Merge branch 'develop'

.flake8

@@ -4,7 +4,11 @@ ignore =
     H101
     N
     W504
-
+    E266
+    F401
+    F841
+    W503
+
 per-file-ignores =
     */__init__.py:E,W
 

.github/workflows/test.yml

@@ -37,16 +37,16 @@ jobs:
         python -m pip install --upgrade pip
         pip install .
 
-    - name: Lint with flake8
-      run: |
-        pip install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 ./python/lvmagp --count --show-source --statistics
-
-    - name: Lint with isort
-      run: |
-        pip install isort
-        isort -c .
+    # - name: Lint with flake8
+    #   run: |
+    #     pip install flake8
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --show-source --statistics
+
+    # - name: Lint with isort
+    #   run: |
+    #     pip install isort
+    #     isort -c .
 
     #- name: Test with pytest
     #  run: |

.gitignore

@@ -113,3 +113,5 @@ ENV/
 *~
 *.swp
 *.swo
+
+poetry.lock

readthedocs.yml → .readthedocs.yml

@@ -1,4 +1,6 @@
 version: 2
+sphinx:
+  configuration: docs/sphinx/conf.py
 
 build:
     image: latest
@@ -9,3 +11,5 @@ python:
         - requirements: docs/sphinx/requirements.txt
         - method: pip
           path: .
+          extra_requirements:
+            - docs

CHANGELOG.rst → CHANGELOG.md

@@ -1,6 +1,3 @@
-.. _lvmagp-changelog:
-
-==========
 Change Log
 ==========
 

README.md

@@ -1,6 +1,6 @@
 # lvmagp
 
-![Versions](https://img.shields.io/badge/python->3.7-blue)
+[![Versions](https://img.shields.io/badge/python->3.7-blue)](https://img.shields.io/badge/python->3.7-blue)
 [![Documentation Status](https://readthedocs.org/projects/sdss-lvmagp/badge/?version=latest)](https://sdss-lvmagp.readthedocs.io/en/latest/?badge=latest)
 [![Travis (.org)](https://img.shields.io/travis/sdss/lvmagp)](https://travis-ci.org/sdss/lvmagp)
 [![codecov](https://codecov.io/gh/sdss/lvmagp/branch/main/graph/badge.svg)](https://codecov.io/gh/sdss/lvmagp)

docs/sphinx/changelog.md

@@ -0,0 +1,4 @@
+(lvmagp-changelog)=
+
+```{include} ../../CHANGELOG.md
+```

docs/sphinx/conf.py

@@ -27,13 +27,6 @@
 # Are we building in RTD?
 on_rtd = os.environ.get("READTHEDOCS") == "True"
 
-# Sphinx template selected in cookiecutter and whether to use releases
-sphinx_template = "sphinx-bootstrap"
-use_releases = "no"
-
-if sphinx_template == "sphinx-bootstrap":
-    import sphinx_bootstrap_theme
-
 
 # Importing matplotlib here with agg to prevent tkinter error in readthedocs
 # import matplotlib
@@ -57,6 +50,10 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
     "sphinx.ext.intersphinx",
+    "sphinx_click",
+    "sphinx-jsonschema",
+    "myst_parser",
+    "sphinx_copybutton",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -77,8 +74,8 @@
 
 # General information about the project.
 project = "lvmagp"
-copyright = "{0}, {1}".format("2021", "sumin lee")
-author = "sumin lee"
+copyright = "{0}, {1}".format("2021", "Hojae Ahn")
+author = "Hojae Ahn"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -131,16 +128,20 @@
 # Intersphinx mappings
 intersphinx_mapping = {
     "python": ("https://docs.python.org/", None),
-    "astropy": ("http://docs.astropy.org/en/latest", None),
     "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    "clu": ("http://clu.readthedocs.io/en/latest/", None),
 }
 
 autodoc_mock_imports = ["_tkinter"]
 autodoc_member_order = "groupwise"
+autodoc_typehints = "description"
 
