Merge branch 'release/5.1.1'

Author: dermatologist

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 ## [Unreleased](https://github.com/dermatologist/fhiry/tree/HEAD)
 
-[Full Changelog](https://github.com/dermatologist/fhiry/compare/5.0.0...HEAD)
+[Full Changelog](https://github.com/dermatologist/fhiry/compare/v5.1.0...HEAD)
 
 **Implemented enhancements:**
 
@@ -39,6 +39,10 @@
 - add utf-8 encoding [\#134](https://github.com/dermatologist/fhiry/pull/134) ([fhirfly](https://github.com/fhirfly))
 - Feature/fix-warnings-1 [\#113](https://github.com/dermatologist/fhiry/pull/113) ([dermatologist](https://github.com/dermatologist))
 
+## [v5.1.0](https://github.com/dermatologist/fhiry/tree/v5.1.0) (2025-08-15)
+
+[Full Changelog](https://github.com/dermatologist/fhiry/compare/5.0.0...v5.1.0)
+
 ## [5.0.0](https://github.com/dermatologist/fhiry/tree/5.0.0) (2025-06-15)
 
 [Full Changelog](https://github.com/dermatologist/fhiry/compare/4.2.1...5.0.0)

README.md

@@ -1,8 +1,8 @@
 # 🔥 fhiry — FHIR to Pandas DataFrame for Data Analytics, AI, and ML
 
 [![Release](https://img.shields.io/github/v/release/dermatologist/fhiry)](https://img.shields.io/github/v/release/dermatologist/fhiry)
-[![Build status](https://img.shields.io/github/actions/workflow/status/dermatologist/fhiry/main.yml?branch=main)](https://github.com/dermatologist/fhiry/actions/workflows/main.yml?query=branch%3Amain)
-[![codecov](https://codecov.io/gh/dermatologist/fhiry/branch/main/graph/badge.svg)](https://codecov.io/gh/dermatologist/fhiry)
+[![Build status](https://img.shields.io/github/actions/workflow/status/dermatologist/fhiry/pytest.yml?branch=develop)](https://github.com/dermatologist/fhiry/actions/workflows/pytest.yml?query=branch%3Adevelop)
+[![codecov](https://codecov.io/gh/dermatologist/fhiry/branch/master/graph/badge.svg)](https://codecov.io/gh/dermatologist/fhiry)
 [![Commit activity](https://img.shields.io/github/commit-activity/m/dermatologist/fhiry)](https://img.shields.io/github/commit-activity/m/dermatologist/fhiry)
 [![License](https://img.shields.io/github/license/dermatologist/fhiry)](https://img.shields.io/github/license/dermatologist/fhiry)
 [![Downloads](https://img.shields.io/pypi/dm/fhiry)](https://pypi.org/project/fhiry)

src/fhiry/base_fhiry.py

@@ -107,7 +107,6 @@ def delete_unwanted_cols(self):
         if len(self.config["REMOVE"]) == 0:
             logger.warning("No columns to remove defined in config")
             return
-        logger.info("Removing columns: {}".format(self.config["REMOVE"]))
         for col in self.config["REMOVE"]:
             cols_to_remove = [
                 c for c in self._df.columns if c == col or c.startswith(f"{col}.")

src/fhiry/main.py

@@ -53,22 +53,6 @@ def cli(
     query,
     config_file,
 ):
-    """Process FHIR data from folder or server and output a dataframe.
-
-    This command can either read FHIR Bundles/NDJSON from a local folder or
-    perform a FHIR search against a server, then optionally flatten resources
-    and write to CSV/XLSX/Parquet.
-
-    Args:
-        input_path (str | None): Path to a folder with FHIR files.
-        output_path (str | None): Destination file path for dataframe output.
-        flatten (bool): Whether to add a flattened text column for resources.
-        url (str | None): FHIR server base URL for search.
-        search_type (str | None): Resource type to search when using --url.
-        resource_types (str | None): CSV string of resource types to filter.
-        query (str | None): JSON string of search parameters for the server.
-        config_file (str | None): Path to config JSON file for column transforms.
-    """
     if url:
         from fhiry.fhirsearch import Fhirsearch