Update python and pre-commits

.github/workflows/code.yml

@@ -46,7 +46,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"] # can add windows-latest, macos-latest
-        python: ["3.12"]
+        python: ["3.12", "3.13"]
         install: ["-e .[dev]"]
         # Make one version be non-editable to test both paths of version code
         include:

.pre-commit-config.yaml

@@ -1,22 +1,21 @@
 repos:
 
-# Automatic source code formatting
-- repo: https://github.com/psf/black
-  rev: 24.1.1
-  hooks:
-  - id: black
-    args: [--safe, --quiet]
-
-
 # Linter
 - repo: local
   hooks:
     - id: ruff
-      name: Run ruff
-      stages: [pre-commit]
+      name: lint with ruff
+      language: system
+      entry: ruff check --force-exclude --fix
+      types: [python]
+      require_serial: true
+
+    - id: ruff-format
+      name: format with ruff
       language: system
-      entry: ruff check
+      entry: ruff format --force-exclude
       types: [python]
+      require_serial: true
 
 
 # Other syntax checks

pyproject.toml

@@ -13,6 +13,7 @@ classifiers = [
     "Natural Language :: English",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 keywords = ["nexus", "NXmx"]
 dependencies = [

src/nexgen/command_line/ED_mrc_to_nexus.py

@@ -344,7 +344,6 @@ def overwrite_from_command_line(
 
 
 def log_dict(logger: Logger, dictionary: dict, skip: list = None) -> None:
-
     if skip is None:
         skip = [1]
 
@@ -366,7 +365,6 @@ def log_dict(logger: Logger, dictionary: dict, skip: list = None) -> None:
 
 
 def main():
-
     args = parse_input_arguments()
     metadata_template = Metadata(args.input_files)
     logger.info("Starting MRC to Nexus conversion.")
@@ -478,7 +476,6 @@ def main():
 
 
 def parse_input_arguments():
-
     msg = "Convert electron diffraction data from an MRC format "
     msg += "to a NeXus format"
     parser = ArgumentParser(description=msg, add_help=True)

src/nexgen/command_line/ED_nexus.py

@@ -25,7 +25,6 @@
 
 
 def write_from_SINGLA(args):
-
     singla_nexus_writer(
         args.master_file,
         args.det_distance,
@@ -60,7 +59,7 @@ def write_from_SINGLA_from_config(args):
         )
         ED_coord_system["convention"] = params.coord_system.convention
     else:
-        logger.info("The following convention will be applied:\n" f"{ED_coord_system}")
+        logger.info(f"The following convention will be applied:\n{ED_coord_system}")
 
     if params.coord_system.origin:
         logger.info(

src/nexgen/command_line/I19_2_cli.py

@@ -307,7 +307,7 @@ def nexgen_writer(args):
     help="Data entry key of dataset in raw .h5 file. Defaults to data.",
 )
 parser_nex.add_argument(
-    "-bits" "--bit-depth",
+    "-bits--bit-depth",
     type=int,
     choices=[8, 16, 32],
     default=32,

src/nexgen/command_line/nexus_generator.py

@@ -393,7 +393,8 @@ def _parse_cli() -> argparse.ArgumentParser:
         help="Data entry key of dataset in raw .h5 file. Defaults to data.",
     )
     nxmx_parser.add_argument(
-        "-bits" "--bit-depth",
+        "-bits",
+        "--bit-depth",
         type=int,
         choices=[8, 16, 32],
         default=32,

src/nexgen/nxs_copy/copy_nexus.py

@@ -41,7 +41,10 @@ def images_nexus(
     original_nexus = Path(original_nexus).expanduser().resolve()
     nxs_filename = get_nexus_filename(data_file[0], copy=True)
     copy_logger.debug(f"New NeXus file name: {nxs_filename}")
-    with h5py.File(original_nexus, "r") as nxs_in, h5py.File(nxs_filename, "x") as nxs_out:
+    with (
+        h5py.File(original_nexus, "r") as nxs_in,
+        h5py.File(nxs_filename, "x") as nxs_out,
+    ):
         if simple_copy is True:
             # Copy the whole tree
             get_nexus_tree(nxs_in, nxs_out, skip=False)
@@ -92,9 +95,10 @@ def pseudo_events_nexus(
     original_nexus = Path(original_nexus).expanduser().resolve()
     nxs_filename = get_nexus_filename(data_file[0], copy=True)
     copy_logger.debug(f"New NeXus file name: {nxs_filename}")
-    with h5py.File(original_nexus, "r") as nxs_in, h5py.File(
-        nxs_filename, "x"
-    ) as nxs_out:
+    with (
+        h5py.File(original_nexus, "r") as nxs_in,
+        h5py.File(nxs_filename, "x") as nxs_out,
+    ):
         nxs_out.attrs["default"] = "entry"
         # Copy the whole tree except for nxdata
         nxentry = get_nexus_tree(nxs_in, nxs_out)

