gapit 0.5.3__tar.gz → 0.5.4__tar.gz

{gapit-0.5.3 → gapit-0.5.4}/CHANGELOG.md

@@ -5,6 +5,19 @@ 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).
 
+## [0.5.4] - 2026-10-03
+
+### Added
+
+- **Rich progress bar on long batch runs** (stderr only; modeled on the gmlst UX).
+  Multi-file contig screening, the positional-FASTQ wildcard batch, and
+  `gapit db fetch all` now show a spinner + bar + M/N + percent + elapsed bar on an
+  interactive stderr, with the description tracking the current file/sample/database and
+  replacing the per-file stderr notes while it runs. Under `--quiet` or a non-TTY stderr
+  (pipes, CI) the bar is disabled and today's plain notes print byte-identically; stdout
+  data streams are untouched in every case (the bar never captures stdout — rich's Live
+  redirection is pinned off), so output bytes are identical with the bar on or off.
+
 ## [0.5.3] - 2026-10-03
 
 ### Added

{gapit-0.5.3 → gapit-0.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: gapit
-Version: 0.5.3
+Version: 0.5.4
 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-0.5.3 → gapit-0.5.4}/docs/agents.md

@@ -13,7 +13,7 @@ Version, as one JSON line:
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.5.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.5.4"}
 ```
 
 Output schemas. Eleven documents are introspectable: `report`, `typing_result`, `reads`,

{gapit-0.5.3 → gapit-0.5.4}/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":"0.5.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.5.4"}
 ```
 
 输出 schema。十一个文档可自省：`report`、`typing_result`、`reads`、`reads2`、`cluster`、

{gapit-0.5.3 → gapit-0.5.4}/docs/databases.md

@@ -496,7 +496,7 @@ versions. A real one, from the plasmidfinder database:
   "upstream_version": "",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "makeblastdb_version": "blastn: 2.17.0+",
   "minimap2_version": "2.31-r1302"

{gapit-0.5.3 → gapit-0.5.4}/docs/databases.zh.md

@@ -474,7 +474,7 @@ manifest，来自 plasmidfinder 数据库：
   "upstream_version": "",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "makeblastdb_version": "blastn: 2.17.0+",
   "minimap2_version": "2.31-r1302"

{gapit-0.5.3 → gapit-0.5.4}/docs/installation.md

@@ -48,9 +48,9 @@ gapit --version
 
 ```console
 $ gapit --version
-gapit 0.5.3
+gapit 0.5.4
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.5.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.5.4"}
 ```
 
 ## External binaries

{gapit-0.5.3 → gapit-0.5.4}/docs/installation.zh.md

@@ -46,9 +46,9 @@ gapit --version
 
 ```console
 $ gapit --version
-gapit 0.5.3
+gapit 0.5.4
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.5.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.5.4"}
 ```
 
 ## 外部二进制

{gapit-0.5.3 → gapit-0.5.4}/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":"0.5.3"}}}
+{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.5.4"}}}
 ```
 
 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": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "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": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "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": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "created_at": "2026-09-20T13:38:39Z",
   "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [

{gapit-0.5.3 → gapit-0.5.4}/docs/mcp.zh.md

@@ -88,7 +88,7 @@ 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":"0.5.3"}}}
+{"jsonrpc":"2.0","id":1,"result":{"protocolVersion":"2025-06-18","capabilities":{"tools":{}},"serverInfo":{"name":"gapit","version":"0.5.4"}}}
 ```
 
 响应第 2 行（真实输出，中段省略；每个工具携带完整的 `inputSchema`）：
@@ -109,7 +109,7 @@ EOF
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "created_at": "2026-09-19T01:15:44Z",
   "params": {"db": "tinyamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [
@@ -163,7 +163,7 @@ EOF
 ```json
 {
   "schema": "gapit.reads/1",
-  "tool": {"name": "gapit", "version": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "created_at": "2026-09-22T00:07:35Z",
   "params": {
     "db": "tinyreads",
@@ -236,7 +236,7 @@ export GAPIT_DATADIR=/tmp/gapit-mcp-demo/datadir
 ```json
 {
   "schema": "gapit.report/1",
-  "tool": {"name": "gapit", "version": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "created_at": "2026-09-20T13:38:39Z",
   "params": {"db": "myamr", "minid": 80.0, "mincov": 80.0, "threads": 1},
   "files": [

