python/tskit/util.py: Add a file name to FileFormatError

Closes #2467
Uses the .add_note method of exception, introduced
in Python 3.11. Also hardcodes the file name in
the raised from exceptions for HDF5 or zip.
Until 3.10 is EOF, needs the sys module.

Author: Alexis Simon

.gitignore

@@ -7,3 +7,6 @@ python/benchmark/*.html
 .env
 .vscode
 env
+# pixi environments
+.pixi/*
+!.pixi/config.toml

python/.gitignore

@@ -5,3 +5,6 @@ build
 .*.swp
 .*.swo
 */.ipynb_checkpoints
+# pixi environments
+.pixi/*
+!.pixi/config.toml

python/tskit/util.py

@@ -30,6 +30,7 @@
 import json
 import numbers
 import os
+import sys
 import textwrap
 from typing import Union
 
@@ -878,6 +879,10 @@ def raise_known_file_format_errors(open_file, existing_exception):
     Sniffs the file for pk-zip or hdf header bytes, then raises an exception
     if these are detected, if not raises the existing exception.
     """
+    if (sys.version_info[0] >= 3) & (sys.version_info[1] > 10):
+        # add_note has been added in python 3.11
+        # This condition can be removed once 3.10 is end-of-life
+        existing_exception.add_note(f"While trying to load {open_file.name}")
     # Check for HDF5 header bytes
     try:
         open_file.seek(0)
@@ -887,14 +892,14 @@ def raise_known_file_format_errors(open_file, existing_exception):
         raise existing_exception
     if header == b"\x89HDF":
         raise tskit.FileFormatError(
-            "The specified file appears to be in HDF5 format. This file "
+            f"The file {open_file.name} appears to be in HDF5 format. This file "
             "may have been generated by msprime < 0.6.0 (June 2018) which "
             "can no longer be read directly. Please convert to the new "
             "kastore format using the ``tskit upgrade`` command from tskit version<0.6.2"
         ) from existing_exception
     if header[:2] == b"\x50\x4b":
         raise tskit.FileFormatError(
-            "The specified file appears to be in zip format, so may be a compressed "
+            f"The file {open_file.name} appears to be in zip format, so may be a compressed "
             "tree sequence. Try using the tszip module to decompress this file before "
             "loading. `pip install tszip; tsunzip <filename>` or use "
             "`tszip.decompress` in Python code."