src/nexgen/nxs_utils/__init__.py

@@ -34,5 +34,5 @@
     "TransformationType",
     "Facility",
     "CetaDetector",
-    "TVIPSDetector"
+    "TVIPSDetector",
 ]

src/nexgen/nxs_write/write_utils.py

@@ -239,8 +239,7 @@ def mask_and_flatfield_writer_for_event_data(
         )
     else:
         NXclassUtils_logger.warning(
-            f"No {dset_name} file found in working directory."
-            "Writing an ExternalLink."
+            f"No {dset_name} file found in working directory.Writing an ExternalLink."
         )
         file_loc = Path(dset_data_file)
         image_key = "image" if "tristan" in detector_name.lower() else "/"

src/nexgen/tools/data_writer.py

@@ -57,14 +57,14 @@ def build_an_eiger(
     for i in range(1, n_modules[0] + 1):
         IM[
             :,
-            i * eiger_mod_size[1]
-            + (i - 1) * eiger_gap_size[1] : i * (eiger_mod_size[1] + eiger_gap_size[1]),
+            i * eiger_mod_size[1] + (i - 1) * eiger_gap_size[1] : i
+            * (eiger_mod_size[1] + eiger_gap_size[1]),
         ] = 65535
     # Vertical modules
     for j in range(1, n_modules[1] + 1):
         IM[
-            j * eiger_mod_size[0]
-            + (j - 1) * eiger_gap_size[0] : j * (eiger_mod_size[0] + eiger_gap_size[0]),
+            j * eiger_mod_size[0] + (j - 1) * eiger_gap_size[0] : j
+            * (eiger_mod_size[0] + eiger_gap_size[0]),
             :,
         ] = 65535
 
@@ -104,17 +104,13 @@ def build_a_tristan(
     for i in range(1, n_modules[0] + 1):
         IM[
             :,
-            i * tristan_mod_size[1]
-            + (i - 1)
-            * tristan_gap_size[1] : i
+            i * tristan_mod_size[1] + (i - 1) * tristan_gap_size[1] : i
             * (tristan_mod_size[1] + tristan_gap_size[1]),
         ] = 65535
     # Vertical modules
     for j in range(1, n_modules[1] + 1):
         IM[
-            j * tristan_mod_size[0]
-            + (j - 1)
-            * tristan_gap_size[0] : j
+            j * tristan_mod_size[0] + (j - 1) * tristan_gap_size[0] : j
             * (tristan_mod_size[0] + tristan_gap_size[0]),
             :,
         ] = 65535
@@ -268,7 +264,7 @@ def generate_event_files(
             )
             EV_dict[(i, j)] = pseudo_event_list(I, J, exp_time)
     t1 = time.process_time()
-    data_logger.info(f"Time taken to generate pseudo-event list: {t1-t0:.2f} s.")
+    data_logger.info(f"Time taken to generate pseudo-event list: {t1 - t0:.2f} s.")
 
     # Find total number of events to be written to file
     num_events = tristan_chunk * num_chunks

src/nexgen/tools/mrc_tools.py

@@ -1,4 +1,4 @@
-""" Helper functions for the MRC to Nexus converter """
+"""Helper functions for the MRC to Nexus converter"""
 
 import logging
 import os
@@ -198,9 +198,7 @@ def to_hdf5_data_file(
 
     # Input is a single MRC file with a stack of images
     if (len(data_shape) == 3) and (n == 1):
-
         with h5py.File(out_file, "w") as hdf5_file:
-
             mrc = mrcfile.open(files[0], mode="r")
 
             bs = hdf5plugin.Bitshuffle
@@ -234,7 +232,6 @@ def to_hdf5_data_file(
 
     # Input is a list of MRC files containing single images
     elif (len(data_shape) == 2) and (n >= 1):
-
         with h5py.File(out_file, "w") as hdf5_file:
             dataset_shape = (n, data_shape[0], data_shape[1])
             dataset = hdf5_file.create_dataset(

tests/tools/test_mrc_tools.py

@@ -10,14 +10,12 @@
 
 
 def test_cal_wavelength():
-
     a = 0.025082356047905176
     epsilon = 1.0e-15
     assert abs(cal_wavelength(200000) - a) < epsilon
 
 
 def test_get_metadata():
-
     make_mrc_file("images.mrc")
     h = get_metadata("images.mrc")
     assert isinstance(h, dict)
@@ -26,7 +24,6 @@ def test_get_metadata():
 
 
 def test_collect_data():
-
     make_mrc_file("images_00001.mrc")
     make_mrc_file("images_00002.mrc")
 
@@ -41,7 +38,6 @@ def test_collect_data():
 
 
 def make_mrc_file(filename):
-
     images = np.zeros((1, 1), dtype=np.int16)
 
     with mrcfile.new(filename, overwrite=True) as mrc: