Merge pull request #53 from FZJ-IEK3-VSA/dev_release

Merge branch 'dev_release' into 'master' (v1.1.1)
FZJ-IEK3-VSA · Aug 10, 2021 · 25c5b39 · 25c5b39
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -7,5 +7,5 @@ conda:
     - conda env update -q --file=requirements.yml
     - conda env update -q --file=requirements_dev.yml
     - source activate tsam
-    - pip install --no-cache-dir .
-    - pytest --cov tsam --cov-report term-missing
+    - pip install -e .
+    - pytest --cov=tsam test/
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 [![Build Status](https://travis-ci.com/FZJ-IEK3-VSA/tsam.svg?branch=master)](https://travis-ci.com/FZJ-IEK3-VSA/tsam) [![Version](https://img.shields.io/pypi/v/tsam.svg)](https://pypi.python.org/pypi/tsam) [![Documentation Status](https://readthedocs.org/projects/tsam/badge/?version=latest)](https://tsam.readthedocs.io/en/latest/) [![PyPI - License](https://img.shields.io/pypi/l/tsam)]((https://github.com/FZJ-IEK3-VSA/tsam/blob/master/LICENSE.txt)) [![codecov](https://codecov.io/gh/FZJ-IEK3-VSA/tsam/branch/master/graph/badge.svg)](https://codecov.io/gh/FZJ-IEK3-VSA/tsam)
 
-<a href="https://www.fz-juelich.de/iek/iek-3/EN/Home/home_node.html"><img src="https://www.fz-juelich.de/SharedDocs/Bilder/IBG/IBG-3/DE/Plant-soil-atmosphere%20exchange%20processes/INPLAMINT%20(BONARES)/Bild3.jpg?__blob=poster" alt="Forschungszentrum Juelich Logo" width="230px"></a> 
+<a href="https://www.fz-juelich.de/iek/iek-3/EN/Forschung/_Process-and-System-Analysis/_node.html"><img src="https://www.fz-juelich.de/SharedDocs/Bilder/IBG/IBG-3/DE/Plant-soil-atmosphere%20exchange%20processes/INPLAMINT%20(BONARES)/Bild3.jpg?__blob=poster" alt="Forschungszentrum Juelich Logo" width="230px"></a> 
 
 # tsam - Time Series Aggregation Module
 tsam is a python package which uses different machine learning algorithms for the aggregation of time series. The data aggregation can be performed in two freely combinable dimensions: By representing the time series by a user-defined number of typical periods or by decreasing the temporal resolution.
@@ -91,7 +91,7 @@ You should have received a copy of the MIT License along with this program.
 If not, see https://opensource.org/licenses/MIT
 
 ## About Us 
-<a href="https://www.fz-juelich.de/iek/iek-3/EN/Home/home_node.html"><img src="https://www.fz-juelich.de/SharedDocs/Bilder/IEK/IEK-3/Abteilungen2015/VSA_DepartmentPicture_2019-02-04_459x244_2480x1317.jpg?__blob=normal" width="400px" alt="Abteilung VSA"></a> 
+<a href="http://www.fz-juelich.de/iek/iek-3/EN/Forschung/_Process-and-System-Analysis/_node.html"><img src="https://www.fz-juelich.de/SharedDocs/Bilder/IEK/IEK-3/Abteilungen2015/VSA_DepartmentPicture_2019-02-04_459x244_2480x1317.jpg?__blob=normal" width="400px" alt="Abteilung VSA"></a> 
 
 We are the [Techno-Economic Energy Systems Analysis](https://www.fz-juelich.de/iek/iek-3/EN/Forschung/_Process-and-System-Analysis/_node.html) department at the [Institute of Energy and Climate Research: Electrochemical Process Engineering (IEK-3)](https://www.fz-juelich.de/iek/iek-3/EN/Home/home_node.html) belonging to the [Forschungszentrum Jülich](https://www.fz-juelich.de/). Our interdisciplinary department's research is focusing on energy-related process and systems analyses. Data searches and system simulations are used to determine energy and mass balances, as well as to evaluate performance, emissions and costs of energy systems. The results are used for performing comparative assessment studies between the various systems. Our current priorities include the development of energy strategies, in accordance with the German Federal Government’s greenhouse gas reduction targets, by designing new infrastructures for sustainable and secure energy supply chains and by conducting cost analysis studies for integrating new technologies into future energy market frameworks.
 

