From e7876a00d87d6b41ca703cbe9bbd1e9ccfe2eff2 Mon Sep 17 00:00:00 2001 From: Josh Carmichael Date: Tue, 20 Feb 2024 08:28:50 -0500 Subject: [PATCH 1/2] replace gemmi loop.val method with updaated getter/setter syntax --- src/aspire/storage/starfile.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/aspire/storage/starfile.py b/src/aspire/storage/starfile.py index 19598c1e06..98b3219607 100644 --- a/src/aspire/storage/starfile.py +++ b/src/aspire/storage/starfile.py @@ -100,11 +100,10 @@ def _initialize_blocks(self): ) loop_tags = gemmi_item.loop.tags # convert loop data to a list of lists - # using the .val(row, col) method of gemmi's Loop class loop_data = [None] * gemmi_item.loop.length() for row in range(gemmi_item.loop.length()): loop_data[row] = [ - gemmi_item.loop.val(row, col) + gemmi_item.loop[row, col] for col in range(gemmi_item.loop.width()) ] if block_has_pair: From 8f805f853e291e0bb3ff3a688a2ea1149a6c690b Mon Sep 17 00:00:00 2001 From: Josh Carmichael Date: Tue, 20 Feb 2024 09:00:37 -0500 Subject: [PATCH 2/2] update dependency version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3aa73f5ed6..a31644435c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ dependencies = [ # finufft 2.2.0 doesn't seemt to run on GHA Windows CI... "finufft==2.2.0 ; sys_platform != 'win32'", "finufft==2.1.0 ; sys_platform == 'win32'", - "gemmi >= 0.4.8", + "gemmi >= 0.6.5", "grpcio >= 1.54.2", "joblib", "matplotlib >= 3.2.0",