Skip to content

Backport fix from PR #409. [ci skip] #410

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
lohedges merged 1 commit into from
Mar 19, 2026
Merged

Backport fix from PR #409. [ci skip] #410

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions doc/source/changelog.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.

* Fixed parsing of AMBER and GROMACS GLYCAM force field topologies.

* Fix hang in ``sire.load`` function when shared GROMACS topology path is missing.

`2025.4.0 <https://github.com/openbiosim/sire/compare/2025.3.0...2025.4.0>`__ - February 2026
---------------------------------------------------------------------------------------------

Expand Down
13 changes: 9 additions & 4 deletions src/sire/_load.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,11 +77,16 @@ def _get_gromacs_dir():

if not os.path.exists(gromacs_tbz2):
try:
import socket
import urllib.request

urllib.request.urlretrieve(f"{tutorial_url}/gromacs.tar.bz2", gromacs_tbz2)
except Exception:
# we cannot download - just give up
with urllib.request.urlopen(
f"{tutorial_url}/gromacs.tar.bz2", timeout=5
) as response:
with open(gromacs_tbz2, "wb") as f:
f.write(response.read())
except (Exception, socket.timeout):
# we cannot download - continue without GROMACS
return None

if not os.path.exists(gromacs_tbz2):
Expand Down Expand Up @@ -443,7 +448,7 @@ def load(
gromacs_path = _get_gromacs_dir()

m = {
"GROMACS_PATH": _get_gromacs_dir(),
"GROMACS_PATH": gromacs_path,
"show_warnings": show_warnings,
"parallel": parallel,
"ignore_topology_frame": ignore_topology_frame,
Expand Down