started big cleanup

MANIFEST.in

@@ -1 +0,0 @@
-include src/scgenerator/data/*

README.md

@@ -1,3 +1,5 @@
+# THIS README IS NOT UP TO DATE
+
 It is recommended to import scgenerator in the following manner :
 `import scgenerator as sc`
 

formulas/main.tex

@@ -1,34 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{siunitx}
-\usepackage{tikz}
-\usepackage[siunitx]{circuitikz}
-\usepackage{babel}
-\usepackage{acronym}
-\newcommand{\At}{A(z, t)}
-\newcommand{\Et}{E(z, t)}
-\newcommand{\Ew}{\tilde{E}(z, \omega)}
-\newcommand{\PNL}{\tilde{\mathrm{P}}^\mathrm{NL}}
-
-\begin{document}
-Complex envelope such that $|A|^2$ is in W with E in V/m~:
-\begin{equation}
-    \At = \sqrt{\frac12 \epsilon_0 c n A_\mathrm{eff}} \Et
-\end{equation}
-
-Equations with E in V/m
-\begin{equation}
-    \frac{\partial \Ew}{\partial z} = i\left(\beta(\omega) - \frac{\omega}{\nu} \right)\Ew + i \frac{\omega^2}{2c\epsilon_0 \beta(\omega)}\PNL(z, \omega)
-\end{equation}
-
-\begin{equation}
-    \tau = t - \frac{z}{\nu}
-    \,, \quad \xi = z
-    \,, \quad \frac{\partial}{\partial z} = -\frac1{\nu}\frac{\partial}{\partial \tau} + \frac{\partial}{\partial \xi} = -\frac{i \omega}{\nu} + \frac{\partial}{\partial \xi}
-    \,, \quad \frac{\partial}{\partial t} = \frac{\partial}{\partial \tau}
-\end{equation}
-$\Rightarrow$
-\begin{equation}
-    \frac{\partial \Ew}{\partial z} = i\beta(\omega)\Ew + i \frac{\omega^2}{2c\epsilon_0 \beta(\omega)}\PNL(z, \omega)
-\end{equation}
-
-\end{document}

pyproject.toml

@@ -0,0 +1,26 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scgenerator"
+version = "0.3.0"
+description = "Simulate nonlinear pulse propagation in optical fibers"
+readme = "README.md"
+authors = [{ name = "Benoit Sierro", email = "benoit.sierro@iap.unibe.ch" }]
+license = "MIT"
+classifiers = [
+    "License :: OSI Approved :: MIT",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.10"
+keywords = ["nonlinear", "fiber optics", "simulation", "runge-kutta"]
+dependencies = ["numpy >= 1.23", "tomli", "numba", "pydantic", "tqdm"]
+
+[tool.ruff]
+line-length = 100
+[tool.ruff.pydocstyle]
+convention = "numpy"
+
+[tool.black]
+line-length = 100

requirements.txt

@@ -1,6 +0,0 @@
-numpy
-matplotlib
-scipy
-tomli
-tomli-w
-tqdm

setup.cfg

@@ -1,42 +0,0 @@
-[metadata]
-name = scgenerator
-version = 0.2.8dev
-description = Simulated PCFs and supercontinuum generation !
-author = Benoit Sierro
-author_email = benoit.sierro@iap.unibe.ch
-long_description = file: README.md
-long_description_content_type = text/markdown
-keywords = supercontinuum, nonlinear optics, GNLSE
-license = MIT
-classifiers =
-    License :: OSI Approved :: MIT
-    Programming Language :: Python :: 3
-
-[options]
-zip_safe = False
-include_package_data = True
-packages = find:
-package_dir = 
-    = src
-install_requires =
-    numpy
-    numba
-    matplotlib
-    scipy
-    tomli
-    tomli-w
-    tqdm
-
-
-[options.package_data]
-scgenerator =
-    data/hr_t.npz
-    data/materials.toml
-
-[options.packages.find]
-where = src
-
-[options.entry_points]
-console_scripts = 
-    scgenerator = scgenerator.cli.cli:main
-    sc-submit = scgenerator.scripts.slurm_submit:main

setup.py

@@ -1,3 +1,6 @@
-from setuptools import setup
+#!/usr/bin/env python
 
-setup()
+import setuptools
+
+if __name__ == "__main__":
+    setuptools.setup()