{gapit-0.5.3 → gapit-0.5.4}/docs/outputs.md

@@ -141,7 +141,7 @@ Real document, same run as the TSV above:
   "schema": "gapit.report/1",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:20Z",
   "params": {
@@ -232,7 +232,7 @@ row by `(%IDENTITY, %COVERAGE)`. Real document (trimmed):
 ```json
 {
   "schema": "gapit.typing_result/1",
-  "tool": {"name": "gapit", "version": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "created_at": "2026-10-02T10:04:55Z",
   "source": ["dec.tsv"],
   "db": "ecoli_dec",
@@ -419,7 +419,7 @@ summarizing two report files, one with a `tetA` hit and one with none:
   "schema": "gapit.summary/1",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:11:09Z",
   "params": {
@@ -539,7 +539,7 @@ An agent can discover the whole contract from the binary alone.
 
 ```console
 $ gapit --version --json
-{"schema":"gapit.version/1","name":"gapit","version":"0.5.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.5.4"}
 ```
 
 `gapit schema <name>` prints the JSON Schema for each document. The eleven names: `report`,

{gapit-0.5.3 → gapit-0.5.4}/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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:20Z",
   "params": {
@@ -219,7 +219,7 @@ 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": "0.5.3"},
+  "tool": {"name": "gapit", "version": "0.5.4"},
   "created_at": "2026-10-02T10:04:55Z",
   "source": ["dec.tsv"],
   "db": "ecoli_dec",
@@ -402,7 +402,7 @@ 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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:11:09Z",
   "params": {
@@ -521,7 +521,7 @@ 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":"0.5.3"}
+{"schema":"gapit.version/1","name":"gapit","version":"0.5.4"}
 ```
 
 `gapit schema <name>` 打印每个文档的 JSON Schema。十一个名字：`report`、

{gapit-0.5.3 → gapit-0.5.4}/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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:11:06Z",
   "params": {

{gapit-0.5.3 → gapit-0.5.4}/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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:11:06Z",
   "params": {

{gapit-0.5.3 → gapit-0.5.4}/docs/reads.md

@@ -108,6 +108,14 @@ Output streams per completed sample, head-of-line in sample order under `--jobs`
   file — the json variant renders nothing at all, since its single document only exists
   at the end.
 
+On an interactive terminal (stderr is a TTY, no `--quiet`) the batch shows a rich progress
+bar on **stderr** — spinner, the current sample's name, bar, M/N count, percent, elapsed
+time — replacing the per-sample `Screening sample …`/`Detected N present genes` notes while
+it runs. Piped or redirected stderr and `--quiet` keep the plain notes byte-identically.
+The bar never touches stdout: streaming bytes are identical with it on or off, and the
+lazy `#SAMPLE` header still leads. The contig path ([./screen.md](./screen.md)) and
+`gapit db fetch all` carry the same bar.
+
 The single-sample `--r1`/`--r2` path differs on two points: no `--jobs`, and its Markdown
 frontmatter keeps the `files:`/`genes_found:` totals (its tsv default renders the same
 table, one chunk for the one sample).
@@ -115,7 +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 0.5.3). Contig-mode flags not listed here
+(transcribed from `gapit screen --help`, gapit 0.5.4). Contig-mode flags not listed here
 (`--minid`, `--mincov`, `--fofn`, `--noheader`, `--nopath`) do not apply; `--jobs` applies
 to the wildcard path only.
 
