Merge pull request #342 from dmgav/zr-gao-pr

Modified data loading for HXN scans using PandABox

Author: dmgav

.github/workflows/black.yml

@@ -13,7 +13,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.11
+          python-version: 3.13
       - name: Install Dependencies
         run: |
           # These packages are installed in the base environment but may be older

.github/workflows/docs.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.13]
       fail-fast: false
 
     steps:

.github/workflows/docs_publish.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.13]
       fail-fast: false
 
     steps:

.github/workflows/testing.yml

@@ -17,8 +17,8 @@ jobs:
     strategy:
       matrix:
         host-os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11"]
-        numpy-version: ["1.26"]
+        python-version: ["3.12", "3.13"]
+        numpy-version: ["2.4.0"]
         pyqt-version: ["5.15"]
         include:
           - host-os: "ubuntu-latest"

pyxrf/core/tests/test_map_processing.py

@@ -51,6 +51,7 @@ def test_dask_client_create(tmpdir):
     client = dask_client_create(n_workers=n_workers_requested)
     n_workers = len(client.scheduler_info()["workers"])
     assert n_workers == n_workers_requested, "The number of workers was set incorrectly"
+
     client.close()
 
     assert not os.path.exists(dask_worker_space_path), "Temporary directory was created in the current directory"

pyxrf/core/tests/test_quant_analysis.py

@@ -347,9 +347,11 @@ def test_get_quant_fluor_data_dict():
         ), "Generated object contains emission lines that are different from expected"
 
         mass_sum = sum([_["density"] for _ in quant_fluor_data_dict["element_lines"].values()])
-        assert (
-            mass_sum == mass_sum_expected
-        ), "The total mass (density) of the components is different from expected"
+        npt.assert_almost_equal(
+            mass_sum,
+            mass_sum_expected,
+            err_msg="The total mass (density) of the components is different from expected",
+        )
 
 
 def gen_xrf_map_dict(nx=10, ny=5, elines=["S_K", "Au_M", "Fe_K"]):

pyxrf/core/tests/test_yaml_param_files.py

@@ -1,4 +1,5 @@
 import os
+import sys
 
 import jsonschema
 import numpy as np
@@ -135,13 +136,21 @@ def _generate_sample_docstring(param_dict, include_section_titles=True):
         d_str.append("    -------")
 
     d_str.extend([""] * n_empty_lines_after)
-
     d_str = "\n".join(d_str)  # Convert the list to a single string
 
+    # Remove initial 4 spaces from all lines to mimick behavior of func.__doc__ in Python 3.13
+    # and later (in Python 3.13, the initial spaces are removed automatically,
+    # but in earlier versions they are not)
+    is_py313 = sys.version_info >= (3, 13)
+    if is_py313:
+        d_str = d_str.split("\n")
+        d_str = [_[4:] if len(_) > 4 else "" for _ in d_str]
+        d_str = "\n".join(d_str)
+
     return d_str, parameters
 
 
-def test_parse_docstring_parameters():
+def test_parse_docstring_parameters_01():
     # Simple test for the successfully parsed docstring. It seems sufficient, since all error cases are trivial.
 
     param_dict = _generate_parameter_set()
@@ -164,7 +173,7 @@ def test_parse_docstring_parameters():
     # Check for exception if the section titles are required, but don't exist
     param_dict = _generate_parameter_set()
     d_str, parameters = _generate_sample_docstring(param_dict, include_section_titles=False)
-    with pytest.raises(AssertionError, match="'Parameters' or 'Return' statement was not found in the docstring"):
+    with pytest.raises(AssertionError, match="'Parameters' or 'Returns' statement was not found in the docstring"):
         _parse_docstring_parameters(d_str, search_param_section=True)
 
 

pyxrf/core/yaml_param_files.py

@@ -1,5 +1,6 @@
 import os
 import re
+import sys
 
 import yaml
 
@@ -51,6 +52,11 @@ def _parse_docstring_parameters(doc_string, search_param_section=True):
 
     str_list = doc_string.split("\n")
 
+    is_py313 = sys.version_info >= (3, 13)
+    if is_py313:
+        # Add initial 4 spaces to all lines
+        str_list = [f"    {_}" for _ in str_list]
+
     # Remove all spaces at the end of the strings (the should be no spaces there, but still)
     str_list = [s.rstrip() for s in str_list]
 
@@ -70,14 +76,15 @@ def _parse_docstring_parameters(doc_string, search_param_section=True):
 
     assert (n_first is not None) or (
         n_last is not None
-    ), "Incorrect docstring format: 'Parameters' or 'Return' statement was not found in the docstring"
+    ), "Incorrect docstring format: 'Parameters' or 'Returns' statement was not found in the docstring"
 
     # The list of strings contains parameter descriptions
     str_list = str_list[n_first : n_last + 1]
     # Each line must start with 4 spaces or be empty. Verify this
     assert all(
         [(not s) or re.search(r"^    ", s) for s in str_list]
     ), "Incorrect docstring format: parameter descriptions should be indented by at least FOUR spaces"
+
     # Now remove the spaces from nonempty lines
     str_list = [s[4:] if s else s for s in str_list]
 
@@ -99,7 +106,7 @@ def _parse_docstring_parameters(doc_string, search_param_section=True):
     #   The fist line of the description is actually the
     assert all(
         [len(s) > 1 for s in param_descriptions]
-    ), "Incomplete docstring: some parameters have not descriptions"
+    ), "Incomplete docstring: some parameters have no descriptions"
 
     params = list(zip(param_names, param_descriptions))
 

pyxrf/db_config/hxn_db_config.py

@@ -3,11 +3,17 @@
 except ModuleNotFoundError:
     from databroker import Broker
 
-from hxntools.handlers.timepix import TimepixHDF5Handler
-from hxntools.handlers.xspress3 import Xspress3HDF5Handler
-
 db = Broker.named("hxn")
+
+from hxntools.handlers import register  # noqa: E402
+
+register(db)
+
+# from hxntools.handlers.xspress3 import Xspress3HDF5Handler
+# from hxntools.handlers.timepix import TimepixHDF5Handler
+#
+# db = Broker.named("hxn")
 # db_analysis = Broker.named('hxn_analysis')
 
-db.reg.register_handler(Xspress3HDF5Handler.HANDLER_NAME, Xspress3HDF5Handler, overwrite=True)
-db.reg.register_handler(TimepixHDF5Handler._handler_name, TimepixHDF5Handler, overwrite=True)
+# db.reg.register_handler(Xspress3HDF5Handler.HANDLER_NAME, Xspress3HDF5Handler, overwrite=True)
+# db.reg.register_handler(TimepixHDF5Handler._handler_name, TimepixHDF5Handler, overwrite=True)

pyxrf/model/fileio.py

@@ -165,6 +165,8 @@ def _get_pyxrf_version_str(self):
         """
 
         # Determine the current version of PyXRF
+        global pyxrf_version  # noqa: F824
+
         pyxrf_version_str = pyxrf_version
         if pyxrf_version_str[0].lower() != "v":
             pyxrf_version_str = f"v{pyxrf_version_str}"