Merge pull request #456 from Ensembl/jalvarez/add_version

Add --version to every entry point

src/python/ensembl/io/genomio/__init__.py

@@ -14,4 +14,4 @@
 # limitations under the License.
 """Genome Input/Output (GenomIO) handling library."""
 
-__version__ = "1.5.0"
+__version__ = "1.6.0"

src/python/ensembl/io/genomio/annotation/update_description.py

@@ -26,6 +26,7 @@
 from sqlalchemy.orm import Session
 from sqlalchemy import and_, select
 
+import ensembl.io.genomio
 from ensembl.core.models import Gene, Transcript, ObjectXref, Xref
 from ensembl.io.genomio.utils import get_json
 from ensembl.utils.argparse import ArgumentParser
@@ -249,6 +250,7 @@ def main() -> None:
     parser.add_argument(
         "--match_xrefs", action="store_true", help="Use xref IDs to match features if IDs do not work"
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/assembly/download.py

@@ -36,6 +36,7 @@
 import time
 from typing import Dict, Optional
 
+import ensembl.io.genomio
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
 
@@ -333,6 +334,7 @@ def main() -> None:
     parser.add_argument_dst_path(
         "--download_dir", default=Path.cwd(), help="Folder where the data will be downloaded"
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/assembly/status.py

@@ -35,6 +35,7 @@
 from sqlalchemy.engine import URL
 from sqlalchemy import text
 
+import ensembl.io.genomio
 from ensembl.io.genomio.utils.json_utils import print_json
 from ensembl.utils import StrPath
 from ensembl.utils.argparse import ArgumentParser
@@ -346,6 +347,7 @@ def generate_report_tsv(
 def main() -> None:
     """Module's entry-point."""
     parser = ArgumentParser(description=__doc__)
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     # Create parser with common arguments to be used by both subparsers
     base_parser = ArgumentParser(add_help=False)
     base_parser.add_argument_dst_path(

src/python/ensembl/io/genomio/database/factory.py

@@ -23,6 +23,7 @@
 
 from sqlalchemy.engine import URL
 
+import ensembl.io.genomio
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
 from .core_server import CoreServer
@@ -136,7 +137,7 @@ def parse_args(arg_list: list[str] | None) -> argparse.Namespace:
     # Add filter arguments
     parser.add_argument("--prefix", default="", help="Prefix to filter the databases")
     parser.add_argument("--build", type=int, default=None, help="Build to filter the databases")
-    parser.add_argument("--version", type=int, default=None, help="EnsEMBL version to filter the databases")
+    parser.add_argument("--release", type=int, default=None, help="EnsEMBL release to filter the databases")
     parser.add_argument("--db_regex", default="", help="Regular expression to match database names against")
     parser.add_argument_src_path("--db_list", help="File with one database per line to load")
     # Add flags
@@ -145,6 +146,7 @@ def parse_args(arg_list: list[str] | None) -> argparse.Namespace:
         action="store_true",
         help="Enable BRC mode, i.e. use organism_abbrev for species, component for division",
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     return parser.parse_args(arg_list)
 
@@ -163,7 +165,7 @@ def main(arg_list: list[str] | None = None) -> None:
         server_url=args.url,
         prefix=args.prefix,
         build=args.build,
-        version=args.version,
+        version=args.release,
         db_regex=args.db_regex,
         db_list=args.db_list,
         brc_mode=args.brc_mode,

src/python/ensembl/io/genomio/database/meta_getter.py

@@ -25,6 +25,7 @@
 
 from sqlalchemy.engine import URL
 
+import ensembl.io.genomio
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils import StrPath
 from ensembl.utils.logging import init_logging_with_args
@@ -95,6 +96,7 @@ def parse_args(arg_list: list[str] | None) -> argparse.Namespace:
     parser.add_argument_src_path(
         "--meta_keys_list", help="Input File | List with >=2 meta_keys to query target database."
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=False)
     return parser.parse_args(arg_list)
 

src/python/ensembl/io/genomio/events/dump.py

@@ -32,6 +32,7 @@
 from sqlalchemy import select, and_, or_
 from sqlalchemy.orm import Session
 
+import ensembl.io.genomio
 from ensembl.core.models import MappingSession, StableIdEvent
 from ensembl.io.genomio.database import DBConnectionLite
 from ensembl.utils.argparse import ArgumentParser
@@ -541,6 +542,7 @@ def main() -> None:
     )
     parser.add_server_arguments(include_database=True)
     parser.add_argument_dst_path("--output_file", required=True, help="Output file")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/events/format.py

