Add pre-commit and fix CI pipeline

.github/workflows/testing.yml

@@ -5,7 +5,7 @@ jobs:
   example_tests:
     name: Example tests
     runs-on: ubuntu-latest
-    container: python:3.8.15
+    container: python:3.10
     steps:
       - name: Check out repository code
         uses: actions/checkout@v3

.gitignore

@@ -19,4 +19,4 @@ docs/_build
 docs/*.rst
 examples_for_ci.py
 examples_output
-replace_placeholders_in_md.py
+replace_placeholders_in_md.py

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.6
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - numpy
+          - types-tqdm

cavity.py

@@ -1,11 +1,11 @@
-import numpy as np
 import matplotlib.pyplot as plt
-
-# from scipy import signal
-from matplotlib import animation
+import numpy as np
 
 # import scipy.constants as con
 from IPython.display import HTML
+
+# from scipy import signal
+from matplotlib import animation
 from tqdm import tqdm
 
 # import matplotlib.cm as cm
@@ -23,7 +23,6 @@ def resonator_modes(
     spectrum_std=1000,
     save_in="",
 ):
-
     # length of the resonator
     L = z.max() - z.min()
     # calculate the frequency difference between two neighbouring modes of

docs/requirements.txt

@@ -2,4 +2,4 @@ librep
 myst-parser~=0.17.0
 pydata-sphinx-theme
 sphinx-autoapi
-Sphinx~=4.2.0
+Sphinx~=4.2.0

docs/source/conf.py

@@ -12,9 +12,10 @@
 
 import os
 import sys
-import panim
 from subprocess import run
 
+import panim
+
 sys.path.insert(0, os.path.abspath("."))
 sys.path.insert(0, os.path.abspath("../../panim"))
 
@@ -74,10 +75,7 @@
     run(command, capture_output=True, check=True).stdout.strip().decode("utf-8")
 )
 
-if "dev" in release:
-    version_match = "master"
-else:
-    version_match = f"v{release}"
+version_match = "master" if "dev" in release else f"v{release}"
 
 html_theme = "pydata_sphinx_theme"
 html_theme_options = {

docs/source/index.rst

@@ -15,4 +15,4 @@ Indices and tables
 * `Git repository <https://github.com/jobirk/panim>`_
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
+* :ref:`search`

docs/source/redirect_index.html

@@ -6,4 +6,4 @@
     <meta http-equiv="refresh" content="0; url=./master/index.html">
     <link rel="canonical" href="https://jobirk.github.io/panim/master/index.html">
   </head>
-</html>
+</html>

docs/sphinx_build_multiversion.py

@@ -12,7 +12,6 @@
 import os
 from shutil import copy
 from subprocess import run
-import subprocess
 
 
 def build_docs_version(version):
@@ -49,13 +48,15 @@ def build_docs_version(version):
 
 def main():
     """main function that is executed when the script is called."""
-    with open("docs/source/_static/switcher.json", "r") as f:  # pylint: disable=W1514
+    with open("docs/source/_static/switcher.json") as f:  # pylint: disable=W1514
         version_switcher = json.load(f)
 
     # get currently active branch
     command = "git rev-parse --abbrev-ref HEAD".split()
-    initial_branch = run(command, capture_output=True, check=True).stdout.strip().decode("utf-8")
-
+    initial_branch = (
+        run(command, capture_output=True, check=True).stdout.strip().decode("utf-8")
+    )
+
     copy("docs/source/conf.py", "./conf_latest.py")
 
     # build docs for main branch no matter what versions are present in the switcher

examples/examples_components_demo.py

@@ -1,7 +1,9 @@
-from panim import *
 import os
+
 import numpy as np
 
+from panim import plot_pulses, sin_sum
+
 z = np.linspace(-20, 200, 10000)
 # +z_max=100 - nice settings to get three good pulses with stretching
 
