started fixing docs

Makefile

@@ -51,7 +51,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8
-	flake8 pyce tests
+	flake8 pycirk tests
 
 test: ## run tests quickly with the default Python
 	py.test
@@ -60,13 +60,13 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source pyce -m pytest
+	coverage run --source pycirk -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/pyce.rst
+	rm -f docs/pycirk.rst
 	rm -f docs/modules.rst
 	sphinx-apidoc -o docs/ pycirk
 	$(MAKE) -C docs clean

README.md

@@ -132,130 +132,7 @@ It is possible to specify:
 - whether the intervention affects domestic, import transactions or both
 
 
+This package was created with Cookiecutter and the `audreyr/cookiecutter-pypackage` project template.
 
-## Important modules
-
-
-### pycirk.py
-
-1. Initiates the operations to set scenarios and to create IOT from SUT based on prodxprod Industry-Technology assumption both under Market Share Coefficient method and Technical Coefficient method.
-2. From start you can launch all the analysis specifications listed under scenarios.xls and save everything
-3. Results will be saved in the output folder
-
-Permitted SUT transformation Methods:
-	- method = 0 >> Prod X Prod Ind-Tech Assumption Technical Coeff method
-	- method = 1 >> Prod X Prod Ind-Tech Assumption Market Share Coeff method
-
-Results options:
-	- results_only = True >> output only results (spec'd in scenarios.xls under analysis)
-	- results_only = False >> output all IOTs and results
-	- scen_no = 0 - n (0 = baseline) 
-	- n = is number of scenarios specified by sheet in scenarios.xls
-	- "scenario_1" is also allowed for scenarios
-	- None, 0, base and baseline are also accepted for baseline
-
-Aggregation types:
-	- aggregation = ["", "bi-regional"](bi-regional EU-ROW), None (Multi-regional 49 countries)
-
-Availability of secondary raw materials in IO:
-	- make_secondary = False (regular database), True (modifies SUTs so that secondary raw materials are avaialable in IO after transformation)
-
-
-### scenarios.xls
-
-From this .xls file it is possible to set different types of interventions and the analysis to perform:
-
-- matrix = specifies in which matrix of IOT the changes are applied
-- intervention = Primary and ancillary are only used to specify the type of intervention from a conceptual level
-- reg_o or reg_d = Regional coordinates (o=origin or row, d=destination or column)
-- cat_o  or cat_d = category (e.g. products or extensions ) coordinates (o=origin or row, d=destination or column)
-- kt = technical change coefficient (max achievable technically); a negative value means reduction; unit = %
-- ka = absolute values for addition
-- kp = penetration coefficient (level of market penetration of the policy); unit = %
-- copy = allows you to copy a specific transation to a different point in the matrices (useful for proxy creation)
-- substitution = tells the software whether it needs to substitute values among specified categories
-- sk = which intervention should be substituted
-- swk = Substitution weighing factor (how much of the original transaction should be substituted); allows to simulate difference in prices and physical properties between categories; unit = %
-
-These can be set for:
-
-- product category e.g. C_STEL (basic iron), C_PULP (pulp), etc.
-- final demand category e.g. F_HOUS (households), F_GOVE (government), etc.
-- primary input category e.g. E_HRHS (employment highly skilled), T_TLSA (taxes less subsidies), etc.
-- emissions extensions e.g. E_CO2_c (CO2 - combustion)
-- material extensions e.g. NI.02 (Nature Inputs: Coking Coal)
-- resource extension e.g. L_1.1 (Land use - Arable Land - Rice)
-
-Furthemore, from the analysis sheet you can set the following variables to be compared in the analysis:
-
-- product categories
-- primary input categories
-- emissions extensions
-- material extensions
-- resource extensions
-- region of interest
-- impact categories # Please see the data_validation_list sheet in the scenarios.xls file for the comprehensive list
-
-### make_secondary.py
-Allows for the modification of secondary material flows in the SUTs so that they are visible in the IO system
-
-## Other modules
-
-### results.py
-
-Class to assemble results for analysis as specified in scenario.xls analysis sheet:
-
-- Output product content in other products
-- Output results for each scenario
-- Output results and all IO tables and extensions 
-
-
-### save_.py
-
-Save class:
-
-- Save one scenario results
-- Save one scenario results + IOTs
-- Save all scenarios + IOTs
-- Save all results
-
-
-### apply_policy.py
-
-Policy interventions class:
-
-- Recreate any matrix in IOT from policy interventions listed in the scenarios scenarios.xls
-
-### base_n_scen.py
-
-Calculate IOT for baseline and scenarios from SUTs
-
-
-### SUTtoIOT.py
-
-Assemblying IOTs and Extensions from: 
-
-- Prod x prod industry technology assumption in market share coefficient method
-- Prod x prod industry technology assumption in technical coefficient method
-
-
-### SUTops.py
-
-Class for fundamental mathematical operations of IOA and SUT
-
-
-### labels.py 
-
-General label manager for tables	
-
-
-## Credits
-
-Thanks to dr. Arnold Tukker, dr. Joao Dias Rodriguez for the supervision 
-dr. Arjan de Koning for knowledge support in exiobase
-MSc. Glenn Auguilar Hernandez for testing
-
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
-
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
+Cookiecutter: https://github.com/audreyr/cookiecutter
+audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

