v0.14.0

shenwei356 · Nov 27, 2022 · a2e7589 · a2e7589
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,8 @@
         - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70)
     - `taxonkit list`:
         - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68)
+    - `taxonkit`:
+        - When environment variable `TAXONKIT_DB` is set, explicitly setting --data-dir will overide the value of `TAXONKIT_DB`.
 - [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
     - `taxonkit reformat`:

diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -6,18 +6,14 @@
 
 ## Current Version
 
-- [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
-    - `taxonkit reformat`:
-        - add a new placeholder `{K}` for rank `kingdom`. [#64](https://github.com/shenwei356/taxonkit/issues/64)
-        - do not panic for invalid TaxIds, e.g., the column name, when using `-I--taxid-field`.
-    - `taxonkit create-taxdump`: 
-        - fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2).
-        - fix bug of handling non-GTDB data when using `-A/--field-accession` and no rank names given:
-          the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
-        - fix the default option value of `--field-accession-re` which wrongly remove prefix like `Sp_`. [#65](https://github.com/shenwei356/taxonkit/issues/65)
+- [TaxonKit v0.14.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
+    - `taxonkit create-taxdump`:
+        - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70)
     - `taxonkit list`:
-        - fix warning message of merged taxids.
+        - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68)
+    - `taxonkit`:
+        - When environment variable `TAXONKIT_DB` is set, explicitly setting --data-dir will overide the value of `TAXONKIT_DB`.
 
 ### Please cite
 
@@ -34,11 +30,11 @@
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/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/v0.13.0/taxonkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/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/v0.13.0/taxonkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/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/v0.13.0/taxonkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/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/v0.13.0/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.13.0/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/v0.13.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_windows_amd64.exe.tar.gz)
 
 ## Installation
 
@@ -159,6 +155,18 @@ All-in-one command:
 
 ## Release history
 
+- [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
+    - `taxonkit reformat`:
+        - add a new placeholder `{K}` for rank `kingdom`. [#64](https://github.com/shenwei356/taxonkit/issues/64)
+        - do not panic for invalid TaxIds, e.g., the column name, when using `-I--taxid-field`.
+    - `taxonkit create-taxdump`: 
+        - fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2).
+        - fix bug of handling non-GTDB data when using `-A/--field-accession` and no rank names given:
+          the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
+        - fix the default option value of `--field-accession-re` which wrongly remove prefix like `Sp_`. [#65](https://github.com/shenwei356/taxonkit/issues/65)
+    - `taxonkit list`:
+        - fix warning message of merged taxids.
 - [TaxonKit v0.12.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.12.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
     - `taxonkit create-taxdump`: 

diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -41,7 +41,7 @@ All-in-one command:
 ```text
 TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit
 
-Version: 0.13.1
+Version: 0.14.0
 
 Author: Wei Shen <[email protected]>
 
@@ -59,6 +59,9 @@ Dataset:
 
     or some other directory, and later you can refer to using flag --data-dir,
     or environment variable TAXONKIT_DB
+    
+    When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will
+    overide the value of TAXONKIT_DB.
 
 Usage:
   taxonkit [command] 

diff --git a/taxonkit/cmd/root.go b/taxonkit/cmd/root.go
@@ -73,7 +73,10 @@ Dataset:
     "%s"
 
     or some other directory, and later you can refer to using flag --data-dir,
-    or environment variable TAXONKIT_DB
+    or environment variable TAXONKIT_DB.
+
+	When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will
+    overide the value of TAXONKIT_DB.
 
 `, VERSION, defaulDataDir)
 

diff --git a/taxonkit/cmd/util-cli.go b/taxonkit/cmd/util-cli.go
@@ -64,7 +64,11 @@ func getConfigs(cmd *cobra.Command) Config {
 
 	var val, dataDir string
 	if val = os.Getenv("TAXONKIT_DB"); val != "" {
-		dataDir = val
+		if cmd.Flags().Lookup("data-dir").Changed { // users explicitly set the option
+			dataDir = getFlagString(cmd, "data-dir")
+		} else {
+			dataDir = val
+		}
 	} else {
 		dataDir = getFlagString(cmd, "data-dir")
 	}