updated change logs to reflect new partition file generated from the …

…create_concat function
JLSteenwyk · Sep 12, 2024 · 1fb406a · 1fb406a
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diff --git a/change_log.txt b/change_log.txt
@@ -1,5 +1,14 @@
 Major changes to PhyKIT are summarized here.
 
+1.21.0
+  - The partition file outputted from the create_concat function has been updated
+  - Column information in the partition file is as follows:
+    - column 1: alignment name
+    - column 2: # of taxa present
+    - column 3: # of taxa missing
+    - column 4: fraction of occupancy
+    - column 5: names of missing taxa (; separated)
+
 1.20.0
   - Fixed bug for thread_dna function when using a ClipKIT log file. Input protein alignment must be the untrimmed alignment.
 

diff --git a/docs/change_log/index.rst b/docs/change_log/index.rst
@@ -8,6 +8,14 @@ Change log
 
 Major changes to PhyKIT are summarized here.
 
+**1.21.0**:
+The partition file outputted from the create_concat function has been updated to the following format:
+- column 1: alignment name
+- column 2: # of taxa present
+- column 3: # of taxa missing
+- column 4: fraction of occupancy
+- column 5: names of missing taxa (; separated)
+
 **1.20.0**:
 Fixed bug for thread_dna function when using a ClipKIT log file. Input protein alignment must be the untrimmed alignment.
 

diff --git a/phykit/phykit.py b/phykit/phykit.py
@@ -2563,11 +2563,11 @@ def create_concatenation_matrix(argv):
                 2) A partition file ready for input into RAxML or IQ-tree.
                 3) An occupancy file that summarizes the taxon occupancy
                    per sequence.
-                   - column 1: alignment name
-                   - column 2: # of taxa present
-                   - column 3: # of taxa missing
-                   - column 4: # fraction of occupancy
-                   - column 5: # names of missing taxa (; separated)
+                        - column 1: alignment name
+                        - column 2: # of taxa present
+                        - column 3: # of taxa missing
+                        - column 4: fraction of occupancy
+                        - column 5: names of missing taxa (; separated)
 
                 Aliases:
                   create_concatenation_matrix, create_concat, cc