README.rst

@@ -173,7 +173,7 @@ It is possible to specify:
 
 
 4.1. pycirk.py
-------------
+--------------
 
 
 1. Initiates the operations to set scenarios and to create IOT from SUT based on prodxprod Industry-Technology assumption both under Market Share Coefficient method and Technical Coefficient method.
@@ -235,71 +235,6 @@ Furthemore, from the analysis sheet you can set the following variables to be co
 - impact categories # Please see the data_validation_list sheet in the scenarios.xls file for the comprehensive list
 
 
-### make_secondary.py
-Allows for the modification of secondary material flows in the SUTs so that they are visible in the IO system
-
-
-================
-5. Other modules
-================
-
-
-5.1. results.py
----------------
-
-Class to assemble results for analysis as specified in scenario.xls analysis sheet:
-
-- Output product content in other products
-- Output results for each scenario
-- Output results and all IO tables and extensions 
-
-
-5.2. save_.py
--------------
-
-Save class:
-
-- Save one scenario results
-- Save one scenario results + IOTs
-- Save all scenarios + IOTs
-- Save all results
-
-
-5.3. apply_policy.py
---------------------
-
-Policy interventions class:
-
-- Recreate any matrix in IOT from policy interventions listed in the scenarios scenarios.xls
-
-
-5.4. base_n_scen.py
--------------------
-
-Calculate IOT for baseline and scenarios from SUTs
-
-
-5.5. SUTtoIOT.py
-----------------
-
-Assemblying IOTs and Extensions from: 
-
-- Prod x prod industry technology assumption in market share coefficient method
-- Prod x prod industry technology assumption in technical coefficient method
-
-
-5.6. SUTops.py
---------------
-
-Class for fundamental mathematical operations of IOA and SUT
-
-
-5.7. labels.py 
---------------
-
-General label manager for tables	
-
-
 
 ==========
 6. Credits

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = pyce
+SPHINXPROJ    = pycirk
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 99d7142f39acbba3c9fe65c805d4ec72
+config: 973b200ac544692cf49b7ad1a82bc8fc
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_modules/index.html

@@ -9,7 +9,7 @@
     <title>Overview: module code &#8212; pycirk 1.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" src="../_static/documentation_options.js"></script>
+    <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../_static/jquery.js"></script>
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
@@ -27,25 +27,52 @@
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
+
+
           <div class="body" role="main">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="pycirk/SUTops.html">pycirk.SUTops</a></li>
-<li><a href="pycirk/SUTtoIOT.html">pycirk.SUTtoIOT</a></li>
-<li><a href="pycirk/apply_policy.html">pycirk.apply_policy</a></li>
-<li><a href="pycirk/base_n_scen.html">pycirk.base_n_scen</a></li>
+<ul><li><a href="pycirk/fundamental_operations.html">pycirk.fundamental_operations</a></li>
 <li><a href="pycirk/labels.html">pycirk.labels</a></li>
+<li><a href="pycirk/make_scenarios.html">pycirk.make_scenarios</a></li>
 <li><a href="pycirk/make_secondary_flows.html">pycirk.make_secondary_flows</a></li>
+<li><a href="pycirk/organize_io.html">pycirk.organize_io</a></li>
+<li><a href="pycirk/positions.html">pycirk.positions</a></li>
 <li><a href="pycirk/pycirk.html">pycirk.pycirk</a></li>
+<li><a href="pycirk/pycirk_settings.html">pycirk.pycirk_settings</a></li>
 <li><a href="pycirk/results.html">pycirk.results</a></li>
-<li><a href="pycirk/save_.html">pycirk.save_</a></li>
+<li><a href="pycirk/save_utils.html">pycirk.save_utils</a></li>
+<li><a href="pycirk/transformation_methods.html">pycirk.transformation_methods</a></li>
 </ul>
 
           </div>
+
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper"><div class="relations">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">pycirk</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../readme.html">pycirk</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">pycirk</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../authors.html">Credits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../history.html">History</a></li>
+</ul>
+
+<div class="relations">
 <h3>Related Topics</h3>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
@@ -64,16 +91,24 @@ <h3>Quick search</h3>
     </div>
 </div>
 <script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
         </div>
       </div>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, Franco Donati.
+      &copy;2019, Franco Donati.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.7.4</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.10</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.2</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>