Merge pull request #6 from ericpre/setup_docs_build

Setup docs build

.github/workflows/build.yml

@@ -56,10 +56,6 @@ jobs:
         run: |
           ls -R
 
-      - name: Install HyperSpy (dev)
-        run: |
-          pip install https://github.com/hyperspy/hyperspy/archive/refs/heads/RELEASE_next_major.zip
-
       - name: Install distribution
         run: |
           pip install --pre --find-links dist holospy[tests]

.github/workflows/tests.yml

@@ -34,11 +34,6 @@ jobs:
           python --version
           pip --version
 
-      - name: Install (HyperSpy dev)
-        # Need to install hyperspy dev until hyperspy 2.0 is released
-        run: |
-          pip install https://github.com/hyperspy/hyperspy/archive/refs/heads/RELEASE_next_major.zip
-
       - name: Install
         shell: bash
         run: |

.gitignore

@@ -1,8 +1,8 @@
-/docs/_build/*
+/doc/_build/*
 /build/*
 /dist/*
 /holospy.egg-info/*
 *__pycache__*
 *pyd
 .spyproject/*
-.idea
+.idea

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - htmlzip
+
+python:
+   install:
+      - method: pip
+        path: .
+        extra_requirements:
+           - doc

CHANGES.rst

@@ -0,0 +1,20 @@
+Changelog
+*********
+
+Changelog entries for the development version are available at
+https://holospy.readthedocs.io/en/latest/changes.html
+
+0.1.dev0 (UNRELEASED)
+=====================
+
+- Add pre-commit configuration file (`#4 <https://github.com/hyperspy/holospy/pull/4>`_)
+- Format code using ``black`` and add workflow to check formatting (`#3 <https://github.com/hyperspy/holospy/pull/3>`_).
+- Add GitHub workflows to tests and build packages (`#2 <https://github.com/hyperspy/holospy/pull/2>`_).
+
+Initiation (2023-07-23)
+=======================
+
+- HoloSpy was split out of the `HyperSpy repository
+  <https://github.com/hyperspy/hyperspy>`_ on July 23, 2023. The electron
+  holography functionalities so far developed in HyperSpy were moved to the
+  `HoloSpy repository <https://github.com/hyperspy/holospy>`_.

CONTRIBUTING.rst

@@ -0,0 +1,104 @@
+.. _contributing_label:
+
+Contributing
+************
+
+HoloSpy is meant to be a community maintained project. We welcome contributions
+in the form of bug reports, documentation, code, feature requests, and more.
+In the following we refer to some resources to help you make useful contributions.
+
+Issues
+======
+
+The `issue tracker <https://github.com/hyperspy/holospy/issues>`_ can be used to
+report bugs or propose new features. When reporting a bug, the following is
+useful:
+
+- give a minimal example demonstrating the bug,
+- copy and paste the error traceback.
+
+Pull Requests
+=============
+
+If you want to contribute to the HoloSpy source code, you can send us a
+`pull request <https://github.com/hyperspy/holospy/pulls>`_. Small bug fixes or
+corrections to the user guide are typically a good starting point. But don't
+hesitate also for significant code contributions - if needed, we'll help you
+to get the code ready to common standards.
+
+Please refer to the
+`HyperSpy developer guide <http://hyperspy.org/hyperspy-doc/current/dev_guide/intro.html>`_
+in order to get started and for detailed contributing guidelines.
+
+The :doc:`kikuchipy contributors guide <kikuchipy:dev/index>`, another HyperSpy
+extension, also is a valuable resource that can get you started and provides useful
+guidelines.
+
+Reviewing
+---------
+
+As quality assurance, to improve the code, and to ensure a generalized
+functionality, pull requests need to be thoroughly reviewed by at least one
+other member of the development team before being merged.
+
+Documentation
+=============
+
+The HoloSpy documentation consists of three elements:
+
+- Docstrings following the `numpy standard
+  <https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard>`_
+  that document the functionality of individual methods on `GitHub
+  <https://github.com/hyperspy/holospy>`_.
+- The `documentation <https://holospy.readthedocs.io>`_ written using `Sphinx
+  <https://www.sphinx-doc.org>`_ and hosted on `Read the Docs
+  <https://holospy.readthedocs.io>`_. The source is part of the `GitHub repository
+  <https://github.com/hyperspy/holospy/tree/main/doc>`_.
+- Jupyter notebooks in the `HoloSpy demos repository
+  <https://github.com/hyperspy/holospy-demos>`_ on GitHub that provide tutorials and example
+  workflows.
+
+Improving documentation is always welcome and a good way of starting out to learn the GitHub
+functionality. You can contribute through pull requests to the respective repositories.
+
+Code style
+==========
+
+HoloSpy follows `Style Guide for Python Code <https://www.python.org/dev/peps/pep-0008/>`_
+with `The Black Code style
+<https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html>`_.
+
+For `docstrings <https://www.python.org/dev/peps/pep-0257/>`_, we follow the `numpydoc
+<https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard>`_ standard.
+
+Package imports should be structured into three blocks with blank lines between
+them:
+
+- standard libraries (like ``os`` and ``typing``),
+- third party packages (like ``numpy`` and ``hyperspy``),
+- and finally ``holospy`` imports.
+
+Writing tests
+=============
+
+All functionality in HoloSpy is tested via the `pytest <https://docs.pytest.org>`_
+framework. The tests reside in the ``test`` directory. Tests are short methods that call
+functions in HoloSpy and compare resulting output values with known answers.
+Please refer to the `HyperSpy development guide
+<https://hyperspy.org/hyperspy-doc/current/dev_guide/testing.html>`_ for further
+information on tests.
+
+Releasing a new version
+=======================
+
+HoloSpy versioning follows `semantic versioning <https://semver.org/spec/v2.0.0.html>`_
+and the version number is therefore a three-part number: MAJOR.MINOR.PATCH.
+Each number will change depending on the type of changes according to the following:
+
+- MAJOR increases when making incompatible API changes,
+- MINOR increases when adding functionality in a backwards compatible manner, and
+- PATCH increases when making backwards compatible bug fixes.
+
+The process to release a new version that is pushed to `PyPI <https://pypi.org>`_ and
+`Conda-Forge <https://conda-forge.org/>`_ is documented in the `Releasing guide
+<https://github.com/hyperspy/holospy/blob/main/releasing_guide.md>`_.