@@ -28,7 +30,7 @@
     0,
     N_frequencies=4000,
     nu_center=0.15,
-    k_i=(1, 3, 2),
+    k_i=[1, 3, 2],
     spec_width=100,
     plotting=True,
     figuresize=(11, 1.2),

examples/first_order_dispersion.py

@@ -1,7 +1,9 @@
-from panim import *
 import os
+
 import numpy as np
 
+from panim import animate, calc_pulses
+
 z = np.linspace(-20, 200, 10000)
 os.makedirs("plots", exist_ok=True)
 

examples/group_equal_phase.py

@@ -1,7 +1,9 @@
-from panim import *
 import os
+
 import numpy as np
 
+from panim import animate, calc_pulses
+
 z = np.linspace(-20, 200, 10000)
 # +z_max=100 - nice settings to get three good pulses with stretching
 os.makedirs("plots", exist_ok=True)

examples/second_order_dispersion.py

@@ -1,7 +1,9 @@
-from panim import *
 import os
+
 import numpy as np
 
+from panim import animate, calc_pulses
+
 z = np.linspace(-20, 200, 10000)
 os.makedirs("plots", exist_ok=True)
 

examples/third_order_dispersion.py

@@ -1,5 +1,5 @@
-from panim import *
 import os
+
 import numpy as np
 
 z = np.linspace(-20, 200, 10000)

mode_locking.ipynb

@@ -2,13 +2,10 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from pulse_animation import *\n",
-    "%config InlineBackend.figure_format = 'retina'"
-   ]
+   "source": "import numpy as np\n\nfrom cavity import animate_resonator\n\n%config InlineBackend.figure_format = 'retina'"
   },
   {
    "cell_type": "code",
@@ -8613,18 +8610,17 @@
     }
    ],
    "source": [
-    "animate_resonator(np.linspace(0, 10, 100), np.linspace(0, 20, 400), n_modes=40, ms_between_frames=60)"
+    "animate_resonator(\n",
+    "    np.linspace(0, 10, 100), np.linspace(0, 20, 400), n_modes=40, ms_between_frames=60\n",
+    ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from cavity import *\n",
-    "%config InlineBackend.figure_format = 'retina'"
-   ]
+   "source": "import numpy as np\n\nfrom cavity import resonator_modes\n\n%config InlineBackend.figure_format = 'retina'"
   },
   {
    "cell_type": "code",
@@ -8667,8 +8663,21 @@
     }
    ],
    "source": [
-    "d = resonator_modes(0.21, np.linspace(0, 1, 2000), 30, spectrum_std=1000, save_in=\"plots/mode_locking/locked_phase\")\n",
-    "b = resonator_modes(0.21, np.linspace(0, 1, 2000), 30, spectrum_std=1000, save_in=\"plots/mode_locking/random_phase\", random_phases=True)"
+    "d = resonator_modes(\n",
+    "    0.21,\n",
+    "    np.linspace(0, 1, 2000),\n",
+    "    30,\n",
+    "    spectrum_std=1000,\n",
+    "    save_in=\"plots/mode_locking/locked_phase\",\n",
+    ")\n",
+    "b = resonator_modes(\n",
+    "    0.21,\n",
+    "    np.linspace(0, 1, 2000),\n",
+    "    30,\n",
+    "    spectrum_std=1000,\n",
+    "    save_in=\"plots/mode_locking/random_phase\",\n",
+    "    random_phases=True,\n",
+    ")"
    ]
   },
   {
@@ -8694,7 +8703,14 @@
     }
    ],
    "source": [
-    "b = resonator_modes(1, np.linspace(0, 1, 2000), 3, spectrum_std=1000, save_in=\"plots/mode_locking/resonator_3modes/illustration\", random_phases=True)"
+    "b = resonator_modes(\n",
+    "    1,\n",
+    "    np.linspace(0, 1, 2000),\n",
+    "    3,\n",
+    "    spectrum_std=1000,\n",
+    "    save_in=\"plots/mode_locking/resonator_3modes/illustration\",\n",
+    "    random_phases=True,\n",
+    ")"
    ]
   },
   {

optical_fibre.py

@@ -1,5 +1,7 @@
-from pulse_animation import *
 import matplotlib
+import numpy as np
+
+from panim import animate_with_time, calc_pulses
 
 matplotlib.rcParams.update({"font.size": 13})
 

panim/__init__.py

@@ -1,12 +1,13 @@
-import numpy as np
+import os
+
 import matplotlib.pyplot as plt
-from scipy import signal
-from matplotlib import animation
+import numpy as np
 
