Merge pull request #1 from INRIM/v0.1.0-init

Merge V0.1.0 init

.readthedocs.yaml

@@ -0,0 +1,12 @@
+version: 2
+
+build:
+  os: "ubuntu-latest"
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - requirements: docs/rtd_requirements.txt

README.md

@@ -1,2 +1,39 @@
 # large-lattice-model
-A python package to model the motional spectra of atoms trapped in a one-dimensional optical lattice
+A python package to model the motional spectra of atoms trapped in a one-dimensional optical lattice.
+
+
+## Requirements
+Large-lattice-model requires the calculation of Mathieu special function.
+The current `scipy` implementation of Mathieu functions [is not continuous.](https://github.com/scipy/scipy/pull/14577)
+It is reccomended to install the [GSL Library](https://www.gnu.org/software/gsl/), for example using:
+
+    sudo apt install libgsl-dev
+
+Large-lattice-model will use `ctypes` to import the GSL implementation and will fallback to `scipy` if it does not find GSL.
+Previous versions of the package used [`pygsl`](https://github.com/pygsl/pygsl), but the current version of `pygsl` does not implement [special functions](https://github.com/pygsl/pygsl/issues/55).
+
+
+
+## License
+
+[MIT](https://opensource.org/licenses/MIT)
+
+## References
+
+This package implements many ideas from the work of NIST Yb optical lattice clock group:
+
+[Beloy et al., Phys. Rev. A, 101, 053416 (2020).](https://doi.org/10.1103/PhysRevA.101.053416)
+
+It is developed for use in the INRIM Yb optical lattice clock IT-Yb1, see for example:
+
+
+[Goti et al., Metrologia, 60, 035002 (2023).](https://dx.doi.org/10.1088/1681-7575/accbc5)
+
+## Acknowledgments
+This work has received funding from the European Partnership on Metrology, co-financed by the European Union’s Horizon Europe Research and Innovation Programme and by the Participating States, under grant number 22IEM01 TOCK.
+
+![badge](./docs/source/Acknowledgement%20badge.png)
+
+## Authors
+
+(c) 2021-2024 Marco Pizzocaro - Istituto Nazionale di Ricerca Metrologica (INRIM)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import importlib.metadata
+from pathlib import Path
+
+project = "Large-lattice-model"
+copyright = "2021-2024 Marco Pizzocaro - Istituto Nazionale di Ricerca Metrologica (INRIM)"
+author = "Marco Pizzocaro"
+release = importlib.metadata.version("large_lattice_model")
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "myst_parser",
+    "sphinx.ext.duration",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "autoapi.extension",
+]
+autoapi_type = "python"
+autoapi_dirs = [f"{Path(__file__).parents[2]}/src"]
+
+myst_enable_extensions = ["dollarmath", "amsmath"]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/source/index.md

@@ -0,0 +1,11 @@
+% Large-lattice-model documentation master file, created by
+% sphinx-quickstart on Thu Sep 12 17:52:22 2024.
+% You can adapt this file completely to your liking, but it should at least
+% contain the root `toctree` directive.
+
+# Large-lattice-model documentation
+
+```{toctree}
+:caption: 'Contents:'
+:maxdepth: 2
+```