csrlite 0.3.0__py3-none-any.whl → 0.3.2__py3-none-any.whl

{csrlite-0.3.0.dist-info → csrlite-0.3.2.dist-info}/METADATA

@@ -1,68 +1,68 @@
-Metadata-Version: 2.4
-Name: csrlite
-Version: 0.3.0
-Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
-Author-email: Yilong Zhang <elong0527@gmail.com>, Ming-Chun Chen <hellomingchun@gmail.com>
-License: MIT
-Project-URL: Homepage, https://github.com/elong0527/csrlite
-Project-URL: Documentation, https://elong0527.github.io/csrlite
-Project-URL: Repository, https://github.com/elong0527/csrlite.git
-Project-URL: Bug Tracker, https://github.com/elong0527/csrlite/issues
-Keywords: clinical-trials,biostatistics,yaml,tlf,tables,listings,figures
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-Requires-Dist: pydantic>=2.0.0
-Requires-Dist: pyyaml>=6.0
-Requires-Dist: polars>=0.20.0
-Requires-Dist: rtflite>=2.1.1
-Provides-Extra: rtf
-Requires-Dist: rtflite; extra == "rtf"
-Provides-Extra: plotting
-Requires-Dist: matplotlib>=3.5.0; extra == "plotting"
-Requires-Dist: plotly>=5.0.0; extra == "plotting"
-Provides-Extra: dev
-Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
-Requires-Dist: pytest>=9.0.1; extra == "dev"
-Requires-Dist: black>=22.0.0; extra == "dev"
-Requires-Dist: isort>=7.0.0; extra == "dev"
-Requires-Dist: ruff>=0.14.8; extra == "dev"
-Requires-Dist: mypy>=1.19.0; extra == "dev"
-Requires-Dist: quarto>=0.1.0; extra == "dev"
-Requires-Dist: pyre-check>=0.9.18; extra == "dev"
-Requires-Dist: jupyter>=1.1.1; extra == "dev"
-Requires-Dist: jupyter-cache>=1.0.1; extra == "dev"
-Requires-Dist: nbformat>=5.10.4; extra == "dev"
-Provides-Extra: all
-Requires-Dist: rtflite; extra == "all"
-Requires-Dist: matplotlib>=3.5.0; extra == "all"
-Requires-Dist: plotly>=5.0.0; extra == "all"
-
-# csrlite
-
-[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
-[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
-[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-
-A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
-
-## Installation
-
-```bash
-pip install csrlite
-```
-
-## Documentation
-
-Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
-
-## License
-
-MIT License - see [LICENSE](LICENSE) file for details.
+Metadata-Version: 2.4
+Name: csrlite
+Version: 0.3.2
+Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
+Author-email: Yilong Zhang <elong0527@gmail.com>, Ming-Chun Chen <hellomingchun@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/elong0527/csrlite
+Project-URL: Documentation, https://elong0527.github.io/csrlite
+Project-URL: Repository, https://github.com/elong0527/csrlite.git
+Project-URL: Bug Tracker, https://github.com/elong0527/csrlite/issues
+Keywords: clinical-trials,biostatistics,yaml,tlf,tables,listings,figures
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: polars>=0.20.0
+Requires-Dist: rtflite>=2.1.1
+Provides-Extra: rtf
+Requires-Dist: rtflite; extra == "rtf"
+Provides-Extra: plotting
+Requires-Dist: matplotlib>=3.5.0; extra == "plotting"
+Requires-Dist: plotly>=5.0.0; extra == "plotting"
+Provides-Extra: dev
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pytest>=9.0.1; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: isort>=7.0.0; extra == "dev"
+Requires-Dist: ruff>=0.14.8; extra == "dev"
+Requires-Dist: mypy>=1.19.0; extra == "dev"
+Requires-Dist: quarto>=0.1.0; extra == "dev"
+Requires-Dist: pyre-check>=0.9.18; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: jupyter-cache>=1.0.1; extra == "dev"
+Requires-Dist: nbformat>=5.10.4; extra == "dev"
+Provides-Extra: all
+Requires-Dist: rtflite; extra == "all"
+Requires-Dist: matplotlib>=3.5.0; extra == "all"
+Requires-Dist: plotly>=5.0.0; extra == "all"
+
+# csrlite
+
+[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
+[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
+
+## Installation
+
+```bash
+pip install csrlite
+```
+
+## Documentation
+
+Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
+
+## License
+
+MIT License - see [LICENSE](LICENSE) file for details.

