Update supported python versions

.azure-pipelines.yml

@@ -19,18 +19,18 @@ stages:
       - task: UsePythonVersion@0
         displayName: Set up python
         inputs:
-          versionSpec: 3.8
+          versionSpec: 3.9
 
       - bash: python .azure-pipelines/syntax-validation.py
-        displayName: Syntax validation (3.8)
+        displayName: Syntax validation (3.9)
 
       - task: UsePythonVersion@0
         displayName: Set up python
         inputs:
-          versionSpec: 3.10
+          versionSpec: 3.11
 
       - bash: python .azure-pipelines/syntax-validation.py
-        displayName: Syntax validation (3.10)
+        displayName: Syntax validation (3.11)
 
       # Run flake8 validation on a shallow clone
       - bash: |
@@ -50,7 +50,7 @@ stages:
       - task: UsePythonVersion@0
         displayName: Set up python
         inputs:
-          versionSpec: 3.10
+          versionSpec: 3.11
 
       - bash: |
           pip install --disable-pip-version-check collective.checkdocs wheel
@@ -86,12 +86,12 @@ stages:
       vmImage: ubuntu-20.04
     strategy:
       matrix:
-        python38:
-          PYTHON_VERSION: 3.8
         python39:
           PYTHON_VERSION: 3.9
         python310:
           PYTHON_VERSION: 3.10
+        python311:
+          PYTHON_VERSION: 3.11
     steps:
     - template: .azure-pipelines/ci-unix.yml
 
@@ -100,12 +100,12 @@ stages:
       vmImage: macOS-latest
     strategy:
       matrix:
-        python38:
-          PYTHON_VERSION: 3.8
         python39:
           PYTHON_VERSION: 3.9
         python310:
           PYTHON_VERSION: 3.10
+        python311:
+          PYTHON_VERSION: 3.11
     steps:
     - template: .azure-pipelines/ci-unix.yml
 
@@ -114,12 +114,12 @@ stages:
       vmImage: windows-latest
     strategy:
       matrix:
-        python38:
-          PYTHON_VERSION: 3.8
         python39:
           PYTHON_VERSION: 3.9
         python310:
           PYTHON_VERSION: 3.10
+        python311:
+          PYTHON_VERSION: 3.11
     steps:
     - template: .azure-pipelines/ci-windows.yml
 
@@ -139,7 +139,7 @@ stages:
       - task: UsePythonVersion@0
         displayName: Set up python
         inputs:
-          versionSpec: 3.10
+          versionSpec: 3.11
 
       - task: DownloadBuildArtifacts@0
         displayName: Get pre-built package

.readthedocs.yaml

@@ -5,7 +5,7 @@
 version: 2
 
 python:
-  version: "3.8"
+  version: "3.9"
   install:
     - method: pip
       path: .

requirements.txt

@@ -1,14 +1,14 @@
-gemmi==0.5.3
-htcondor==10.7.0
-importlib_metadata==6.8.0
-matplotlib==3.5.1
-mrcfile==1.4
-numpy==1.25.0
-opencv-python-headless==4.7.0.72
-pandas==1.4.2
-pillow==10.0.1
-plotly==5.7.0
+gemmi==0.6.5
+htcondor==23.5.2
+importlib_metadata==7.0.2
+matplotlib==3.8.3
+mrcfile==1.5.0
+numpy==1.26.4
+opencv-python-headless==4.9.0.80
+pandas==2.2.1
+pillow==10.2.0
+plotly==5.20.0
 pydantic==1.10.7
-starfile==0.4.11
+starfile==0.5.6
 workflows==2.26
-zocalo==0.30.0
+zocalo==0.30.2

requirements_dev.txt

@@ -1,18 +1,18 @@
 bump2version==1.0.1
-dials_data==2.4.18
-gemmi==0.5.3
-graphviz==0.19.2
-ispyb==6.10.0
-matplotlib==3.5.1
-mrcfile==1.4
-opencv-python==4.7.0.72
-pandas==1.4.2
-pillow==10.0.1
-plotly==5.7.0
+dials_data==2.4.81
+gemmi==0.6.5
+graphviz==0.20.2
+ispyb==10.0.0
+matplotlib==3.8.3
+mrcfile==1.5.0
+opencv-python==4.9.0.80
+pandas==2.2.1
+pillow==10.2.0
+plotly==5.20.0
 pydantic==1.10.7
-pytest-cov==3.0.0
-pytest-mock==3.10.0
-pytest==7.1.1
-starfile==0.4.11
-workflows==2.21.1
-zocalo==0.18.0
+pytest-cov==4.1.0
+pytest-mock==3.12.0
+pytest==8.1.1
+starfile==0.5.6
+workflows==2.26
+zocalo==0.30.2

requirements_doc.txt

@@ -1,10 +1,10 @@
-gemmi==0.5.3
-ispyb==6.10.0
-matplotlib==3.5.1
-mrcfile==1.4
-pandas==1.4.2
-pillow==10.0.1
-plotly==5.7.0
+gemmi==0.6.5
+ispyb==10.0.0
+matplotlib==3.8.3
+mrcfile==1.5.0
+pandas==2.2.1
+pillow==10.2.0
+plotly==5.20.0
 pydantic==1.10.7
 Sphinx==4.5.0
 sphinx-rtd-theme==1.0.0

setup.cfg

@@ -13,9 +13,9 @@ classifiers =
     License :: OSI Approved :: GNU General Public License v2 (GPLv2)
     Natural Language :: English
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
 keywords = relion
 project_urls =
     Documentation = https://python-relion.readthedocs.io/
@@ -45,7 +45,7 @@ install_requires =
 packages = find:
 package_dir =
     =src
-python_requires = >=3.8
+python_requires = >=3.9
 zip_safe = False
 
 [options.entry_points]

src/relion/zocalo/class2d_wrapper.py

@@ -275,11 +275,11 @@
                     f"/run_it{class2d_params.class2d_nr_iter:03}_classes_{class_id+1}.jpeg"
                 ),
                 "particles_per_class": (
-                    float(classes_loop.val(class_id, 1)) * particles_in_batch
+                    float(classes_loop[class_id, 1]) * particles_in_batch
                 ),
-                "class_distribution": classes_loop.val(class_id, 1),
-                "rotation_accuracy": classes_loop.val(class_id, 2),
-                "translation_accuracy": classes_loop.val(class_id, 3),
+                "class_distribution": classes_loop[class_id, 1],
+                "rotation_accuracy": classes_loop[class_id, 2],
+                "translation_accuracy": classes_loop[class_id, 3],
             }
             if job_is_rerun:
                 class_ispyb_parameters["buffer_lookup"].update(
@@ -295,12 +295,12 @@
                 ]
 
             # Add the resolution and fourier completeness if they are valid numbers
-            estimated_resolution = float(classes_loop.val(class_id, 4))
+            estimated_resolution = float(classes_loop[class_id, 4])
             if np.isfinite(estimated_resolution):
                 class_ispyb_parameters["estimated_resolution"] = estimated_resolution
             else:
                 class_ispyb_parameters["estimated_resolution"] = 0.0
-            fourier_completeness = float(classes_loop.val(class_id, 5))
+            fourier_completeness = float(classes_loop[class_id, 5])
             if np.isfinite(fourier_completeness):
                 class_ispyb_parameters[
                     "overall_fourier_completeness"

src/relion/zocalo/class3d_wrapper.py

@@ -465,11 +465,11 @@
                     f"run_it{class3d_params.class3d_nr_iter:03}_class{class_id+1:03}.mrc"
                 ),
                 "particles_per_class": (
-                    float(classes_loop.val(class_id, 1)) * class3d_params.batch_size
+                    float(classes_loop[class_id, 1]) * class3d_params.batch_size
                 ),
-                "class_distribution": classes_loop.val(class_id, 1),
-                "rotation_accuracy": classes_loop.val(class_id, 2),
-                "translation_accuracy": classes_loop.val(class_id, 3),
+                "class_distribution": classes_loop[class_id, 1],
+                "rotation_accuracy": classes_loop[class_id, 2],
+                "translation_accuracy": classes_loop[class_id, 3],
             }
             if job_is_rerun:
                 class_ispyb_parameters["buffer_lookup"].update(
@@ -485,12 +485,12 @@
                 ]
 
             # Add the resolution and fourier completeness if they are valid numbers
-            estimated_resolution = float(classes_loop.val(class_id, 4))
+            estimated_resolution = float(classes_loop[class_id, 4])
             if np.isfinite(estimated_resolution):
                 class_ispyb_parameters["estimated_resolution"] = estimated_resolution
             else:
                 class_ispyb_parameters["estimated_resolution"] = 0.0
-            fourier_completeness = float(classes_loop.val(class_id, 5))
+            fourier_completeness = float(classes_loop[class_id, 5])
             if np.isfinite(fourier_completeness):
                 class_ispyb_parameters[
                     "overall_fourier_completeness"

src/relion/zocalo/select_particles.py

@@ -141,9 +141,7 @@ def dummy(self, *args, **kwargs):
                 new_row = []
                 for col in range(extracted_parts_loop.width()):
                     new_row.append(
-                        extracted_parts_loop.val(
-                            num_new_parts - num_remaining_parts, col
-                        )
+                        extracted_parts_loop[num_new_parts - num_remaining_parts, col]
                     )
                 prev_parts_loop.add_row(new_row)
 
@@ -197,9 +195,7 @@ def dummy(self, *args, **kwargs):
                 new_row = []
                 for col in range(extracted_parts_loop.width()):
                     new_row.append(
-                        extracted_parts_loop.val(
-                            num_new_parts - num_remaining_parts, col
-                        )
+                        extracted_parts_loop[num_new_parts - num_remaining_parts, col]
                     )
                 new_split_loop.add_row(new_row)