src/scgenerator/cli/__main__.py

@@ -1,4 +0,0 @@
-from .cli import main
-
-if __name__ == "__main__":
-    main()

src/scgenerator/cli/cli.py

@@ -1,248 +0,0 @@
-import argparse
-import os
-import re
-from collections import ChainMap
-from pathlib import Path
-
-import matplotlib.pyplot as plt
-import numpy as np
-
-from .. import const, env, scripts, utils
-from ..logger import get_logger
-from ..physics.fiber import dispersion_coefficients
-from ..physics.simulate import SequencialSimulations, run_simulation
-
-try:
-    import ray
-except ImportError:
-    ray = None
-
-
-def set_env_variables(cmd_line_args: dict[str, str]):
-    cm = ChainMap(cmd_line_args, os.environ)
-    for env_key in env.global_config:
-        k = env_key.replace(env.ENVIRON_KEY_BASE, "").lower()
-        v = cm.get(k)
-        if v is not None:
-            os.environ[env_key] = str(v)
-
-
-def create_parser():
-    parser = argparse.ArgumentParser(description="scgenerator command", prog="scgenerator")
-    subparsers = parser.add_subparsers(help="sub-command help")
-
-    for key, args in env.global_config.items():
-        names = ["--" + key.replace(env.ENVIRON_KEY_BASE, "").replace("_", "-").lower()]
-        if "short_name" in args:
-            names.append(args["short_name"])
-        parser.add_argument(
-            *names, **{k: v for k, v in args.items() if k not in {"short_name", "type"}}
-        )
-    parser.add_argument("--version", action="version", version=const.__version__)
-
-    run_parser = subparsers.add_parser("run", help="run a simulation from a config file")
-    run_parser.add_argument("config", help="path(s) to the toml configuration file(s)")
-    run_parser.set_defaults(func=run_sim)
-
-    merge_parser = subparsers.add_parser("merge", help="merge simulation results")
-    merge_parser.add_argument(
-        "path", help="path to the final simulation folder containing 'initial_config.toml'"
-    )
-    merge_parser.set_defaults(func=merge)
-
-    plot_parser = subparsers.add_parser("plot", help="generate basic plots of a simulation")
-    plot_parser.add_argument(
-        "sim_dir",
-        help="path to the root directory of the simulation (i.e. the "
-        "directory directly containing 'initial_config0.toml'",
-    )
-    plot_parser.add_argument(
-        "spectrum_limits",
-        nargs=argparse.REMAINDER,
-        help="comma-separated list of left limit, right limit and unit. "
-        "One plot is made for each limit set provided. Example : 600,1200,nm or -2,2,ps",
-    )
-    plot_parser.add_argument("--options", "-o", default=None)
-    plot_parser.add_argument(
-        "--show", action="store_true", help="show the plots instead of saving them"
-    )
-    plot_parser.set_defaults(func=plot_all)
-
-    dispersion_parser = subparsers.add_parser(
-        "dispersion", help="show the dispersion of the given config"
-    )
-    dispersion_parser.add_argument("config", help="path to the config file")
-    dispersion_parser.add_argument(
-        "--limits", "-l", default=None, type=float, nargs=2, help="left and right limits in nm"
-    )
-    dispersion_parser.set_defaults(func=plot_dispersion)
-
-    init_pulse_plot_parser = subparsers.add_parser(
-        "plot-spec-field", help="plot the initial field and spectrum"
-    )
-    init_pulse_plot_parser.add_argument("config", help="path to the config file")
-    init_pulse_plot_parser.add_argument(
-        "--wavelength-limits",
-        "-l",
-        default=None,
-        type=float,
-        nargs=2,
-        help="left and right limits in nm",
-    )
-    init_pulse_plot_parser.add_argument(
-        "--time-limit", "-t", default=None, type=float, help="time axis limit in fs"
-    )
-    init_pulse_plot_parser.set_defaults(func=plot_init_field_spec)
-
-    init_plot_parser = subparsers.add_parser("plot-init", help="plot initial values")
-    init_plot_parser.add_argument("config", help="path to the config file")
-    init_plot_parser.add_argument(
-        "--dispersion-limits",
-        "-d",
-        default=None,
-        type=float,
-        nargs=2,
-        help="left and right limits for dispersion plots in nm",
-    )
-    init_plot_parser.add_argument(
-        "--time-limit", "-t", default=None, type=float, help="time axis limit in fs"
-    )
-    init_plot_parser.add_argument(
-        "--wavelength-limits",
-        "-l",
-        default=None,
-        nargs=2,
-        type=float,
-        help="wavelength axis limit in nm",
-    )
-    init_plot_parser.set_defaults(func=plot_init)
-
-    preview_parser = subparsers.add_parser("preview", help="preview a currently running simulation")
-    plc_hld = "XX"
-    preview_parser.add_argument(
-        "path", help=f"path to the directory containing {const.SPEC1_FN.format(plc_hld)!r}"
-    )
-    preview_parser.add_argument(
-        "spectrum_limits",
-        nargs=argparse.REMAINDER,
-        help="comma-separated list of left limit, right limit and unit. "
-        "One plot is made for each limit set provided. Example : 600,1200,nm or -2,2,ps",
-    )
-    preview_parser.set_defaults(func=preview)
-
-    return parser
-
-
-def main():
-    parser = create_parser()
-    args = parser.parse_args()
-
-    set_env_variables({k: v for k, v in vars(args).items() if v is not None})
-
-    args.func(args)
-
-    logger = get_logger(__name__)
-    logger.info(f"dispersion cache : {dispersion_coefficients.cache_info()}")
-
-
-def run_sim(args):
-    method = prep_ray()
-    run_simulation(args.config, method=method)
-    # if sys.platform == "darwin" and sys.stdout.isatty():
-    #     subprocess.run(
-    #         [
-    #             "osascript",
-    #             "-e",
-    #             'tell app "System Events" to display dialog "simulation finished !"',
-    #         ],
-    #         stdout=subprocess.DEVNULL,
-    #         stderr=subprocess.DEVNULL,
-    #     )
-
-
-def merge(args):
-    path_trees = utils.build_path_trees(Path(args.path))
-
-    output = env.output_path()
-    if output is None:
-        output = path_trees[0][-1][0].parent.name + " merged"
-
-    utils.merge(output, path_trees)
-
-
-def preview(args):
-    for path in utils.simulations_list(args.path):
-        lims = args.spectrum_limits or [None, "-10,10,ps"]
-        for lim in lims:
-            scripts.partial_plot(path, lim)
-            plt.show()
-            plt.close()
-
-
-def prep_ray():
-    logger = get_logger(__name__)
-    if ray:
-        if env.get(env.START_RAY):
-            init_str = ray.init()
-        elif not env.get(env.NO_RAY):
-            try:
-                init_str = ray.init(
-                    address="auto",
-                    _redis_password=os.environ.get("redis_password", "caco1234"),
-                )
-                logger.info(init_str)
-            except ConnectionError as e:
-                logger.warning(e)
-    return SequencialSimulations if env.get(env.NO_RAY) else None
-
-
-def plot_all(args):
-    opts = {}
-    if args.options is not None:
-        opts |= dict([o.split("=")[:2] for o in re.split("[, ]+", args.options)])
-    root = Path(args.sim_dir).resolve()
-    scripts.plot_all(root, args.spectrum_limits, show=args.show, **opts)
-
-
-def plot_init_field_spec(args):
-    if args.wavelength_limits is None:
-        l = None
-    else:
-        l = list(args.wavelength_limits)
-
-    if args.time_limit is None:
-        t = None
-    else:
-        t = [-args.time_limit, args.time_limit]
-
-    scripts.plot_init_field_spec(args.config, t, l)
-
-
-def plot_init(args):
-    if args.wavelength_limits is None:
-        l = None
-    else:
-        l = list(args.wavelength_limits)
-    if args.dispersion_limits is None:
-        d = None
-    else:
-        d = list(args.dispersion_limits)
-
-    if args.time_limit is None:
-        t = None
-    else:
-        t = [-args.time_limit, args.time_limit]
-
-    scripts.plot_init(args.config, t, l, d)
-
-
-def plot_dispersion(args):
-    if args.limits is None:
-        lims = None
-    else:
-        lims = 1e-9 * np.array(args.limits, dtype=float)
-    scripts.plot_dispersion(args.config, lims)
-
-
-if __name__ == "__main__":
-    main()