diff --git a/.gitignore b/.gitignore index 198af6f..bb9305f 100644 --- a/.gitignore +++ b/.gitignore @@ -32,4 +32,10 @@ MANIFEST # perso dev **/*.egg-info -.idea \ No newline at end of file +.idea + +## docs +docs/_build +docs/md/generated +_docs +**/.ipynb_checkpoints diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..3c598b7 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,15 @@ +version: 2 + +build: + os: "ubuntu-22.04" + tools: + python: "3.8" + jobs: + post_create_environment: + - pip install poetry + - poetry config virtualenvs.create false + post_install: + - poetry install --with docs + +sphinx: + configuration: docs/conf.py \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/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) diff --git a/docs/_static/logo.png b/docs/_static/logo.png new file mode 100644 index 0000000..0af4ada Binary files /dev/null and b/docs/_static/logo.png differ diff --git a/docs/_static/style.css b/docs/_static/style.css new file mode 100644 index 0000000..4e72abe --- /dev/null +++ b/docs/_static/style.css @@ -0,0 +1,190 @@ +:root { + /* --pst-color-inline-code: 33, 125, 224; */ + --mystnb-source-margin-color: darkgrey; + --pst-color-secondary: var(--pst-color-primary) !important; + --pst-color-link-hover: var(--pst-color-primary) !important; +} + +html { + --pst-color-secondary: var(--pst-color-primary) !important; + --pst-color-inline-code: #e5448b !important; + --pst-color-inline-code-links: var(--pst-color-primary) !important; +} + + +/* Block read write */ + +.blockread, +.blockwrite, +.blockmodify { + width: 50px; + text-align: center; + border-radius: 9px; + font-size: 13px; + margin-bottom: 0px; + padding: 2px 6px 2px 6px; + /* margin-right: 5px; */ + opacity: 85%; +} + +.blockread { + color: rgb(65, 65, 65); + background-color: rgba(65, 65, 65, 0.082); + border-color: rgb(65, 65, 65); +} + +.blockwrite { + color: rgb(76, 120, 201); + background-color: rgb(76, 120, 201, 0.082); + border-color: rgb(76, 120, 201); +} + +.blockmodify { + color: rgb(201, 84, 76); + background-color: rgb(201, 84, 76, 0.082); + border-color: rgb(201, 84, 76); +} + + +/* Headings */ + +h2 { + text-decoration: underline; + font-size: 22px; +} + + +/* Code cells */ + +.highlight pre { + line-height: 20px !important; + font-weight: 500 !important; + font-family: ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, Liberation Mono, monospace !important; + font-size: 13px; +} + +div.cell_output pre { + background-color: white !important; +} + +.highlight pre { + padding: 12px !important; +} + + +/* no cell number */ + +.prompt { + display: none !important; +} + +.rst-content code.literal { + color: #575757 +} + +.docutils.literal.notranslate pre { + color: #575757 +} + +.xr-attrs dt { + background: inherit !important; + color: inherit !important; + border-top: inherit !important; +} + +div.nboutput.container div.output_area>div { + text-align: left !important; +} + +div.nboutput.container div.output_area { + text-align: center !important; +} + +.highlight .nn { + color: black !important; + font-weight: normal !important; +} + +.highlight .kn, +.highlight .k, +.highlight .kc, +.highlight .ow { + color: #d73a49 !important; + font-weight: normal !important; +} + +.highlight .mi, +.highlight .mf, +.highlight .nb, +.highlight .bp { + color: #005cc5 !important +} + +.highlight .c1, +.highlight .o { + color: #6a737d !important +} + +.highlight .sa, +.highlight .sé, +.highlight .s2, +.highlight .sd { + color: #032f62 !important +} + +.highlight .nd { + color: #005cc5 !important; + font-weight: normal !important; +} + +.highlight .p, +.highlight .mi, +.highlight .mf { + font-weight: normal !important; +} + +.highlight .si { + color: #70a0d0 !important; +} + +/* code, +code span.pre { + background: none; + color: var(--color-brand-primary) +} */ + +/* Dataframe */ + +.cell_output .dataframe { + font-size: 0.85em; + width: 100%; +} + +/* prose logo font */ +.navbar-brand.logo .logo__title { + font-style: italic; + font-weight: bold; + font-family: Georgia, 'Times New Roman', Times, serif; + color: #404040; + font-size: 2rem; +} + +.version-nb { + margin-top: -12px; + font-style: italic; + font-weight: bold; + color: var(--pst-color-primary); + font-size: 15px; +} + +.navbar-brand:hover { + text-decoration: none !important; +} + +nav.bd-links li>a:hover { + text-decoration: none; +} + +/* nav.bd-links .current > a { +box-shadow: none; +} */ \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..f353c56 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,99 @@ +# 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 ----------------------------------------------------- + +project = "verse" +copyright = "2023, Mathilde Timmermans" +author = "Mathilde Timmermans" + + +# -- 