osiris-utils 1.1.7__tar.gz → 1.1.9__tar.gz

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/.github/workflows/ci.yml

@@ -28,12 +28,6 @@ jobs:
 
       - name: Run pre-commit
         uses: pre-commit/action@v3.0.1
-      
-      - name: Static type check (mypy)
-        run: |
-          python -m pip install mypy types-tqdm types-Pillow
-          mypy osiris_utils
-
 
       - name: Run test suite
         run: |

{osiris_utils-1.1.7/osiris_utils.egg-info → osiris_utils-1.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.1.7
+Version: 1.1.9
 Summary: Utilities to manipulate and visualise OSIRIS plasma PIC output data
 Author: João Cândido, Diogo Carvalho
 Author-email: João Pedro Ferreira Biu <joaopedrofbiu@tecnico.ulisboa.pt>
@@ -34,7 +34,6 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pre-commit>=3.7; extra == "dev"
 Requires-Dist: ruff>=0.4; extra == "dev"
 Requires-Dist: isort>=5.13; extra == "dev"
-Requires-Dist: mypy>=1.10; extra == "dev"
 Requires-Dist: types-tqdm; extra == "dev"
 Requires-Dist: types-Pillow; extra == "dev"
 Provides-Extra: docs
@@ -44,8 +43,6 @@ Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: sphinx-copybutton<=0.5.2; extra == "docs"
 Requires-Dist: sphinx-rtd-theme<3.0.3; extra == "docs"
 Requires-Dist: sphinx-github-style<=1.2.2; extra == "docs"
-Provides-Extra: plot
-Requires-Dist: seaborn>=0.13; extra == "plot"
 Dynamic: license-file
 
 OSIRIS_UTILS
@@ -99,10 +96,6 @@ Quick-start
    cd osiris_utils
    python examples/quick_start.py examples/example_data/thermal.1d
 
-.. image:: docs/source/_static/quick_start_ez.png
-   :alt: Example Ez plot produced by the quick-start
-   :width: 400px
-
 Documentation
 -------------
 

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/README.rst

@@ -49,10 +49,6 @@ Quick-start
    cd osiris_utils
    python examples/quick_start.py examples/example_data/thermal.1d
 
-.. image:: docs/source/_static/quick_start_ez.png
-   :alt: Example Ez plot produced by the quick-start
-   :width: 400px
-
 Documentation
 -------------
 

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/docs/source/conf.py

@@ -26,7 +26,7 @@ sys.path.append(os.path.abspath("../.."))
 project = "osiris_utils"
 copyright = "2025, João Biu, João Cândido, Diogo Carvalho"
 author = "João Biu, João Cândido, Diogo Carvalho"
-version = "v1.1.7"
+version = "v1.1.9"
 release = version
 
 

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/osiris_utils/data/data.py

@@ -203,7 +203,7 @@ class OsirisGridFile(OsirisData):
                 "units": self._file["AXIS/" + ax].attrs["UNITS"][0].decode("utf-8"),
                 "long_name": self._file["AXIS/" + ax].attrs["LONG_NAME"][0].decode("utf-8"),
                 "type": self._file["AXIS/" + ax].attrs["TYPE"][0].decode("utf-8"),
-                "plot_label": rf'${self._file["AXIS/"+ax].attrs["LONG_NAME"][0].decode("utf-8")}$ $[{self._file["AXIS/"+ax].attrs["UNITS"][0].decode("utf-8")}]$',
+                "plot_label": rf'${self._file["AXIS/" + ax].attrs["LONG_NAME"][0].decode("utf-8")}$ $[{self._file["AXIS/" + ax].attrs["UNITS"][0].decode("utf-8")}]$',
             }
             self._axis.append(axis_data)
 
@@ -777,9 +777,7 @@ def reorder_track_data(unordered_data, indexes, field_names):
         for time_iter in range(num_time_iter):
             index = indexes[particle][time_iter]
             if len(unordered_data[index]) != len(field_names):
-                raise ValueError(
-                    f"Data at index {index} has {len(unordered_data[index])} elements, " f"but {len(field_names)} are expected."
-                )
+                raise ValueError(f"Data at index {index} has {len(unordered_data[index])} elements, but {len(field_names)} are expected.")
             data_sorted[particle, time_iter] = tuple(unordered_data[index])
 
     return data_sorted

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/osiris_utils/decks/species.py

@@ -35,7 +35,7 @@ class Specie:
         self._q = q
         self._m = rqm * q
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return f"Specie(name={self._name}, rqm={self._rqm}, q={self._q}, m={self._m})"
 
     @property

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/osiris_utils/utils.py

@@ -1,4 +1,7 @@
+from __future__ import annotations
+
 from datetime import datetime
+from typing import cast
 
 import h5py
 import numpy as np
@@ -6,7 +9,7 @@ import pandas as pd
 import scipy
 
 
-def courant2D(dx, dy):
+def courant2D(dx: float, dy: float) -> float:
     """
     Compute the Courant number for a 2D simulation.
 