@@ -21,6 +21,7 @@
 import re
 from typing import Dict, List
 
+import ensembl.io.genomio
 from ensembl.io.genomio.events.load import EventCollection
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -79,6 +80,7 @@ def main() -> None:
     parser.add_argument("--release_name", required=True, metavar="NAME", help="Release name for all events")
     parser.add_argument("--release_date", required=True, metavar="DATE", help="Release date for all events")
     parser.add_argument_dst_path("--output_file", required=True, help="Output formatted event file")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/events/load.py

@@ -28,6 +28,7 @@
 
 from sqlalchemy.orm import Session
 
+import ensembl.io.genomio
 from ensembl.io.genomio.database import DBConnectionLite
 from ensembl.core.models import MappingSession, StableIdEvent
 from ensembl.utils.argparse import ArgumentParser
@@ -243,6 +244,7 @@ def main() -> None:
         ),
     )
     parser.add_argument("--update", action="store_true", help="Make changes to the database")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/fasta/chunk.py

@@ -38,6 +38,7 @@
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 
+import ensembl.io.genomio
 from ensembl.utils.archive import open_gz_file
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -386,7 +387,7 @@ def main() -> None:
         action="store_true",
         help="Append zero-based offset to chunk name ('_off_{offset}').",
     )
-
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/fasta/process.py

@@ -23,6 +23,7 @@
 
 from Bio import SeqIO
 
+import ensembl.io.genomio
 from ensembl.utils.archive import open_gz_file
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -99,6 +100,7 @@ def main() -> None:
     parser.add_argument_src_path("--genbank_infile", help="Input GenBank GBFF file")
     parser.add_argument_dst_path("--fasta_outfile", required=True, help="Output FASTA file")
     parser.add_argument("--peptide_mode", action="store_true", help="Process proteins instead of DNA")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/genbank/download.py

@@ -22,6 +22,7 @@
 
 import requests
 
+import ensembl.io.genomio
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
 
@@ -70,6 +71,7 @@ def main() -> None:
     parser = ArgumentParser(description="Download a sequence from GenBank.")
     parser.add_argument("--accession", required=True, help="Sequence accession")
     parser.add_argument_dst_path("--output_file", required=True, help="Output GenBank file")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/genbank/extract_data.py

@@ -42,6 +42,7 @@
 from Bio.SeqRecord import SeqRecord
 from Bio.SeqFeature import SeqFeature
 
+import ensembl.io.genomio
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
 
@@ -526,6 +527,7 @@ def main() -> None:
     parser.add_argument_dst_path(
         "--out_dir", default=Path.cwd(), help="output folder where the generated files will be stored"
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/genome_metadata/dump.py

@@ -33,6 +33,7 @@
 from sqlalchemy.engine import URL
 
 from ensembl.core.models import Meta
+import ensembl.io.genomio
 from ensembl.io.genomio.utils.json_utils import get_json
 from ensembl.io.genomio.database import DBConnectionLite
 from ensembl.utils.argparse import ArgumentParser
@@ -289,6 +290,7 @@ def parse_args(arg_list: list[str] | None) -> argparse.Namespace:
         help="Perform assembly and genebuild 'version' metadata checks & update if needed.",
     )
     parser.add_argument("--append_db", action="store_true", help="Append core database name to output JSON.")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     return parser.parse_args(arg_list)
 

src/python/ensembl/io/genomio/genome_metadata/extend.py

@@ -29,6 +29,7 @@
 
 from Bio import SeqIO
 
+import ensembl.io.genomio
 from ensembl.io.genomio.utils import get_json, print_json
 from ensembl.utils.archive import open_gz_file
 from ensembl.utils.argparse import ArgumentParser
@@ -163,6 +164,7 @@ def main() -> None:
     )
     parser.add_argument_src_path("--report_file", help="INSDC/RefSeq sequences report file")
     parser.add_argument_src_path("--genbank_file", help="INSDC/RefSeq GBFF file")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/genome_metadata/prepare.py

@@ -31,6 +31,7 @@
 from os import PathLike
 from typing import Dict
 
+import ensembl.io.genomio
 from ensembl.io.genomio.utils import get_json, print_json
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -199,6 +200,7 @@ def main() -> None:
     parser.add_argument_src_path(
         "--ncbi_meta", required=True, help="JSON file from NCBI datasets for this genome."
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/genome_stats/compare.py

