Migrate to Numpy 2.2+ and Python 3.11+ (#87)

* refact: Move minimum python version to 3.11

Python 3.11 is the minimum version supported by NumPy 2.3. Additionally, removed .python-version, which pins the development version of Python to 3.9.

* refact: Updates Numpy to >2.2

From personal experience, there was a not-insignificant depreciation between 2.1 and 2.2 that caught me out before related to indexing arrays. Skipping to 2.2 avoids this deprecation.

* refact: Disable UP007 Linting Rule

UP007 is related to a change in typing detailed in PEP604. Typing Unions can now be written as `X | Y` instead of `Union[int, str]`. There is no deprecation for this feature, and a significant amount of legacy code needs to be updated.

* refact: Update `zip()` calls to include `strict=False` per B905

Adds `strict=False` to all `zip()` calls to fix Ruff linter Rule B905 (https://docs.astral.sh/ruff/rules/zip-without-explicit-strict/). `strict=False` maintains current behaviour while fixing the linter error. 

There is no impact on unit tests with this change.

* Bump test version

---------

Co-authored-by: Codie <5020407+codie3611@users.noreply.github.com>

Author: DCHartlen

.github/workflows/ci-cd.yml

@@ -12,13 +12,13 @@ jobs:
     runs-on: ubuntu-latest
 
     strategy:
-      # If either the tests for 3.9 or 3.12 fail, all workflows
+      # If either the tests for 3.11 or 3.12 fail, all workflows
       # are terminated to save computing resources.
       fail-fast: true
       # To safe runtime least and latest version supported are
       # chosen. For more info see the pyproject.toml
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v3

.python-version

@@ -13,22 +13,20 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
 
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 dependencies = [
     "h5py==3.*",
     "scipy==1.*",
-    "numpy==1.*",
+    "numpy>2.2",
     "plotly==5.*",
     "psutil==5.*",
     "rich==13.*",
     "pandas==2.*",
-    "scikit_learn==1.*"
+    "scikit_learn==1.*",
 ]
 
 [tool.setuptools]
@@ -89,6 +87,7 @@ select = [
     "YTT", # flake8-2020 (Detects outdated Python 2/3 compatibility issues)
     "FLY", # flynt (Converts old-style string formatting to f-strings)
     "PIE", # flake8-pie
+    "NPY201",   # numpy2-deprecations
     # "PL",  # pylint
     # "RUF", # Ruff-specific rules (Additional optimizations and best practices)
 ]
@@ -99,6 +98,7 @@ ignore = [
     "S311",     # [suspicious-non-cryptographic-random-usage](https://docs.astral.sh/ruff/rules/suspicious-non-cryptographic-random-usage/)
     "S404",     # [suspicious-subprocess-import](https://docs.astral.sh/ruff/rules/suspicious-subprocess-import/)
     "S603",     # [subprocess-without-shell-equals-true](https://docs.astral.sh/ruff/rules/subprocess-without-shell-equals-true/)
+    "UP007",    # [non-pep604-annotation-union](https://docs.astral.sh/ruff/rules/non-pep604-annotation-union/#non-pep604-annotation-union-up007)
 ]
 
 [tool.ruff.lint.per-file-ignores]

pyproject.toml

@@ -97,7 +97,7 @@ def _laplacian_gauss_idw(
     for i, (j, d, e, k) in enumerate(
         zip(
             *tree.query_radius(points, return_distance=True, r=search_radius),
-            *tree.query(points, return_distance=True, k=1 + min_neighbors),
+            *tree.query(points, return_distance=True, k=1 + min_neighbors), strict=False,
         )
     ):
         # Always search for k neighbors, this prevents strongly connected local areas

src/lasso/dimred/graph_laplacian.py

@@ -211,7 +211,7 @@ def _join_hash_comparison_thread_files(
                 thread_weights = thread_file["weights"]
 
                 for (i_row, i_col), values, matches in zip(
-                    matrix_indexes, matrix_similarities, matrix_matches
+                    matrix_indexes, matrix_similarities, matrix_matches, strict=False
                 ):
                     smatrix[i_row, i_col] = values
                     ds_matches[i_row, i_col] = matches

src/lasso/dimred/hashing.py

@@ -200,7 +200,9 @@ def as_df(self, *args) -> pd.DataFrame:
             if args[0] == "rcforc":
                 ids = [
                     (str(i) + "m") if j else (str(i) + "s")
-                    for i, j in zip(self.read("rcforc", "ids"), self.read("rcforc", "side"))
+                    for i, j in zip(
+                        self.read("rcforc", "ids"), self.read("rcforc", "side"), strict=False
+                    )
                 ]
             else:
                 ids = self.read(*args[:-1], "ids")

src/lasso/dyna/binout.py

@@ -7162,7 +7162,9 @@ def _write_geom_rigid_road_surface(
         rigid_road_segment_road_id = self.arrays[ArrayType.rigid_road_segment_road_id]
         rigid_road_segment_node_ids = self.arrays[ArrayType.rigid_road_segment_node_ids]
 
-        for segment_id, node_ids in zip(rigid_road_segment_road_id, rigid_road_segment_node_ids):
+        for segment_id, node_ids in zip(
+            rigid_road_segment_road_id, rigid_road_segment_node_ids, strict=False
+        ):
             n_bytes_written += fp.write(settings.pack(segment_id))
             n_bytes_written += fp.write(settings.pack(len(node_ids)))
             n_bytes_written += fp.write(settings.pack(node_ids, dtype_hint=np.integer))
@@ -7347,7 +7349,7 @@ def _write_header_part_contact_interface_titles(
             title_wordsize = 4
             max_len = 18 * title_wordsize
             fmt_name = "{0:" + str(max_len) + "}"
-            for pid, title in zip(part_titles_ids, part_titles):
+            for pid, title in zip(part_titles_ids, part_titles, strict=False):
                 title = title.decode("utf-8")
                 n_bytes_written += fp.write(settings.pack(pid))
 
@@ -7387,7 +7389,7 @@ def _write_header_part_contact_interface_titles(
 
             max_len = 18 * self.header.wordsize
             fmt_name = "{0:" + str(max_len) + "}"
-            for pid, title in zip(titles_ids, titles):
+            for pid, title in zip(titles_ids, titles, strict=False):
                 n_bytes_written += fp.write(settings.pack(pid))
 
                 formatted_title = fmt_name.format(title[:max_len])

src/lasso/dyna/d3plot.py

@@ -334,7 +334,7 @@ def test_write(self):
 
         with tempfile.TemporaryDirectory() as dirpath:
             for d3plot_kwargs in d3plot_kwargs_list:
-                for d3plot_filepath, _ in zip(filepaths, d3plot_kwargs_list):
+                for d3plot_filepath, _ in zip(filepaths, d3plot_kwargs_list, strict=False):
                     print(d3plot_filepath)
 
                     # read d3plot