fix: use POSIX/GNU conventions for option word separators (#521)

the general recommendation is to use hyphens to separate words for
reasons like visibility in certain terminal contexts and how some html
documentation handles it. This is something we've been bad about in the
past but it'd be good to get it cleaned up

Author: jsstevenson

docs/extras/vcf_annotator.md

@@ -15,37 +15,37 @@ vrs-annotate vcf --help
 
 ### Configuring the sequence data proxy
 
-Like other VRS-Python tools, the VCF annotator requires access to [sequence and identifier data services](https://vrs.ga4gh.org/en/stable/impl-guide/required_data.html#data-services), as implemented in libraries like [SeqRepo](https://github.com/biocommons/biocommons.seqrepo). By default, the CLI will attempt to connect to a [SeqRepo REST instance](https://github.com/biocommons/seqrepo-rest-service) at `http://localhost:5000/seqrepo`, but a URI can be passed with the `--dataproxy_uri` option or set with the `GA4GH_VRS_DATAPROXY_URI` environment variable (the former takes priority over the latter).
+Like other VRS-Python tools, the VCF annotator requires access to [sequence and identifier data services](https://vrs.ga4gh.org/en/stable/impl-guide/required_data.html#data-services), as implemented in libraries like [SeqRepo](https://github.com/biocommons/biocommons.seqrepo). By default, the CLI will attempt to connect to a [SeqRepo REST instance](https://github.com/biocommons/seqrepo-rest-service) at `http://localhost:5000/seqrepo`, but a URI can be passed with the `--dataproxy-uri` option or set with the `GA4GH_VRS_DATAPROXY_URI` environment variable (the former takes priority over the latter).
 
 For example, to use a local set of SeqRepo data, you can use an absolute file path:
 
 ```commandline
-vrs-annotate vcf --dataproxy_uri="seqrepo+file:///usr/local/share/seqrepo/2024-12-20/" --vcf_out=out.vcf.gz input.vcf.gz
+vrs-annotate vcf --dataproxy-uri="seqrepo+file:///usr/local/share/seqrepo/2024-12-20/" --vcf-out=out.vcf.gz input.vcf.gz
 ```
 
 Alternative, a relative file path:
 
 ```commandline
-vrs-annotate vcf --dataproxy_uri="seqrepo+../seqrepo/2024-12-20/" --vcf_out=out.vcf.gz input.vcf.gz
+vrs-annotate vcf --dataproxy-uri="seqrepo+../seqrepo/2024-12-20/" --vcf-out=out.vcf.gz input.vcf.gz
 ```
 
 Or an alternate REST path:
 
 ```commandline
-vrs-annotate vcf --dataproxy_uri="seqrepo+http://mylabwebsite.org/seqrepo" --vcf_out=out.vcf.gz input.vcf.gz
+vrs-annotate vcf --dataproxy-uri="seqrepo+http://mylabwebsite.org/seqrepo" --vcf-out=out.vcf.gz input.vcf.gz
 ```
 
 ### Other Options
-`--vrs_attributes`
+`--vrs-attributes`
 >Will include VRS_Start, VRS_End, VRS_State fields in the INFO field.
 
 `--assembly` [TEXT]
->The assembly that the `vcf_in` data uses. [default: GRCh38]
+>The assembly that the `vcf-in` data uses. [default: GRCh38]
 
-`--skip_ref`
+`--skip-ref`
 >Skip VRS computation for REF alleles.
 
-`--require_validation`
+`--require-validation`
 >Require validation checks to pass in order to return a VRS object
 
 `--help`

src/ga4gh/vrs/extras/annotator/cli.py

@@ -30,7 +30,7 @@ def _cli() -> None:
 
 
 class _LogLevel(str, Enum):
-    """Define legal values for `--log_level` option."""
+    """Define legal values for `--log-level` option."""
 
     DEBUG = "debug"
     INFO = "info"
@@ -42,7 +42,7 @@ class _LogLevel(str, Enum):
 def _log_level_option(func: Callable) -> Callable:
     """Provide reusable log level CLI option decorator.
 
-    Adds a `--log_level` CLI option to any decorated command. Doesn't pass on any
+    Adds a `--log-level` CLI option to any decorated command. Doesn't pass on any
     values, just sets the logging level for this module.
 