README.md

@@ -0,0 +1,13 @@
+
+HoloSpy is a Python package extending the functionality for multi-dimensional
+data analysis provided by the [HyperSpy](https://hyperspy.org) library. It is
+aimed at helping with the analysis of (off-axis) electron holography data.
+
+Go to the documentation for instructions on how to install HoloSpy and start an
+analysis: [Read the docs](https://holospy.readthedocs.io).
+
+Everyone is welcome to contribute. Please read our
+[contributing guidelines](https://github.com/hyperspy/holospy/blob/main/CONTRIBUTING.rst) and get started!
+
+Development of HoloSpy is documented in the
+[changelog](https://github.com/hyperspy/holospy/blob/main/CHANGES.rst).

doc/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)

doc/api/datasets.rst

@@ -0,0 +1,5 @@
+:mod:`holospy.datasets`
+-----------------------
+
+.. automodule:: holospy.datasets
+   :members:

doc/api/index.rst

@@ -0,0 +1,14 @@
+.. _reference:
+
+#########
+Reference
+#########
+
+.. toctree::
+   :caption: API Reference
+   :maxdepth: 2
+
+   datasets
+   reconstruct
+   signals
+   tools

doc/api/reconstruct.rst

@@ -0,0 +1,5 @@
+:mod:`holospy.reconstruct`
+--------------------------
+
+.. automodule:: holospy.reconstruct
+   :members:

doc/api/signals.rst

@@ -0,0 +1,5 @@
+:mod:`holospy.signals.hologram_image`
+-------------------------------------
+
+.. automodule:: holospy.signals.hologram_image
+   :members:

doc/api/tools.rst

@@ -0,0 +1,5 @@
+:mod:`holospy.tools`
+--------------------------
+
+.. automodule:: holospy.tools
+   :members:

doc/changes.rst

@@ -0,0 +1,3 @@
+.. This is a stub, see the top level CHANGELOG.rst file for the changelog.
+
+.. include:: ../CHANGES.rst

doc/citing.rst

@@ -0,0 +1,15 @@
+Citing HoloSpy
+**************
+
+HoloSpy is maintained by the HyperSpy community
+<https://github.com/hyperspy/holospy/contributors>`_.
+
+If HoloSpy has been significant to a project that leads to an academic
+publication, please acknowledge that fact by citing it. The DOI in the
+badge below is the `Concept DOI <https://help.zenodo.org/fag/#versioning>`_ --
+it can be used to cite the project without referring to a specific
+version. If you are citing HoloSpy because you have used it to process data,
+please use the DOI of the specific version that you have employed. You can
+find it by clicking on the DOI badge below:
+
+To be updated after first release.

doc/conf.py

@@ -0,0 +1,107 @@
+# 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('.'))
+
+import numpydoc
+from packaging.version import Version
+
+# -- Project information -----------------------------------------------------
+
+project = "HoloSpy"
+copyright = "2023, HyperSpy Developers"
+author = "HyperSpy Developers"
+
+
+# -- 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 = [
+    # numpydoc is necessary to parse the docstring using sphinx
+    # otherwise the nitpicky option will raise many warnings
+    # "numpydoc",
+    "sphinx_favicon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+]
+
+intersphinx_mapping = {
+    "dask": ("https://docs.dask.org/en/latest", None),
+    "hyperspy": ("https://hyperspy.org/hyperspy-doc/current/", None),
+    "kikuchipy": ("https://kikuchipy.org/en/latest/", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "python": ("https://docs.python.org/3", None),
+}
+
+# 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 = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- 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 = "pydata_sphinx_theme"
+
+# 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_theme_options = {
+    "github_url": "https://github.com/hyperspy/holospy",
+    "icon_links": [
+        {
+            "name": "Gitter",
+            "url": "https://gitter.im/hyperspy/hyperspy",
+            "icon": "fab fa-gitter",
+        },
+    ],
+    "logo": {
+        "image_light": "_static/hyperspy_logo.png",
+        "image_dark": "_static/hyperspy_logo.png",
+    },
+    "header_links_before_dropdown": 6,
+}
+
+# -- Options for sphinx_favicon extension -----------------------------------
+
+favicons = {"rel": "icon", "href": "logo_sq.svg", "type": "image/svg+xml"}
+
+# Check links to API when building documentation
+nitpicky = False
+# Remove when fixed in hyperspy
+nitpick_ignore_regex = [(r"py:.*", r"hyperspy.api.*")]
+
+# -- Options for numpydoc extension -----------------------------------
+
+numpydoc_xref_param_type = True
+numpydoc_xref_ignore = {"type", "optional", "default", "of"}
+
+if Version(numpydoc.__version__) >= Version("1.6.0rc0"):
+    numpydoc_validation_checks = {"all", "ES01", "EX01", "GL02", "GL03", "SA01", "SS06"}
+
+# def setup(app):
+#     app.add_css_file("custom-styles.css")

doc/contributing.rst

@@ -0,0 +1,3 @@
+.. This is a stub, see the top level CONTRIBUTING.rst file for the changelog.
+
+.. include:: ../CONTRIBUTING.rst