Merge pull request #68 from CMT-MU/develop

Releasing for 1.1.30

.gitignore

@@ -1,104 +1,102 @@
-# Byte-compiled / optimized / DLL files
+# Compiled source #
+###################
+*.pyc
+*.pyd
+*.so
+*.o
 __pycache__/
-*.py[cod]
-*$py.class
 
-# C extensions
-*.so
+# Cython generated files #
+##########################
+#pymeshfix/cython/_meshfix.cpp
+
+# OS generated files #
+######################
+.fuse_hidden*
+*~
 
-# Distribution / packaging
-.Python
-env/
+# Pip generated folders #
+#########################
+*.egg-info/
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
 
-# Translations
-*.mo
-*.pot
+# MISC #
+########
+.mypy_cache
+
+
+# doc generated #
+#################
+docs/_build
+_build
 
-# Django stuff:
-*.log
-local_settings.py
+# testing coverage and cache #
+##############################
+.pytest_cache/
+tests/.coverage
+tests/htmlcov/
 
-# Flask stuff:
-instance/
-.webassets-cache
+# windows #
+###########
+test.bat
 
-# Scrapy stuff:
-.scrapy
+# Jupyter notebook cache #
+##########################
+**/.ipynb_checkpoints
 
-# Sphinx documentation
-docs/_build/
+# Code coverage results #
+#########################
+htmlcov
+.coverage
+*,cover
 
-# PyBuilder
-target/
+# Mac #
+#######
+.DS_Store
+**/.DS_Store
 
-# IPython Notebook
-.ipynb_checkpoints/
+# Testing output #
+##################
+tests/ERROR_OUTPUT.txt
 
-# pyenv
-.python-version
+# hypothesis #
+##############
+.hypothesis
 
-# celery beat schedule file
-celerybeat-schedule
+# emacs #
+#########
+*#
+.#
+flycheck*
 
-# dotenv
-.env
+# vim #
+#######
+*.swp
 
-# virtualenv
-.venv/
-venv/
-ENV/
+# benchmark cache from pytest-benchmark #
+#########################################
+.benchmarks
 
-# Spyder project settings
-.spyderproject
+# PyCharm #
+###########
+.idea/
 
-# Rope project settings
-.ropeproject
+# virtual environments #
+########################
+venv/
+.venv/
 
-# MacOS
-.DS_Store
+# VSCode #
+##########
+.vscode/
 
-# latex
+# LaTeX #
+#########
 .dvi
 .fdb_latexmk
 .fls
 .aux
 .log
 .out
 .synctex.gz
-
-.vscode

docs/Makefile

@@ -0,0 +1,8 @@
+build:
+	jupyter book build --all -v .
+
+upload:	build
+	ghp-import -n -p -f _build/html
+
+clean:
+	rm -rf _build

