merge

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)

docs/conf.py

@@ -0,0 +1,87 @@
+import datetime
+
+# 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 -----------------------------------------------------
+
+year = datetime.date.today().year
+project = "PyAutoFit"
+copyright = "2020, James Nightingale, Richard Hayes"
+author = "James Nightingale, Richard Hayes"
+
+# The full version, including alpha/beta/rc tags
+release = "0.39.3"
+master_doc = "index"
+
+
+# -- 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 = []
+
+# 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"]
+
+
+sphinx_gallery_conf = {
+    # Remove the "Download all examples" button from the top level gallery
+    "download_all_examples": False,
+    # directory where function granular galleries are stored
+    "backreferences_dir": "api/generated/backreferences",
+    # Modules for which function level galleries are created.
+    "doc_module": "pyautofit",
+    # Insert links to documentation of objects in the examples
+    "reference_url": {"pyautofit": None},
+}
+
+# -- 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_rtd_theme"
+html_last_updated_fmt = "%b %d, %Y"
+html_title = "PyAutoFit"
+html_short_title = "PyAutoFit"
+pygments_style = "default"
+add_function_parentheses = False
+html_show_sourcelink = False
+html_show_sphinx = True
+html_show_copyright = True
+
+html_context = {
+    "menu_links_name": "Repository",
+    # Custom variables to enable "Improve this page"" and "Download notebook"
+    # links
+    "doc_path": "docs",
+    "github_project": "pyautofit",
+    "github_repo": "pyautofit",
+    "github_version": "development",
+}
+
+# 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"]

docs/credits.rst

@@ -0,0 +1,6 @@
+.. _credits:
+
+Credits
+-------
+
+test

docs/howtofit.rst

@@ -0,0 +1,16 @@
+.. _howtofit:
+
+HowToFit Lectures
+------------------
+
+To build a **PyAutoFit** project, the best starting point is the **HowToFit** lecture series on the
+`autofit workspace <https://github.com/Jammy2211/autofit_workspace>`_.
+
+The lectures are provided as Jupyter notebooks - checkout
+`this link <https://github.com/Jammy2211/autofit_workspace/blob/master/howtofit/chapter_1_introduction/tutorial_1_model_mapping/tutorial_1_model_mapping.ipynb>`_
+for an example of the first notebook.
+
+The lectures consists of 1 chapter:
+
+- **Introduction** - How to perform non-linear model-fitting with **PyAutoFit** and write a *phase* module to exploit
+                     **PyAutoFits**'s advanced modeling features.

docs/index.rst

@@ -0,0 +1,19 @@
+.. include:: ../README.rst
+
+.. toctree::
+   :caption: Getting Started:
+   :maxdepth: 2
+   :hidden:
+
+   installation
+   api
+   workspace
+   howtofit
+
+.. toctree::
+   :caption: Getting Involved:
+   :maxdepth: 1
+   :hidden:
+
+   papers
+   credits