@@ -329,7 +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 0.5.3
+tool: gapit 0.5.4
 created_at: 2026-09-20T14:23:33Z
 db: homologs
 read_type: map-ont
@@ -425,7 +433,7 @@ $ gapit screen --r1 tetx_full.fq --db tinyreads --format json
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:25Z",
   "params": {
@@ -520,7 +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 0.5.3
+tool: gapit 0.5.4
 created_at: 2026-09-19T01:12:25Z
 db: tinyreads
 read_type: sr
@@ -622,7 +630,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T14:23:00Z",
   "params": {
@@ -681,7 +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 0.5.3):
+single-threaded, gapit 0.5.4):
 
 ```console
 $ # Stage 1: survey, ~0.9 s

{gapit-0.5.3 → gapit-0.5.4}/docs/reads.zh.md

@@ -99,6 +99,13 @@ $ gapit screen -d ecoli_dec *.gz
   *k* 个样本批量中途失败，已流式写出的样本 1..*k-1* 会保留在文件里 —— json 变体
   什么都不写，因为它的单文档只在结尾才存在。
 
+在交互式终端上（stderr 为 TTY 且未用 `--quiet`）批量会在 **stderr** 上显示 rich 进度
+条 —— 转轮、当前样本名、进度条、M/N 计数、百分比、已用时间 —— 并在其运行期间取代
+逐样本的 `Screening sample …`/`Detected N present genes` 提示。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。进度条绝不触碰 stdout：开与关的
+流式字节完全一致，惰性的 `#SAMPLE` 表头依然最先发出。contig 路径
+（[./screen.zh.md](./screen.zh.md)）与 `gapit db fetch all` 使用同一条进度条。
+
 单样本的 `--r1`/`--r2` 路径在两点上不同：不接受 `--jobs`，其 Markdown
 frontmatter 保留 `files:`/`genes_found:` 运行总计（它的 tsv 默认渲染同一张表，
 单个样本一个分块）。
@@ -106,7 +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 0.5.3）。这里未列出的 contig 模式参数（`--minid`、`--mincov`、
+--help`，gapit 0.5.4）。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 |
@@ -311,7 +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 0.5.3
+tool: gapit 0.5.4
 created_at: 2026-09-20T14:23:33Z
 db: homologs
 read_type: map-ont
@@ -403,7 +410,7 @@ $ gapit screen --r1 tetx_full.fq --db tinyreads --format json
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:25Z",
   "params": {
@@ -498,7 +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 0.5.3
+tool: gapit 0.5.4
 created_at: 2026-09-19T01:12:25Z
 db: tinyreads
 read_type: sr
@@ -598,7 +605,7 @@ Detected 2 present genes in /tmp/gapit-demo/assembly.fa
   "schema": "gapit.reads/1",
   "tool": {
     "name": "gapit",
-    "version": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T14:23:00Z",
   "params": {
@@ -656,7 +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 0.5.3）：
+单线程，gapit 0.5.4）：
 
 ```console
 $ # Stage 1: survey, ~0.9 s

{gapit-0.5.3 → gapit-0.5.4}/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 0.5.3). Flags marked *reads mode* apply only when
+Transcribed from `gapit screen --help` (gapit 0.5.4). 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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:04Z",
   "params": {
@@ -192,6 +192,16 @@ tests/data/contigs/gap.fa	contig1	1	97	+	sul1	1-94/94	========/======	1/3	100.00
 With `--jobs 2` the two files are screened concurrently but stdout stays in input order, so the
 output is identical to the sequential run.
 
+### Progress bar on long batch runs
+
+On an interactive terminal (stderr is a TTY, no `--quiet`) a multi-file batch shows a rich
+progress bar on **stderr** — spinner, the current file's basename, bar, M/N count, percent,
+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.
+
 ### Typed gene databases: designation is a second command
 
 When `--db` names a gene database built with a `typing.json` (the bundled `ecoli_dec`, or

{gapit-0.5.3 → gapit-0.5.4}/docs/screen.zh.md

@@ -9,7 +9,7 @@
 
 ## 选项
 
-转写自 `gapit screen --help`（gapit 0.5.3）。标记为 *reads 模式* 的参数只在传入
+转写自 `gapit screen --help`（gapit 0.5.4）。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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:04Z",
   "params": {
@@ -189,6 +189,16 @@ tests/data/contigs/gap.fa	contig1	1	97	+	sul1	1-94/94	========/======	1/3	100.00
 用 `--jobs 2` 时两个文件并发筛查，但 stdout 仍按输入顺序排列，输出与串行运行完全
 一致。
 
+### 长批量任务的进度条
+
+在交互式终端上（stderr 为 TTY 且未用 `--quiet`）多文件批量筛查会在 **stderr** 上显示
+rich 进度条 —— 转轮、当前文件基名、进度条、M/N 计数、百分比、已用时间 —— 并在其运行
+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。
+
 ### typed 基因数据库：判定是第二条命令
 
 当 `--db` 指向带 `typing.json` 构建的基因数据库（捆绑的 `ecoli_dec`，或任何

{gapit-0.5.3 → gapit-0.5.4}/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 0.5.3):
+Transcribed from `gapit summary --help` (gapit 0.5.4):
 
 | 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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:48Z",
   "params": {

