gapit 0.2.2__tar.gz → 0.3.0__tar.gz

{gapit-0.2.2 → gapit-0.3.0}/AGENTS.md

@@ -60,7 +60,7 @@ gapit/
 │   └── ci.yml           # gates matrix 3.11/3.13/3.14 + parity job
 ├── src/gapit/
 │   ├── __init__.py
-│   ├── cli.py           # typer entrypoint: screen / summary / db / list / setupdb / schema / mcp
+│   ├── cli.py           # typer entrypoint: screen / summary / db / setupdb / schema / mcp
 │   ├── config.py        # datadir resolution, defaults, env vars
 │   ├── dispatch.py      # shared CLI dispatch (error envelope → exit codes) + --datadir option
 │   ├── proctools.py     # external-tool plumbing: argv subprocess runner + stderr notes
@@ -149,7 +149,7 @@ This is what distinguishes gapit from abricate. Treat it as a public API.
   `db_fetch` (installs provider databases; may download) and `db_build` (writes a custom db);
   tool failures carry the `gapit.error/1` envelope.
 - **stdout purity**: data on stdout, diagnostics on stderr, always. `--quiet` only affects stderr.
-- **Self-description**: `gapit --version --json`, `gapit list --json`, `gapit schema` — an agent
+- **Self-description**: `gapit --version --json`, `gapit db list --json`, `gapit schema` — an agent
   must be able to discover everything without reading docs.
 
 ## 6. Testing strategy

{gapit-0.2.2 → gapit-0.3.0}/CHANGELOG.md

@@ -5,6 +5,14 @@ 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).
 
+## [0.3.0] - 2026-09-28
+
+### Removed
+
+- `gapit list` command and the `gapit.list/1` schema (breaking; rightsholder decision to
+  drop abricate `--list` strict parity for this surface). `gapit db list` / `gapit.dblist/1`
+  is the single listing surface; `gapit schema` now introspects six documents.
+
 ## [0.2.2] - 2026-09-24
 
 ### Security

{gapit-0.2.2 → gapit-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: gapit
-Version: 0.2.2
+Version: 0.3.0
 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/
@@ -49,8 +49,15 @@ byte-compatible TSV plus first-class JSON and Markdown.
 
 ## Install
 
-[pixi](https://pixi.sh) manages the environment, including the external binaries
-(BLAST+, minimap2):
+From PyPI (external BLAST+ and minimap2 binaries required on PATH — see
+[docs/installation.md](docs/installation.md)):
+
+```bash
+pip install gapit
+```
+
+Or from a git clone with [pixi](https://pixi.sh), which manages the environment including
+the external binaries:
 
 ```bash
 git clone https://github.com/indexofire/gapit.git
@@ -87,7 +94,6 @@ gapit db search "tet(M)"         # look up genes across every installed database
 gapit db build mydb my_genes.fa --tsv my_meta.tsv   # custom db from any FASTA
 
 # Introspection
-gapit list              # installed databases (abricate --list compatible)
 gapit schema report     # JSON Schema of gapit.report/1
 ```
 

{gapit-0.2.2 → gapit-0.3.0}/PLAN.md

@@ -142,8 +142,15 @@ consumes abricate-built datadirs.
   `run_screen_reads`/`run_screen_assemblies` use-cases. Additive `gapit.mcp` contract
   (9 tools; the other 8 entries byte-identical), no output-schema version bump. See
   docs/mcp.md.
-- **Deferred by decision (2026-09-18):** PyPI and bioconda publication — recipe remains
-  in-repo; sha256 placeholder to be replaced at submission time.
+- **PyPI published (first release 0.2.2, 2026-09-27):** `pip install gapit`; passwordless
+  releases via `.github/workflows/release.yml` (OIDC trusted publishing, `workflow_dispatch`
+  or `v*` tag). **Deferred by decision (2026-09-18, still open):** bioconda submission —
+  recipe remains in-repo; sha256 placeholder to be replaced at submission time.
+- **Contract change (2026-09-27, rightsholder decision):** `gapit list` and its
+  `gapit.list/1` document removed; `gapit db list` (`gapit.dblist/1`) is the single
+  listing surface and abricate `--list` byte-parity is intentionally dropped for it.
+  Schema registry is now six documents (report, reads, reads2, summary, error, version).
+  Breaking; recorded under \[Unreleased\] in CHANGELOG.md for the next minor bump.
 
 ## Milestones
 

{gapit-0.2.2 → gapit-0.3.0}/README.md

@@ -19,8 +19,15 @@ byte-compatible TSV plus first-class JSON and Markdown.
 
