initial commit

.gitignore

+MANIFEST
+dist/*
+doc/build/*
+doc/source/_autosummary/*
+*/__pycache__/*
+*.egg-info
+other/*

.gitlab-ci.yml

+stages:
+  - build
+  - test
+  - documentation
+  - staging
+  - production
+
+Build distribution:
+  stage: build
+  before_script:
+    - export PATH=$PATH:/opt/anaconda3/bin/
+    - conda env create -f sam_env.yml
+    - conda activate sam
+  script:
+    - python setup.py sdist
+  after_script:
+    - conda deactivate
+    - conda env remove -n sam
+  artifacts:
+    paths:
+      - dist/*.tar.gz
+    expire_in: 1 day
+
+Run test:
+  stage: test
+  before_script:
+    - export PATH=$PATH:/opt/anaconda3/bin/
+    - conda env create -f sam_env.yml
+    - conda activate sam
+  script:
+    - pip install dist/*.tar.gz
+    - cd test
+    - python -m pytest
+  after_script:
+    - conda deactivate
+    - conda env remove -n sam
+
+Generate documentation:
+  stage: documentation
+  before_script:
+    - export PATH=$PATH:/opt/anaconda3/bin/
+    - conda env create -f sam_env.yml
+    - conda activate sam
+  script:
+    - pip install dist/*.tar.gz
+    - cd doc
+    - make html
+  after_script:
+    - conda deactivate
+    - conda env remove -n sam
+  artifacts:
+    paths:
+      - doc/build/html
+    expire_in: 1 day
+
+Deploy on Staging:
+  stage: staging
+  script:
+    - cp dist/*.tar.gz /www/people/delisle/public/staging/sam
+    - rm -rf /www/people/delisle/public/staging/sam/doc/*
+    - cp -R doc/build/html/* /www/people/delisle/public/staging/sam/doc
+
+Release and deploy on Production:
+  stage: production
+  before_script:
+    # According to documentation, gitlab uses detached HEAD and we need to go back to master to release.
+    # See https://gitlab.com/gitlab-org/gitlab-ce/issues/19421
+    - git checkout -B master origin/master
+    - git config --global user.name 'Gitlab CI'
+    - git config --global user.email ''
+    - git remote set-url origin "https://gitlab-ci-token:$RELEASE_TOKEN@gitlab.unige.ch/jean-baptiste.delisle/sam.git"
+  script:
+    # Tag
+    - VERSION=`grep __version__ sam/__info__.py | sed 's/.*version__ = "//' | sed 's/"//'`
+    - TAG_VERSION="v$VERSION"
+    - git tag -a "$TAG_VERSION" -m "Release sam $TAG_VERSION"
+    - git push origin "$TAG_VERSION" --quiet
+    - CHANGES=`cat CHANGES.txt`
+    # Add release on gitlab (via gitlab API)
+    - curl -X POST -H "PRIVATE-TOKEN:$RELEASE_TOKEN" -F "name=Release sam $TAG_VERSION" -F "tag_name=$TAG_VERSION" -F "ref=$TAG_VERSION" -F "description=Changes:$CHANGES" 'https://gitlab.unige.ch/api/v4/projects/1383/releases'
+    # Deploy on production
+    - cp dist/*.tar.gz /www/people/delisle/public/sam
+    - rm -rf /www/people/delisle/public/sam/doc/*
+    - cp -R doc/build/html/* /www/people/delisle/public/sam/doc
+    # Upgrade to next version
+    - MAJOR_DIGIT=`echo $VERSION | awk -F. '{print $1}'`
+    - MINOR_DIGIT=`echo $VERSION | awk -F. '{print $2}'`
+    - PATCH_DIGIT=`echo $VERSION | awk -F. '{print $3}'`
+    - PATCH_DIGIT=$((PATCH_DIGIT + 1))
+    - NEW_VERSION="$MAJOR_DIGIT.$MINOR_DIGIT.$PATCH_DIGIT"
+    - echo $NEW_VERSION
+    # Need to hack sed to work on both mac and unix. See details here : https://stackoverflow.com/questions/5694228/sed-in-place-flag-that-works-both-on-mac-bsd-and-linux
+    - sed -i.bak s"/version__ = \"$VERSION\"/version__ = \"$NEW_VERSION\"/g" sam/__info__.py
+    - git add sam/__info__.py
+    - git commit -m "Upgrade project to next version $NEW_VERSION"
+    - git push origin master --quiet
+  when: manual

CHANGES.txt

+ 

MANIFEST.in

+graft sam

README.rst

+sam: Scaled Adaptive Metropolis
+===============================
+
+Read the documentation at `<https://obswww.unige.ch/~delisle/sam/doc/>`_.

