disposition analysis
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- "study_plan_to_disposition_summary",
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- # Count functions
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- "count_subject",
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- "count_subject_with_observation",
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- # Parse utilities
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- "StudyPlanParser",
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- "parse_filter_to_sql",
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- # IE analysis
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- "ie_ard",
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- "ie_df",
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- "ie_rtf",
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- "study_plan_to_ie_summary",
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- "study_plan_to_ie_listing",
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- ]
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+ import logging
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+ import sys
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+
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+ from .ae.ae_listing import ( # AE listing functions
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+ ae_listing,
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+ study_plan_to_ae_listing,
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+ )
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+ from .ae.ae_specific import ( # AE specific functions
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+ ae_specific,
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+ study_plan_to_ae_specific,
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+ )
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+ from .ae.ae_summary import ( # AE summary functions
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+ ae_summary,
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+ study_plan_to_ae_summary,
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+ )
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+ from .cm.cm_listing import ( # CM listing functions
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+ cm_listing,
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+ study_plan_to_cm_listing,
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+ )
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+ from .cm.cm_summary import (
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+ cm_summary,
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+ study_plan_to_cm_summary,
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+ )
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+ from .common.config import config
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+ from .common.count import (
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+ count_subject,
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+ count_subject_with_observation,
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+ )
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+ from .common.parse import (
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+ StudyPlanParser,
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+ parse_filter_to_sql,
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+ )
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+ from .common.plan import ( # Core classes
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+ load_plan,
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+ )
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+ from .disposition.disposition import study_plan_to_disposition_summary
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+ from .ie.ie_listing import (
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+ ie_listing_df,
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+ ie_listing_rtf,
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+ study_plan_to_ie_listing,
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+ )
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+ from .ie.ie_summary import (
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+ ie_ard,
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+ ie_df,
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+ ie_rtf,
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+ study_plan_to_ie_summary,
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+ )
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+ from .mh.mh_listing import (
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+ mh_listing,
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+ study_plan_to_mh_listing,
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+ )
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+ from .mh.mh_summary import (
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+ mh_summary,
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+ study_plan_to_mh_summary,
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+ )
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+ from .pd.pd_listing import (
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+ pd_listing,
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+ study_plan_to_pd_listing,
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+ )
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+
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+ # Configure logging
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+ logging.basicConfig(
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+ level=config.logging_level,
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+ format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
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+ stream=sys.stdout,
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+ )
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+ logger = logging.getLogger("csrlite")
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+
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+ # Main exports for common usage
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+ __all__ = [
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+ # Primary user interface
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+ "load_plan",
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+ # AE analysis (direct pipeline wrappers)
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+ "ae_summary",
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+ "ae_specific",
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+ "ae_listing",
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+ # AE analysis (StudyPlan integration)
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+ "study_plan_to_ae_summary",
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+ "study_plan_to_ae_specific",
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+ "study_plan_to_ae_listing",
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+ # CM analysis
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+ "cm_listing",
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+ "study_plan_to_cm_listing",
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+ "cm_summary",
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+ "study_plan_to_cm_summary",
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+ # Disposition analysis
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+ "study_plan_to_disposition_summary",
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+ # Count functions
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+ "count_subject",
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+ "count_subject_with_observation",
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+ # Parse utilities
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+ "StudyPlanParser",
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+ "parse_filter_to_sql",
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+ # IE analysis
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+ "ie_ard",
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+ "ie_df",
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+ "ie_rtf",
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+ "study_plan_to_ie_summary",
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+ "ie_listing_df",
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+ "ie_listing_rtf",
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+ "study_plan_to_ie_listing",
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+ # PD analysis
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+ "pd_listing",
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+ "study_plan_to_pd_listing",
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+ # MH analysis
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+ "mh_listing",
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+ "study_plan_to_mh_listing",
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+ "mh_summary",
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+ "study_plan_to_mh_summary",
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+ ]
csrlite/ae/__init__.py CHANGED
@@ -1 +1 @@
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- # pyre-strict
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+ # pyre-strict