Test docs

.readthedocs.yaml

@@ -0,0 +1,12 @@
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: "3.9"
+   install:
+   - method: pip
+     path: .[docs]

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "restructuredtext.preview.name": "docutils"
+}

docs/api.rst

@@ -0,0 +1,17 @@
+API
+====
+
+.. currentmodule:: flip
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   flip.covariance
+   flip.likelihood
+   flip.fitter
+   flip.gridding
+   flip.model_evaluation
+   flip.power_spectra
+   flip.utils
+

docs/api/flip.covariance.rst

@@ -0,0 +1,23 @@
+flip.covariance
+===============
+
+.. automodule:: flip.covariance
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/basicusage.rst

@@ -0,0 +1,2 @@
+Getting started
+===============

docs/conf.py

@@ -0,0 +1,128 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+import sys
+import os
+import numpy
+sys.path.insert(0, os.path.abspath('..'))
+import flip 
+
+project = 'flip'
+copyright = '2023, C. Ravoux'
+author = 'C. Ravoux, B. Carreres'
+
+# The full version, including alpha/beta/rc tags
+release = flip.__version__
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'astropy': ('http://docs.astropy.org/en/stable/', None),
+    'sncosmo': ('https://sncosmo.readthedocs.io/en/stable/', None),
+    'pandas': ('https://pandas.pydata.org/docs/', None)}
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+
+extensions = ['myst_parser', 'sphinx.ext.napoleon', 'sphinx_markdown_tables', 'sphinx.ext.autosectionlabel',
+              'sphinx.ext.linkcode', 'sphinx.ext.intersphinx', 'sphinx.ext.autodoc', 'sphinx.ext.autosummary']
+
+napoleon_google_docstring = True
+myst_enable_extensions = ["dollarmath"]
+myst_dmath_double_inline = True
+
+autosectionlabel_prefix_document = True
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+html_logo = ""
+
+html_theme_options = {
+                        "sidebar_hide_name": True,
+                     }
+
+import inspect
+from os.path import relpath
+
+
+# Copied on sncosmo documentation
+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:
+            obj = getattr(obj, part)
+        except:
+            return None
+
+    try:
+        fn = inspect.getsourcefile(obj)
+    except:
+        fn = None
+    if not fn:
+        return None
+
+    try:
+        source, lineno = inspect.findsource(obj)
+    except:
+        lineno = None
+
+    if lineno:
+        linespec = "#L%d" % (lineno + 1)
+    else:
+        linespec = ""
+
+    fn = relpath(fn, start=flip.__flip_dir_path__)
+
+    return "https://github.com/corentinravoux/flip/tree/main/%s%s" % (fn, linespec)

docs/index.rst

@@ -0,0 +1,24 @@
+
+Welcome to flip's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation.rst
+   basicusage.rst
+
+.. toctree::
+   :hidden:
+   :titlesonly:
+
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation.rst

@@ -0,0 +1,10 @@
+Installation
+============
+
+Clone the repository from github and install using pip.
+
+.. code:: bash
+
+   git clone https://github.com/corentinravoux/flip.git
+   cd flip
+   pip install .

flip/__init__.py

@@ -1,4 +1,9 @@
 """Init file of the flip package."""
-from . import covariance 
+from . import covariance
+from . import fitter
+from . import gridding
+from . import likelihood
+from . import model_evaluation
+from . import utils
 
 __version__ = "1.0.0"

flip/model_evaluation.py

@@ -1,5 +1,4 @@
 import numpy as np
-from fitfs8 import grid_utils, joint_cov
 import itertools
 import matplotlib.pyplot as plt
 

requirements.txt

@@ -0,0 +1 @@
+-e .

setup.cfg

@@ -6,16 +6,6 @@ email = corentin.ravoux.research@gmail.com
 author = Corentin Ravoux
 long_description = file : README.md
 license = MIT
-classifiers =
-    # Trove classifiers
-    # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
-    License :: OSI Approved :: MIT License
-    Programming Language :: Python
-    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: Implementation :: CPython
-    Programming Language :: Python :: Implementation :: PyPy
 
 
 [options]
@@ -26,3 +16,18 @@ install_requires =
     scipy
     matplotlib
     importlib-metadata
+    cosmoprimo @ git+https://github.com/cosmodesi/cosmoprimo
+
+
+[options.extras_require]
+docs =
+    markdown
+    sphinx >= 5.2.3
+    sphinx-markdown-tables >= 0.0.15
+    numpydoc
+    furo
+    myst-parser
+    sphinx-copybutton
+    sphinx-design
+    sphinx-inline-tabs
+    sphinx-tabs