cms-icd 0.1.0__tar.gz

cms_icd-0.1.0/CITATION.cff

@@ -0,0 +1,22 @@
+cff-version: 1.2.0
+title: cms-icd
+message: >-
+  If you use this software in research or published work, please cite cms-icd
+  and acknowledge IPOL at MGH.
+type: software
+authors:
+  - given-names: Pawel
+    family-names: Renc
+    affiliation: IPOL at MGH
+version: 0.1.0
+license: Apache-2.0
+repository-code: https://github.com/ipolharvard/cms-icd
+url: https://ipolharvard.github.io/cms-icd/
+abstract: >-
+  Version-aware structured access to official CMS ICD-10-CM, ICD-10-PCS, and
+  General Equivalence Mapping materials.
+keywords:
+  - CMS
+  - ICD-10-CM
+  - ICD-10-PCS
+  - clinical informatics

cms_icd-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
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cms_icd-0.1.0/MANIFEST.in

@@ -0,0 +1,3 @@
+include CITATION.cff
+include LICENSE
+include NOTICE

cms_icd-0.1.0/NOTICE

@@ -0,0 +1,5 @@
+cms-icd
+Copyright 2026 Paweł Renc
+
+This software was developed by IPOL at MGH.
+https://ipol.mgh.harvard.edu/