     :param func: incoming click command
@@ -60,7 +60,7 @@ def _set_log_level(ctx: dict, param: str, value: _LogLevel) -> None:  # noqa: AR
         logging.getLogger(__name__).setLevel(level_map[value])
 
     return click.option(
-        "--log_level",
+        "--log-level",
         type=click.Choice([v.value for v in _LogLevel.__members__.values()]),
         default="info",
         help="Set the logging level.",
@@ -73,42 +73,42 @@ def _set_log_level(ctx: dict, param: str, value: _LogLevel) -> None:  # noqa: AR
 @_cli.command(name="vcf")
 @_log_level_option
 @click.argument(
-    "vcf_in",
+    "vcf-in",
     nargs=1,
     type=click.Path(exists=True, readable=True, dir_okay=False, path_type=Path),
 )
 @click.option(
-    "--vcf_out",
+    "--vcf-out",
     required=False,
     type=click.Path(writable=True, allow_dash=False, path_type=Path),
     help=(
         "Declare save location for output annotated VCF. At least one form of output must be declared."
     ),
 )
 @click.option(
-    "--pkl_out",
+    "--pkl-out",
     required=False,
     type=click.Path(writable=True, allow_dash=False, path_type=Path),
     help=(
         "Declare save location for output PKL file mapping VRS IDs to alleles. At least one form of output must be declared."
     ),
 )
 @click.option(
-    "--ndjson_out",
+    "--ndjson-out",
     required=False,
     type=click.Path(writable=True, allow_dash=False, path_type=Path),
     help=(
         "Declare save location for output NDJSON file dump of VRS alleles. At least one form of output must be declared."
     ),
 )
 @click.option(
-    "--vrs_attributes",
+    "--vrs-attributes",
     is_flag=True,
     default=False,
     help="Include VRS_Start, VRS_End, and VRS_State fields in the VCF output INFO field.",
 )
 @click.option(
-    "--dataproxy_uri",
+    "--dataproxy-uri",
     required=False,
     default="seqrepo+http://localhost:5000/seqrepo",
     help="URI declaring source of sequence data. See subcommand description for more information.",
@@ -123,13 +123,13 @@ def _set_log_level(ctx: dict, param: str, value: _LogLevel) -> None:  # noqa: AR
     type=str,
 )
 @click.option(
-    "--skip_ref",
+    "--skip-ref",
     is_flag=True,
     default=False,
     help="Skip VRS computation for REF alleles.",
 )
 @click.option(
-    "--require_validation",
+    "--require-validation",
     is_flag=True,
     default=False,
     help="Require validation checks to pass to construct a VRS object.",
@@ -155,12 +155,12 @@ def _annotate_vcf_cli(
 ) -> None:
     """Extract VRS objects from VCF located at VCF_IN.
 
-        $ vrs-annotate vcf input.vcf.gz --vcf_out output.vcf.gz --pkl_out vrs_objects.pkl
+        $ vrs-annotate vcf input.vcf.gz --vcf-out output.vcf.gz --pkl-out vrs_objects.pkl
 
-    Note that at least one of --vcf_out, --pkl_out, or --ndjson_out must be selected and
+    Note that at least one of --vcf-out, --pkl-out, or --ndjson-out must be selected and
     defined; otherwise, this process will terminate immediately.
 
-    Sequence data from a provider such as SeqRepo is required. Use the `--dataproxy_uri`
+    Sequence data from a provider such as SeqRepo is required. Use the `--dataproxy-uri`
     option or the environment variable `GA4GH_VRS_DATAPROXY_URI` to define its location
     (the former will take priority over the latter when both are set).
 
@@ -199,7 +199,7 @@ def _annotate_vcf_cli(
             output_ndjson_path=ndjson_out,
         )
     except VcfAnnotatorArgsError:
-        msg = "No VCF, PKL, or NDJSON output path provided -- must set at least one of --vcf_out, --pkl_out, or --ndjson_out"
+        msg = "No VCF, PKL, or NDJSON output path provided -- must set at least one of --vcf-out, --pkl-out, or --ndjson-out"
         if not silent:
             click.echo(msg)
         _logger.exception(msg)