 ## Install
 
-[pixi](https://pixi.sh) manages the environment, including the external binaries
-(BLAST+, minimap2):
+From PyPI (external BLAST+ and minimap2 binaries required on PATH — see
+[docs/installation.md](docs/installation.md)):
+
+```bash
+pip install gapit
+```
+
+Or from a git clone with [pixi](https://pixi.sh), which manages the environment including
+the external binaries:
 
 ```bash
 git clone https://github.com/indexofire/gapit.git
@@ -57,7 +64,6 @@ gapit db search "tet(M)"         # look up genes across every installed database
 gapit db build mydb my_genes.fa --tsv my_meta.tsv   # custom db from any FASTA
 
 # Introspection
-gapit list              # installed databases (abricate --list compatible)
 gapit schema report     # JSON Schema of gapit.report/1
 ```
 

{gapit-0.2.2 → gapit-0.3.0}/docs/agents.md

@@ -13,17 +13,17 @@ Version, as one JSON line:
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.2.2"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.3.0"}
 ```
 
 Output schemas. Six documents are introspectable: `report`, `reads`,
-`summary`, `list`, `error`, `version`. Each prints its full JSON Schema:
+`reads2`, `summary`, `error`, `version`. Each prints its full JSON Schema:
 
 ```console
 $ gapit schema report      # gapit.report/1 (contig screening)
 $ gapit schema reads       # gapit.reads/1  (FASTQ screening)
+$ gapit schema reads2      # gapit.reads/2  (filtered FASTQ screening)
 $ gapit schema summary     # gapit.summary/1
-$ gapit schema list        # gapit.list/1
 $ gapit schema error       # gapit.error/1
 $ gapit schema version     # gapit.version/1
 ```
@@ -56,18 +56,27 @@ For example, `gapit schema version` (real output):
 }
 ```
 
-Installed databases (real output against a datadir holding one database):
+Databases: the provider catalog and install state (`gapit db list --json`; real output,
+first two of twelve shown, trimmed):
 
 ```console
-$ gapit list --json
+$ gapit db list --json
 {
-  "schema": "gapit.list/1",
-  "databases": [
+  "schema": "gapit.dblist/1",
+  "providers": [
     {
-      "name": "tinyamr",
-      "sequences": 3,
+      "name": "argannot",
+      "description": "ARG-ANNOT acquired resistance genes",
       "dbtype": "nucl",
-      "date": "2026-Sep-19"
+      "installed": true,
+      "records": 2224
+    },
+    {
+      "name": "bacmet2",
+      "description": "BacMet2 experimentally confirmed biocide/resistance genes (protein)",
+      "dbtype": "prot",
+      "installed": true,
+      "records": 746
     }
   ]
 }
@@ -103,7 +112,7 @@ Envelope details and error codes: `./outputs.md`.
 ## JSON stability policy
 
 - Every document self-identifies with a version string: `gapit.report/1`,
-  `gapit.reads/1`, `gapit.summary/1`, `gapit.list/1`, `gapit.error/1`,
+  `gapit.reads/1`, `gapit.summary/1`, `gapit.error/1`,
   `gapit.version/1`. Check `schema` first, dispatch on it.
 - Schemas follow semver. A minor bump never renames or retypes an existing
   field; new fields may appear, so ignore unknown keys rather than rejecting
@@ -148,7 +157,7 @@ Parsing guidance:
 Discover, screen, parse, summarize. Session below run against the repo's test
 fixture datadir (setup recipe in `./mcp.md`).
 
-1. Discover available databases (`gapit list --json`, or the `db_list` MCP
+1. Discover available databases (`gapit db list --json`, or the `db_list` MCP
    tool), pick a `db` name.
 
 2. Screen each sample as JSON and parse hits straight out of the document:

{gapit-0.2.2 → gapit-0.3.0}/docs/custom-db.md

@@ -271,9 +271,9 @@ gapit: generated /tmp/opencode/customdb-default/db/labenv/sequences
 gapit: self-check passed for labenv
 gapit: BLAST index built (nucl)
 {"db":"labenv","records":2,"dbtype":"nucl","destination":"/tmp/opencode/customdb-default/db/labenv"}
-$ gapit list
-DATABASE	SEQUENCES	DBTYPE	DATE
-labenv	2	nucl	2026-Sep-19
+$ gapit db outdated
+NAME	FETCHED_AT	AGE_DAYS	STATUS
+labenv	2026-09-27T14:46:27Z	0.00	ok
 ```
 
 Unlike screening, a build creates a missing datadir instead of failing, so a fresh machine bootstraps on the first build. The scratch datadir was deleted after this capture.