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+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)
\ No newline at end of file

doc/source/_templates/autosummary/attribute.rst

+:orphan:
+
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoattribute:: {{ objname }}
\ No newline at end of file

doc/source/_templates/autosummary/class.rst

+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
+
+  {% block methods %}
+   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
+      .. autosummary::
+         :toctree:
+      {% for item in all_methods %}
+         {%- if not item.startswith('_') or item in ['__call__', '__mul__', '__getitem__', '__len__'] %}
+         {{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endfor %}
+      {% for item in inherited_members %}
+         {%- if item in ['__call__', '__mul__', '__getitem__', '__len__'] %}
+         {{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endfor %}
+  {% endblock %}
+
+  {% block attributes %}
+  {% if attributes %}
+   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
+      .. autosummary::
+         :toctree:
+      {% for item in all_attributes %}
+         {%- if not item.startswith('_') %}
+         {{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endfor %}
+  {% endif %}
+  {% endblock %}

doc/source/_templates/autosummary/custom_module.rst

+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+

doc/source/_templates/autosummary/method.rst

+:orphan:
+
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. automethod:: {{ objname }}
\ No newline at end of file

doc/source/_templates/autosummary/property.rst

+:orphan:
+
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoproperty:: {{ objname }}
\ No newline at end of file

doc/source/_templates/indexsidebar.html

+            <h3>Resources</h3>
+            <ul>
+              <li><a href="https://scipy.org/">Scipy.org website</a></li>
+              <li>&nbsp;</li>
+            </ul>

doc/source/_templates/layout.html

+{% extends "!layout.html" %}
+
+{% block sidebarsearch %}
+{%- if sourcename %}
+<ul class="this-page-menu">
+{%- if 'generated/' in sourcename %}
+  <li><a href="/scipy/docs/{{ sourcename.replace('generated/', '').replace('.txt', '') |e }}">{{_('Edit page')}}</a></li>
+{%- else %}
+  <li><a href="/scipy/docs/scipy-docs/{{ sourcename.replace('.txt', '.rst') |e }}">{{_('Edit page')}}</a></li>
+{%- endif %}
+</ul>
+{%- endif %}
+{{ super() }}
+{% endblock %}