@@ -21,6 +21,7 @@
 import re
 from typing import Any, Dict
 
+import ensembl.io.genomio
 from ensembl.io.genomio.utils import get_json
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -222,6 +223,7 @@ def main() -> None:
     )
     parser.add_argument_src_path("--ncbi_stats", required=True, help="NCBI dataset stats JSON file")
     parser.add_argument_src_path("--core_stats", required=True, help="core database stats JSON file")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
 

src/python/ensembl/io/genomio/genome_stats/dump.py

@@ -24,6 +24,7 @@
 from sqlalchemy.orm import Session
 
 from ensembl.core.models import SeqRegionAttrib, AttribType, Gene, Transcript
+import ensembl.io.genomio
 from ensembl.io.genomio.database import DBConnectionLite
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.database import StrURL
@@ -149,6 +150,7 @@ def main() -> None:
     """Main script entry-point."""
     parser = ArgumentParser(description=__doc__)
     parser.add_server_arguments(include_database=True)
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/gff3/overlaps.py

@@ -32,6 +32,7 @@
 from Bio.SeqRecord import SeqRecord
 from intervaltree import Interval, IntervalTree
 
+import ensembl.io.genomio
 from ensembl.io.genomio.utils import print_json
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -182,15 +183,14 @@ def get_intervals(record: SeqRecord, genes_dict: dict, seq_dict: dict, seq_name:
 def main() -> None:
     """Module entry-point."""
     parser = ArgumentParser(description=__doc__)
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     # Create parser with common arguments to be used by both subparsers
     base_parser = ArgumentParser(add_help=False)
     base_parser.add_argument_src_path("--input_gff", required=True, help="path of GFF3 file to process")
     base_parser.add_log_arguments(add_log_file=True)
     # Add subparsers with their parent being the base parser with the common arguments
     subparsers = parser.add_subparsers(title="Parse GFF3 and ", required=True, dest="subcommand")
-    gff3_stats_parser = subparsers.add_parser(  # pylint: disable=unused-variable
-        "stats", parents=[base_parser], help="Provide summary of feature types"
-    )
+    _ = subparsers.add_parser("stats", parents=[base_parser], help="Provide summary of feature types")
     overlaps_parser = subparsers.add_parser("overlaps", parents=[base_parser], help="Find feature overlaps")
     overlaps_parser.add_argument_dst_path(
         "--output_file", default="feature_overlaps.txt", help="path of output file"

src/python/ensembl/io/genomio/gff3/process.py

@@ -18,6 +18,7 @@
 import logging
 from pathlib import Path
 
+import ensembl.io.genomio
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
 
@@ -44,6 +45,7 @@ def main() -> None:
         default=Path("functional_annotation.json"),
         help="Output functional annotation JSON file",
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/manifest/check_integrity.py

@@ -23,6 +23,7 @@
 import re
 from typing import Any
 
+import ensembl.io.genomio
 from ensembl.io.genomio.manifest.manifest_stats import InvalidIntegrityError, ManifestStats
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -389,6 +390,7 @@ def main() -> None:
     parser.add_argument(
         "--no_fail", action="store_true", help="In case of errors, don't fail but print errors to stdout."
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments(add_log_file=True)
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/manifest/compute_stats.py

@@ -29,6 +29,7 @@
 
 from BCBio import GFF
 
+import ensembl.io.genomio
 from ensembl.utils import StrPath
 from ensembl.utils.archive import open_gz_file
 from ensembl.utils.argparse import ArgumentParser
@@ -418,6 +419,7 @@ def main() -> None:
     parser.add_argument("--accession", help="Sequence accession ID to compare stats with NCBI")
     parser.add_argument("--datasets_bin", help="Datasets bin status")
     parser.add_argument_dst_path("--stats_file", help="Output file with the stats")
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/manifest/generate.py

@@ -14,6 +14,7 @@
 # limitations under the License.
 """Creates a manifest file in a folder depending on the file names ends."""
 
+import ensembl.io.genomio
 from ensembl.io.genomio.manifest.manifest import Manifest
 from ensembl.utils.argparse import ArgumentParser
 from ensembl.utils.logging import init_logging_with_args
@@ -27,6 +28,7 @@ def main() -> None:
     parser.add_argument_dst_path(
         "--manifest_dir", required=True, help="Folder where to create a manifest file"
     )
+    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)

src/python/ensembl/io/genomio/manifest/manifest_stats.py

@@ -104,7 +104,7 @@ def add_error(self, error: str) -> None:
     def load_seq_regions(self) -> None:
         """Retrieve seq_regions lengths and circular information from the seq_region JSON file."""
 
-        if not "seq_region" in self.manifest_files:
+        if "seq_region" not in self.manifest_files:
             return
         logging.info("Manifest contains seq_region JSON")
         seq_regions = get_json(Path(self.manifest_files["seq_region"]))