csrlite-0.3.2.dist-info/RECORD

@@ -0,0 +1,23 @@
+csrlite/__init__.py,sha256=TotlI9TWnCkOxP8OOG5AfTMKjWLhM2-AJOEA6YF5ZLQ,2190
+csrlite/ae/__init__.py,sha256=Pp661SGbsoYoXLmd24dUQB_lx1jYKWEsCEPjgVg5UUU,15
+csrlite/ae/ae_listing.py,sha256=fZWhYmi_Vzp974z-3o7EQ9joizEjF0mio2eB5_I8ghU,18883
+csrlite/ae/ae_specific.py,sha256=P1glCd5K_ur_KexxbVaC79BmowgQSMI9K8xdzL6OmIM,17505
+csrlite/ae/ae_summary.py,sha256=Vk4bUonnjAji2zeJkiPHW7nwgpwUG1UfbuzH4M0w1MM,14093
+csrlite/ae/ae_utils.py,sha256=tOVOdsj-TRTw1w5T4JqFTYUwTfOppZWGlRHi6nkNWRA,2073
+csrlite/cm/cm_listing.py,sha256=VRgEdwWNlgjqU5W_-ObAxUwqapDf2G44xffwDiybIa4,18904
+csrlite/cm/cm_summary.py,sha256=DDWvubtENtf_Hr537xyGjYP2MOxS-meLs-yInFRynXM,10479
+csrlite/common/config.py,sha256=qWFTNSaeWnqAagXM6FwACdQafXLG_nFWxFHEk5dAo-I,912
+csrlite/common/count.py,sha256=T9nB9hYdc2jIIuV9HISK2ZS0wXNV_FUBDCKW_VVM1fQ,9078
+csrlite/common/parse.py,sha256=J4UkmNlG10mrJ-O68-po1LlfLchK_kSvfdU1GOaAYgQ,9627
+csrlite/common/plan.py,sha256=tYnK-5TVCoGWobxkqmasYYYkc9DJlHmOiTIcrP3MFRo,13293
+csrlite/common/rtf.py,sha256=fbube-5QoWYE8u6GCjE5qCMS6BzmXqJhoZI8GpOYXJM,5610
+csrlite/common/utils.py,sha256=XLUQqYtEm4SLNImvNDxAuj9OOu6Eogm3_uIp0vyfpfQ,1143
+csrlite/common/yaml_loader.py,sha256=ZPgXw5X9eitMHCPEJBHzeYtcjesEQ8sP0hOFSYnzrgk,3142
+csrlite/disposition/__init__.py,sha256=AiLW7Os7SBFrvvkaUMrxYEntK15_XXT0HYpZQxBx7ro,87
+csrlite/disposition/disposition.py,sha256=W1Oik5hqDfalQ69NXullH7XYWP3oRw2x2nFuFWlE3Qo,10679
+csrlite/ie/ie.py,sha256=9kEAe4aY3xfHe7O-o2ZD3LNfL5eTha2ZPkAflopjPYU,13544
+csrlite/pd/pd_listing.py,sha256=xPqpJFuxx_7vzjADGDSBo7RK2GpGWpR6SIMnCjKNirI,17632
+csrlite-0.3.2.dist-info/METADATA,sha256=RDlBzyKYUN2AGe_k-ZOOB0USa6g-qdl4OZPa-FwJFGk,2896
+csrlite-0.3.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+csrlite-0.3.2.dist-info/top_level.txt,sha256=59zJTvGH5zx2FY4vCl4kgnH8awT0cZrg21Mace7IFlU,8
+csrlite-0.3.2.dist-info/RECORD,,

{csrlite-0.3.0.dist-info → csrlite-0.3.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