doc/source/_templates/searchbox.html

+{#
+    basic/searchbox.html
+    ~~~~~~~~~~~~~~~~~~~~
+
+    Sphinx sidebar template: quick search box.
+
+    :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{%- if pagename != "search" and builder != "singlehtml" %}
+<div id="searchbox" style="display: none" role="search">
+  <h4>{{ _('Quick search') }}</h4>
+    <div>
+    <form class="search" action="{{ pathto('search') }}" method="get">
+      <input type="text" style="width: inherit;" name="q" />
+      <input type="submit" value="{{ _('search') }}" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    </div>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+{%- endif %}
\ No newline at end of file

doc/source/_theme/scipy/layout.html

+{#
+    scipy/layout.html
+    ~~~~~~~~~~~~~~~~~
+
+    Master layout template for Sphinx themes.
+
+    :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{%- block doctype -%}
+<!DOCTYPE html>
+{%- endblock %}
+{%- set url_root = pathto('', 1) %}
+{%- if url_root == '#' %}{% set url_root = '' %}{% endif %}
+{%- if not embedded and docstitle %}
+  {%- set titlesuffix = " &mdash; "|safe + docstitle|e %}
+{%- else %}
+  {%- set titlesuffix = "" %}
+{%- endif %}
+
+{%- macro relbar_top() %}
+    <ul class="nav nav-pills pull-left">
+        {%- for link in theme_rootlinks %}
+        <li class="active"><a href="{{ link[0] }}">{{ link[1] }}</a></li>
+        {%- endfor %}
+        {%- block rootrellink %}
+	{% if pagename != master_doc %}
+        <li class="active"><a href="{{ pathto(master_doc) }}">{{ shorttitle|e }}</a></li>
+	{% endif %}
+        {%- endblock %}
+        {%- for parent in parents %}
+          <li class="active"><a href="{{ parent.link|e }}" {% if loop.last %}{{ accesskey("U") }}{% endif %}>{{ parent.title }}</a></li>
+        {%- endfor %}
+        {%- block relbaritems %} {% endblock %}
+    </ul>
+{%- endmacro %}
+
+{%- macro relbar_top_right() %}
+    <ul class="nav nav-pills pull-right">
+      {%- for rellink in rellinks %}
+      <li class="active">
+        <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+           {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+      </li>
+      {%- endfor %}
+    </ul>
+{%- endmacro %}
+
+{%- macro relbar_bottom() %}
+{%- endmacro %}
+
+{%- macro sidebar() %}
+      <div class="spc-rightsidebar span3">
+        <div class="sphinxsidebarwrapper">
+          {%- block sidebarlogo %}
+          {%- if logo %}
+            <p class="logo"><a href="{{ pathto(master_doc) }}">
+              <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo">
+            </a></p>
+          {%- endif %}
+          {%- endblock %}
+          {%- if sidebars != None %}
+            {#- new style sidebar: explicitly include/exclude templates #}
+            {%- for sidebartemplate in sidebars %}
+            {%- include sidebartemplate %}
+            {%- endfor %}
+          {%- else %}
+            {#- old style sidebars: using blocks -- should be deprecated #}
+            {%- block sidebartoc %}
+            {%- include "localtoc.html" %}
+            {%- endblock %}
+            {%- block sidebarrel %}
+            {%- include "relations.html" %}
+            {%- endblock %}
+            {%- block sidebarsourcelink %}
+            {%- include "sourcelink.html" %}
+            {%- endblock %}
+            {%- if customsidebar %}
+            {%- include customsidebar %}
+            {%- endif %}
+            {%- block sidebarsearch %}
+            {%- include "searchbox.html" %}
+            {%- endblock %}
+          {%- endif %}
+        </div>
+      </div>
+{%- endmacro %}
+
+{%- macro script() %}
+    <script type="text/javascript" id="documentation_options" data-url_root="{{ pathto('', 1) }}" src="{{ pathto('_static/documentation_options.js', 1) }}"></script>
+    {%- for scriptfile in script_files %}
+    <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+    {%- endfor %}
+    <script type="text/javascript" src="{{ pathto('_static/js/copybutton.js', 1) }}"></script>
+{%- endmacro %}
+
+{%- macro css() %}
+    <link rel="stylesheet" type="text/css" href="{{ pathto('_static/css/spc-bootstrap.css', 1) }}">
+    <link rel="stylesheet" type="text/css" href="{{ pathto('_static/css/spc-extend.css', 1) }}">
+    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" >
+    <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" >
+    {%- for cssfile in css_files %}
+    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" >
+    {%- endfor %}
+{%- endmacro %}
+
+<html>
+  <head>
+    <meta charset="{{ encoding }}">
+    {{ metatags }}
+    {%- block htmltitle %}
+    <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
+    {%- endblock %}
+    {{ css() }}
+    {%- if not embedded %}
+    {%- block scripts %}
+    {{ script() }}
+    {%- endblock %}
+    {%- if use_opensearch %}
+    <link rel="search" type="application/opensearchdescription+xml"
+          title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
+          href="{{ pathto('_static/opensearch.xml', 1) }}">
+    {%- endif %}
+    {%- if favicon %}
+    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}">
+    {%- endif %}
+    {%- endif %}
+{%- block linktags %}
+    {%- if hasdoc('about') %}
+    <link rel="author" title="{{ _('About these documents') }}" href="{{ pathto('about') }}" >
+    {%- endif %}
+    {%- if hasdoc('genindex') %}
+    <link rel="index" title="{{ _('Index') }}" href="{{ pathto('genindex') }}" >
+    {%- endif %}
+    {%- if hasdoc('search') %}
+    <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}" >
+    {%- endif %}
+    {%- if hasdoc('copyright') %}
+    <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}" >
+    {%- endif %}
+    <link rel="top" title="{{ docstitle|e }}" href="{{ pathto('index') }}" >
+    {%- if parents %}
+    <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}" >
+    {%- endif %}
+    {%- if next %}
+    <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}" >
+    {%- endif %}
+    {%- if prev %}
+    <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}" >
+    {%- endif %}
+{%- endblock %}
+{%- block extrahead %} {% endblock %}
+  </head>
+  <body>
+{%- block header %}
+{% if theme_scipy_org_logo %}
+<div class="container">
+  <div class="top-scipy-org-logo-header">
+    <a href="{{ pathto('index') }}">
+      <img style="border: 0;" alt="SciPy" src="{{ pathto('_static/img/scipy_org_logo.png', 1) }}"></a>
+    </div>
+  </div>
+</div>
+{% else %}
+  <div class="container">
+    <div class="header">
+    </div>
+  </div>
+{% endif %}
+{% endblock %}
+
+{%- block content %}
+    <div class="container">
+      <div class="main">
+{%- block navbar %}
+        {% if theme_navigation_links or sidebar == 'left' %}
+	<div class="row-fluid">
+	  <div class="span12">
+	    <div class="spc-navbar">
+              {{ relbar_top() }}
+              {% if theme_navigation_links %}
+              {{ relbar_top_right() }}
+              {% endif %}
+	    </div>
+	  </div>
+	</div>
+        {% endif %}
+{% endblock %}
+	<div class="row-fluid">
+	  {%- if theme_sidebar == 'left' -%}
+            {{ sidebar() }}
+          {%- endif %}
+	  {%- if theme_sidebar == 'none' -%}
+          <div class="span1"></div>
+          <div class="span10">
+	  {% else %}
+          <div class="span9">
+	  {%- endif %}
+            {% if not theme_navigation_links and sidebar != 'left' %}
+	      <div class="row-fluid">
+		<div class="span9">
+  		  <div class="spc-navbar">
+		    {{ relbar_top() }}
+		  </div>
+		</div>
+	      </div>
+            {% endif %}
+  {%- block document %}
+        <div class="bodywrapper">
+          <div class="body" id="spc-section-body">
+            {% block body %} {% endblock %}
+          </div>
+        </div>
+  {%- endblock %}
+          </div>
+	  {%- if theme_sidebar == 'right' -%}
+          {{ sidebar() }}
+	  {%- elif theme_sidebar == 'none' -%}
+          <div class="span1"></div>
+	  {%- endif %}
+        </div>
+      </div>
+    </div>
+{%- endblock %}
+
+    <div class="container container-navbar-bottom">
+      <div class="spc-navbar">
+        {{ relbar_bottom() }}
+      </div>
+    </div>
+
+{%- block footer %}
+    <div class="container">
+    <div class="footer">
+    <div class="row-fluid">
+    <ul class="inline pull-left">
+    {%- if show_copyright %}
+      <li>
+      {%- if hasdoc('copyright') %}
+        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
+      {%- else %}
+        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
+      {%- endif %}
+      </li>
+    {%- endif %}
+    {%- if last_updated %}
+      <li>
+      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
+      </li>
+    {%- endif %}
+    {%- if show_sphinx %}
+      <li>
+      {% trans sphinx_version=sphinx_version|e %}Created using <a href="https://www.sphinx-doc.org">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
+      </li>
+    {%- endif %}
+    </ul>
+    </div>
+    </div>
+    </div>
+{%- endblock %}
+  </body>
+</html>