@@ -23,10 +26,10 @@ def courant2D(dx, dy):
         The limit for dt.
     """
     dt = 1 / (np.sqrt(1 / dx**2 + 1 / dy**2))
-    return dt
+    return cast(float, dt)
 
 
-def time_estimation(n_cells, ppc, t_steps, n_cpu, push_time=1e-7, hours=False):
+def time_estimation(n_cells: int, ppc: int, t_steps: int, n_cpu: int, push_time: float = 1e-7, hours: bool = False) -> float:
     """
     Estimate the simulation time.
 
@@ -57,11 +60,11 @@ def time_estimation(n_cells, ppc, t_steps, n_cpu, push_time=1e-7, hours=False):
         return time
 
 
-def filesize_estimation(n_gridpoints):
+def filesize_estimation(n_gridpoints: int) -> float:
     return n_gridpoints * 4 / (1024**2)
 
 
-def transverse_average(data):
+def transverse_average(data: np.ndarray) -> np.ndarray:
     """
     Computes the transverse average of a 2D array.
 
@@ -81,10 +84,10 @@ def transverse_average(data):
 
     if len(data.shape) != 2:
         raise ValueError("The input data must be a 2D array.")
-    return np.mean(data, axis=1)
+    return cast(np.ndarray, np.mean(data, axis=1))
 
 
-def integrate(array, dx):
+def integrate(array: np.ndarray, dx: float) -> np.ndarray:
     """
     Integrate a 1D from the left to the right. This may be changed in the future to allow
     for integration in both directions or for other more general cases.
@@ -109,10 +112,10 @@ def integrate(array, dx):
     flip_array = np.flip(array)
     # int = -scipy.integrate.cumulative_trapezoid(flip_array, dx = dx, initial = flip_array[0])
     int = -scipy.integrate.cumulative_simpson(flip_array, dx=dx, initial=0)
-    return np.flip(int)
+    return cast(np.ndarray, np.flip(int))
 
 
-def save_data(data, savename, option="numpy"):
+def save_data(data: np.ndarray, savename: str, option: str = "numpy") -> None:
     """
     Save the data to a .txt (with Numpy) or .csv (with Pandas) file.
 
@@ -133,7 +136,7 @@ def save_data(data, savename, option="numpy"):
         raise ValueError("Option must be 'numpy' or 'pandas'.")
 
 
-def read_data(filename, option="numpy"):
+def read_data(filename: str, option: str = "numpy") -> np.ndarray:
     """
     Read the data from a .txt file.
 
@@ -151,7 +154,7 @@ def read_data(filename, option="numpy"):
     return np.loadtxt(filename) if option == "numpy" else pd.read_csv(filename).values
 
 
-def convert_tracks(filename_in):
+def convert_tracks(filename_in: str) -> str:
     """
     Converts a new OSIRIS track file aka IDL-formatted aka tracks-2 to an older format that is more human-readable.
     In the old format, each particle is stored in a separate folder, with datasets for each quantity.
@@ -245,7 +248,7 @@ def convert_tracks(filename_in):
     return filename_out
 
 
-def create_file_tags(filename, tags_array):
+def create_file_tags(filename: str, tags_array: np.ndarray) -> str:
     """
     Function to write a file_tags file from a (number_of_tags, 2) NumPy array of tags.
     this file is used to choose particles for the OSIRIS track diagnostic.

{osiris_utils-1.1.7 → osiris_utils-1.1.9/osiris_utils.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.1.7
+Version: 1.1.9
 Summary: Utilities to manipulate and visualise OSIRIS plasma PIC output data
 Author: João Cândido, Diogo Carvalho
 Author-email: João Pedro Ferreira Biu <joaopedrofbiu@tecnico.ulisboa.pt>
@@ -34,7 +34,6 @@ Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pre-commit>=3.7; extra == "dev"
 Requires-Dist: ruff>=0.4; extra == "dev"
 Requires-Dist: isort>=5.13; extra == "dev"
-Requires-Dist: mypy>=1.10; extra == "dev"
 Requires-Dist: types-tqdm; extra == "dev"
 Requires-Dist: types-Pillow; extra == "dev"
 Provides-Extra: docs
@@ -44,8 +43,6 @@ Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: sphinx-copybutton<=0.5.2; extra == "docs"
 Requires-Dist: sphinx-rtd-theme<3.0.3; extra == "docs"
 Requires-Dist: sphinx-github-style<=1.2.2; extra == "docs"
-Provides-Extra: plot
-Requires-Dist: seaborn>=0.13; extra == "plot"
 Dynamic: license-file
 
 OSIRIS_UTILS
@@ -99,10 +96,6 @@ Quick-start
    cd osiris_utils
    python examples/quick_start.py examples/example_data/thermal.1d
 
-.. image:: docs/source/_static/quick_start_ez.png
-   :alt: Example Ez plot produced by the quick-start
-   :width: 400px
-
 Documentation
 -------------
 

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/osiris_utils.egg-info/SOURCES.txt

@@ -1076,4 +1076,5 @@ osiris_utils/postprocessing/postprocess.py
 osiris_utils/postprocessing/pressure_correction.py
 tests/__init__.py
 tests/test_imports.py
+tests/test_utils.py
 tests/test_version.py

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/osiris_utils.egg-info/requires.txt

@@ -11,7 +11,6 @@ pytest-cov
 pre-commit>=3.7
 ruff>=0.4
 isort>=5.13
-mypy>=1.10
 types-tqdm
 types-Pillow
 
@@ -22,6 +21,3 @@ myst-parser
 sphinx-copybutton<=0.5.2
 sphinx-rtd-theme<3.0.3
 sphinx-github-style<=1.2.2
-
-[plot]
-seaborn>=0.13

{osiris_utils-1.1.7 → osiris_utils-1.1.9}/pyproject.toml

@@ -56,7 +56,6 @@ dev  = [
   "pre-commit>=3.7",
   "ruff>=0.4",
   "isort>=5.13",
-  "mypy>=1.10",
   "types-tqdm",
   "types-Pillow",
 ]
@@ -68,15 +67,6 @@ docs = [
     "sphinx-rtd-theme<3.0.3",
     "sphinx-github-style<=1.2.2"
 ]
-plot = ["seaborn>=0.13"]
-
-[tool.mypy]
-python_version = "3.10"
-strict = true                      # enables all *safe* strict flags
-show_error_codes = true
-plugins = []
-ignore_missing_imports = true      # relax; tighten gradually
-namespace_packages = true
 
 # -----------------------  setuptools-specific knobs  ------------------------ #
 [tool.setuptools]
@@ -94,6 +84,7 @@ fallback_version = "0.0.0"
   "docs/_static/*.png"
 ]
 
+# -----------------------------  pre-commit hooks  ---------------------------- #
 [tool.ruff]
 line-length = 140          # instead of 88
 target-version = "py310"   # matches your min python

osiris_utils-1.1.9/tests/test_utils.py

@@ -0,0 +1,46 @@
+# tests/test_utils.py
+import math
+
+import numpy as np
+import pytest
+
+from osiris_utils.utils import courant2D, transverse_average
+
+
+@pytest.mark.parametrize(
+    ("dx", "dy", "expected"),
+    [
+        (1.0, 1.0, 1.0 / math.sqrt(1.0 / 1.0**2 + 1.0 / 1.0**2)),
+        (2.0, 2.0, 1.0 / math.sqrt(1.0 / 2.0**2 + 1.0 / 2.0**2)),
+        (0.5, 1.0, 1.0 / math.sqrt(1.0 / 0.5**2 + 1.0 / 1.0**2)),
+    ],
+)
+def test_courant2D(dx, dy, expected):
+    dt = courant2D(dx, dy)
+    assert pytest.approx(dt, rel=1e-9) == expected
+
+
+def test_courant2D_bad_input():
+    with pytest.raises(TypeError):
+        # passing a non-float should error
+        _ = courant2D("a", 1.0)
+
+
+@pytest.mark.parametrize(
+    "data, expected",
+    [
+        (np.array([[1, 2, 3], [4, 5, 6]]), np.array([2.0, 5.0])),
+        (np.ones((5, 4)), np.ones(5)),
+    ],
+)
+def test_transverse_average(data, expected):
+    out = transverse_average(data)
+    # shape and values
+    assert isinstance(out, np.ndarray)
+    assert out.shape == (data.shape[0],)
+    assert np.allclose(out, expected)
+
+
+def test_transverse_average_bad_dim():
+    with pytest.raises(ValueError):
+        transverse_average(np.zeros((3, 3, 3)))