afquery 0.4.1__tar.gz → 0.4.2__tar.gz

{afquery-0.4.1 → afquery-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: afquery
-Version: 0.4.1
+Version: 0.4.2
 Summary: Genomic allele frequency query engine with bitmap-encoded genotypes
 License: MIT
 License-File: LICENSE

{afquery-0.4.1 → afquery-0.4.2}/docs/reference/cli.md

@@ -4,6 +4,19 @@ All AFQuery commands follow the pattern `afquery <command> [OPTIONS]`.
 
 ---
 
+## Global options
+
+| Option | Description |
+|--------|-------------|
+| `--version` | Print the AFQuery version and exit |
+| `--help` | Show help for the command and exit |
+
+`afquery --version` prints the installed package version (e.g. `afquery 0.4.2`),
+taken from the Git release tag at build time. In an editable install
+(`pip install -e .`) it reflects the last build, not later local commits.
+
+---
+
 ## create-db
 
 Build a new AFQuery database from a manifest of single-sample VCFs.

{afquery-0.4.1 → afquery-0.4.2}/docs/troubleshooting.md

@@ -81,84 +81,6 @@ AFQuery requires DuckDB to use Parquet for all temporary files. Arrow IPC is not
 
 ---
 
-## Samples Added by update-db Are Missing From Queries
-
-**Symptom:** After `afquery update-db --add-samples`, the new samples show up in
-`afquery info --db ./db/ --samples` and `AN` grows by the expected amount, but they
-never appear as carriers: `AC` does not increase at variants you know they carry, and
-`afquery variant-info` does not list them. Allele frequencies across the whole database
-drift downward after every update.
-
-`afquery check --db ./db/` reports one error per affected chromosome:
-
-```
-ERROR  chr1: both variants/chr1/ (bucketed) and variants/chr1.parquet exist.
-```
-
-**Cause:** `update-db --add-samples` before 0.4.1 only understood the
-single-file-per-chromosome variant layout. `create-db` produces the bucketed layout
-(`variants/<chrom>/bucket_N.parquet`), so the merge found nothing to merge and wrote the
-new samples to a fresh `variants/<chrom>.parquet` instead. Queries read the bucketed
-files and ignore that one, so the added samples counted toward `AN` through the capture
-index but never as carriers — they were treated as homozygous reference everywhere.
-
-**Fix:** Upgrade to 0.4.1 or later, then repair the database. `afquery info --db ./db/
---changelog` lists the samples added by each `add_samples` event.
-
-```bash
-# 0. Stop all writers and back up the small files.
-cp ./db/manifest.json ./db/manifest.json.bak
-cp ./db/metadata.sqlite ./db/metadata.sqlite.bak
-
-# 1. Record the affected samples BEFORE removing them: removal deletes their
-#    phenotype rows, and you need them to rebuild the manifest.
-sqlite3 ./db/metadata.sqlite \
-  "SELECT s.sample_name, s.sex, t.tech_name, s.vcf_path,
-          group_concat(p.phenotype_code)
-   FROM samples s
-   JOIN technologies t ON s.tech_id = t.tech_id
-   LEFT JOIN sample_phenotype p ON p.sample_id = s.sample_id
-   WHERE s.sample_name IN ('SAMPLE_1','SAMPLE_2') GROUP BY s.sample_id;"
-
-# 2. List the flat files before deleting anything. Only those with a sibling
-#    directory of the same name are orphans; one without a sibling is the only
-#    copy of that chromosome and queries still read it.
-for f in ./db/variants/*.parquet; do
-  [ -d "${f%.parquet}" ] && echo "orphan: $f" || echo "KEEP (no sibling): $f"
-done
-
-# 3. Remove the affected samples. This clears their bits from both layouts and is
-#    safe on a split database. Every bucket is read, so budget minutes, not
-#    seconds, and do not interrupt it.
-afquery update-db --db ./db/ --remove-samples SAMPLE_1 --remove-samples SAMPLE_2
-
-# 4. Delete only the orphans listed in step 2. A flat file with no sibling
-#    directory must be kept: deleting it would drop that chromosome entirely.
-for f in ./db/variants/*.parquet; do
-  [ -d "${f%.parquet}" ] && rm "$f"
-done
-
-# 5. Confirm the errors are gone.
-afquery check --db ./db/
-
-# 6. Re-add the samples with the fixed version.
-afquery update-db --db ./db/ --add-samples repair.tsv --bed-dir ./beds/
-
-# 7. Verify a variant you know they carry.
-afquery variant-info --db ./db/ --locus chr1:887801
-```
-
-Re-added samples receive new sample IDs — IDs are never reused after a removal. That is
-expected and does not affect results.
-
-If the original VCFs are no longer available, stop after step 5. The samples are then
-absent from both the metadata and `AN`, which is a correct smaller cohort rather than a
-biased larger one. Rebuilding with `create-db` is always a valid fallback.
-
-Databases that were only ever built with `create-db`, and never updated, are unaffected.
-
----
-
 ## Compact Takes a Long Time
 
 **Symptom:** `afquery update-db --compact` runs for many minutes or hours.

{afquery-0.4.1 → afquery-0.4.2}/src/afquery/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.4.1'
-__version_tuple__ = version_tuple = (0, 4, 1)
+__version__ = version = '0.4.2'
+__version_tuple__ = version_tuple = (0, 4, 2)
 
 __commit_id__ = commit_id = None

{afquery-0.4.1 → afquery-0.4.2}/src/afquery/cli.py

@@ -4,6 +4,8 @@ import sys
 
 import click
 
+from afquery import __version__
+
 from .database import Database
 
 
@@ -168,15 +170,18 @@ def _print_carriers(carriers, variant_key, fmt: str) -> None:
             click.echo(fmt_row.format(*row))
 
 
-@click.group()
-def cli():
-    """AFQuery: bitmap-indexed allele frequency engine for local genomic cohorts.
+_CLI_HELP = f"""\
+AFQuery v{__version__} — bitmap-indexed allele frequency engine for local genomic cohorts.
 
-    Enables fast AC/AN/AF queries on user-defined subcohorts (phenotype, sex,
-    technology) without rescanning VCFs.
+Enables fast AC/AN/AF queries on user-defined subcohorts (phenotype, sex,
+technology) without rescanning VCFs.
+"""
 
-    Commands: query, variant-info, annotate, dump, info, version, create-db, update-db, check, benchmark
-    """
+
+@click.group(help=_CLI_HELP)
+@click.version_option(version=__version__, prog_name="afquery", message="%(prog)s %(version)s")
+def cli():
+    pass
 
 
 @cli.command()

{afquery-0.4.1 → afquery-0.4.2}/tests/test_cli.py

@@ -375,6 +375,29 @@ def test_version_set_then_show(runner, db_copy):
     assert "MYVER" in result.output
 
 
+# --- afquery --version / --help ---
+
+def test_version_flag(runner):
+    from afquery import __version__
+    result = runner.invoke(cli, ["--version"])
+    assert result.exit_code == 0
+    assert __version__ in result.output
+
+
+def test_help_shows_program_name_and_version(runner):
+    from afquery import __version__
+    result = runner.invoke(cli, ["--help"])
+    assert result.exit_code == 0
+    assert f"AFQuery v{__version__}" in result.output
+
+
+def test_help_lists_all_commands(runner):
+    result = runner.invoke(cli, ["--help"])
+    for cmd in ("query", "variant-info", "annotate", "dump", "info",
+                "version", "create-db", "update-db", "check", "benchmark"):
+        assert cmd in result.output
+
+
 # --- afquery check ---
 
 def test_check_ok(runner, test_db):