{gapit-0.2.2 → gapit-0.3.0}/docs/databases.md

@@ -85,8 +85,10 @@ $ gapit db list --json
 | `providers[].installed` | boolean | True when a manifest exists in the datadir |
 | `providers[].records` | integer | Record count, omitted when the database isn't installed |
 
-`gapit list` gives the abricate-compatible view of installed databases; `gapit list --json`
-returns a `gapit.list/1` document. See [outputs.md](./outputs.md).
+`gapit db list` is the single listing surface: the provider catalog above, with `--json`
+returning the `gapit.dblist/1` document. (The former standalone listing command and its
+schema were removed; abricate `--list` byte-parity is intentionally dropped for this
+surface.) See [outputs.md](./outputs.md).
 
 ## Checking database freshness
 
@@ -343,7 +345,7 @@ versions. A real one, from the plasmidfinder database:
   "upstream_version": "",
   "tool": {
     "name": "gapit",
-    "version": "0.2.2"
+    "version": "0.3.0"
   },
   "makeblastdb_version": "blastn: 2.17.0+",
   "minimap2_version": "2.31-r1302"

{gapit-0.2.2 → gapit-0.3.0}/docs/index.md

@@ -9,7 +9,7 @@ first-class JSON and Markdown outputs with versioned schemas.
 
 | Page | Contents |
 |---|---|
-| [Installation](./installation.md) | Prerequisites, pixi setup, verification, database bootstrap, shell completions |
+| [Installation](./installation.md) | PyPI wheel and pixi paths, external binaries, verification, database bootstrap, shell completions |
 | [Quickstart](./quickstart.md) | A complete first session on the bundled test fixture, offline |
 | [Screening contigs](./screen.md) | `gapit screen` on FASTA/GBK/EMBL inputs: thresholds, filters, formats |
 | [Screening reads](./reads.md) | FASTQ and assembly FASTA through minimap2: `--r1`/`--r2`, presets, breadth-based presence, two-stage survey |
@@ -30,9 +30,8 @@ first-class JSON and Markdown outputs with versioned schemas.
 | `gapit db fetch` | Fetch and build provider database(s) into the datadir | [Databases](./databases.md) |
 | `gapit db list` | List database providers and their installed state | [Databases](./databases.md) |
 | `gapit db install` | Install a local file after verifying its SHA256 | [Databases](./databases.md) |
-| `gapit list` | List installed databases (abricate `--list` compatible) | here |
 | `gapit setupdb` | Build BLAST indices for all databases under the datadir | here |
-| `gapit schema` | Print the JSON Schema of a gapit output document (`report`, `reads`, `summary`, `list`, `error`, `version`) | [Outputs](./outputs.md) |
+| `gapit schema` | Print the JSON Schema of a gapit output document (`report`, `reads`, `reads2`, `summary`, `error`, `version`) | [Outputs](./outputs.md) |
 | `gapit mcp` | Run the MCP stdio server (also installed as the `gapit-mcp` console script) | [MCP server](./mcp.md) |
 
 ## Project documents

{gapit-0.2.2 → gapit-0.3.0}/docs/installation.md

@@ -1,16 +1,29 @@
 # Installing gapit
 
-gapit is installed from a git clone: [pixi](https://pixi.sh) creates the environment, so
-you don't manage Python or external tools yourself.
+Two install paths: the PyPI wheel (you provide the external binaries) or a git clone with
+[pixi](https://pixi.sh) (binaries managed for you).
 
-## Prerequisites
+## From PyPI
+
+```bash
+pip install gapit
+```
+
+The wheel bundles the Python package, the `gapit`/`gapit-mcp` console scripts, and the
+offline `card`/`vfdb` snapshots. It does **not** bundle BLAST+ or minimap2 — install them
+first ([External binaries](#external-binaries), e.g. `conda create -n gapit-env -c
+bioconda blast minimap2`).
+
+## From source (pixi)
+
+### Prerequisites
 
 - [git](https://git-scm.com) and [pixi](https://pixi.sh). On macOS/Linux:
   `curl -fsSL https://pixi.sh/install.sh | bash`
 - Python 3.11+ if you install the package outside pixi (pip/pyproject). With pixi this is
   moot: the environment ships its own Python (the dev env pins 3.14).
 
