diff --git a/doc/source/conf.py b/doc/source/conf.py
index fb3c486..768a7bd 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -3,25 +3,64 @@
# For the full list of built-in configuration values, 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
+
+from recommonmark.transform import AutoStructify
+
+sys.path.insert(0, os.path.abspath(".."))
+import qibochem
+
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
project = "qibochem"
-copyright = "2023, qiboteam"
-author = "qiboteam"
-release = "0.0.1"
+copyright = "The Qibo team"
+author = "The Qibo team"
+
+# The full version, including alpha/beta/rc tags
+release = qibochem.__version__
# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+# https://stackoverflow.com/questions/56336234/build-fail-sphinx-error-contents-rst-not-found
+master_doc = "index"
extensions = [
"sphinx.ext.autodoc",
"sphinx.ext.doctest",
"sphinx.ext.coverage",
"sphinxcontrib.katex",
+ "sphinx.ext.napoleon",
+ "sphinx.ext.intersphinx",
+ "sphinx_copybutton",
+ "recommonmark",
+ "nbsphinx",
]
+# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]
+
+# Markdown configuration
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = {".rst": "restructuredtext", ".txt": "markdown", ".md": "markdown"}
+
+autosectionlabel_prefix_document = True
+# Allow to embed rst syntax in markdown files.
+enable_eval_rst = True
+
+# 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 = []
@@ -31,21 +70,66 @@
# a list of builtin themes.
#
html_theme = "furo"
+html_favicon = "favicon.ico"
# custom title
-html_title = "Version " + release
+html_title = "Qibochem ยท v" + release
# custom html theme options (colors and font)
html_theme_options = {
+ "top_of_page_button": "edit",
+ "source_repository": "https://github.com/qiboteam/qibochem/",
+ "source_branch": "main",
+ "source_directory": "doc/source/",
+ "light_logo": "qibo_logo_dark.svg",
+ "dark_logo": "qibo_logo_light.svg",
"light_css_variables": {
"color-brand-primary": "#6400FF",
"color-brand-secondary": "#6400FF",
"color-brand-content": "#6400FF",
- }
+ },
+ "footer_icons": [
+ {
+ "name": "GitHub",
+ "url": "https://github.com/qiboteam/qibochem",
+ "html": """
+
+ """,
+ "class": "",
+ },
+ ],
}
# 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"]
+
+
+# -- Intersphinx -------------------------------------------------------------
+
+intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
+
+
+# -- Doctest ------------------------------------------------------------------
+#
+
+doctest_path = [os.path.abspath("../examples")]
+
+# -- Autodoc ------------------------------------------------------------------
+#
+autodoc_member_order = "bysource"
+
+
+# Adapted this from
+# https://github.com/readthedocs/recommonmark/blob/ddd56e7717e9745f11300059e4268e204138a6b1/docs/conf.py
+# app setup hook
+def setup(app):
+ app.add_config_value("recommonmark_config", {"enable_eval_rst": True}, True)
+ app.add_transform(AutoStructify)
+ app.add_css_file("css/style.css")
+
+
+html_show_sourcelink = False
diff --git a/doc/source/favicon.ico b/doc/source/favicon.ico
new file mode 100644
index 0000000..62c493a
Binary files /dev/null and b/doc/source/favicon.ico differ
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 1d44428..57a57ea 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -16,6 +16,27 @@ Qibochem key features:
* PySCF or Psi4 for calculation of 1- and 2-electron integrals
* Unitary Coupled Cluster Ansatz
+
+How to Use the Documentation
+============================
+
+Welcome to the comprehensive documentation for ``Qibo``! This guide will help
+you navigate through the various sections and make the most of the resources
+available.
+
+1. **Installation and Setup**: Begin by referring to the
+ :doc:`/getting-started/index` guide to set up the ``Qibochem`` library in your environment.
+
+2. **Tutorials**: Explore the :doc:`/code-examples/index` section for a range of
+ tutorials that cater to different levels of expertise. These tutorials cover
+ basic examples, advanced examples and tutorials with algorithm for specific
+ applications.
+
+3. **API Documentation**: Dive into the :doc:`/api-reference/index` section,
+ which offers a detailed overview of the main components that constitute the
+ ``Qibochem`` API. This section provides a comprehensive understanding of the key
+ elements, helping you build a holistic view of the API's capabilities.
+
Contents
========
@@ -31,3 +52,19 @@ Contents
api-reference/index
developer-guides/index
+
+.. toctree::
+ :maxdepth: 1
+ :caption: Documentation links
+
+ Qibo docs
+ Qibolab docs
+ Qibocal docs
+ Qibosoq docs
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`
diff --git a/doc/source/logo.png b/doc/source/logo.png
new file mode 100644
index 0000000..610c713
Binary files /dev/null and b/doc/source/logo.png differ
diff --git a/doc/source/qibo_logo.svg b/doc/source/qibo_logo.svg
new file mode 100644
index 0000000..ab201d2
--- /dev/null
+++ b/doc/source/qibo_logo.svg
@@ -0,0 +1,121 @@
+
+
diff --git a/poetry.lock b/poetry.lock
index 49277e2..0dba932 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
[[package]]
name = "alabaster"
@@ -24,39 +24,35 @@ files = [
[[package]]
name = "astroid"
-version = "2.15.6"
+version = "3.0.1"
description = "An abstract syntax tree for Python with inference support."
