Merge branch 'main' into feat/anyvar-http-client

Author: jsstevenson

.github/CODEOWNERS

@@ -1 +1 @@
-* @GenomicMedLab/vlm-in-a-box-maintainers
+* @GenomicMedLab/anyvlm-maintainers

.gitignore

@@ -85,7 +85,7 @@ ipython_config.py
 # pyenv
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -199,7 +199,7 @@ cython_debug/
 #   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
 #   and can be added to the global gitignore or merged into this file. However, if you prefer,
 #   you could uncomment the following to ignore the entire vscode folder
-# .vscode/
+.vscode/
 
 # Ruff stuff:
 .ruff_cache/
@@ -217,3 +217,6 @@ __marimo__/
 
 # uv
 uv.lock
+
+# Mac things:
+.DS_Store

Makefile

@@ -8,7 +8,7 @@
 SHELL:=/bin/bash -e -o pipefail
 SELF:=$(firstword $(MAKEFILE_LIST))
 
-PKG=vlm
+PKG=anyvlm
 PKGD=$(subst .,/,${PKG})
 PYV:=3.11
 VEDIR=venv/${PYV}

README.md

@@ -1 +1 @@
-# VLM in a Box
+# AnyVLM

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "vlm"
+name = "anyvlm"
 authors = [
   { name="biocommons contributors", email="[email protected]" },
 ]
@@ -46,14 +46,14 @@ dev = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/genomicmedlab/vlm_in_a_box"
-Documentation = "https://github.com/genomicmedlab/vlm_in_a_box/"
-Changelog = "https://github.com/genomicmedlab/vlm_in_a_box/releases"
-Source = "https://github.com/genomicmedlab/vlm_in_a_box/"
-"Bug Tracker" = "https://github.com/genomicmedlab/vlm_in_a_box/issues"
+Homepage = "https://github.com/genomicmedlab/anyvlm"
+Documentation = "https://github.com/genomicmedlab/anyvlm/"
+Changelog = "https://github.com/genomicmedlab/anyvlm/releases"
+Source = "https://github.com/genomicmedlab/anyvlm/"
+"Bug Tracker" = "https://github.com/genomicmedlab/anyvlm/issues"
 
 [project.scripts]
-vlm = "vlm.cli:_cli"
+anyvlm = "anyvlm.cli:_cli"
 
 
 [build-system]
@@ -66,7 +66,7 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 
 [tool.pytest.ini_options]
-addopts = "--cov=vlm --cov-report term-missing"
+addopts = "--cov=anyvlm --cov-report term-missing"
 testpaths = ["tests"]
 pythonpath = ["src"]
 

src/vlm/__init__.py src/anyvlm/__init__.pysrc/vlm/__init__.py renamed to src/anyvlm/__init__.py

@@ -3,7 +3,7 @@
 from importlib.metadata import PackageNotFoundError, version
 
 try:
-    __version__ = version("vlm")
+    __version__ = version("anyvlm")
 except PackageNotFoundError:
     __version__ = "unknown"
 finally:

src/vlm/anyvar/__init__.py src/anyvlm/anyvar/__init__.pysrc/vlm/anyvar/__init__.py renamed to src/anyvlm/anyvar/__init__.py

@@ -1,10 +1,10 @@
-"""Provide abstraction for a VLM-to-AnyVar connection."""
+"""Provide abstraction for a AnyVLM-to-AnyVar connection."""
 
 import abc
 
 from anyvar.utils.types import VrsObject
 
-from vlm.schemas.domain import AlleleFrequencyAnnotation
+from anyvlm.schemas.domain import AlleleFrequencyAnnotation
 
 # define constant to use as AnyVar annotation type
 AF_ANNOTATION_TYPE = "cohort_allele_frequency"

src/vlm/anyvar/base_client.py src/anyvlm/anyvar/base_client.pysrc/vlm/anyvar/base_client.py renamed to src/anyvlm/anyvar/base_client.py

@@ -0,0 +1,17 @@
+"""CLI for interacting with AnyVLM instance"""
+
+import click
+
+import anyvlm
+
+
+@click.version_option(anyvlm.__version__)
+@click.group()
+def _cli() -> None:
+    """Manage AnyVLM data."""
+
+
+@_cli.command()
+def ingest_vcf() -> None:
+    """Deposit variants and allele frequencies from VCF into AnyVLM instance"""
+    raise NotImplementedError