Merge pull request #445 from biothings/1.1.x

Release v1.1.0

Author: DylanWelzel

.github/workflows/pypi-publish.yml

@@ -21,9 +21,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/run-tests.yml

@@ -5,15 +5,15 @@ on:
   pull_request:
     branches:
       - master
-      - 1.0.x
+      - 1.1.x
 
 jobs:
   install_and_run_tests:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12', '3.13' ]
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14t']
 
     services:
       # mongo:
@@ -41,9 +41,9 @@ jobs:
 
     steps:
       - name: Checkout source
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.github/workflows/test-build.yml

@@ -11,12 +11,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12', '3.13' ]
+        python-version: [ '3.9', '3.10', '3.11', '3.12', '3.13', '3.14t' ]
     steps:
       - name: Checkout source
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

CHANGES.txt

@@ -1,4 +1,67 @@
 
+v1.1.0 (2026/05/27)
+    Highlights:
+        - Added Python 3.14 support and dropped Python 3.8 support.
+        - Reworked biothings CLI configuration, pathing, and dataplugin command organization.
+        - Added MongoDB build cleanup management APIs and commands.
+
+    biothings.hub improvements:
+        - Added prefix support to DataTransformMDB. ([#411](https://github.com/biothings/biothings.api/pull/411))
+        - Added TAR and Zstandard file handling. ([#424](https://github.com/biothings/biothings.api/pull/424), [#428](https://github.com/biothings/biothings.api/pull/428))
+        - Added support for custom local uploader and dumper classes in dataplugin manifests. ([#431](https://github.com/biothings/biothings.api/pull/431))
+        - Added MongoDB build cleanup validation and deletion tooling. ([#437](https://github.com/biothings/biothings.api/pull/437))
+
+    biothings.utils improvements:
+        - Fixed dict_sweep handling for NaN-like values, including pandas.NA and pandas.NaT. ([#442](https://github.com/biothings/biothings.api/pull/442))
+        - Centralized orjson usage across the library. ([#435](https://github.com/biothings/biothings.api/pull/435))
+
+    biothings.web improvements:
+        - Removed deprecated Google Analytics event support. ([#439](https://github.com/biothings/biothings.api/pull/439))
+        - Removed old doc_type and deprecated Elasticsearch compatibility code.
+        - Improved Elasticsearch exception handling and query response behavior.
+        - Optimized Elasticsearch memory usage when using scroll API.
+
+    biothings.cli improvements:
+        - Added CLI config and pathing commands. ([#418](https://github.com/biothings/biothings.api/pull/418), [#422](https://github.com/biothings/biothings.api/pull/422))
+        - Added CLI dump mark-success support. ([#423](https://github.com/biothings/biothings.api/pull/423))
+        - Fixed Typer/rich_utils loading behavior. ([#426](https://github.com/biothings/biothings.api/pull/426))
+
+    Misc improvements:
+        - Updated dependencies and package metadata for Python 3.9+, including tornado, typer, pymongo, orjson, and zstandard.
+        - Updated GitHub Actions test, build, and publish workflows.
+
+
+v1.1.0 (2026/05/27)
+    Highlights:
+        - Added Python 3.14 support and dropped Python 3.8 support.
+        - Reworked biothings CLI configuration, pathing, and dataplugin command organization.
+        - Added MongoDB build cleanup management APIs and commands.
+
+    biothings.hub improvements:
+        - Added prefix support to DataTransformMDB. ([#411](https://github.com/biothings/biothings.api/pull/411))
+        - Added TAR and Zstandard file handling. ([#424](https://github.com/biothings/biothings.api/pull/424), [#428](https://github.com/biothings/biothings.api/pull/428))
+        - Added support for custom local uploader and dumper classes in dataplugin manifests. ([#431](https://github.com/biothings/biothings.api/pull/431))
+        - Added MongoDB build cleanup validation and deletion tooling. ([#437](https://github.com/biothings/biothings.api/pull/437))
+
+    biothings.utils improvements:
+        - Fixed dict_sweep handling for NaN-like values, including pandas.NA and pandas.NaT. ([#442](https://github.com/biothings/biothings.api/pull/442))
+        - Centralized orjson usage across the library. ([#435](https://github.com/biothings/biothings.api/pull/435))
+
+    biothings.web improvements:
+        - Removed deprecated Google Analytics event support. ([#439](https://github.com/biothings/biothings.api/pull/439))
+        - Removed old doc_type and deprecated Elasticsearch compatibility code.
+        - Improved Elasticsearch exception handling and query response behavior.
+        - Optimized Elasticsearch memory usage when using scroll API.
+
+    biothings.cli improvements:
+        - Added CLI config and pathing commands. ([#418](https://github.com/biothings/biothings.api/pull/418), [#422](https://github.com/biothings/biothings.api/pull/422))
+        - Added CLI dump mark-success support. ([#423](https://github.com/biothings/biothings.api/pull/423))
+        - Fixed Typer/rich_utils loading behavior. ([#426](https://github.com/biothings/biothings.api/pull/426))
+
+    Misc improvements:
+        - Updated dependencies and package metadata for Python 3.9+, including tornado, typer, pymongo, orjson, and zstandard.
+        - Updated GitHub Actions test, build, and publish workflows.
+
 v1.0.2 (2025/10/15)
     Bugfix:
         - Fixed an import issue in inspector.py that was causing the mapping inspect to fail.