docs/installation.rst

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+.. _installation:
+
+Installation
+============
+
+We strive to make **PyAutoFit** as easy to install as possible. However, one of our dependencies, **PyMultiNest**,
+has proven difficult to install on many machines. We therefore recommend users to install **PyAutoFit** via conda
+following the instructions below, which handles the installation of **PyMultiNest**.
+
+Users who wish to install PyAutoFit via pip or fork the respository will need to install **PyMultiNest** manually.
+
+Dependencies
+------------
+
+**PyAutoFit** dependencies can be found in the requirements.txt file and they are automatically installed with
+**PyAutoFit**. The libraries are:
+
+**PyAutoConf** https://github.com/rhayes777/PyAutoConf
+
+**PyMultiNest** http://johannesbuchner.github.io/pymultinest-tutorial/install.html
+
+**Dynesty** https://github.com/joshspeagle/dynesty
+
+**emcee** https://github.com/dfm/emcee
+
+**astropy** https://www.astropy.org/
+
+**GetDist** https://getdist.readthedocs.io/en/latest/
+
+**matplotlib** https://matplotlib.org/
+
+**numpy** https://numpy.org/
+
+**scipy** https://www.scipy.org/
+
+Installation with conda
+-----------------------
+
+We recommend installation using a conda environment as this circumvents a number of compatibility issues when
+installing **PyMultiNest**.
+
+First, install `conda <https://conda.io/miniconda.html>`_.
+
+Create a conda environment:
+
+.. code-block:: bash
+
+    >> conda create -n autofit python=3.7 anaconda
+
+
+Activate the conda environment:
+
+.. code-block:: bash
+
+    conda activate autofit
+
+
+Install multinest:
+
+.. code-block:: bash
+
+    conda install -c conda-forge multinest
+
+
+Install autofit:
+
+.. code-block:: bash
+
+    pip install autofit
+
+
+Clone the autofit workspace & set WORKSPACE environment model:
+
+.. code-block:: bash
+
+    cd /path/where/you/want/autofit_workspace
+    git clone https://github.com/Jammy2211/autofit_workspace
+    export WORKSPACE=/path/to/autofit_workspace/
+
+
+Set PYTHONPATH to include the autofit_workspace directory:
+
+.. code-block:: bash
+
+    export PYTHONPATH=/path/to/autofit_workspace/
+
+Matplotlib uses the default backend on your computer, as set in the config file:
+
+.. code-block:: bash
+
+    autofit_workspace/config/visualize/general.ini
+
+If unchanged, the backend is set to 'default', meaning it will use the backend automatically set up for Python on
+your system.
+
+.. code-block:: bash
+
+    [general]
+    backend = default
+
+There have been reports that using the default backend causes crashes when running the test script below (either the
+code crashes without a error or your computer restarts). If this happens, change the config's backend until the test
+works (TKAgg has worked on Linux machines, Qt5Agg has worked on new MACs). For example:
+
+.. code-block:: bash
+
+    [general]
+    backend = TKAgg
+
+
+You can test everything is working by running the example pipeline runner in the autofit_workspace
+
+.. code-block:: bash
+
+    python3 /path/to/autofit_workspace/runners/beginner/no_fit_light/fit_sie__source_inversion.py
+
+
+Installation with pip
+---------------------
+
+Installation is also available via pip, however there are reported issues with
+installing **PyMultiNest** that can make installation difficult, see
+`here <https://github.com/rhayes777/PyAutoFit/blob/master/INSTALL.notes>`_
+
+If **PyMultiNest** has installed correctly you may install **PyAutoFit** via pip as follows.
+
+.. code-block:: bash
+
+    pip install autofit
+
+Clone autofit workspace & set WORKSPACE enviroment model:
+
+.. code-block:: bash
+
+    cd /path/where/you/want/autofit_workspace
+    git clone https://github.com/Jammy2211/autofit_workspace
+    export WORKSPACE=/path/to/autofit_workspace/
+
+
+Set PYTHONPATH to include the autofit_workspace directory:
+
+.. code-block:: bash
+
+    export PYTHONPATH=/path/to/autofit_workspace
+
+
+Matplotlib uses the default backend on your computer, as set in the config file:
+
+.. code-block:: bash
+
+    autofit_workspace/config/visualize/general.ini
+
+If unchanged, the backend is set to 'default', meaning it will use the backend automatically set up for Python on
+your system.
+
+.. code-block:: bash
+
+    [general]
+    backend = default
+
+There have been reports that using the default backend causes crashes when running the test script below (either the
+code crashes without a error or your computer restarts). If this happens, change the config's backend until the test
+works (TKAgg has worked on Linux machines, Qt5Agg has worked on new MACs). For example:
+
+.. code-block:: bash
+
+    [general]
+    backend = TKAgg
+
+
+You can test everything is working by running the example pipeline runner in the autofit_workspace
+
+You can test everything is working by running the example pipeline runner in the autofit_workspace
+
+.. code-block:: bash
+
+    python3 /path/to/autofit_workspace/runners/beginner/no_fit_light/fit_sie__source_inversion.py
+
+Forking / Cloning
+-----------------
+
+Alternatively, you can fork or clone the **PyAutoFit** github repository. Note that **PyAutoFit** requires a valid
+config to run. Therefore, if you fork or clone the **PyAutoFit** repository, you need the
+`autofit_workspace <https://github.com/Jammy2211/autofit_workspace>`_ with the PYTHONPATH and WORKSPACE environment
+variables set up as described on the `autofit_workspace <https://github.com/Jammy2211/autofit_workspace>`_ repository
+or the installation instructions below.

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.http://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

docs/software.rst

@@ -0,0 +1,15 @@
+.. _software:
+
+Software
+--------
+
+The following software projects use **PyAutoFit**:
+
+`PyAutoLens <https://github.com/Jammy2211/PyAutoLens>`_ -
+Astronomy software for modeling Strong Gravitational Lenses.
+
+`PyAutoGalaxy <https://github.com/Jammy2211/PyAutoGalaxy>`_ -
+Astronomy software for modeling galaxy light profiles and dynamics.
+
+`PyAutoCTI <https://github.com/Jammy2211/PyAutoCTI>`_ -
+Software for modeling Charge Transfer Inefficiency induced by radiation damage to CCDs.