csrlite/ie/ie_listing.py

@@ -1,109 +0,0 @@
-# pyre-strict
-"""
-Inclusion/Exclusion (IE) Listing Analysis Functions
-"""
-
-from pathlib import Path
-
-import polars as pl
-
-from ..common.parse import StudyPlanParser
-from ..common.plan import StudyPlan
-from ..common.rtf import create_rtf_listing
-from ..common.utils import apply_common_filters
-
-
-def study_plan_to_ie_listing(
-    study_plan: StudyPlan,
-) -> list[str]:
-    """
-    Generate IE Listing outputs.
-    """
-    # Meta data
-    analysis_type = "ie_listing"
-    output_dir = study_plan.output_dir
-    title = "Listing of Protocol Deviations"
-
-    # Ensure output directory exists
-    Path(output_dir).mkdir(parents=True, exist_ok=True)
-
-    # Initialize parser
-    parser = StudyPlanParser(study_plan)
-
-    # Get expanded plan (Manually expansion to avoid AttributeError)
-    plans = study_plan.study_data.get("plans", [])
-    all_specs = []
-    for plan_data in plans:
-        expanded = study_plan.expander.expand_plan(plan_data)
-        for p in expanded:
-            all_specs.append(study_plan.expander.create_analysis_spec(p))
-
-    plan_df = pl.DataFrame(all_specs)
-
-    if "analysis" in plan_df.columns:
-        listing_plans = plan_df.filter(pl.col("analysis") == analysis_type)
-    else:
-        listing_plans = pl.DataFrame()
-
-    generated_files = []
-
-    # If listing_plans is empty, create a dummy row to force generation
-    if listing_plans.height == 0:
-        listing_plans = pl.DataFrame([{"population": "enrolled", "analysis": analysis_type}])
-
-    for analysis in listing_plans.iter_rows(named=True):
-        # Load ADSL
-        pop_name = analysis.get("population", "enrolled")
-
-        try:
-            (adsl_raw,) = parser.get_datasets("adsl")
-            pop_filter = parser.get_population_filter(pop_name)
-
-            adsl, _ = apply_common_filters(
-                population=adsl_raw,
-                observation=None,
-                population_filter=pop_filter,
-                observation_filter=None,
-            )
-
-        except ValueError as e:
-            print(f"Error loading population: {e}")
-            continue
-
-        # Output filename
-        filename = f"{analysis_type}_{pop_name}.rtf".lower()
-        output_path = f"{output_dir}/{filename}"
-
-        # Generate DF
-        df = ie_listing_df(adsl)
-
-        # Generate RTF
-        ie_listing_rtf(df, output_path, title=title)
-
-        generated_files.append(output_path)
-
-    return generated_files
-
-
-def ie_listing_df(adsl: pl.DataFrame) -> pl.DataFrame:
-    """Select columns for Listing."""
-    # Check if DCSREAS exists
-    cols = ["USUBJID", "DCSREAS"]
-    available = [c for c in cols if c in adsl.columns]
-    return adsl.select(available)
-
-
-def ie_listing_rtf(df: pl.DataFrame, output_path: str, title: str | list[str] = "") -> None:
-    """Generate RTF Listing."""
-    col_widths = [1.5, 3.5]  # Approximate ratio
-
-    rtf_doc = create_rtf_listing(
-        df=df,
-        col_header=list(df.columns),
-        col_widths=col_widths,
-        title=title,
-        footnote=[],
-        source=[],
-    )
-
-    rtf_doc.write_rtf(output_path)