biothings/__init__.py

@@ -8,7 +8,7 @@ class _version_info(NamedTuple):
     micro: int
 
 
-version_info = _version_info(1, 0, 2)
+version_info = _version_info(1, 1, 0)
 __version__ = ".".join(map(str, version_info))
 
 

biothings/cli/__init__.py

@@ -2,34 +2,41 @@
 Entrypoint for the biothings-cli tool
 """
 
+from typing import Literal
 import importlib.util
 import logging
 import os
 import sys
 
+import typer
+from rich.logging import RichHandler
 
-from biothings.cli.settings import (
-    setup_biothings_configuration,
-    setup_commandline_configuration,
-    setup_logging_configuration,
-)
+from biothings.cli.commands.admin import build_admin_application
+from biothings.cli.commands.config import config_application, load_configuration
+from biothings.cli.commands.dataplugin import dataplugin_application
+from biothings.cli.commands.pathing import path_application
 
 
-def check_module_import_status(module: str) -> bool:
+def setup_logging_configuration(logging_level: Literal[10, 20, 30, 40, 50]) -> None:
     """
-    Verify that we can import a module prior to proceeding with creating our commandline
-    tooling that depends on those modules
+    Configures the logging based off our environment configuration
     """
-    module_specification = importlib.util.find_spec(module)
-    status = module_specification is not None
-    return status
+    rich_handler = RichHandler(
+        level=logging_level,
+        markup=True,
+        rich_tracebacks=False,  # typer creates it already
+        show_path=False,
+        tracebacks_suppress=[typer],
+    )
+    logging.basicConfig(level=logging_level, format="%(message)s", datefmt="[%X]", handlers=[rich_handler])
 
 
 def main():
     """
-    The entrypoint for running the BioThings CLI to test your local data plugin
+    The entrypoint for running the BioThings CLI
     """
-    typer_status = check_module_import_status("typer")
+    module_specification = importlib.util.find_spec("typer")
+    typer_status = module_specification is not None
     if not typer_status:
         logging.error(
             (
@@ -48,14 +55,14 @@ def main():
     cli_debug_flag = os.environ.get("BTCLI_DEBUG", False)
     cli_rich_traceback_flag = os.environ.get("BTCLI_RICH_TRACEBACK", False)
 
-    cli = setup_commandline_configuration(debug=cli_debug_flag, rich_traceback=cli_rich_traceback_flag)
+    admin_application = build_admin_application(debug=cli_debug_flag, rich_traceback=cli_rich_traceback_flag)
     logging_level = logging.WARNING
     if cli_debug_flag:
         logging_level = logging.DEBUG
     setup_logging_configuration(logging_level)
-    setup_biothings_configuration()
+    load_configuration()
 
-    from biothings.cli.dataplugin import dataplugin_application
-
-    cli.add_typer(dataplugin_application, name="dataplugin")
-    return cli()
+    admin_application.add_typer(dataplugin_application, name="dataplugin")
+    admin_application.add_typer(config_application, name="config")
+    admin_application.add_typer(path_application, name="path")
+    return admin_application()

biothings/cli/assistant.py

@@ -38,7 +38,7 @@ class CLIAssistant(BaseAssistant):
 
     plugin_type = "CLI"
 
-    def __init__(self, plugin_name: Optional[str] = None, job_manager: "JobManager" = None):
+    def __init__(self, plugin_name: Optional[str] = None, job_manager: CLIJobManager = None):
         from biothings import config
         from biothings.hub.databuild.builder import BuilderManager
         from biothings.hub.dataindex.indexer import IndexManager

biothings/cli/commands/__init__.py

@@ -0,0 +1,48 @@
+"""
+Configuration settings for the biothings-cli tool
+
+> Logging
+> Tool Configuration
+    > Creates a mock config used in the biothings.api backend
+"""
+
+import sys
+
+import typer
+import typer.rich_utils
+
+
+def build_admin_application(debug: bool, rich_traceback: bool) -> typer.Typer:
+    """
+    Builds the main administrative command line application for the
+    biothings-cli application
+    """
+    pretty_exceptions_show_locals = False
+    pretty_exceptions_enable = False
+    sys.tracebacklimit = 1
+
+    if rich_traceback:
+        pretty_exceptions_enable = True
+        sys.tracebacklimit = 1000
+
+    if debug:
+        pretty_exceptions_enable = True
+        pretty_exceptions_show_locals = True
+        sys.tracebacklimit = 1000
+
+    # prevent dimming the help text from the 2nd line
+    # see: https://github.com/tiangolo/typer/issues/437#issuecomment-1224149402
+    typer.rich_utils.STYLE_HELPTEXT = ""
+
+    context_settings = {"help_option_names": ["-h", "--help"]}
+    typer_instance = typer.Typer(
+        help="[green]BioThings Admin CLI to test your local data plugins. See helps for each command for specific usage.[/green]",
+        rich_help_panel="Help and Others",
+        rich_markup_mode="rich",
+        context_settings=context_settings,
+        no_args_is_help=True,
+        pretty_exceptions_show_locals=pretty_exceptions_show_locals,
+        pretty_exceptions_enable=pretty_exceptions_enable,
+    )
+
+    return typer_instance