doc/source/_theme/scipy/searchbox.html

+{%- if theme_edit_link -%}
+{% block edit_link %}
+{%- if sourcename %}
+<div class="this-page-menu">
+{%- if 'generated/' in sourcename %}
+  <a href="/scipy/docs/{{ sourcename.replace('generated/', '').replace('.txt', '') |e }}">{{_('Edit page')}}</a>
+{%- else %}
+  <a href="/scipy/docs/scipy-docs/{{ sourcename.replace('.txt', '.rst') |e }}">{{_('Edit page')}}</a>
+{%- endif %}
+</div>
+{%- endif %}
+{% endblock %}
+{%- endif -%}

doc/source/_theme/scipy/sourcelink.html

+{%- if show_source and has_source and sourcename %}
+  <h3>{{ _('This Page') }}</h3>
+  <div>
+    <a href="{{ pathto('_sources/' + sourcename, true)|e }}"
+       rel="nofollow">{{ _('Show Source') }}</a>
+  </div>
+{%- endif %}

doc/source/_theme/scipy/static/css/extend.css

+.container {
+  width: 80%;
+}
+.navbar1 {
+  padding-bottom: 10px;
+}
+.navbar1 .nav-pills {
+  margin-bottom: 0px;
+  font-size: 12px;
+}
+.navbar1 .nav-pills > li > a {
+  padding-top: 2.5px;
+  padding-bottom: 2.5px;
+}
+.navbar1 .dropdown.dropdown-menu {
+	padding: 0px;
+}
+.header {
+  padding-top: 30px;
+  padding-bottom: 18px;
+}
+.SearchBar .form-search {
+  margin-bottom: 0px;
+}
+.SearchBar .input-append input {
+  height: 12px;
+}
+body {