Merge pull request #204 from pymzml/dev

Update to v2.4.6

.github/auto_assign.yml

@@ -0,0 +1,10 @@
+addReviewers: true
+addAssignees: true
+reviewers:
+  - MKoesters
+
+skipKeywords:
+  - wip
+  - WIP
+
+numberOfReviewers: 0

.gitignore

@@ -19,3 +19,4 @@ dist
 .tox
 pymzml.egg-info
 docs/source/code_inc/
+/.github/

README.rst

@@ -64,7 +64,7 @@ Please refer to:
     | Germany
     | eMail: [email protected]
     |
-    | http:// <in transition >
+    | https://fufezan.net
 
 
 *******

docs/requirements.txt

@@ -1,3 +1,3 @@
-sphinx >= 1.3.0
-sphinx_rtd_theme >= 0.1.9
+sphinx==2.3.1
+sphinx_rtd_theme==0.4.3
 regex

example_scripts/_playground2.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+import bisect
+import pprint
+import click
+import os
+import hashlib
+
+import random
+import pickle
+import pymzml
+
+from xml.etree.ElementTree import ParseError
+
+
+@click.command()
+@click.argument('input_files', nargs=-1)
+@click.option('--shuffle', '-s', is_flag=True)
+@click.option('--suffix')
+def main(input_files, shuffle, suffix=''):
+    print(suffix)
+    output_name = f'failing_spectra{suffix}.txt'
+    with open(output_name, 'wt') as fout:
+        for file in input_files:
+            print(file)
+            fails = 0
+            fail_info = []
+            reader = pymzml.run.Reader(file)
+            indices = list(range(1, reader.get_spectrum_count()))
+            if shuffle:
+                random.seed(a=1570010244.2805517)
+                random.shuffle(indices)
+                m = hashlib.md5()
+                m.update(pickle.dumps(indices))
+                md5_digest = m.hexdigest()
+                print(f"Shuffled indices md5: {md5_digest}")
+                # exit(1)
+            number_of_specs = len(indices)
+            basic_off_set_dict = reader.info["file_object"].file_handler.offset_dict.copy()
+            basic_seek_list = reader.info["file_object"].file_handler.seek_list.copy()
+            for pos, i in enumerate(indices):
+                # reader.info["file_object"].file_handler.offset_dict = basic_off_set_dict.copy()
+                # reader.info["file_object"].file_handler.seek_list = basic_seek_list.copy()
+                current_precentage = 100 * float(pos) / float(number_of_specs)
+                print(f"[{current_precentage:0>3.1f}%] Access spectrum {i:<10}".format(), end='\r')
+                #spec = reader[i]
+                try:
+                    spec = reader[i]
+                    # 100 / 0
+                except Exception as e:
+                    fails += 1
+                    fout.write(f'{os.path.basename(file)}\t{i}\n')
+                    print(f"failed on spec {i}")
+
+                    # pprint.pprint(reader.info["file_object"].file_handler.offset_dict)
+                    # pprint.pprint(reader.info["file_object"].file_handler.seek_list)
+                    spec = reader[i]
+                    exit(1)
+                # break
+            print()
+            perc = fails / len(indices) * 100
+            print(f'{fails} of {len(indices)} spectra could not be accessed ({perc}%)')
+            print('\n\n')
+
+
+if __name__ == '__main__':
+    main()