{gapit-0.5.3 → gapit-0.5.4}/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 0.5.3）：
+转写自 `gapit summary --help`（gapit 0.5.4）：
 
 | 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": "0.5.3"
+    "version": "0.5.4"
   },
   "created_at": "2026-09-19T01:12:48Z",
   "params": {

{gapit-0.5.3 → gapit-0.5.4}/pixi.lock

@@ -1136,8 +1136,8 @@ packages:
   timestamp: 1694615932610
 - pypi: ./
   name: gapit
-  version: 0.5.3
-  sha256: 05a60639a36ad46653768cc89bc37fc2c49baa91e992a1d1ff516f1fd45fd9e9
+  version: 0.5.4
+  sha256: 3aa9e1214291caa3a95976acca90fd7aa1faf072c27d09cd1a377d0d53e618ba
   requires_dist:
   - typer>=0.12
   - pydantic>=2.7

{gapit-0.5.3 → gapit-0.5.4}/pixi.toml

@@ -3,7 +3,7 @@ authors = ["indexofire <indexofire@gmail.com>"]
 channels = ["conda-forge", "bioconda"]
 name = "gapit"
 platforms = ["linux-64"]
-version = "0.5.3"
+version = "0.5.4"
 
 [tasks]
 lint = "ruff check"

{gapit-0.5.3 → gapit-0.5.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "gapit"
-version = "0.5.3"
+version = "0.5.4"
 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-0.5.3 → gapit-0.5.4}/recipe/meta.yaml

@@ -2,10 +2,10 @@
 # Field sources: version/license/python/deps mirror pyproject.toml exactly; the
 # external binaries mirror pixi.toml's conda dependencies. sha256 below hashes
 # the official PyPI sdist (verified against the release-workflow upload log).
-# NOTE: the sha256 is still the 0.3.1 sdist hash — replace it with the 0.5.3
-# sdist hash (dist/gapit-0.5.3.tar.gz) at bioconda submission time.
+# NOTE: the sha256 is still the 0.3.1 sdist hash — replace it with the 0.5.4
+# sdist hash (dist/gapit-0.5.4.tar.gz) at bioconda submission time.
 {% set name = "gapit" %}
-{% set version = "0.5.3" %}
+{% set version = "0.5.4" %}
 
 package:
   name: {{ name|lower }}

{gapit-0.5.3 → gapit-0.5.4}/src/gapit/__init__.py

@@ -1,3 +1,3 @@
 """gapit — agent-first Python reimplementation of abricate."""
 
-__version__ = "0.5.3"
+__version__ = "0.5.4"

{gapit-0.5.3 → gapit-0.5.4}/src/gapit/db_ops.py

@@ -21,6 +21,7 @@ from gapit.bundled import BundledDatabase, bundled_databases
 from gapit.db import Database, discover_databases, mol_type
 from gapit.errors import UsageError
 from gapit.fasta import iter_fasta
+from gapit.progress import screen_progress
 from gapit.providers import REGISTRY
 from gapit.providers.cluster_common import ClusterProvider, fetch_cluster_provider
 from gapit.providers.common import Dbtype, fetch_provider
@@ -97,7 +98,9 @@ def perform_fetch(
     """Fetch database(s) into <datadir>/NAME — the shared CLI + MCP
     path. NAME ``all`` installs every database in DEFAULT_DBS order; each
     receipt yields as its install completes (streaming, like the CLI's
-    per-db stdout lines).
+    per-db stdout lines). On an interactive stderr the batch rides the
+    shared progress bar; under --quiet / non-TTY stderr the no-op shim
+    keeps today's byte-identical behavior.
     """
 
     def fetch_one(provider_name: str) -> ProviderReceipt:
@@ -135,8 +138,14 @@ def perform_fetch(
             destination=str(db_dir),
         )
 
-    for provider_name in DEFAULT_DBS if name == FETCH_ALL else (name,):
-        yield fetch_one(provider_name)
+    names = DEFAULT_DBS if name == FETCH_ALL else (name,)
+    with screen_progress(names, quiet=quiet, description="Fetching") as (bar, task_id):
+        for provider_name in names:
+            if task_id is not None:
+                bar.describe(provider_name)
+            receipt = fetch_one(provider_name)
+            bar.advance()
+            yield receipt
 
 
 def _detected_dbtype(database: Database) -> str: