Adding first attempt of documentation

.gitignore

@@ -4,3 +4,5 @@ input_data/
 **.pyc**
 **.nc
 **.zarr
+docs/_build/*
+docs/_downloads

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     = .
+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/conf.py

@@ -0,0 +1,119 @@
+# 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 datetime
+import inspect
+import os
+import sys
+import warnings
+
+project = 'PlasticParcels'
+copyright = f'{datetime.datetime.now().year}, The OceanParcels Team'
+author = 'The OceanParcels Team'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'pydata_sphinx_theme'
+html_static_path = ['_static']
+
+html_theme_options = {
+    "logo": {
+        "image_light": "plasticparcelslogo.png",
+        "image_dark": "plasticparcelslogo-inverted.png",  # TODO create this
+    },
+    # "use_edit_page_button": True,
+    "github_url": "https://github.com/OceanParcels/plasticparcels",
+    "icon_links": [
+        {
+            "name": "Conda Forge",
+            "url": "https://anaconda.org/conda-forge/plasticparcels",  # required
+            "icon": "fa-solid fa-box",
+            "type": "fontawesome",
+        }
+    ]
+}
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.todo',
+    "sphinx.ext.linkcode",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "myst_parser",
+    "nbsphinx",
+    "numpydoc",
+]
+
+# based on pandas doc/source/conf.py
+def linkcode_resolve(domain, info):
+    """Determine the URL corresponding to Python object."""
+    if domain != "py":
+        return None
+
+    modname = info["module"]
+    fullname = info["fullname"]
+
+    submod = sys.modules.get(modname)
+    if submod is None:
+        return None
+
+    obj = submod
+    for part in fullname.split("."):
+        try:
+            with warnings.catch_warnings():
+                # Accessing deprecated objects will generate noisy warnings
+                warnings.simplefilter("ignore", FutureWarning)
+                obj = getattr(obj, part)
+        except AttributeError:
+            return None
+
+    try:
+        fn = inspect.getsourcefile(inspect.unwrap(obj))
+    except TypeError:
+        try:  # property
+            fn = inspect.getsourcefile(inspect.unwrap(obj.fget))
+        except (AttributeError, TypeError):
+            fn = None
+    if not fn:
+        return None
+
+    try:
+        source, lineno = inspect.getsourcelines(obj)
+    except TypeError:
+        try:  # property
+            source, lineno = inspect.getsourcelines(obj.fget)
+        except (AttributeError, TypeError):
+            lineno = None
+    except OSError:
+        lineno = None
+
+    if lineno:
+        linespec = f"#L{lineno}-L{lineno + len(source) - 1}"
+    else:
+        linespec = ""
+
+    fn = os.path.relpath(fn, start=os.path.dirname(parcels.__file__))
+
+    if "-" in parcels.__version__:
+        return f"https://github.com/OceanParcels/plasticparcels/blob/master/parcels/{fn}{linespec}"
+    else:
+        return (
+            f"https://github.com/OceanParcels/plasticparcels/blob/"
+            f"{parcels.__version__}/parcels/{fn}{linespec}"
+        )

docs/examples.rst

@@ -0,0 +1,12 @@
+Examples
+========
+
+PlasticParcels has a few example notebooks, see below.
+
+
+
+.. nbgallery::
+   :caption: Running simulations
+   :name: running-simulations
+
+   examples/example_Italy_coast.ipynb

docs/examples/example_Italy_coast.ipynb

@@ -4,8 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# PlasticParcels Example\n",
-    "## The pathways and fate of Italian coastal plastic pollution\n",
+    "# The pathways and fate of Italian coastal plastic pollution\n",
     "In this example, we will use `plasticparcels` to run a basic simulation of microplastic pollution along the Italian coastline."
    ]
   },

docs/index.rst

@@ -0,0 +1,20 @@
+.. plasticparcels documentation master file, created by
+   sphinx-quickstart on Fri May  3 09:55:52 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PlasticParcels documentation
+============================
+
+Welcome to the documentation of PlasticParcels.
+
+``plasticparcels`` is a python package for simulating the transport and dispersion of plastics in the ocean. The tool is based on the ``parcels`` computational Lagrangian ocean analysis framework, providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents
+
+   Home <self>
+   Examples <examples>
+   OceanParcels website <https://oceanparcels.org/>

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=.
+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