initial restructuring and sphinx setup

Author: luward

.envrc

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+source activate rust-data
+
+export PROJECT_DIR=$PWD
+export PATH=$PWD/bin:$PATH
+export PYTHONPATH=$PWD/python:$PYTHONPATH
+export MATPLOTLIBRC=$PWD/configurations
+export JUPYTER_CONFIG_DIR=$PWD/configurations/jupyter
+export IPYTHONDIR=$PWD/configurations/ipython

.github/workflows/ci.yml

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+name: Continuous Integration
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+           activate-environment: rust-data
+           environment-file: configurations/environment.yml
+           python-version: 3.6
+           auto-activate-base: false
+    - name: check notebook formatting
+      shell: bash -l {0}
+      run: |
+        export PATH="$PATH:/usr/share/miniconda/bin"
+        source .envrc
+        flake8-nb; [ $? -eq 0 ] || exit 1
+        black-nb --check .; [ $? -eq 0 ] || exit 1
+   - name: run project
+      shell: bash -l {0}
+      run: |
+        export PATH="$PATH:/usr/share/miniconda/bin"
+        source .envrc
+        py.test        
+        run-project

.zenodo.json

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+# 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)

Makefile

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+.. |logo| image:: https://raw.githubusercontent.com/OpenSourceEconomics/ose-corporate-design/master/logos/OSE_logo_no_type_RGB.svg
+  :width: 4 %
+
+|logo| Rust data
+==================
+
+This repository contains the raw data from Rust (1987) and data reading and processing functions.
+
+The data and the provided documentation can be found at John Rust's `homepage <https://editorialexpress.com/jrust/nfxp.html>`_. 
+Please see the `documentation <https://rust-data.readthedocs.io/en/latest/index.html>`_ for details.
+
+
+Supported by
+------------
+
+
+.. image:: https://raw.githubusercontent.com/OpenSourceEconomics/ose-corporate-design/master/logos/OSE_logo_RGB.svg
+    :width: 22 %
+    :target: https://github.com/OpenSourceEconomics

README.md

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+../scripts/run_project.py

README.rst

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+# 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 = 'Rust data'
+copyright = '2021, OpenSourceEconomics'
+author = 'OpenSourceEconomics'
+
+
+# -- 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 = [
+    "sphinx.ext.mathjax",
+    "nbsphinx",
+    "sphinx.ext.extlinks",
+    "sphinx_rtd_theme",
+    "sphinx.ext.doctest",
+    "sphinxcontrib.bibtex",
+]
+
+
+# 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 nbsphinx  ----------------------------------------
+nbsphinx_execute = "auto"
+
+nbsphinx_prolog = r"""
+{% set docname = env.doc2path(env.docname, base=None) %}
+.. |binder| image:: https://mybinder.org/badge_logo.svg
+    :target: https://mybinder.org/v2/gh/OpenSourceEconomics/rust-data/upgrade?filepath={{ docname|e }}
+
+.. only:: html
+
+    .. nbinfo::
+        Download the notebook :download:`here <https://nbviewer.jupyter.org/github/OpenSourceEconomics/rust-data/blob/upgrade/{{ docname }}>`!
+        Interactive online version: |binder|
+"""
+
+# -- 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"
+
+# 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']

bin/run-project

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+name: rust-data
+
+channels:
+  - defaults
+  - conda-forge
+  - OpenSourceEconomics
+
+dependencies:
+  - python=3
+  - pip=19.0.3
+  - jupyterlab
+  - matplotlib>=3.0.0
+  - mkl
+  - nbsphinx=0.4.2
+  - numba>=0.43.1
+  - numpydoc
+  - pyaml
+  - pytest-cov
+  - pytest-xdist    
+  - numpy
+  - restructuredtext_lint
+  - scipy>=1.2.1
+  - Sphinx>=2.0.0
+  - black>=20.8b1
+  - flake8
+  - pytest-flake8
+  - pytest
+  - sphinx-autobuild
+  - tox-conda
+  - markupsafe<2.0
+  - pip:
+      - git+https://github.com/OpenSourceEconomics/respy
+      - apprise
+      - pre-commit
+      - pysftp
+      - pytest-black
+      - Py-BOBYQA
+      - DFO-LS
+      - jupyterlab
+      - sphinx-rtd-theme
+      - sphinxcontrib-bibtex==1.0
+      - sphinxcontrib-svg2pdfconverter[CairoSVG]

conf.py

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+This is the IPython startup directory
+
+.py and .ipy files in this directory will be run *prior* to any code or files specified
+via the exec_lines or exec_files configurables whenever you load this profile.
+
+Files will be run in lexicographical order, so you can control the execution order of files
+with a prefix, e.g.::
+
+    00-first.py
+    50-middle.py
+    99-last.ipy

configurations/environment.yml

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+from IPython import get_ipython
+
+ipython = get_ipython()
+ipython.magic("matplotlib inline")
+ipython.magic("load_ext autoreload")
+ipython.magic("autoreload 2")
+
+import warnings
+
+warnings.simplefilter(action="ignore", category=RuntimeWarning)