docs/README.md

@@ -0,0 +1,31 @@
+# [QtDraw](https://cmt-mu.github.io/QtDraw/)
+
+3D drawing tool for molecules and crystals based on [PyVista](https://docs.pyvista.org/) and [Qt](https://www.riverbankcomputing.com/static/Docs/PyQt5/#).
+Drawings are associated with crystallographic symmetry operations provided by [MultiPie](https://github.com/CMT-MU/MultiPie).
+
+- **Authors**: Hiroaki Kusunose
+
+- **Citing QtDraw and MultiPie**: If you are using QtDraw and/or MultiPie in your scientific research, please help our scientific visibility by citing our work:
+    > Hiroaki Kusunose, Rikuto Oiwa, and Satoru Hayami, Symmetry-adapted modeling for molecules and crystals, Phys. Rev. B <b>107</b>, 195118 (2023).<br>
+    > DOI: [https://doi.org/10.1103/PhysRevB.107.195118](https://doi.org/10.1103/PhysRevB.107.195118)
+
+- **Installation**: QtDraw can be installed from PyPI using pip on Python >= 3.9:
+    ```
+    pip install qtdraw
+    ```
+    - It is useful to associate with the following application with `.qtdw` and `.cif` extension.
+      - [Mac](https://github.com/CMT-MU/QtDraw/tree/main/others/QtDraw_MacApp.zip)
+      - [Windows](https://github.com/CMT-MU/QtDraw/tree/main/others/QtDraw_WinApp.zip)
+    - You can also visit [PyPI](https://pypi.org/project/qtdraw/) or [GitHub](https://github.com/CMT-MU/QtDraw) to download the source.
+    - See also, [Install Guide (in Japanese)](./src/install_guide.pdf)
+    - Shell command `qtdraw [filename]` is available.
+
+- **Requirements**:
+  - This library requires [TeXLive](https://www.tug.org/texlive/) environment.
+  - Symmetry operation supports are provided by [MultiPie](https://github.com/CMT-MU/MultiPie).
+
+- **See also**:
+  - [Manual (QtDraw and MultiPie)](https://github.com/CMT-MU/QtDraw/blob/main/docs/manual.pdf).
+  - [MyST syntax cheat sheet](https://jupyterbook.org/en/stable/reference/cheatsheet.html)
+  - [MultiPie tutorial (in Japanese)](https://cmt-mu.github.io/MultiPieTutorial/)
+  - [QtDraw tutorial (in Japanese)](https://cmt-mu.github.io/QtDrawTutorial/)

docs/_config.yml

@@ -1,5 +1,91 @@
-remote_theme: pages-themes/cayman@v0.2.0
-plugins:
-- jekyll-remote-theme # add this line to the plugins list if you already have one
+# Learn more at https://jupyterbook.org/customize/config.html
+
+# ==================================================
+# Book settings
 title: QtDraw
-description: 3D drawing tool for molecules and crystals based on PyVista and Qt.
+author: Hiroaki Kusunose
+copyright: '2021-2024'
+logo: qtdraw_logo.png
+
+# ==================================================
+# Execution settings
+execute:
+  execute_notebooks: cache
+  stderr_output: "remove"
+  allow_errors: true
+  timeout: 120
+
+# ==================================================
+# Parse and render settings
+parse:
+  myst_substitutions:
+      sub3: My _global_ value!
+  myst_enable_extensions:
+    - amsmath
+    - colon_fence
+    - deflist
+    - dollarmath
+    - html_admonition
+    - html_image
+    - linkify
+    - replacements
+    - smartquotes
+    - substitution
+
+# ==================================================
+# HTML-specific settings
+html:
+  home_page_in_navbar: false
+  use_edit_page_button: false
+  use_repository_button: true
+  use_issues_button: false
+  collapse_navigation: true
+
+# ==================================================
+# LaTeX-specific settings
+latex:
+  latex_engine: "xelatex"
+  latex_documents:
+    targetname: book.tex
+
+bibtex_bibfiles:
+  - "references.bib"
+
+# ==================================================
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/CMT-MU/QtDraw.git
+  branch: main
+
+# ==================================================
+# Sphinx setting
+sphinx:
+  root_doc: "README.md"
+  recursive_update: true
+  extra_extensions:
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.napoleon'
+  - 'sphinx.ext.viewcode'
+  config:
+    add_module_names: false
+    autodoc_default_options:
+      members: true
+      # member-order: 'bysource'
+      undoc-members": false
+      show-inheritance: true,
+      special-members: '__init__'
+    html_theme: sphinx_book_theme
+    html_theme_options:
+      show_prev_next: false
+      navigation_with_keys: false
+    html_show_sourcelink: false
+    html_copy_source : false
+    bibtex_reference_style: label
+    bibtex_default_style: "unsrt"
+    language: jp
+    mathjax_path: "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
+    mathjax3_config:
+      loader:
+        load: ['[tex]/physics']
+      tex:
+        packages: { '[+]': ['physics'] }

docs/_toc.yml

@@ -0,0 +1,13 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: README
+parts:
+- caption: Feature
+  chapters:
+    - file: src/object
+    - file: src/api
+- caption: Change Log
+  chapters:
+    - file: src/change_log