optional = false
-python-versions = ">=3.7.2"
+python-versions = ">=3.8.0"
files = [
- {file = "astroid-2.15.6-py3-none-any.whl", hash = "sha256:389656ca57b6108f939cf5d2f9a2a825a3be50ba9d589670f393236e0a03b91c"},
- {file = "astroid-2.15.6.tar.gz", hash = "sha256:903f024859b7c7687d7a7f3a3f73b17301f8e42dfd9cc9df9d4418172d3e2dbd"},
+ {file = "astroid-3.0.1-py3-none-any.whl", hash = "sha256:7d5895c9825e18079c5aeac0572bc2e4c83205c95d416e0b4fee8bc361d2d9ca"},
+ {file = "astroid-3.0.1.tar.gz", hash = "sha256:86b0bb7d7da0be1a7c4aedb7974e391b32d4ed89e33de6ed6902b4b15c97577e"},
]
[package.dependencies]
-lazy-object-proxy = ">=1.4.0"
typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
-wrapt = [
- {version = ">=1.11,<2", markers = "python_version < \"3.11\""},
- {version = ">=1.14,<2", markers = "python_version >= \"3.11\""},
-]
[[package]]
name = "asttokens"
-version = "2.4.0"
+version = "2.4.1"
description = "Annotate AST trees with source code positions"
optional = false
python-versions = "*"
files = [
- {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"},
- {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"},
+ {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+ {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
]
[package.dependencies]
six = ">=1.12.0"
[package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
[[package]]
name = "attrs"
@@ -78,25 +74,17 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
[[package]]
name = "babel"
-version = "2.12.1"
+version = "2.13.1"
description = "Internationalization utilities"
optional = false
python-versions = ">=3.7"
files = [
- {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
- {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+ {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+ {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
]
-[[package]]
-name = "backcall"
-version = "0.2.0"
-description = "Specifications for callback functions passed in to an API"
-optional = false
-python-versions = "*"
-files = [
- {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
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-]
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
[[package]]
name = "beautifulsoup4"
@@ -118,13 +106,13 @@ lxml = ["lxml"]
[[package]]
name = "bleach"
-version = "6.0.0"
+version = "6.1.0"
description = "An easy safelist-based HTML-sanitizing tool."
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "bleach-6.0.0-py3-none-any.whl", hash = "sha256:33c16e3353dbd13028ab4799a0f89a83f113405c766e9c122df8a06f5b85b3f4"},
- {file = "bleach-6.0.0.tar.gz", hash = "sha256:1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414"},
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+ {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
]
[package.dependencies]
@@ -132,17 +120,17 @@ six = ">=1.9.0"
webencodings = "*"
[package.extras]
-css = ["tinycss2 (>=1.1.0,<1.2)"]
+css = ["tinycss2 (>=1.1.0,<1.3)"]
[[package]]
name = "cachetools"
-version = "5.3.1"
+version = "5.3.2"
description = "Extensible memoizing collections and decorators"
optional = false
python-versions = ">=3.7"
files = [
- {file = "cachetools-5.3.1-py3-none-any.whl", hash = "sha256:95ef631eeaea14ba2e36f06437f36463aac3a096799e876ee55e5cdccb102590"},
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+ {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
]
[[package]]
@@ -158,75 +146,63 @@ files = [
[[package]]
name = "cffi"
-version = "1.15.1"
+version = "1.16.0"
description = "Foreign Function Interface for Python calling C code."
optional = false
-python-versions = "*"
+python-versions = ">=3.8"
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[[package]]
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optional = false
python-versions = ">=3.7.0"
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[[package]]
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symfont = ["sympy"]
type1 = ["xattr"]
ufo = ["fs (>=2.2.0,<3)"]
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optional = false
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+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
[[package]]
name = "jinja2"
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[[package]]
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[[package]]
name = "zipp"
-version = "3.16.2"
+version = "3.17.0"
description = "Backport of pathlib-compatible object wrapper for zip files"
optional = false
python-versions = ">=3.8"
files = [
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]
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
[metadata]
lock-version = "2.0"
python-versions = ">3.9,<3.12"
-content-hash = "d21a07b03df50b2ec6ef31640ba9a6f38c2b8a2ad5d1ce338909f97f25335768"
+content-hash = "41f0a87eb0875f8dea1d122a32c86b5d8ae444bbfa046268f85dc1a8c2e626b1"
diff --git a/pyproject.toml b/pyproject.toml
index 6f9bda4..27f5026 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ authors = ["The Qibo team"]
license = "Apache License 2.0"
readme = "README.md"
repository = "https://github.com/qiboteam/qibochem/"
-documentation = ""
+documentation = "https://qibo.science/qibochem/latest/"
keywords = []
classifiers = [
"Programming Language :: Python :: 3",
@@ -16,7 +16,7 @@ packages = [{ include = "qibochem", from = "src" }]
[tool.poetry.dependencies]
python = ">3.9,<3.12"
-qibo = "^0.1.10"
+qibo = ">0.1.10"
openfermion = "^1.5"
pyscf = "^2.3.0"
scipy = "^1.10.1"
diff --git a/src/qibochem/__init__.py b/src/qibochem/__init__.py
index 47bcd18..362d74a 100644
--- a/src/qibochem/__init__.py
+++ b/src/qibochem/__init__.py
@@ -1 +1 @@
-__version__ = "0.0.1.dev0"
+__version__ = "0.0.1"