# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1718632470 0
# Node ID 39ab361e6d59b33fb6ce35aec083d739ab8c8470
# Parent  2ceaa943a2ad49b2780a468d2a76b8df316f50f3
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 71cee2ed96b69a2e78a1eb3dadbd2e81bf332798

diff -r 2ceaa943a2ad -r 39ab361e6d59 common.py
--- a/common.py	Thu Apr 11 09:01:48 2024 +0000
+++ b/common.py	Mon Jun 17 13:54:30 2024 +0000
@@ -1,3 +1,4 @@
+import re
 from typing import Iterable
 
 from larch.io import extract_athenagroup, read_athena
@@ -168,3 +169,7 @@
 def read_groups(dat_files: "list[str]", key: str = None) -> Iterable[Group]:
     for dat_file in dat_files:
         yield read_group(dat_file=dat_file, key=key)
+
+
+def sorting_key(filename: str) -> str:
+    return re.findall(r"\d+", filename)[-1]
diff -r 2ceaa943a2ad -r 39ab361e6d59 larch_artemis.py
--- a/larch_artemis.py	Thu Apr 11 09:01:48 2024 +0000
+++ b/larch_artemis.py	Mon Jun 17 13:54:30 2024 +0000
@@ -5,7 +5,7 @@
 import os
 import sys
 
-from common import read_group
+from common import read_group, sorting_key
 
 from larch.fitting import guess, param, param_group
 from larch.symboltable import Group
@@ -351,7 +351,7 @@
             filepaths = [
                 os.path.join(prj_file, p) for p in os.listdir(prj_file)
             ]
-            filepaths.sort()
+            filepaths.sort(key=sorting_key)
         else:
             # DO NOT sort if we have multiple Galaxy datasets - the filenames
             # are arbitrary but should be in order
diff -r 2ceaa943a2ad -r 39ab361e6d59 larch_artemis.xml
--- a/larch_artemis.xml	Thu Apr 11 09:01:48 2024 +0000
+++ b/larch_artemis.xml	Mon Jun 17 13:54:30 2024 +0000
@@ -4,7 +4,7 @@
         <!-- version of underlying tool (PEP 440) -->
         <token name="@TOOL_VERSION@">0.9.75</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">0</token>
+        <token name="@WRAPPER_VERSION@">1</token>
         <!-- citation should be updated with every underlying tool version -->
         <!-- typical fields to update are version, month, year, and doi -->
         <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
@@ -315,6 +315,26 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 7: Zipped numerical sort -->
+        <test expect_num_outputs="2">
+            <param name="execution" value="zipped"/>
+            <param name="prj_file" value="numeric_sort.zip"/>
+            <param name="variable" value="rfactor"/>
+            <param name="action" value="log"/>
+            <param name="feff_paths" value="[FEFF_paths_of_test.inp].zip"/>
+            <param name="gds_file" value="gds.csv"/>
+            <param name="sp_file" value="sp.csv"/>
+            <param name="fitspace" value="r"/>
+            <param name="kmin" value="3"/>
+            <param name="kmax" value="14"/>
+            <param name="kweight" value="2"/>
+            <param name="dk" value="1"/>
+            <param name="window" value="hanning"/>
+            <param name="rmin" value="1.4"/>
+            <param name="rmax" value="3.0"/>
+            <output_collection name="fit_report_collection" type="list" count="3"/>
+            <output name="criteria_report" file="numeric_sort_criteria_report.csv" compare="re_match"/>
+        </test>
     </tests>
     <help><![CDATA[
         Using Larch, perform fitting on an Athena project file, originally from the input X-ray Absorption Fine Structure (XAFS) data file.
diff -r 2ceaa943a2ad -r 39ab361e6d59 test-data/numeric_sort.zip
Binary file test-data/numeric_sort.zip has changed
diff -r 2ceaa943a2ad -r 39ab361e6d59 test-data/numeric_sort_criteria_report.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/numeric_sort_criteria_report.csv	Mon Jun 17 13:54:30 2024 +0000
@@ -0,0 +1,4 @@
+     rfactor
+    0\.35\d{4}
+    0\.35\d{4}
+    0\.25\d{4}