-## Install
+### Install
 
 ```bash
 git clone https://github.com/indexofire/gapit.git
@@ -31,9 +44,9 @@ gapit --version
 
 ```console
 $ gapit --version
-gapit 0.2.2
+gapit 0.3.0
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.2.2"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.3.0"}
 ```
 
 ## External binaries
@@ -71,7 +84,8 @@ gapit: BLAST index built (nucl)
 {"db":"vfdb","records":4769,"dbtype":"nucl","destination":"/tmp/gapit-docs/dd/vfdb"}
 ```
 
-Confirm what's installed any time with `gapit list` (or `gapit list --json`).
+Confirm the provider catalog and what's installed any time with `gapit db list` (or
+`gapit db list --json`).
 
 ## Shell completions
 

{gapit-0.2.2 → gapit-0.3.0}/docs/mcp.md

@@ -40,7 +40,7 @@ transcribed from the live `tools/list` `inputSchema` objects.
 | `screen` | `files` (array of strings, required), `db` (string, default `ncbi`), `minid` (number), `mincov` (number), `format` (string: `json` \| `tsv` \| `md`, default `json`), `aligner` (string: `blastn` \| `minimap2`, default `blastn`), `min_breadth` (number 0–100, default `90`; minimap2 only), `min_identity` (number 0–100, default `0`; minimap2 only), `min_mapq` (integer ≥ 0, default `0`; minimap2 only), `datadir` (string) | Report text: `gapit.report/1` JSON by default, TSV or Markdown per `format`; `aligner minimap2` runs the reads engine and emits `gapit.reads/1` |
 | `screen_reads` | `r1` (array of strings, required — one path per lane), `r2` (array of strings, same count as `r1`), `read_type` (string: `sr` \| `map-ont` \| `map-hifi`, default `sr`), `min_breadth` (number 0–100, default `90`), `min_identity` (number 0–100, default `0`), `min_mapq` (integer ≥ 0, default `0`), `format` (string: `json` \| `md`, default `json`), `db` (string, default `ncbi`), `datadir` (string) | `gapit.reads/1` JSON by default or Markdown per `format`; `min_identity`/`min_mapq` > 0 switches to `gapit.reads/2` |
 | `summary` | `files` (array of report table paths, required), `identity` (boolean), `nopath` (boolean) | `gapit.summary/1` JSON |
-| `schema` | `name` (string, required, one of `error`, `list`, `reads`, `report`, `summary`, `version`) | The JSON Schema of that output document |
+| `schema` | `name` (string, required, one of `error`, `reads`, `reads2`, `report`, `summary`, `version`) | The JSON Schema of that output document |
 | `db_list` | none | `gapit.dblist/1`: provider names, install state, record counts |
 | `db_fetch` | `name` (string), `datadir` (string), `force` (boolean, default `false`) | One JSON receipt line per database (`db`, `records`, `dbtype`, `destination`). Name omitted: the card+vfdb default set from bundled snapshots. Network installs can take minutes |
 | `db_build` | `name` (string, required), `fasta` (string, required — a LOCAL filesystem path), `tsv` (string), `dbtype` (string: `nucl` \| `prot`), `description` (string), `datadir` (string), `force` (boolean, default `false`) | One JSON receipt line (`db`, `records`, `dbtype`, `destination`) |
@@ -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":"0.2.2"}}}
+{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.3.0"}}}
 ```
 
 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": "0.2.2"},
+  "tool": {"name": "gapit", "version": "0.3.0"},
   "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": "0.2.2"},
+  "tool": {"name": "gapit", "version": "0.3.0"},
   "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": "0.2.2"},
+  "tool": {"name": "gapit", "version": "0.3.0"},
   "created_at": "2026-09-20T13:38:39Z",
   "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [

{gapit-0.2.2 → gapit-0.3.0}/docs/outputs.md

@@ -115,7 +115,7 @@ Real document, same run as the TSV above:
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.2.2"
+    "version": "0.3.0"
   },
   "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": "0.2.2"
+    "version": "0.3.0"
   },
   "created_at": "2026-09-19T01:11:09Z",
   "params": {
@@ -364,42 +364,11 @@ An agent can discover the whole contract from the binary alone.
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.2.2"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.3.0"}
 ```
 
-`gapit list --json` describes installed databases (`gapit.list/1`, first two of twelve
-shown, trimmed):
-
-```json
-{
-  "schema": "gapit.list/1",
-  "databases": [
-    {
-      "name": "argannot",
-      "sequences": 2224,
-      "dbtype": "nucl",
-      "date": "2026-Sep-18"
-    },
-    {
-      "name": "bacmet2",
-      "sequences": 746,
-      "dbtype": "prot",
-      "date": "2026-Sep-18"
-    }
-  ]
-}
-```
-
-| Field | Type | Meaning |
-|---|---|---|
-| `schema` | string | Always `gapit.list/1` |
-| `databases[].name` | string | Database name, usable as `--db` |
-| `databases[].sequences` | integer | Sequence count in the database |
-| `databases[].dbtype` | string | `nucl` or `prot` |
-| `databases[].date` | string | Build date, abricate `%d-%b-%Y` format |
-
 `gapit schema <name>` prints the JSON Schema for each document. The six names: `report`,
-`reads`, `summary`, `list`, `error`, `version`. A trimmed fragment of `gapit schema report`:
+`reads`, `reads2`, `summary`, `error`, `version`. A trimmed fragment of `gapit schema report`:
 
 ```json
 {

{gapit-0.2.2 → gapit-0.3.0}/docs/quickstart.md

@@ -22,14 +22,20 @@ makeblastdb -in /tmp/gapit-quickstart/db/tinyamr/sequences \
 export GAPIT_DATADIR=/tmp/gapit-quickstart/db
 ```
 
-`gapit list` confirms the database is visible:
+`gapit db list` shows the provider catalog and install state (trimmed below; `--json`
+returns the `gapit.dblist/1` document). The fixture `tinyamr` is a plain custom database,
+not a provider, so it does not appear there — the screen in the next section confirms it
+is usable:
 
 ```console
-$ gapit list
-DATABASE	SEQUENCES	DBTYPE	DATE
-tinyamr	3	nucl	2026-Sep-19
+$ gapit db list
+PROVIDER	STATUS	DBTYPE	DESCRIPTION
+argannot	available	nucl	ARG-ANNOT acquired resistance genes
+ncbi	available	nucl	NCBI AMRFinderPlus (reference finder) curated AMR
 ```
 
+(twelve providers in total, all `available` in this throwaway datadir)
+
 ## 2. Screen a contig file
 
 ```console
@@ -73,7 +79,7 @@ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.2.2"
+    "version": "0.3.0"
   },
   "created_at": "2026-09-19T01:11:06Z",
   "params": {

{gapit-0.2.2 → gapit-0.3.0}/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 0.2.2). Contig-mode flags not listed here
+(transcribed from `gapit screen --help`, gapit 0.3.0). 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 0.2.2
+tool: gapit 0.3.0
 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": "0.2.2"
+    "version": "0.3.0"
   },
   "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 0.2.2
+tool: gapit 0.3.0
 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": "0.2.2"
+    "version": "0.3.0"
   },
   "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 0.2.2):
+single-threaded, gapit 0.3.0):
 
 ```console
 $ # Stage 1: survey, ~0.9 s

{gapit-0.2.2 → gapit-0.3.0}/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 0.2.2). Flags marked *reads mode* apply only when
+Transcribed from `gapit screen --help` (gapit 0.3.0). 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": "0.2.2"
+    "version": "0.3.0"
   },
   "created_at": "2026-09-19T01:12:04Z",
   "params": {

{gapit-0.2.2 → gapit-0.3.0}/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 0.2.2):
+Transcribed from `gapit summary --help` (gapit 0.3.0):
 
 | 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": "0.2.2"
+    "version": "0.3.0"
   },
   "created_at": "2026-09-19T01:12:48Z",
   "params": {

{gapit-0.2.2 → gapit-0.3.0}/pixi.lock

@@ -1135,8 +1135,8 @@ packages:
   timestamp: 1694615932610
 - pypi: ./
   name: gapit
-  version: 0.2.2
-  sha256: 7ddd019d0bc6e998bf772d75f8cdc26856074cf4ed1c76c71d048d7486df5b43
+  version: 0.3.0
+  sha256: 079317f27b81dd25126368906a19acb3934a200b6fcdf3f2ac1490e9e60d4c46
   requires_dist:
   - typer>=0.12
   - pydantic>=2.7

{gapit-0.2.2 → gapit-0.3.0}/pixi.toml

@@ -3,7 +3,7 @@ authors = ["indexofire <indexofire@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 name = "gapit"
 platforms = ["linux-64"]
-version = "0.2.2"
+version = "0.3.0"
 
 [tasks]
 lint = "ruff check"

{gapit-0.2.2 → gapit-0.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "gapit"
-version = "0.2.2"
+version = "0.3.0"
 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-0.2.2 → gapit-0.3.0}/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 = "0.2.2" %}
+{% set version = "0.3.0" %}
 
 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-0.2.2.tar.gz)
+  # The value below hashes the LOCAL hatchling sdist (dist/gapit-0.3.0.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-0.2.2 → gapit-0.3.0}/src/gapit/__init__.py

@@ -1,3 +1,3 @@
 """gapit — agent-first Python reimplementation of abricate."""
 
-__version__ = "0.2.2"
+__version__ = "0.3.0"