gapit 0.3.0__tar.gz → 0.3.1__tar.gz

{gapit-0.3.0 → gapit-0.3.1}/CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to gapit are documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this
 project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.1] - 2026-09-28
+
+### Added
+
+- `-h` now works as an alias for `--help` on every command (root, subcommands,
+  and nested `db` sub-app).
+
 ## [0.3.0] - 2026-09-28
 
 ### Removed

{gapit-0.3.0 → gapit-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: gapit
-Version: 0.3.0
+Version: 0.3.1
 Summary: Mass screening of contigs for antimicrobial resistance and virulence genes — agent-first Python reimplementation of abricate
 Project-URL: Homepage, https://github.com/indexofire/gapit
 Project-URL: Documentation, https://indexofire.github.io/gapit/

{gapit-0.3.0 → gapit-0.3.1}/docs/agents.md

@@ -13,7 +13,7 @@ Version, as one JSON line:
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.3.0"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.3.1"}
 ```
 
 Output schemas. Six documents are introspectable: `report`, `reads`,

{gapit-0.3.0 → gapit-0.3.1}/docs/databases.md

@@ -345,7 +345,7 @@ versions. A real one, from the plasmidfinder database:
   "upstream_version": "",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "makeblastdb_version": "blastn: 2.17.0+",
   "minimap2_version": "2.31-r1302"

{gapit-0.3.0 → gapit-0.3.1}/docs/installation.md

@@ -44,9 +44,9 @@ gapit --version
 
 ```console
 $ gapit --version
-gapit 0.3.0
+gapit 0.3.1
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.3.0"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.3.1"}
 ```
 
 ## External binaries

{gapit-0.3.0 → gapit-0.3.1}/docs/mcp.md

@@ -94,7 +94,7 @@ EOF
 Response line 1, verbatim:
 
 ```text
-{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.3.0"}}}
+{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.3.1"}}}
 ```
 
 Response line 2 (real output, elided in the middle; each tool carries its full
@@ -117,7 +117,7 @@ the same run):
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.3.0"},
+  "tool": {"name": "gapit", "version": "0.3.1"},
   "created_at": "2026-09-19T01:15:44Z",
   "params": {"db": "tinyamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [
@@ -173,7 +173,7 @@ the same run):
 ```json
 {
   "schema": "gapit.reads/1",
-  "tool": {"name": "gapit", "version": "0.3.0"},
+  "tool": {"name": "gapit", "version": "0.3.1"},
   "created_at": "2026-09-22T00:07:35Z",
   "params": {
     "db": "tinyreads",
@@ -248,7 +248,7 @@ hit is the gene the agent just built the database from (real output):
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.3.0"},
+  "tool": {"name": "gapit", "version": "0.3.1"},
   "created_at": "2026-09-20T13:38:39Z",
   "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [

{gapit-0.3.0 → gapit-0.3.1}/docs/outputs.md

@@ -115,7 +115,7 @@ Real document, same run as the TSV above:
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T01:12:20Z",
   "params": {
@@ -246,7 +246,7 @@ summarizing two report files, one with a `tetA` hit and one with none:
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T01:11:09Z",
   "params": {
@@ -364,7 +364,7 @@ An agent can discover the whole contract from the binary alone.
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.3.0"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.3.1"}
 ```
 
 `gapit schema <name>` prints the JSON Schema for each document. The six names: `report`,

{gapit-0.3.0 → gapit-0.3.1}/docs/quickstart.md

@@ -79,7 +79,7 @@ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T01:11:06Z",
   "params": {

{gapit-0.3.0 → gapit-0.3.1}/docs/reads.md

@@ -28,7 +28,7 @@ gapit screen --r1 R1[,R1b,...] [--r2 R2[,R2b,...]] --db NAME [--read-type sr|map
 ## Options
 
 Reads mode runs through the same `gapit screen` command; these are the flags that apply
-(transcribed from `gapit screen --help`, gapit 0.3.0). Contig-mode flags not listed here
+(transcribed from `gapit screen --help`, gapit 0.3.1). Contig-mode flags not listed here
 (`--minid`, `--mincov`, `--jobs`, `--fofn`, `--noheader`, `--nopath`) do not apply.
 
 | Flag | Type | Default | Description |
@@ -223,7 +223,7 @@ The short-read fixture behaves the same with one calibration: `sr` soft-clipping
 $ gapit screen --r1 ont_homologs.fq --db homologs --read-type map-ont --min-identity 95 --format md --quiet
 ---
 schema: gapit.reads/2
-tool: gapit 0.3.0
+tool: gapit 0.3.1
 created_at: 2026-09-20T14:23:33Z
 db: homologs
 read_type: map-ont
@@ -262,7 +262,7 @@ Detected 1 present genes in tetx_full.fq
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T01:12:25Z",
   "params": {
@@ -359,7 +359,7 @@ $ gapit screen --r1 tetx_lane1.fq,tetx_lane2.fq --db tinyreads --quiet
 $ gapit screen --r1 tetx_full.fq --db tinyreads --format md
 ---
 schema: gapit.reads/1
-tool: gapit 0.3.0
+tool: gapit 0.3.1
 created_at: 2026-09-19T01:12:25Z
 db: tinyreads
 read_type: sr
@@ -455,7 +455,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T14:23:00Z",
   "params": {
@@ -514,7 +514,7 @@ cost of allele-level precision. That trade suggests a two-stage workflow over ma
    pipeline, which applies the identity and coverage floors at abricate parity.
 
 Real numbers, one K. pneumoniae RefSeq assembly (GCF_000240185.1, 5.3 Mb, `--db ncbi`,
-single-threaded, gapit 0.3.0):
+single-threaded, gapit 0.3.1):
 
 ```console
 $ # Stage 1: survey, ~0.9 s

{gapit-0.3.0 → gapit-0.3.1}/docs/screen.md

@@ -9,7 +9,7 @@ Database setup is covered in [./databases.md](./databases.md); a full walk-throu
 
 ## Options
 
-Transcribed from `gapit screen --help` (gapit 0.3.0). Flags marked *reads mode* apply only when
+Transcribed from `gapit screen --help` (gapit 0.3.1). Flags marked *reads mode* apply only when
 you pass `--r1`/`--r2`; they are documented in [./reads.md](./reads.md).
 
 | Flag | Type | Default | Description |
@@ -86,7 +86,7 @@ $ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T01:12:04Z",
   "params": {

{gapit-0.3.0 → gapit-0.3.1}/docs/summary.md

@@ -10,7 +10,7 @@ exactly what `gapit screen` writes. See [./screen.md](./screen.md) for producing
 
 ## Options
 
-Transcribed from `gapit summary --help` (gapit 0.3.0):
+Transcribed from `gapit summary --help` (gapit 0.3.1):
 
 | Flag | Type | Default | Description |
 |---|---|---|---|
@@ -110,7 +110,7 @@ $ gapit summary tests/data/summary/sample_a.tsv tests/data/summary/sample_b.tsv
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-19T01:12:48Z",
   "params": {

{gapit-0.3.0 → gapit-0.3.1}/pixi.lock

@@ -1135,8 +1135,8 @@ packages:
   timestamp: 1694615932610
 - pypi: ./
   name: gapit
-  version: 0.3.0
-  sha256: 079317f27b81dd25126368906a19acb3934a200b6fcdf3f2ac1490e9e60d4c46
+  version: 0.3.1
+  sha256: db655bb2b9f4c9843304958d45db24f7e9fe0f0f9b15460f54d03b9d00968b1c
   requires_dist:
   - typer>=0.12
   - pydantic>=2.7

{gapit-0.3.0 → gapit-0.3.1}/pixi.toml

@@ -3,7 +3,7 @@ authors = ["indexofire <indexofire@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 name = "gapit"
 platforms = ["linux-64"]
-version = "0.3.0"
+version = "0.3.1"
 
 [tasks]
 lint = "ruff check"

{gapit-0.3.0 → gapit-0.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "gapit"
-version = "0.3.0"
+version = "0.3.1"
 description = "Mass screening of contigs for antimicrobial resistance and virulence genes — agent-first Python reimplementation of abricate"
 readme = "README.md"
 authors = [{ name = "indexofire", email = "indexofire@gmail.com" }]

{gapit-0.3.0 → gapit-0.3.1}/recipe/meta.yaml

@@ -4,7 +4,7 @@
 # version/license/python/deps mirror pyproject.toml exactly; the external
 # binaries mirror pixi.toml's conda dependencies.
 {% set name = "gapit" %}
-{% set version = "0.3.0" %}
+{% set version = "0.3.1" %}
 
 package:
   name: {{ name|lower }}
@@ -13,7 +13,7 @@ package:
 source:
   # gapit is not on PyPI yet. This is the standard noarch-python source URL;
   # replace the sha256 with the PyPI sdist hash at submission time.
-  # The value below hashes the LOCAL hatchling sdist (dist/gapit-0.3.0.tar.gz)
+  # The value below hashes the LOCAL hatchling sdist (dist/gapit-0.3.1.tar.gz)
   # — local and PyPI sdists are not byte-identical (gzip), do not trust it.
   url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
   sha256: 24df143ed9647fc784fa29c776babfd880d3730d22004b997ed0aea3f105f5e3

{gapit-0.3.0 → gapit-0.3.1}/src/gapit/__init__.py

@@ -1,3 +1,3 @@
 """gapit — agent-first Python reimplementation of abricate."""
 
-__version__ = "0.3.0"
+__version__ = "0.3.1"

{gapit-0.3.0 → gapit-0.3.1}/src/gapit/cli.py

@@ -21,6 +21,8 @@ app = typer.Typer(
     help="Mass screening of contigs for antimicrobial resistance and virulence genes.",
     no_args_is_help=True,
     add_completion=True,
+    # -h alias for --help; click Context propagates this to all subcommands/sub-apps.
+    context_settings={"help_option_names": ["-h", "--help"]},
 )
 
 

{gapit-0.3.0 → gapit-0.3.1}/tests/golden/reads_tinyamr.json

@@ -2,7 +2,7 @@
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-17T12:00:00Z",
   "params": {

{gapit-0.3.0 → gapit-0.3.1}/tests/golden/reads_tinyamr.md

@@ -1,6 +1,6 @@
 ---
 schema: gapit.reads/1
-tool: gapit 0.3.0
+tool: gapit 0.3.1
 created_at: 2026-09-17T12:00:00Z
 db: tinyreads
 read_type: sr

{gapit-0.3.0 → gapit-0.3.1}/tests/golden/screen_multi.json

@@ -2,7 +2,7 @@
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-17T12:00:00Z",
   "params": {

{gapit-0.3.0 → gapit-0.3.1}/tests/golden/screen_multi.md

@@ -1,6 +1,6 @@
 ---
 schema: gapit.report/1
-tool: gapit 0.3.0
+tool: gapit 0.3.1
 created_at: 2026-09-17T12:00:00Z
 db: tinyamr
 minid: 80.0

{gapit-0.3.0 → gapit-0.3.1}/tests/golden/summary_multi.json

@@ -2,7 +2,7 @@
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.3.0"
+    "version": "0.3.1"
   },
   "created_at": "2026-09-17T12:00:00Z",
   "params": {

{gapit-0.3.0 → gapit-0.3.1}/tests/golden/summary_multi.md

@@ -1,6 +1,6 @@
 ---
 schema: gapit.summary/1
-tool: gapit 0.3.0
+tool: gapit 0.3.1
 created_at: 2026-09-17T12:00:00Z
 metric: '%COVERAGE'
 nopath: false

{gapit-0.3.0 → gapit-0.3.1}/tests/test_cli_completion.py

@@ -23,6 +23,15 @@ def test_root_help_lists_completion_options() -> None:
     assert "--show-completion" in help_text
 
 
+def test_short_help_alias_works_on_every_level() -> None:
+    """Given -h instead of --help, When invoked on the root app, a
+    subcommand, and a nested sub-app, Then each prints its help and exits 0."""
+    for argv in (["-h"], ["screen", "-h"], ["db", "-h"], ["db", "fetch", "-h"]):
+        result = runner.invoke(app, argv, env={"COLUMNS": "100"})
+        assert result.exit_code == 0, argv
+        assert "Usage:" in ANSI_STYLE.sub("", result.stdout), argv
+
+
 def test_show_completion_emits_shell_script() -> None:
     """Given --show-completion under a pinned SHELL, When run, Then a bash
     completion script referencing the gapit completion env var is printed