# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1718632479 0
# Node ID 30cdfd70f28d1d29caf8016f4707aff73bff1047
# Parent  27015eaf9a78dd0d97c9e6f1cb0541d46c4f1b47
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 71cee2ed96b69a2e78a1eb3dadbd2e81bf332798

diff -r 27015eaf9a78 -r 30cdfd70f28d common.py
--- a/common.py	Mon May 20 15:34:58 2024 +0000
+++ b/common.py	Mon Jun 17 13:54:39 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 27015eaf9a78 -r 30cdfd70f28d larch_athena.py
--- a/larch_athena.py	Mon May 20 15:34:58 2024 +0000
+++ b/larch_athena.py	Mon Jun 17 13:54:39 2024 +0000
@@ -1,13 +1,13 @@
 import gc
 import json
 import os
-import re
 import sys
 
 from common import (
     pre_edge_with_defaults,
     read_all_groups,
     read_group,
+    sorting_key,
     xftf_with_defaults,
 )
 
@@ -142,15 +142,16 @@
         return xafs_group
 
     def load_zipped_files(self) -> "dict[str, Group]":
-        def sorting_key(filename: str) -> str:
-            return re.findall(r"\d+", filename)[-1]
-
         all_paths = list(os.walk("dat_files"))
         all_paths.sort(key=lambda x: x[0])
         file_total = sum([len(f) for _, _, f in all_paths])
         print(f"{file_total} files found")
         keyed_data = {}
         for dirpath, _, filenames in all_paths:
+            if dirpath.endswith("__MACOSX"):
+                print(f"Skipping {dirpath}")
+                continue
+
             try:
                 filenames.sort(key=sorting_key)
             except IndexError as e:
diff -r 27015eaf9a78 -r 30cdfd70f28d larch_athena.xml
--- a/larch_athena.xml	Mon May 20 15:34:58 2024 +0000
+++ b/larch_athena.xml	Mon Jun 17 13:54:39 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@">1</token>
+        <token name="@WRAPPER_VERSION@">2</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>
@@ -457,6 +457,14 @@
             <output_collection name="athena_project_file_collection" type="list" count="2"/>
             <output_collection name="plot_collection" type="list" count="2"/>
         </test>
+        <!-- 19: MACOSX zip -->
+        <test expect_num_outputs="2">
+            <param name="is_zipped" value="true"/>
+            <param name="dat_file" value="macosx.zip"/>
+            <param name="plot_graph" value="edge,flat,dmude"/>
+            <output_collection name="athena_project_file_collection" type="list" count="10"/>
+            <output_collection name="plot_collection" type="list" count="10"/>
+        </test>
     </tests>
     <help><![CDATA[
         Using Larch, create an Athena project file from the input X-ray Absorption Fine Structure (XAFS) data file.
diff -r 27015eaf9a78 -r 30cdfd70f28d test-data/macosx.zip
Binary file test-data/macosx.zip has changed