From 816451e51ed60c4b1fa1fb1e64db300eb86df29f Mon Sep 17 00:00:00 2001
From: hugolefeuvre <hugo.lefeuvre@univ-nantes.fr>
Date: Mon, 2 Dec 2024 11:53:48 +0100
Subject: [PATCH] include the commit in the tool version, add .lint_skip file
 to skip ToolVersionPEP404 error

---
 data_managers/data_manager_mmseqs2_database/.lint_skip |  1 +
 .../data_manager/data_manager_mmseqs2_download.xml     | 10 ++++------
 .../mmseqs2_aminoacid_taxonomy_databases.loc.test      |  1 +
 .../mmseqs2_nucleotide_taxonomy_databases.loc.test     |  1 +
 tools/mmseqs2/.lint_skip                               |  1 +
 tools/mmseqs2/macro.xml                                |  5 +----
 6 files changed, 9 insertions(+), 10 deletions(-)
 create mode 100644 data_managers/data_manager_mmseqs2_database/.lint_skip
 create mode 100644 tools/mmseqs2/.lint_skip

diff --git a/data_managers/data_manager_mmseqs2_database/.lint_skip b/data_managers/data_manager_mmseqs2_database/.lint_skip
new file mode 100644
index 00000000000..9d5b5e4801f
--- /dev/null
+++ b/data_managers/data_manager_mmseqs2_database/.lint_skip
@@ -0,0 +1 @@
+ToolVersionPEP404
\ No newline at end of file
diff --git a/data_managers/data_manager_mmseqs2_database/data_manager/data_manager_mmseqs2_download.xml b/data_managers/data_manager_mmseqs2_database/data_manager/data_manager_mmseqs2_download.xml
index d1ff3f561e8..4cfbea2b016 100644
--- a/data_managers/data_manager_mmseqs2_database/data_manager/data_manager_mmseqs2_download.xml
+++ b/data_managers/data_manager_mmseqs2_database/data_manager/data_manager_mmseqs2_download.xml
@@ -1,13 +1,11 @@
 <tool id="data_manager_mmseqs2_download" name="Download MMseqs2 databases" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
     <description></description>
     <macros>
-        <token name="@TOOL_VERSION@">15</token>
+        <token name="@TOOL_VERSION@">15.6f452</token>
         <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@COMMIT@">6f452</token>
-        <token name="@FULL_TOOL_VERSION@">@TOOL_VERSION@.@COMMIT@</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@FULL_TOOL_VERSION@">mmseqs2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">mmseqs2</requirement>
     </requirements>
     <stdio>
         <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/>
@@ -32,10 +30,10 @@ cp '$dmjson' '$out_file'
   "data_tables":{
     "$data_table":[
       {
-        "value": "${database}-@FULL_TOOL_VERSION@-#echo date.today().strftime('%d%m%Y')#",
+        "value": "${database}-@TOOL_VERSION@-#echo date.today().strftime('%d%m%Y')#",
         "name": "${database} #echo date.today().strftime('%d%m%Y')#",
         "path": "$database_name",
-        "version": "@FULL_TOOL_VERSION@"
+        "version": "@TOOL_VERSION@"
       }
     ]
   }
diff --git a/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_aminoacid_taxonomy_databases.loc.test b/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_aminoacid_taxonomy_databases.loc.test
index b6afa55a3b1..194112cb99c 100644
--- a/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_aminoacid_taxonomy_databases.loc.test
+++ b/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_aminoacid_taxonomy_databases.loc.test
@@ -1 +1,2 @@
 UniProtKB/Swiss-Prot-15.6f452-21112024	UniProtKB/Swiss-Prot 21112024		/tmp/tmp7bz_wtyd/galaxy-dev/tool-data/mmseqs2/Swiss-Prot	15.6f452
+UniProtKB/Swiss-Prot-15.6f452-02122024	UniProtKB/Swiss-Prot 02122024		/tmp/tmp2pnsc413/galaxy-dev/tool-data/mmseqs2/Swiss-Prot	15.6f452
diff --git a/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_nucleotide_taxonomy_databases.loc.test b/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_nucleotide_taxonomy_databases.loc.test
index 413090ca8fd..58710a908f6 100644
--- a/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_nucleotide_taxonomy_databases.loc.test
+++ b/data_managers/data_manager_mmseqs2_database/test-data/mmseqs2_nucleotide_taxonomy_databases.loc.test
@@ -1 +1,2 @@
 SILVA-15.6f452-21112024	SILVA 21112024		/tmp/tmp7bz_wtyd/galaxy-dev/tool-data/mmseqs2/SILVA	15.6f452
+SILVA-15.6f452-02122024	SILVA 02122024		/tmp/tmp2pnsc413/galaxy-dev/tool-data/mmseqs2/SILVA	15.6f452
diff --git a/tools/mmseqs2/.lint_skip b/tools/mmseqs2/.lint_skip
new file mode 100644
index 00000000000..9d5b5e4801f
--- /dev/null
+++ b/tools/mmseqs2/.lint_skip
@@ -0,0 +1 @@
+ToolVersionPEP404
\ No newline at end of file
diff --git a/tools/mmseqs2/macro.xml b/tools/mmseqs2/macro.xml
index f9f6f99958c..15f8b477601 100644
--- a/tools/mmseqs2/macro.xml
+++ b/tools/mmseqs2/macro.xml
@@ -1,10 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">15</token>
+    <token name="@TOOL_VERSION@">15.6f452</token>
     <token name="@VERSION_SUFFIX@">0</token>
-    <!-- Remove token COMMIT and FULL_TOOL_VERSION if bioconda version fixed like 16 instead of 15.6f452 -->
-    <token name="@COMMIT@">6f452</token>
-    <token name="@FULL_TOOL_VERSION@">@TOOL_VERSION@.@COMMIT@</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="version_command">
         <version_command><![CDATA[mmseqs version]]></version_command>