From f5505e830313228bf78dec51f95c87545aec1eab Mon Sep 17 00:00:00 2001
From: Wei Shen <shenwei356@gmail.com>
Date: Wed, 3 Jul 2024 15:13:07 +0100
Subject: [PATCH] v0.17.0

---
 CHANGELOG.md         |  2 +-
 doc/docs/download.md | 39 +++++++++++++++++++++++++--------------
 doc/docs/usage.md    |  2 +-
 3 files changed, 27 insertions(+), 16 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a1e08a3..6848c22 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@
     - `taxonkit name2taxid`:
         - Add support of fuzzy match with `-f/--fuzzy`. [#88](https://github.com/shenwei356/taxonkit/issues/88)
     - `taxonkit profile2cami`:
-        - New flag `-S/--no-sum-up` to disable summing up abundances. [#99](https://github.com/shenwei356/taxonkit/issues/99)
+        - Add a new flag `-S/--no-sum-up` to disable summing up abundances. [#99](https://github.com/shenwei356/taxonkit/issues/99)
 - [TaxonKit v0.16.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
     - `taxonkit create-taxdump`:
diff --git a/doc/docs/download.md b/doc/docs/download.md
index 79ed30f..3bb3f7b 100644
--- a/doc/docs/download.md
+++ b/doc/docs/download.md
@@ -6,15 +6,16 @@
 
 ## Current Version
 
-- [TaxonKit v0.16.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
-    - `taxonkit create-taxdump`:
-        - TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). [#92](https://github.com/shenwei356/taxonkit/issues/92).
-    - `taxonkit taxid-changelog/create-taxdump`:
-        - Add notes about the possible error records in taxid-changelog built from taxonomic data created by `create-taxdump`. [#91](https://github.com/shenwei356/taxonkit/issues/91)
-        - Dont't worry, a single version of taxonomic data created by `taxonkit create-taxdump` has no problem, it's just the changelog might not be perfect.
-    - `taxonkit lca`:
-        - new flag `-K/--keep-invalid`: print the query even if no single valid taxid left. [#89](https://github.com/shenwei356/taxonkit/issues/89)
+- [TaxonKit v0.17.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.17.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.17.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.17.0)
+    - `taxonkit filter`:
+        - Fix keeping taxids with a rank of "no rank" or "clade". [#97](https://github.com/shenwei356/taxonkit/issues/97)
+    - `taxonkit list`:
+        - Accept input TaxIds from stdin/files, not just the flag `--ids`. [#93](https://github.com/shenwei356/taxonkit/issues/93)
+    - `taxonkit name2taxid`:
+        - Add support of fuzzy match with `-f/--fuzzy`. [#88](https://github.com/shenwei356/taxonkit/issues/88)
+    - `taxonkit profile2cami`:
+        - Add a new flag `-S/--no-sum-up` to disable summing up abundances. [#99](https://github.com/shenwei356/taxonkit/issues/99)
 
 ### Please cite
 
@@ -31,11 +32,11 @@
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_amd64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_arm64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_amd64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_arm64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_windows_amd64.exe.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.16.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_amd64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_arm64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_amd64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_arm64.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_windows_amd64.exe.tar.gz),<br/> [中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.17.0/taxonkit_windows_amd64.exe.tar.gz)
 
 ## Installation
 
@@ -156,6 +157,16 @@ All-in-one command:
 
 ## Release history
 
+
+- [TaxonKit v0.16.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
+    - `taxonkit create-taxdump`:
+        - TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). [#92](https://github.com/shenwei356/taxonkit/issues/92).
+    - `taxonkit taxid-changelog/create-taxdump`:
+        - Add notes about the possible error records in taxid-changelog built from taxonomic data created by `create-taxdump`. [#91](https://github.com/shenwei356/taxonkit/issues/91)
+        - Dont't worry, a single version of taxonomic data created by `taxonkit create-taxdump` has no problem, it's just the changelog might not be perfect.
+    - `taxonkit lca`:
+        - new flag `-K/--keep-invalid`: print the query even if no single valid taxid left. [#89](https://github.com/shenwei356/taxonkit/issues/89)
 - [TaxonKit v0.15.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.1)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.15.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.1)
     - `taxonkit name2taxid`:
diff --git a/doc/docs/usage.md b/doc/docs/usage.md
index d171bcf..b804b89 100644
--- a/doc/docs/usage.md
+++ b/doc/docs/usage.md
@@ -42,7 +42,7 @@ All-in-one command:
 ```text
 TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit
 
-Version: 0.16.0
+Version: 0.17.0
 
 Author: Wei Shen <shenwei356@gmail.com>