gapit 0.6.3__tar.gz → 0.6.4__tar.gz

{gapit-0.6.3 → gapit-0.6.4}/CHANGELOG.md

@@ -5,6 +5,18 @@ 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).
 
+## [0.6.4] - 2026-10-27
+
+### Fixed
+
+- **Batch progress vs stdout data.** The progress bar now uses the gside/gmlst
+  hand-off: `transient=True`, stdout chunks go through `BatchProgress.write`
+  (stop -> `sys.stdout.write` + flush -> start), and stderr notices have a
+  `notice()` hand-off. The bar is inactive for a single input. On a shared TTY
+  data rows no longer start inside the bar line; stdout bytes are unchanged when
+  output is piped. Applies to contig batches and positional FASTQ samples;
+  `db fetch` receipts use the same suspend/restore path.
+
 ## [0.6.3] - 2026-10-26
 
 ### Added

{gapit-0.6.3 → gapit-0.6.4}/CITATION.cff

@@ -7,7 +7,7 @@ authors:
 repository-code: "https://github.com/indexofire/gapit"
 url: "https://indexofire.github.io/gapit/"
 license: MIT
-version: "0.6.3"
+version: "0.6.4"
 date-released: "2026-10-26"
 keywords:
   - bioinformatics

{gapit-0.6.3 → gapit-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: gapit
-Version: 0.6.3
+Version: 0.6.4
 Summary: Mass screening of contigs and reads for known genes — agent-first Python reimplementation of abricate
 Project-URL: Homepage, https://github.com/indexofire/gapit
 Project-URL: Documentation, https://indexofire.github.io/gapit/

{gapit-0.6.3 → gapit-0.6.4}/docs/agents.md

@@ -13,7 +13,7 @@ Version, as one JSON line:
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.6.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.6.4"}
 ```
 
 Output schemas. Fifteen documents are introspectable: `report`, `typing_result`,

{gapit-0.6.3 → gapit-0.6.4}/docs/agents.zh.md

@@ -12,7 +12,7 @@ gapit 生来就是被程序驱动的。每个输出都以机器可读为设计
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.6.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.6.4"}
 ```
 
 输出 schema。十五个文档可自省：`report`、`typing_result`、`reads`、`reads2`、

{gapit-0.6.3 → gapit-0.6.4}/docs/databases.md

@@ -564,7 +564,7 @@ versions. A real one, from the plasmidfinder database:
   "upstream_version": "",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "makeblastdb_version": "blastn: 2.17.0+",
   "minimap2_version": "2.31-r1302"

{gapit-0.6.3 → gapit-0.6.4}/docs/databases.zh.md

@@ -526,7 +526,7 @@ manifest，来自 plasmidfinder 数据库：
   "upstream_version": "",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "makeblastdb_version": "blastn: 2.17.0+",
   "minimap2_version": "2.31-r1302"

{gapit-0.6.3 → gapit-0.6.4}/docs/datadir.md

@@ -180,7 +180,7 @@ docker run --rm -it \
   --user "$(id -u):$(id -g)" \
   -v gapit-data:/data/gapit \
   -e GAPIT_DATADIR=/data/gapit \
-  gapit:0.6.3 gapit db list
+  gapit:0.6.4 gapit db list
 ```
 
 For CI, mount or cache a workspace directory and pin versions:
@@ -189,7 +189,7 @@ For CI, mount or cache a workspace directory and pin versions:
 docker run --rm \
   -v "$PWD/.gapit-db:/data/gapit" \
   -e GAPIT_DATADIR=/data/gapit \
-  gapit:0.6.3 gapit screen sample.fna --db ecoli_dec
+  gapit:0.6.4 gapit screen sample.fna --db ecoli_dec
 ```
 
 You can bake reference databases into an image for **read-only** screening:

{gapit-0.6.3 → gapit-0.6.4}/docs/datadir.zh.md

@@ -164,7 +164,7 @@ docker run --rm -it \
   --user "$(id -u):$(id -g)" \
   -v gapit-data:/data/gapit \
   -e GAPIT_DATADIR=/data/gapit \
-  gapit:0.6.3 gapit db list
+  gapit:0.6.4 gapit db list
 ```
 
 CI 中挂载或缓存 workspace 目录，并固定版本：
@@ -173,7 +173,7 @@ CI 中挂载或缓存 workspace 目录，并固定版本：
 docker run --rm \
   -v "$PWD/.gapit-db:/data/gapit" \
   -e GAPIT_DATADIR=/data/gapit \
-  gapit:0.6.3 gapit screen sample.fna --db ecoli_dec
+  gapit:0.6.4 gapit screen sample.fna --db ecoli_dec
 ```
 
 可以为**只读**筛查把参考库烤进镜像：

{gapit-0.6.3 → gapit-0.6.4}/docs/installation.md

@@ -48,9 +48,9 @@ gapit --version
 
 ```console
 $ gapit --version
-gapit 0.6.3
+gapit 0.6.4
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.6.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.6.4"}
 ```
 
 ## Optional gseek engine

{gapit-0.6.3 → gapit-0.6.4}/docs/installation.zh.md

@@ -46,9 +46,9 @@ gapit --version
 
 ```console
 $ gapit --version
-gapit 0.6.3
+gapit 0.6.4
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.6.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.6.4"}
 ```
 
 ## 可选 gseek 引擎

{gapit-0.6.3 → gapit-0.6.4}/docs/mcp.md

@@ -59,7 +59,7 @@ reads-engine parameters); `minid`/`mincov` are ignored by `minimap2`.
 Notes:
 
 - Screen parameters use snake_case (`merge_fragments`, `min_gene_cov`,
-  `min_gene_id`, `min_cluster_cov`). The pre-0.6.3 camelCase spellings are still
+  `min_gene_id`, `min_cluster_cov`). The pre-0.6.4 camelCase spellings are still
   accepted as aliases for compatibility, but new clients should use snake_case.
 - File paths resolve relative to the server's working directory; absolute
   paths are safest.
@@ -102,7 +102,7 @@ EOF
 Response line 1, verbatim:
 
 ```text
-{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.3"}}}
+{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.4"}}}
 ```
 
 Response line 2 (real output, elided in the middle; each tool carries its full
@@ -125,7 +125,7 @@ the same run):
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-09-19T01:15:44Z",
   "params": {"db": "tinyamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [
@@ -181,7 +181,7 @@ the same run):
 ```json
 {
   "schema": "gapit.reads/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-09-22T00:07:35Z",
   "params": {
     "db": "tinyreads",
@@ -256,7 +256,7 @@ hit is the gene the agent just built the database from (real output):
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-09-20T13:38:39Z",
   "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [

{gapit-0.6.3 → gapit-0.6.4}/docs/mcp.zh.md

@@ -56,7 +56,7 @@ shell 外调或解析终端输出。协议是手写的换行分隔 JSON-RPC 2.0
 注意事项：
 
 - screen 参数使用 snake_case（`merge_fragments`、`min_gene_cov`、`min_gene_id`、
-  `min_cluster_cov`）；0.6.3 之前的 camelCase 拼写仍作为兼容别名接受，新客户端
+  `min_cluster_cov`）；0.6.4 之前的 camelCase 拼写仍作为兼容别名接受，新客户端
   应使用 snake_case。
 - 文件路径相对服务器的工作目录解析；绝对路径最稳妥。
 - 数据目录来自 `--datadir`（可用时），然后 `$GAPIT_DATADIR`，然后
@@ -98,7 +98,7 @@ EOF
 响应第 1 行，原样：
 
 ```text
-{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.3"}}}
+{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.6.4"}}}
 ```
 
 响应第 2 行（真实输出，中段省略；每个工具携带完整的 `inputSchema`）：
@@ -119,7 +119,7 @@ EOF
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-09-19T01:15:44Z",
   "params": {"db": "tinyamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [
@@ -173,7 +173,7 @@ EOF
 ```json
 {
   "schema": "gapit.reads/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-09-22T00:07:35Z",
   "params": {
     "db": "tinyreads",
@@ -246,7 +246,7 @@ export GAPIT_DATADIR=/tmp/gapit-mcp-demo/datadir
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-09-20T13:38:39Z",
   "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [

{gapit-0.6.3 → gapit-0.6.4}/docs/outputs.md

@@ -141,7 +141,7 @@ Real document, same run as the TSV above:
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:20Z",
   "params": {
@@ -233,7 +233,7 @@ row by `(%IDENTITY, %COVERAGE)`. Real document (trimmed):
 ```json
 {
   "schema": "gapit.typing_result/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-10-02T10:04:55Z",
   "source": ["dec.tsv"],
   "db": "ecoli_dec",
@@ -420,7 +420,7 @@ summarizing two report files, one with a `tetA` hit and one with none:
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:11:09Z",
   "params": {
@@ -544,7 +544,7 @@ An agent can discover the whole contract from the binary alone.
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.6.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.6.4"}
 ```
 
 `gapit schema <name>` prints the JSON Schema for each document. The eleven names: `report`,

{gapit-0.6.3 → gapit-0.6.4}/docs/outputs.zh.md

@@ -130,7 +130,7 @@ non-DEC。零命中文件不产生筛查行，因此不会出现在判定输出
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:20Z",
   "params": {
@@ -220,7 +220,7 @@ non-DEC。零命中文件不产生筛查行，因此不会出现在判定输出
 ```json
 {
   "schema": "gapit.typing_result/1",
-  "tool": {"name": "gapit", "version": "0.6.3"},
+  "tool": {"name": "gapit", "version": "0.6.4"},
   "created_at": "2026-10-02T10:04:55Z",
   "source": ["dec.tsv"],
   "db": "ecoli_dec",
@@ -403,7 +403,7 @@ typing 的数据库是同一个表头去掉 `PHENOTYPE`。没有位点判定的
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:11:09Z",
   "params": {
@@ -526,7 +526,7 @@ agent 只凭二进制就能发现整个契约。
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.6.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.6.4"}
 ```
 
 `gapit schema <name>` 打印每个文档的 JSON Schema。十二个名字：`report`、

{gapit-0.6.3 → gapit-0.6.4}/docs/quickstart.md

@@ -94,7 +94,7 @@ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:11:06Z",
   "params": {

{gapit-0.6.3 → gapit-0.6.4}/docs/quickstart.zh.md

@@ -89,7 +89,7 @@ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:11:06Z",
   "params": {

{gapit-0.6.3 → gapit-0.6.4}/docs/reads.md

@@ -123,7 +123,7 @@ table, one chunk for the one sample).
 ## Options
 
 Reads mode runs through the same `gapit screen` command; these are the flags that apply
-(transcribed from `gapit screen --help`, gapit 0.6.3). Contig-mode flags not listed here
+(transcribed from `gapit screen --help`, gapit 0.6.4). Contig-mode flags not listed here
 (`--minid`, `--mincov`, `--fofn`, `--noheader`, `--nopath`) do not apply; `--jobs` applies
 to the wildcard path only.
 
@@ -337,7 +337,7 @@ 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 0.6.3
+tool: gapit 0.6.4
 created_at: 2026-09-20T14:23:33Z
 db: homologs
 read_type: map-ont
@@ -433,7 +433,7 @@ $ gapit screen --r1 tetx_full.fq --db tinyreads --format json
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:25Z",
   "params": {
@@ -528,7 +528,7 @@ $ gapit screen --r1 tetx_lane1.fq,tetx_lane2.fq --db tinyreads --format json --q
 $ gapit screen --r1 tetx_full.fq --db tinyreads --format md
 ---
 schema: gapit.reads/1
-tool: gapit 0.6.3
+tool: gapit 0.6.4
 created_at: 2026-09-19T01:12:25Z
 db: tinyreads
 read_type: sr
@@ -630,7 +630,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T14:23:00Z",
   "params": {
@@ -689,7 +689,7 @@ 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 0.6.3):
+single-threaded, gapit 0.6.4):
 
 ```console
 $ # Stage 1: survey, ~0.9 s

{gapit-0.6.3 → gapit-0.6.4}/docs/reads.zh.md

@@ -113,7 +113,7 @@ frontmatter 保留 `files:`/`genes_found:` 运行总计（它的 tsv 默认渲
 ## 选项
 
 reads 模式走同一条 `gapit screen` 命令；以下是适用的参数（转写自 `gapit screen
---help`，gapit 0.6.3）。这里未列出的 contig 模式参数（`--minid`、`--mincov`、
+--help`，gapit 0.6.4）。这里未列出的 contig 模式参数（`--minid`、`--mincov`、
 `--fofn`、`--noheader`、`--nopath`）不适用；`--jobs` 只适用于通配符路径（见上文）。
 
 | 参数 | 类型 | 默认值 | 说明 |
@@ -318,7 +318,7 @@ Markdown 形式：
 $ gapit screen --r1 ont_homologs.fq --db homologs --read-type map-ont --min-identity 95 --format md --quiet
 ---
 schema: gapit.reads/2
-tool: gapit 0.6.3
+tool: gapit 0.6.4
 created_at: 2026-09-20T14:23:33Z
 db: homologs
 read_type: map-ont
@@ -410,7 +410,7 @@ $ gapit screen --r1 tetx_full.fq --db tinyreads --format json
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:25Z",
   "params": {
@@ -505,7 +505,7 @@ $ gapit screen --r1 tetx_lane1.fq,tetx_lane2.fq --db tinyreads --format json --q
 $ gapit screen --r1 tetx_full.fq --db tinyreads --format md
 ---
 schema: gapit.reads/1
-tool: gapit 0.6.3
+tool: gapit 0.6.4
 created_at: 2026-09-19T01:12:25Z
 db: tinyreads
 read_type: sr
@@ -605,7 +605,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T14:23:00Z",
   "params": {
@@ -663,7 +663,7 @@ minimap2 一段完全跳过 BLAST 索引，把 assembly 送进 minimap2 引擎
    性应用一致性与覆盖度下限。
 
 真实数字，一株 K. pneumoniae RefSeq assembly（GCF_000240185.1，5.3 Mb，`--db ncbi`，
-单线程，gapit 0.6.3）：
+单线程，gapit 0.6.4）：
 
 ```console
 $ # Stage 1: survey, ~0.9 s

{gapit-0.6.3 → gapit-0.6.4}/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 0.6.3). Flags marked *reads mode* apply only when
+Transcribed from `gapit screen --help` (gapit 0.6.4). Flags marked *reads mode* apply only when
 you pass `--r1`/`--r2`; they are documented in [./reads.md](./reads.md).
 
 Every option also accepts the single-dash short form listed in the **Short** column (e.g.
@@ -107,7 +107,7 @@ $ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:04Z",
   "params": {
@@ -199,8 +199,10 @@ progress bar on **stderr** — spinner, the current file's basename, bar, M/N co
 elapsed time — replacing the per-file `Processing:`/`Found N genes` notes while it runs (the
 `--jobs × --threads` oversubscription note still prints). Piped or redirected stderr and
 `--quiet` keep the plain notes byte-identically — progress bars in logs are noise. The bar
-lives entirely on stderr: stdout bytes are identical with it on or off. The positional-FASTQ
-wildcard batch ([./reads.md](./reads.md)) and `gapit db fetch all` carry the same bar.
+lives entirely on stderr: stdout bytes are identical with it on or off. Before each
+stdout chunk the bar is suspended, so rows start on a clean line and the bar redraws below
+them instead of mixing with the data. The positional-FASTQ wildcard batch
+([./reads.md](./reads.md)) and `gapit db fetch all` carry the same bar.
 
 ### Typed gene databases: designation is a second command
 

{gapit-0.6.3 → gapit-0.6.4}/docs/screen.zh.md

@@ -9,7 +9,7 @@
 
 ## 选项
 
-转写自 `gapit screen --help`（gapit 0.6.3）。标记为 *reads 模式* 的参数只在传入
+转写自 `gapit screen --help`（gapit 0.6.4）。标记为 *reads 模式* 的参数只在传入
 `--r1`/`--r2` 时生效，记录在 [./reads.md](./reads.md)。
 
 每个选项都接受 **短** 列给出的单横线短形式（例如 `--db` 的 `-d`）；长形式仍是规范写法，
@@ -104,7 +104,7 @@ $ gapit screen tests/data/contigs/full.fa --db tinyamr --format json
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:04Z",
   "params": {
@@ -196,8 +196,9 @@ rich 进度条 —— 转轮、当前文件基名、进度条、M/N 计数、百
 期间取代逐文件的 `Processing:`/`Found N genes` 提示（`--jobs × --threads` 超订用提示
 仍然打印）。stderr 被管道或重定向、以及 `--quiet` 时，保持与今天逐字节相同的纯文本
 提示 —— 日志里的进度条只是噪音。进度条完全生存在 stderr 一侧：开与关的 stdout 字节
-完全一致。位置参数 FASTQ 通配符批量（[./reads.zh.md](./reads.zh.md)）与
-`gapit db fetch all` 使用同一条进度条。
+完全一致。每次写 stdout 数据块前会暂停进度条，因此数据行从干净的新行开始，进度条在
+其下方重绘，而不是与数据混在同一行。位置参数 FASTQ 通配符批量
+（[./reads.zh.md](./reads.zh.md)）与 `gapit db fetch all` 使用同一条进度条。
 
 ### typed 基因数据库：判定是第二条命令
 

{gapit-0.6.3 → gapit-0.6.4}/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 0.6.3):
+Transcribed from `gapit summary --help` (gapit 0.6.4):
 
 | Flag | Type | Default | Description |
 |---|---|---|---|
@@ -150,7 +150,7 @@ $ gapit summary tests/data/summary/sample_a.tsv tests/data/summary/sample_b.tsv
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:48Z",
   "params": {

{gapit-0.6.3 → gapit-0.6.4}/docs/summary.zh.md

@@ -10,7 +10,7 @@ screen` 写出的格式。如何产生报告见 [./screen.md](./screen.md)；输
 
 ## 选项
 
-转写自 `gapit summary --help`（gapit 0.6.3）：
+转写自 `gapit summary --help`（gapit 0.6.4）：
 
 | 参数 | 类型 | 默认值 | 说明 |
 |---|---|---|---|
@@ -143,7 +143,7 @@ $ gapit summary tests/data/summary/sample_a.tsv tests/data/summary/sample_b.tsv
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.6.3"
+    "version": "0.6.4"
   },
   "created_at": "2026-09-19T01:12:48Z",
   "params": {

{gapit-0.6.3 → gapit-0.6.4}/pixi.lock

@@ -923,8 +923,8 @@ packages:
   timestamp: 1694615932610
 - pypi: ./
   name: gapit
-  version: 0.6.3
-  sha256: d6169fdb74f9fd131a20c1e011fce5a915ff82328f3862c78ae511c7c55758ff
+  version: 0.6.4
+  sha256: 5a3b9387d4bbec0acf7e69021610599ff52129bc02237f19aba0a79bfa317acd
   requires_dist:
   - click>=8.2
   - pydantic>=2.7

{gapit-0.6.3 → gapit-0.6.4}/pixi.toml

@@ -3,7 +3,7 @@ authors = ["indexofire <indexofire@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 name = "gapit"
 platforms = ["linux-64"]
-version = "0.6.3"
+version = "0.6.4"
 
 [tasks]
 lint = "ruff check"

{gapit-0.6.3 → gapit-0.6.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "gapit"
-version = "0.6.3"
+version = "0.6.4"
 description = "Mass screening of contigs and reads for known genes — agent-first Python reimplementation of abricate"
 readme = "README.md"
 authors = [{ name = "indexofire", email = "indexofire@gmail.com" }]

{gapit-0.6.3 → gapit-0.6.4}/src/gapit/__init__.py

@@ -1,3 +1,3 @@
 """gapit — agent-first Python reimplementation of abricate."""
 
-__version__ = "0.6.3"
+__version__ = "0.6.4"

{gapit-0.6.3 → gapit-0.6.4}/src/gapit/cmd_db.py

@@ -73,8 +73,15 @@ def db_fetch_command(
         # invocation with no NAME reaches this guard.
         if name is None:
             usage_fail("db fetch requires a database NAME or 'all' (see: gapit db list)")
-        for receipt in perform_fetch(name, datadir, force=force, quiet=quiet, debug=debug):
-            click.echo(receipt.model_dump_json())
+        for _receipt in perform_fetch(
+            name,
+            datadir,
+            force=force,
+            quiet=quiet,
+            debug=debug,
+            emit=lambda receipt: click.echo(receipt.model_dump_json()),
+        ):
+            pass
 
     dispatch(run)
 

{gapit-0.6.3 → gapit-0.6.4}/src/gapit/cmd_screen.py

@@ -299,6 +299,7 @@ def screen_command(
                     jobs=jobs,
                     emit=deliver,
                     all_genes=all_genes,
+                    stdout_emit=output is None,
                 )
             elif aligner is AlignerEnum.minimap2:
                 if merge_fragments:
@@ -350,6 +351,7 @@ def screen_command(
                     min_gene_id=min_gene_id,
                     min_cluster_cov=min_cluster_cov,
                     emit=deliver,
+                    stdout_emit=output is None,
                 )
 
     dispatch(run)

{gapit-0.6.3 → gapit-0.6.4}/src/gapit/db_ops.py

@@ -7,7 +7,7 @@ the gapit.dblist/1 database listing. The CLI commands
 callers — this module owns the behavior and imports no CLI plumbing.
 """
 
-from collections.abc import Iterator, Sequence
+from collections.abc import Callable, Iterator, Sequence
 from datetime import UTC, datetime
 from pathlib import Path
 from typing import Literal
@@ -112,6 +112,7 @@ def perform_fetch(
     force: bool = False,
     quiet: bool = True,
     debug: bool = False,
+    emit: Callable[[ProviderReceipt], None] | None = None,
 ) -> Iterator[ProviderReceipt]:
     """Fetch database(s) into <datadir>/NAME — the shared CLI + MCP
     path. NAME ``all`` installs every database in DEFAULT_DBS order; each
@@ -163,6 +164,9 @@ def perform_fetch(
                 bar.describe(provider_name)
             receipt = fetch_one(provider_name)
             bar.advance()
+            if emit is not None:
+                with bar.suspend():
+                    emit(receipt)
             yield receipt