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_nb", + "sphinx_copybutton", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.autosummary", + "sphinx_design", +] + + +# 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 = "sphinx_book_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"] + +# Title +# get version number from pyproject.toml +# -------------------------------------- +import toml + +pyproject = toml.load("../pyproject.toml") +version = pyproject["tool"]["poetry"]["version"] +html_short_title = "verse" +html_title = f"{html_short_title}" +# ----- + +source_suffix = { + ".rst": "restructuredtext", + ".ipynb": "myst-nb", + ".myst": "myst-nb", +} + +root_doc = "index" + +html_theme_options = { + "repository_url": "https://github.com/mathtimm/verse", + "use_repository_button": True, +} + +nb_render_image_options = {"align": "center"} + +myst_enable_extensions = [ + "dollarmath", +] + +templates_path = ["_templates"] +nb_execution_mode = "auto" +nb_execution_raise_on_error = True +remove_code_source = True + +html_css_files = ["style.css"] + +autodoc_typehints = "signature" +autoclass_content = "both" diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..23fd40c --- /dev/null +++ b/docs/index.md @@ -0,0 +1,31 @@ +--- +sd_hide_title: true +--- + +# verse + +```{image} _static/logo.png +:width: 400px +:align: center +``` + + verse is an extension of the prose package for TESS follow-up observations and results reporting. + It gives access to additional features and properties specific to TESS Objects of Interest observations. +A built-in function allows the user to model quickly the transit by making use of the exoplanet and pymc3 packages and by retrieving priors directly from the TESS Transit Finder and the ExoFOP database. +verse creates observation reports and uploads the files directly onto ExoFOP for registered members of the TESS Follow-Up Observing Program (TFOP). + +```{toctree} +:maxdepth: 0 +:caption: Get started + +md/installation +ipynb/quickstart +ipynb/acknowledgement +``` + +```{toctree} +:maxdepth: 0 +:caption: Tutorials + +ipynb/photometry +``` diff --git a/docs/ipynb/photometry.ipynb b/docs/ipynb/photometry.ipynb new file mode 100644 index 0000000..5e59ed8 --- /dev/null +++ b/docs/ipynb/photometry.ipynb @@ -0,0 +1,24 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Photomerty" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..153be5e --- /dev/null +++ b/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 + +if "%1" == "" goto help + +%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 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/md/installation.md b/docs/md/installation.md new file mode 100644 index 0000000..f9c0bc7 --- /dev/null +++ b/docs/md/installation.md @@ -0,0 +1,20 @@ +# Installation + +## Using pip + +The easiest way to install the most recent stable version of `verse` is +with [pip](https://pip.pypa.io): + +```bash +python -m pip install verse +``` + +## From source + +Alternatively, you can get the source: + +```bash +git clone https://github.com/mathtimm/verse +cd verse +python -m pip install -e . +``` diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..636c2b5 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,31 @@ +[tool.poetry] +name = "verse" +version = "0.0.1" +description = "Annex to prose package for TESS reporting" +authors = ["Mathilde Timmermans"] +license = "MIT" +readme = "README.md" +homepage = "https://github.com/mathtimm/verse" + +[tool.poetry.dependencies] +prose = "^3.0.0" + +[tool.poetry.group.dev.dependencies] +pytest = "*" +black = "*" + +[tool.poetry.group.docs.dependencies] +sphinx = "*" +docutils = "*" +jupyterlab = "*" +myst-parser = "*" +sphinx-book-theme = "^1.0.0" +myst-nb = "*" +sphinx-copybutton = "*" +sphinx-design = "*" +toml = "*" +ipywidgets = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/setup.py b/setup.py deleted file mode 100644 index 53bca46..0000000 --- a/setup.py +++ /dev/null @@ -1,48 +0,0 @@ -from pathlib import Path -from setuptools import find_packages, setup - -HERE = Path(__file__).parent -README = (HERE / "README.md").read_text(encoding='utf-8') - -setup( - name="verse", - version="0.0.1", - author="Mathilde Timmermans", - description="Annex to prose package for TESS reporting", - packages=find_packages(exclude=["test"]), - #include_package_data = True, - license="MIT", - url="https://github.com/mathtimm/verse", - # entry_points=""" - # [console_scripts] - # prose=main:cli - # """, - long_description=README, - long_description_content_type="text/markdown", - install_requires=[ - "prose", - "exoplanet", - "pymc3", - "pymc3_ext", - "corner" - ], - extras_require={ - 'docs': [ - "sphinx", - "nbsphinx", - "jupyter-sphinx", - "sphinx_rtd_theme", - "sphinx-copybutton", - "docutils", - "jupyterlab", - "myst-parser", - "twine", - ] - }, - zip_safe=True, - classifiers=[ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", - ], -)