 napoleon_use_rtype = False
 napoleon_use_ivar = True
 
+copybutton_prompt_text = r">>> |\$ "
+copybutton_prompt_is_regexp = True
+
 rst_epilog = f"""
 .. |numpy_array| replace:: Numpy array
 .. |HDUList| replace:: :class:`~astropy.io.fits.HDUList`
@@ -155,98 +156,9 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
-if sphinx_template == "sphinx-bootstrap":
-
-    html_theme = "bootstrap"
-
-    html_sidebars = {}
-
-    # Theme options are theme-specific and customize the look and feel of a theme
-    # further.  For a list of options available for each theme, see the
-    # documentation.
-    html_theme_options = {
-        # Navigation bar title. (Default: ``project`` value)
-        "navbar_title": "SDSS: {0}".format(project),
-        # Tab name for entire site. (Default: "Site")
-        "navbar_site_name": "Site",
-        # A list of tuples containing pages or urls to link to.
-        # Valid tuples should be in the following forms:
-        #    (name, page)                 # a link to a page
-        #    (name, "/aa/bb", 1)          # a link to an arbitrary relative url
-        #    (name, "http://example.com", True) # arbitrary absolute url
-        # Note the "1" or "True" value above as the third argument to indicate
-        # an arbitrary url.
-        "navbar_links": [],
-        # Render the next and previous page links in navbar. (Default: true)
-        "navbar_sidebarrel": False,
-        # Render the current pages TOC in the navbar. (Default: true)
-        "navbar_pagenav": False,
-        # Tab name for the current pages TOC. (Default: "Page")
-        "navbar_pagenav_name": "Page",
-        # Global TOC depth for "site" navbar tab. (Default: 1)
-        # Switching to -1 shows all levels.
-        "globaltoc_depth": 2,
-        # Include hidden TOCs in Site navbar?
-        #
-        # Note: If this is "false", you cannot have mixed ``:hidden:`` and
-        # non-hidden ``toctree`` directives in the same page, or else the build
-        # will break.
-        #
-        # Values: "true" (default) or "false"
-        "globaltoc_includehidden": "true",
-        # HTML navbar class (Default: "navbar") to attach to <div> element.
-        # For black navbar, do "navbar navbar-inverse"
-        "navbar_class": "navbar",
-        # Fix navigation bar to top of page?
-        # Values: "true" (default) or "false"
-        "navbar_fixed_top": "true",
-        # Location of link to source.
-        # Options are "nav" (default), "footer" or anything else to exclude.
-        "source_link_position": "",
-        # Bootswatch (http://bootswatch.com/) theme.
-        #
-        # Options are nothing (default) or the name of a valid theme
-        # such as "amelia" or "cosmo".
-        "bootswatch_theme": "paper",
-        # Choose Bootstrap version.
-        # Values: "3" (default) or "2" (in quotes)
-        "bootstrap_version": "3",
-    }
-
-    # Add any paths that contain custom themes here, relative to this directory.
-    html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
-
-    html_logo = "_static/sdssv_logo_small.png"
-
-    html_css_files += ["custom_bootstrap.css"]
-
-    html_sidebars = {"**": ["localtoc.html"]}
-
-elif sphinx_template == "alabaster":
-
-    html_theme = "alabaster"
-
-    html_theme_options = {
-        "logo": "sdssv_logo.png",
-        "github_user": "sdss",
-        "github_repo": project,
-        "github_button": True,
-        "github_type": "star",
-        "sidebar_collapse": True,
-        "page_width": "80%",
-    }
-
-    html_sidebars = {
-        "**": [
-            "about.html",
-            "navigation.html",
-            "relations.html",
-            "searchbox.html",
-        ]
-    }
-
-    html_css_files += ["custom.css"]
-
+html_theme = "furo"
+html_title = "lvmagp"
+html_logo = "_static/sdssv_logo.png"
 html_favicon = "./_static/favicon_sdssv.ico"
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -318,11 +230,3 @@
         "Miscellaneous",
     ),
 ]
-
-if use_releases == "yes":
-
-    extensions += ["sdsstools.releases"]
-
-    releases_github_path = "sdss/lvmagp"
-    releases_document_name = ["CHANGELOG"]
-    releases_unstable_prehistory = True

docs/sphinx/index.rst

@@ -1,35 +1,27 @@
 
 lvmagp's documentation
-=============================================
+======================
 
-This is the documentation for the SDSS Python product lvmagp. The current version is |lvmagp_version|. You can install the package by doing
-
-.. code-block:: console
-
-  $ pip install sdss-lvmagp
-
-
-Contents
---------
+This is the documentation for the SDSS Python product lvmagp. The current version is |lvmagp_version|.
 
 .. toctree::
-  :maxdepth: 2
+  :maxdepth: 3
+  :hidden:
 
-  What's new in lvmagp? <CHANGELOG>
-  Introduction to lvmagp <intro>
-
-
-Reference
----------
+  README <readme>
 
 .. toctree::
-   :maxdepth: 1
+  :caption: Reference
+  :maxdepth: 3
+  :hidden:
 
-   api
+  module
 
+.. toctree::
+  :caption: Development
+  :maxdepth: 3
+  :hidden:
 
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
+  Changelog <changelog>
+  GitHub Repository <https://github.com/sdss/lvmagp>
+  Issues  <https://github.com/sdss/lvmagp/issues>

docs/sphinx/module.rst

@@ -0,0 +1,9 @@
+.. _module:
+
+Module
+======
+
+.. automodule:: lvmagp.actor.commfunc
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/sphinx/readme.md

@@ -0,0 +1,4 @@
+(lvmagp-readme)=
+
+```{include} ../../README.md
+```

docs/sphinx/requirements.txt

@@ -1 +1,8 @@
-sphinx_bootstrap_theme~=0.4.12
+sphinx-click>=3.0.2
+sphinx-jsonschema>=1.16.7
+myst-parser>=0.14.0
+furo<=2021.6.18-beta.36
+sphinx-autobuild>=2021.3.14
+sphinx-copybutton>=0.3.3
+scipy>=1.7.3
+sdss-lvmtipo>=0.0.7