csrlite/mh/mh_listing.py

@@ -1,209 +0,0 @@
-# pyre-strict
-"""
-Medical History (MH) Listing Analysis Functions
-"""
-
-from pathlib import Path
-
-import polars as pl
-
-from ..common.parse import StudyPlanParser
-from ..common.plan import StudyPlan
-from ..common.rtf import create_rtf_listing
-from ..common.utils import apply_common_filters
-
-
-def mh_listing(
-    population: pl.DataFrame,
-    observation: pl.DataFrame,
-    population_filter: str | None = "SAFFL = 'Y'",
-    observation_filter: str | None = "MHOCCUR = 'Y'",
-    id: tuple[str, str] = ("USUBJID", "Subject ID"),
-    title: list[str] | None = None,
-    footnote: list[str] | None = None,
-    source: list[str] | None = None,
-    output_file: str = "mh_listing.rtf",
-    population_columns: list[tuple[str, str]] | None = None,
-    observation_columns: list[tuple[str, str]] | None = None,
-    sort_columns: list[str] | None = None,
-) -> str:
-    """
-    Generate Medical History Listing.
-    """
-    if title is None:
-        title = ["Listing of Medical History"]
-
-    # Generate DF
-    df = mh_listing_df(
-        population=population,
-        observation=observation,
-        population_filter=population_filter,
-        observation_filter=observation_filter,
-        id_col=id[0],
-        pop_cols=population_columns,
-        obs_cols=observation_columns,
-        sort_cols=sort_columns,
-    )
-
-    # Generate RTF
-    mh_listing_rtf(df=df, output_path=output_file, title=title, footnote=footnote, source=source)
-
-    return output_file
-
-
-def mh_listing_df(
-    population: pl.DataFrame,
-    observation: pl.DataFrame,
-    population_filter: str | None,
-    observation_filter: str | None,
-    id_col: str,
-    pop_cols: list[tuple[str, str]] | None,
-    obs_cols: list[tuple[str, str]] | None,
-    sort_cols: list[str] | None,
-) -> pl.DataFrame:
-    # Defaults
-    if pop_cols is None:
-        # Default interesting cols from ADSL
-        pop_cols = [("TRT01A", "Treatment"), ("AGE", "Age"), ("SEX", "Sex")]
-
-    if obs_cols is None:
-        # Default from ADMH
-        obs_cols = [
-            ("MHSEQ", "Seq"),
-            ("MHBODSYS", "System Organ Class"),
-            ("MHDECOD", "Preferred Term"),
-            ("MHSTDTC", "Start Date"),
-            ("MHENRTPT", "Status"),
-        ]
-
-    # Apply filters
-    adsl, adq = apply_common_filters(
-        population=population,
-        observation=observation,
-        population_filter=population_filter,
-        observation_filter=observation_filter,
-    )
-
-    if adq is None:
-        raise ValueError("Observation data is missing")
-
-    # Join
-    # Select specific columns from ADSL
-    pop_col_names = [c[0] for c in pop_cols]
-    # Ensure ID is there
-    if id_col not in pop_col_names:
-        pop_col_names = [id_col] + pop_col_names
-
-    adsl_sub = adsl.select(pop_col_names)
-
-    joined = adq.join(adsl_sub, on=id_col, how="inner")
-
-    # Sort
-    if sort_cols:
-        # Check if cols exist
-        valid_sorts = [c for c in sort_cols if c in joined.columns]
-        if valid_sorts:
-            joined = joined.sort(valid_sorts)
-
-    # Select display columns (id + pop + obs)
-    display_cols = [id_col] + [c[0] for c in pop_cols if c[0] != id_col] + [c[0] for c in obs_cols]
-    final_df = joined.select([c for c in display_cols if c in joined.columns])
-
-    # Rename for display?
-    # Usually listing keeps raw names or we Map them.
-    # The create_rtf_listing function takes col_header list.
-
-    return final_df
-
-
-def mh_listing_rtf(
-    df: pl.DataFrame,
-    output_path: str,
-    title: list[str] | str,
-    footnote: list[str] | None,
-    source: list[str] | None,
-) -> None:
-    if df.is_empty():
-        return
-
-    # Generate headers from predefined mapping or current logic?
-    # Here we just use column names for simplicity or we could pass headers.
-    # We didn't output headers from mh_listing_df.
-    # Let's assume the order is maintained.
-
-    headers = list(df.columns)
-
-    # Approximate widths
-    # ID: 1, TRT: 1.5, AGE: 0.5, SEX: 0.5, SEQ: 0.5, SOC: 2, PT: 2, DATE: 1, STATUS: 1
-    # Total ~ 10 units?
-    # Simple uniform distribution or weighted?
-    n_cols = len(headers)
-    col_widths = [1.0] * n_cols
-
-    rtf_doc = create_rtf_listing(
-        df=df,
-        col_header=headers,
-        col_widths=col_widths,
-        title=title,
-        footnote=footnote,
-        source=source,
-    )
-
-    rtf_doc.write_rtf(output_path)
-
-
-def study_plan_to_mh_listing(study_plan: StudyPlan) -> list[str]:
-    """
-    Batch generate MH listings.
-    """
-    analysis_type = "mh_listing"
-    output_dir = study_plan.output_dir
-
-    parser = StudyPlanParser(study_plan)
-
-    plans = study_plan.study_data.get("plans", [])
-    all_specs = []
-    for plan_data in plans:
-        expanded = study_plan.expander.expand_plan(plan_data)
-        for p in expanded:
-            all_specs.append(study_plan.expander.create_analysis_spec(p))
-
-    plan_df = pl.DataFrame(all_specs)
-
-    if "analysis" in plan_df.columns:
-        mh_plans = plan_df.filter(pl.col("analysis") == analysis_type)
-    else:
-        mh_plans = pl.DataFrame()
-
-    generated_files = []
-
-    for analysis in mh_plans.iter_rows(named=True):
-        pop_name = analysis.get("population", "enrolled")
-
-        try:
-            # Load Population
-            adsl, _ = parser.get_population_data(pop_name, "trt01a")  # dummy group
-
-            (admh,) = parser.get_datasets("admh")
-
-            filename = f"{analysis_type}_{pop_name}.rtf".lower()
-            output_path = f"{output_dir}/{filename}"
-            Path(output_path).parent.mkdir(parents=True, exist_ok=True)
-
-            mh_listing(
-                population=adsl,
-                observation=admh,
-                population_filter=None,
-                observation_filter=None,  # Show all?
-                output_file=output_path,
-                title=["Listing of Medical History", f"({pop_name} Population)"],
-                source=["Source: ADSL, ADMH"],
-            )
-
-            generated_files.append(output_path)
-
-        except Exception as e:
-            print(f"Error generating MH listing: {e}")
-            continue
-
-    return generated_files