 # import scipy.constants as con
 from IPython.display import HTML
+from matplotlib import animation
+from scipy.signal import windows
 from tqdm import tqdm
-import os
 
 __version__ = "0.1.1dev"
 
@@ -52,7 +53,7 @@ def sin_sum(
     nu_min: float = 0.001,
     N_frequencies: int = 4000,
     spec_width: float = 200,
-    k_i: list = [1, 5, 0],
+    k_i: list | None = None,
     plotting: bool = False,
     z_arrow: bool = False,
     figuresize: tuple = (11, 4),
@@ -108,11 +109,13 @@ def sin_sum(
         E-field amplitude along the z-axis at time t.
 
     """
+    if k_i is None:
+        k_i = [1, 5, 0]
 
     # create array of frequency spectrum and the corresponding weight
     # i.e. how much the given frequency contributes
     frequencies = np.linspace(nu_min, nu_center * 2, N_frequencies)
-    spectrum = signal.gaussian(len(frequencies), std=spec_width)
+    spectrum = windows.gaussian(len(frequencies), std=spec_width)
 
     # create array for spectral components
     E_field_spec_components = np.zeros([len(frequencies), len(z)])
@@ -141,12 +144,11 @@ def sin_sum(
             2 * np.pi * frequencies[i] * t - phi_nu
         )
 
-        if plotting:
-            if frequencies[i] in plotting_frequencies:
-                ax.plot(
-                    z, E_field_spec_components[i], label=frequencies[i]
-                )  # , color=colors[n_plotted])
-                n_plotted += 1
+        if plotting and frequencies[i] in plotting_frequencies:
+            ax.plot(
+                z, E_field_spec_components[i], label=frequencies[i]
+            )  # , color=colors[n_plotted])
+            n_plotted += 1
 
     # Calculate the total E-field as the sum over all spectral components
     E_field = E_field_spec_components.sum(axis=0)
@@ -186,7 +188,7 @@ def sin_sum(
     return E_field
 
 
-def calc_pulses(z, t_start, t_end, n_steps, nu_center=1, k_i=[1, 5, 0], spec_width=100):
+def calc_pulses(z, t_start, t_end, n_steps, nu_center=1, k_i=None, spec_width=100):
     """Calculates the spatial form of the pulse at different times
 
     Parameters
@@ -220,6 +222,8 @@ def calc_pulses(z, t_start, t_end, n_steps, nu_center=1, k_i=[1, 5, 0], spec_wid
         the wave at all time steps.
 
     """
+    if k_i is None:
+        k_i = [1, 5, 0]
 
     times = np.linspace(t_start, t_end, n_steps)
     pulses = np.zeros([n_steps, len(z)])
@@ -425,14 +429,14 @@ def plot_pulses(
     z,
     times,
     nu_center=0.5,
-    k_i=[1, 10, 0],
+    k_i=None,
     spec_width=400,
     no_axes=False,
     plotname="",
     dpi=100,
     figuresize=(11, 4),
     z_arrow=False,
-    colors=["steelblue" for i in range(10)],
+    colors=None,
 ):
     """Plots the pulse at different times
 
@@ -474,6 +478,10 @@ def plot_pulses(
         time steps are plotted with the standard python 'steelblue'.
 
     """
+    if k_i is None:
+        k_i = [1, 10, 0]
+    if colors is None:
+        colors = ["steelblue" for _ in range(10)]
 
     pulses = [
         sin_sum(z, t, nu_center=nu_center, k_i=k_i, spec_width=spec_width)