osiris-utils 1.1.7__py3-none-any.whl → 1.1.9__py3-none-any.whl

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/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/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/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.dist-info → osiris_utils-1.1.9.dist-info}/METADATA

@@ -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.dist-info → osiris_utils-1.1.9.dist-info}/RECORD

@@ -1,4 +1,4 @@
-docs/source/conf.py,sha256=JpYzgkHPpf9Nvy50zDB2jH7Ptbq_5L1acv2FT4MwFjM,6141
+docs/source/conf.py,sha256=EJ1e_TprMsuEl1MRnzuhGi30MLJ3jWBJjnX5HE_1ZNA,6141
 docs/source/contrib.rst,sha256=CkYSzy3msde38fy0zROAjDsdRHYYvQSAJwjkJczFmGI,35
 docs/source/index.rst,sha256=9DQxea3_rZIe9g_nQs9MDJ7XXmeWpB59lDflyrKi66Q,508
 docs/source/_static/custom.css,sha256=aLsKMK8rejJzzCdISkHhDG8Eq-f7T4v4DmQInYzeRDI,909
@@ -1038,14 +1038,14 @@ examples/example_data/MS/UDIST/electrons/vfl1/vfl1-electrons-000253.h5,sha256=Kt
 examples/example_data/TIMINGS/timings-final,sha256=1i_dcQ1hIxs78eeD4e6WNWUxJ_vXKRvbIVDAPGl9_R4,2910
 osiris_utils/__init__.py,sha256=YcD7gApMN-CPz_rkx7ZHnIoqA2yAWetUhgd7b0hABto,2461
 osiris_utils/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-osiris_utils/utils.py,sha256=Y935G6ryagoHnxb0dtc02I_a0zaUFZ4K_1VRXurqBJY,8056
+osiris_utils/utils.py,sha256=5XxFFZd1cK-xujlKIR1-21jPZwNJge7rqkNZlTyCgCs,8401
 osiris_utils/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-osiris_utils/data/data.py,sha256=Hzz2HS-PK0rVP3sw1ExVZvn7hZ27Vo5fxWColesfv3M,28017
+osiris_utils/data/data.py,sha256=OdmArrWPmLlBwibZZL0ct1Mg_ApPL15HPQna49EvnNs,27979
 osiris_utils/data/diagnostic.py,sha256=Ed3w4G7X3vxwvwWpnIXl3QeXIe5IvPsCYjyjgrGlp4E,48710
 osiris_utils/data/simulation.py,sha256=r3YN9jdyLtF5fpovc8-xYDYkKJ3eTibNNqxWdHudNjg,6854
 osiris_utils/decks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 osiris_utils/decks/decks.py,sha256=r0dyg4lZyxvEFcL6p-H7rn-UyawPlYItcftJ4Xb_GpI,9925
-osiris_utils/decks/species.py,sha256=uZA1oMSltofc2m1s3rK__wjxXfTAQ_3wB2aKRG_PmKo,1066
+osiris_utils/decks/species.py,sha256=hHWfK0vPGcEiFfRWssMjRleDHjlqgsN47655yeVlWNM,1073
 osiris_utils/postprocessing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 osiris_utils/postprocessing/derivative.py,sha256=_AO8qEEAXRQKrRNGpk8lpFOeKycGZ-cIlF3AsxgPE7Y,10120
 osiris_utils/postprocessing/fft.py,sha256=rPu7-qJ2joaiP9I_saVj6V1pKGo58OEIgloIr0BBDj8,8954
@@ -1055,8 +1055,8 @@ osiris_utils/postprocessing/mft.py,sha256=KPoUZmwXcKbOGSHz01FPsDKlMSZDUrSeHQhlVb
 osiris_utils/postprocessing/mft_for_gridfile.py,sha256=EGTghHliN9Q7KDYasnkKdc2QolD4tdlAxWnkPonS2aQ,1502
 osiris_utils/postprocessing/postprocess.py,sha256=tcYVJR5eWeCTiWfnu9OKUfHk_E7-H8ek_QkMGVvRRg4,1077
 osiris_utils/postprocessing/pressure_correction.py,sha256=FFi-KaV0pD5I6vBPFMRkyRZym2n8lb_m-CB0onihpRQ,6443
-osiris_utils-1.1.7.dist-info/licenses/LICENSE.txt,sha256=Cawy2v7wKc7n8yL8guFu-cH9sQw9r1gll1pEFPFAB-Q,1084
-osiris_utils-1.1.7.dist-info/METADATA,sha256=KCJYK2elZlNe3swt4REjQDb0bdYTRt6r2q-xyeoBOAU,4575
-osiris_utils-1.1.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-osiris_utils-1.1.7.dist-info/top_level.txt,sha256=8FzwamPQqVoj13it2XTog8aXYQ7cuyYyCFyGNz4tn3s,27
-osiris_utils-1.1.7.dist-info/RECORD,,
+osiris_utils-1.1.9.dist-info/licenses/LICENSE.txt,sha256=Cawy2v7wKc7n8yL8guFu-cH9sQw9r1gll1pEFPFAB-Q,1084
+osiris_utils-1.1.9.dist-info/METADATA,sha256=QM6FOq4Kc4gmTDtPSuWJl2yM5jvgBb_j3bhbbOmIvnA,4345
+osiris_utils-1.1.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+osiris_utils-1.1.9.dist-info/top_level.txt,sha256=8FzwamPQqVoj13it2XTog8aXYQ7cuyYyCFyGNz4tn3s,27
+osiris_utils-1.1.9.dist-info/RECORD,,