cms_icd-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: cms-icd
+Version: 0.1.0
+Summary: Version-aware structured access to official CMS ICD-10 materials
+Author: Pawel Renc
+License-Expression: Apache-2.0
+Project-URL: Documentation, https://ipolharvard.github.io/cms-icd/
+Project-URL: Issues, https://github.com/ipolharvard/cms-icd/issues
+Project-URL: Repository, https://github.com/ipolharvard/cms-icd
+Keywords: CMS,ICD-10,ICD-10-CM,ICD-10-PCS,healthcare
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: beautifulsoup4
+Requires-Dist: pypdf<7,>=6.16.1
+Requires-Dist: requests
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material; extra == "docs"
+Requires-Dist: mkdocstrings[python]; extra == "docs"
+Dynamic: license-file
+
+# CMS ICD
+
+[![CI](https://github.com/ipolharvard/cms-icd/actions/workflows/ci.yml/badge.svg)](https://github.com/ipolharvard/cms-icd/actions/workflows/ci.yml)
+[![Documentation](https://github.com/ipolharvard/cms-icd/actions/workflows/docs.yml/badge.svg)](https://ipolharvard.github.io/cms-icd/)
+[![CMS catalog](https://github.com/ipolharvard/cms-icd/actions/workflows/catalog-cms.yml/badge.svg)](https://github.com/ipolharvard/cms-icd/actions/workflows/catalog-cms.yml)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12%2B-blue.svg)](https://www.python.org/downloads/)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-green.svg)](https://github.com/ipolharvard/cms-icd/blob/main/LICENSE)
+
+`cms-icd` provides version-aware, structured access to official CMS ICD-10-CM
+and ICD-10-PCS materials. Downloads and parsing are lazy: using diagnosis codes
+does not download PCS files, and reading a tabular list does not parse indexes
+or guideline PDFs.
+
+Python 3.12 or newer is required. The package is tested on Python 3.12–3.14.
+CMS-backed discovery supports production ICD-10 releases from FY 2016 onward,
+including advertised intra-year updates.
+
+Full documentation is available at
+[ipolharvard.github.io/cms-icd](https://ipolharvard.github.io/cms-icd/).
+
+The package also exposes the official ICD-9/ICD-10 General Equivalence Mappings
+without imposing an application-specific target-selection policy:
+
+```python
+from cms_icd import GEMKnowledgeBase
+
+gems = GEMKnowledgeBase.from_cms(fiscal_year=2018)
+entries = gems.cm.icd9_to_icd10["4280"]
+```
+
+Use a retrospectively corrected view when historical target-code validity must be
+preserved while later correction-only GEM revisions are incorporated:
+
+```python
+gems = GEMKnowledgeBase.corrected_from_cms(
+    fiscal_year=2016,
+)
+mapping = gems.cm.icd9_to_icd10.mapping("27906")
+provenance = gems.cm.icd9_to_icd10.provenance("27906")
+```
+
+The same exact and retrospectively corrected views apply to procedure GEMs through
+`gems.pcs`. The package also exports the stable ordered `ICD10_PCS_CHARACTERS` alphabet
+for consumers that need a complete, fold-independent PCS vocabulary.
+
+The correction horizon defaults to FY2018, the final CMS GEM release, and can be
+overridden explicitly for a narrower audit. A source stops accepting later revisions
+when its mapping encounters an introduced or retired source/target code.
+
+## Installation
+
+Install the published package with `uv`:
+
+```bash
+uv add cms-icd
+```
+
+For development, install an editable checkout:
+
+```bash
+uv pip install -e /path/to/cms-icd
+```
+
+## Choosing a release
+
+Select the release using the date that controls coding:
+
+```python
+from datetime import date
+
+from cms_icd import ICD10KnowledgeBase
+
+icd = ICD10KnowledgeBase.for_date(
+    date(2026, 5, 1),
+    cache_dir="data/cms_icd",
+)
+cm = icd.cm
+code = cm["I10"]  # downloads and parses CM tabular material on first use
+```
+
+Use the discharge date for inpatient ICD-10-CM and ICD-10-PCS, and the encounter
+or date of service for other ICD-10-CM coding.
+
+For reproducible research, select an exact effective snapshot:
+
+```python
+icd = ICD10KnowledgeBase.from_cms(
+    fiscal_year=2026,
+    release_date=date(2026, 4, 1),
+    cache_dir="data/cms_icd",
+)
+```
+
+CMS commonly publishes an October release and an April 1 update. Materials not
+changed in an update are inherited from the latest earlier revision in that
+fiscal year. CMS does not always retain every historical revision, so snapshot
+selection is strict by default. Pass `fallback="latest_for_fy"` only when using
+the latest available fiscal-year material is scientifically acceptable.
+
+The [release guide](https://ipolharvard.github.io/cms-icd/guide/releases-and-caching/)
+documents supported guideline years and the exact October/April selection
+rules.
+
+## Offline and custom stores
+
+An existing directory is not inspected until a material is requested:
+
+```pycon
+>>> from datetime import date
+>>> from pathlib import Path
+>>> from tempfile import TemporaryDirectory
+>>> from cms_icd import ICD10KnowledgeBase
+>>> with TemporaryDirectory() as directory:
+...     kb = ICD10KnowledgeBase.from_directory(
+...         directory,
+...         fiscal_year=2026,
+...         release_date=date(2025, 10, 1),
+...     )
+...     repr(kb)
+'ICD10KnowledgeBase(release=Release(fiscal_year=2026, release_date=datetime.date(2025, 10, 1)), loaded=[])'
+
+```
+
+Small custom or synthetic stores can be supplied directly:
+
+```pycon
+>>> from cms_icd import Code, ICD10CMKnowledgeBase
+>>> from cms_icd.models import Node
+>>> from cms_icd.stores import TabularStore
+>>> root = Node("cm", "cm", children_ids=("I10",))
+>>> code = Code("I10", "I10", "Essential hypertension", parent_id="cm")
+>>> tabular = TabularStore({"cm": root, "I10": code}, {"I10": "I10"}, ("cm",))
+>>> cm = ICD10CMKnowledgeBase.from_stores(tabular=tabular)
+>>> cm["I10"].description
+'Essential hypertension'
+>>> cm.get_leaves("cm")
+['I10']
+
+```
+
+## Citation and acknowledgment
+
+If you use `cms-icd` in research or published work, please cite the software
+using
+[`CITATION.cff`](https://github.com/ipolharvard/cms-icd/blob/main/CITATION.cff)
+and acknowledge IPOL at MGH.
+
+The source code is licensed under the
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0). See
+[`NOTICE`](https://github.com/ipolharvard/cms-icd/blob/main/NOTICE) for
+attribution information.
+
+## Development
+
+```bash
+make install-dev
+make test
+make install-docs
+make docs
+```
+
+Normal tests are offline. `make test-live` accesses CMS and must be run only
+when live integration testing is explicitly intended.
+
+CMS compatibility is validated in separate catalog, fresh-current, historical,
+and manual exhaustive lanes. See the
+[testing strategy](https://ipolharvard.github.io/cms-icd/testing/).
+
+`cms-icd` is an independent open-source project. It is not affiliated with,
+endorsed by, or sponsored by the Centers for Medicare & Medicaid Services.

cms_icd-0.1.0/README.md

@@ -0,0 +1,170 @@
+# CMS ICD
+
+[![CI](https://github.com/ipolharvard/cms-icd/actions/workflows/ci.yml/badge.svg)](https://github.com/ipolharvard/cms-icd/actions/workflows/ci.yml)
+[![Documentation](https://github.com/ipolharvard/cms-icd/actions/workflows/docs.yml/badge.svg)](https://ipolharvard.github.io/cms-icd/)
+[![CMS catalog](https://github.com/ipolharvard/cms-icd/actions/workflows/catalog-cms.yml/badge.svg)](https://github.com/ipolharvard/cms-icd/actions/workflows/catalog-cms.yml)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12%2B-blue.svg)](https://www.python.org/downloads/)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-green.svg)](https://github.com/ipolharvard/cms-icd/blob/main/LICENSE)
+
+`cms-icd` provides version-aware, structured access to official CMS ICD-10-CM
+and ICD-10-PCS materials. Downloads and parsing are lazy: using diagnosis codes
+does not download PCS files, and reading a tabular list does not parse indexes
+or guideline PDFs.
+
+Python 3.12 or newer is required. The package is tested on Python 3.12–3.14.
+CMS-backed discovery supports production ICD-10 releases from FY 2016 onward,
+including advertised intra-year updates.
+
+Full documentation is available at
+[ipolharvard.github.io/cms-icd](https://ipolharvard.github.io/cms-icd/).
+
+The package also exposes the official ICD-9/ICD-10 General Equivalence Mappings
+without imposing an application-specific target-selection policy:
+
+```python
+from cms_icd import GEMKnowledgeBase
+
+gems = GEMKnowledgeBase.from_cms(fiscal_year=2018)
+entries = gems.cm.icd9_to_icd10["4280"]
+```
+
+Use a retrospectively corrected view when historical target-code validity must be
+preserved while later correction-only GEM revisions are incorporated:
+
+```python
+gems = GEMKnowledgeBase.corrected_from_cms(
+    fiscal_year=2016,
+)
+mapping = gems.cm.icd9_to_icd10.mapping("27906")
+provenance = gems.cm.icd9_to_icd10.provenance("27906")
+```
+
+The same exact and retrospectively corrected views apply to procedure GEMs through
+`gems.pcs`. The package also exports the stable ordered `ICD10_PCS_CHARACTERS` alphabet
+for consumers that need a complete, fold-independent PCS vocabulary.
+
+The correction horizon defaults to FY2018, the final CMS GEM release, and can be
+overridden explicitly for a narrower audit. A source stops accepting later revisions
+when its mapping encounters an introduced or retired source/target code.
+
+## Installation
+
+Install the published package with `uv`:
+
+```bash
+uv add cms-icd
+```
+
+For development, install an editable checkout:
+
+```bash
+uv pip install -e /path/to/cms-icd
+```
+
+## Choosing a release
+
+Select the release using the date that controls coding:
+
+```python
+from datetime import date
+
+from cms_icd import ICD10KnowledgeBase
+
+icd = ICD10KnowledgeBase.for_date(
+    date(2026, 5, 1),
+    cache_dir="data/cms_icd",
+)
+cm = icd.cm
+code = cm["I10"]  # downloads and parses CM tabular material on first use
+```
+
+Use the discharge date for inpatient ICD-10-CM and ICD-10-PCS, and the encounter
+or date of service for other ICD-10-CM coding.
+
+For reproducible research, select an exact effective snapshot:
+
+```python
+icd = ICD10KnowledgeBase.from_cms(
+    fiscal_year=2026,
+    release_date=date(2026, 4, 1),
+    cache_dir="data/cms_icd",
+)
+```
+
+CMS commonly publishes an October release and an April 1 update. Materials not
+changed in an update are inherited from the latest earlier revision in that
+fiscal year. CMS does not always retain every historical revision, so snapshot
+selection is strict by default. Pass `fallback="latest_for_fy"` only when using
+the latest available fiscal-year material is scientifically acceptable.
+
+The [release guide](https://ipolharvard.github.io/cms-icd/guide/releases-and-caching/)
+documents supported guideline years and the exact October/April selection
+rules.
+
+## Offline and custom stores
+
+An existing directory is not inspected until a material is requested:
+
+```pycon
+>>> from datetime import date
+>>> from pathlib import Path
+>>> from tempfile import TemporaryDirectory
+>>> from cms_icd import ICD10KnowledgeBase
+>>> with TemporaryDirectory() as directory:
+...     kb = ICD10KnowledgeBase.from_directory(
+...         directory,
+...         fiscal_year=2026,
+...         release_date=date(2025, 10, 1),
+...     )
+...     repr(kb)
+'ICD10KnowledgeBase(release=Release(fiscal_year=2026, release_date=datetime.date(2025, 10, 1)), loaded=[])'
+
+```
+
+Small custom or synthetic stores can be supplied directly:
+
+```pycon
+>>> from cms_icd import Code, ICD10CMKnowledgeBase
+>>> from cms_icd.models import Node
+>>> from cms_icd.stores import TabularStore
+>>> root = Node("cm", "cm", children_ids=("I10",))
+>>> code = Code("I10", "I10", "Essential hypertension", parent_id="cm")
+>>> tabular = TabularStore({"cm": root, "I10": code}, {"I10": "I10"}, ("cm",))
+>>> cm = ICD10CMKnowledgeBase.from_stores(tabular=tabular)
+>>> cm["I10"].description
+'Essential hypertension'
+>>> cm.get_leaves("cm")
+['I10']
+
+```
+
+## Citation and acknowledgment
+
+If you use `cms-icd` in research or published work, please cite the software
+using
+[`CITATION.cff`](https://github.com/ipolharvard/cms-icd/blob/main/CITATION.cff)
+and acknowledge IPOL at MGH.
+
+The source code is licensed under the
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0). See
+[`NOTICE`](https://github.com/ipolharvard/cms-icd/blob/main/NOTICE) for
+attribution information.
+
+## Development
+
+```bash
+make install-dev
+make test
+make install-docs
+make docs
+```
+
+Normal tests are offline. `make test-live` accesses CMS and must be run only
+when live integration testing is explicitly intended.
+
+CMS compatibility is validated in separate catalog, fresh-current, historical,
+and manual exhaustive lanes. See the
+[testing strategy](https://ipolharvard.github.io/cms-icd/testing/).
+
+`cms-icd` is an independent open-source project. It is not affiliated with,
+endorsed by, or sponsored by the Centers for Medicare & Medicaid Services.

cms_icd-0.1.0/pyproject.toml

@@ -0,0 +1,78 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cms-icd"
+version = "0.1.0"
+description = "Version-aware structured access to official CMS ICD-10 materials"
+readme = "README.md"
+requires-python = ">=3.12"
+license = "Apache-2.0"
+license-files = ["LICENSE", "NOTICE"]
+keywords = ["CMS", "ICD-10", "ICD-10-CM", "ICD-10-PCS", "healthcare"]
+authors = [
+    { name = "Pawel Renc" },
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Healthcare Industry",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = [
+    "beautifulsoup4",
+    "pypdf>=6.16.1,<7",
+    "requests",
+]
+
+[project.urls]
+Documentation = "https://ipolharvard.github.io/cms-icd/"
+Issues = "https://github.com/ipolharvard/cms-icd/issues"
+Repository = "https://github.com/ipolharvard/cms-icd"
+
+[project.optional-dependencies]
+dev = ["pre-commit", "pytest"]
+docs = [
+    "mkdocs-material",
+    "mkdocstrings[python]",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules --doctest-glob=README.md --doctest-glob=docs/*.md -m 'not live_cms'"
+doctest_optionflags = ["NORMALIZE_WHITESPACE", "ELLIPSIS"]
+markers = [
+    "live_cms: integration tests that access official CMS endpoints",
+    "live_catalog: fetch and validate CMS catalog pages without artifacts",
+    "live_current: freshly download and parse the latest complete CMS snapshot",
+    "live_historical: parse representative historical CMS artifact formats",
+    "live_exhaustive: manually download and parse every advertised snapshot",
+]
+
+[tool.ruff]
+target-version = "py312"
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    "E",
+    "F",
+    "I",
+    "UP",
+    "B",
+    "C4",
+    "DTZ",
+    "RUF",
+    "N",
+    "TC",
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["cms_icd"]