Merge branch 'main' into renovate/mariadb-11.x

Author: stephen-riggs

.github/workflows/ci.yml

@@ -17,7 +17,7 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
     services:
       mariadb:
-        image: mariadb:11.8.5 # released 2024-05-06
+        image: mariadb:12.1.2 # released 2024-05-06
         # Pulls image from DockerHub
         # Docker images: https://hub.docker.com/_/mariadb
         # Previous version(s):
@@ -43,7 +43,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Use Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/codeql.yml

@@ -27,16 +27,16 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@v4
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v3
+        uses: github/codeql-action/autobuild@v4
         if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }}
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
+        uses: github/codeql-action/analyze@v4
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/publish-version.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Use Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Check current tag
@@ -66,7 +66,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install pypa/build
@@ -128,7 +128,7 @@ jobs:
           name: package-distributions
           path: dist/
       - name: Sign the dists with Sigstore
-        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        uses: sigstore/gh-action-sigstore-python@v3.2.0
         with:
           inputs: >-
             ./dist/*.tar.gz

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Syntax validation
@@ -37,7 +37,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install pypa/build

.github/workflows/version-bump.yml

@@ -36,7 +36,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install package

src/murfey/server/feedback.py

@@ -1115,12 +1115,12 @@ def _find_initial_model(visit: str, machine_config: MachineConfig) -> Path | Non
 
 
 def _downscaled_box_size(
-    particle_diameter: int, pixel_size: float
+    particle_diameter_ang: float, pixel_size: float
 ) -> Tuple[int, float]:
+    particle_diameter = particle_diameter_ang / pixel_size
     box_size = int(math.ceil(1.2 * particle_diameter))
     box_size = box_size + box_size % 2
     for small_box_pix in (
-        48,
         64,
         96,
         128,
@@ -1145,9 +1145,9 @@ def _downscaled_box_size(
         # Don't go larger than the original box
         if small_box_pix > box_size:
             return box_size, pixel_size
-        # If Nyquist freq. is better than 8.5 A, use this downscaled box, else step size
+        # If Nyquist freq. is better than 7.5 A, use this downscaled box, else step size
         small_box_angpix = pixel_size * box_size / small_box_pix
-        if small_box_angpix < 4.25:
+        if small_box_angpix < 3.75:
             return small_box_pix, small_box_angpix
     raise ValueError(f"Box size is too large: {box_size}")
 
@@ -1161,9 +1161,9 @@ def _resize_intial_model(
     env: Dict[str, str],
 ) -> None:
     with mrcfile.open(input_path) as input_mrc:
-        input_size_x = input_mrc.nx
-        input_size_y = input_mrc.ny
-        input_size_z = input_mrc.nz
+        input_size_x = input_mrc.header.nx
+        input_size_y = input_mrc.header.ny
+        input_size_z = input_mrc.header.nz
     if executables.get("clip") and not input_size_x == input_size_y == input_size_z:
         # If the initial model is not a cube, do some padding
         clip_proc = subprocess.run(
@@ -1198,6 +1198,8 @@ def _resize_intial_model(
                 str(downscaled_box_size),
                 "--rescale_angpix",
                 str(downscaled_pixel_size),
+                "--force_header_angpix",
+                str(downscaled_pixel_size),
                 "--o",
                 str(output_path),
             ],

src/murfey/server/gain.py

@@ -3,6 +3,7 @@
 import asyncio
 import logging
 import os
+import shutil
 from enum import Enum
 from pathlib import Path
 from typing import Dict, Tuple
@@ -130,4 +131,6 @@ async def prepare_eer_gain(
             f"{stderr.decode('utf-8').strip()}"
         )
         return None, None
+    # Also copy the gain as a .gain file
+    shutil.copy(secure_path(gain_path), secure_path(gain_out.with_suffix(".gain")))
     return gain_out, None