diff --git a/docs/source/aboutUsDoc.rst b/docs/source/aboutUsDoc.rst
@@ -0,0 +1,33 @@
+########
+About Us
+########
+
+.. image:: https://www.fz-juelich.de/iek/iek-3/DE/_Documents/Pictures/IEK-3Team_2019-02-04.jpg?__blob=poster
+    :target: https://www.fz-juelich.de/iek/iek-3/EN/Home/home_node.html
+    :alt: Abteilung TSA
+    :align: center
+
+We are the `Institute of Energy and Climate Research: Techno-Economic Energy Systems Analysis (IEK-3)
+<https://www.fz-juelich.de/iek/iek-3/DE/Home/home_node.html>`_ belonging to the Forschungszentrum Jülich.
+Our interdisciplinary department's research is focusing on energy-related process and systems analyses. Data searches and
+system simulations are used to determine energy and mass balances, as well as to evaluate performance, emissions and
+costs of energy systems. The results are used for performing comparative assessment studies between the various systems.
+Our current priorities include the development of energy strategies, in accordance with the German Federal Government’s
+greenhouse gas reduction targets, by designing new infrastructures for sustainable and secure energy supply chains and
+by conducting cost analysis studies for integrating new technologies into future energy market frameworks.
+
+**Contributions and Users**
+
+Within the BMWi funded project `METIS <http://www.metis-platform.net/>`_ we develop together with the RWTH-Aachen
+`(Prof. Aaron Praktiknjo) <http://www.wiwi.rwth-aachen.de/cms/Wirtschaftswissenschaften/Die-Fakultaet/Institute-und-Lehrstuehle/Professoren/~jgfr/Praktiknjo-Aaron/?allou=1&lidx=1>`_,
+the EDOM Team at FAU `(PD Lars Schewe) <http://www.mso.math.fau.de/de/edom/team/schewe-lars/dr-lars-schewe>`_ and the
+`Jülich Supercomputing Centre (JSC) <http://www.fz-juelich.de/ias/jsc/DE/Home/home_node.html>`_ energy system models
+on both, global and national scales, and new methods for effectively solving them.
+
+.. image:: http://www.metis-platform.net/metis-platform/DE/_Documents/Pictures/projectTeamAtKickOffMeeting_640x338.jpg?__blob=normal
+    :target: http://www.metis-platform.net
+    :alt: METIS Team
+    :align: center
+
+Dr. Martin Robinius is teaching a `course <https://www.campus-elgouna.tu-berlin.de/energy/v_menu/msc_business_engineering_energy/modules_and_curricula/project_market_coupling/>`_
+at TU Berlin in which he is introducing tsam to students.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -66,9 +66,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.1.0'
+version = '1.1.1'
 # The full version, including alpha/beta/rc tags.
-release = '1.1.0'
+release = '1.1.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/source/gettingStartedDoc.rst b/docs/source/gettingStartedDoc.rst
@@ -4,10 +4,6 @@
 Getting started
 ###############
 
-************
-Installation
-************
-
 In the following, instructions for installing and using the tsam package on Windows are given. The installation
 instructions for installing and using tsam on Linux/macOS systems are however quite similar and can be, hopefully
 easily, derived from the instructions below.
@@ -41,37 +37,3 @@ or install directly via python as
 **Installation of an optimization solver**
 
 Some clustering algorithms implemented in tsam are based on Mixed-Integer Linear Programming. Accordingy, an appropriate solver for using these functionalities is required that can be accessed by `Pyomo <https://github.com/Pyomo/pyomo/>`_. In theory many solvers can be used (e.g. `GUROBI <http://www.gurobi.com/>`_  or `GLPK <https://sourceforge.net/projects/winglpk/files/latest/download>`_). For the installation of GUROBI, follow the instructions on the solver's website. For installation of GLPK, move the downloaded folder to a desired location. Then, manually append the Environment Variable *Path* with the absolute path leading to the folder in which the glpsol.exe is located (c.f. w32/w64 folder, depending on operating system type).
-
-********
-About Us
-********
-
-.. image:: https://www.fz-juelich.de/iek/iek-3/DE/_Documents/Pictures/IEK-3Team_2019-02-04.jpg?__blob=poster
-    :target: https://www.fz-juelich.de/iek/iek-3/EN/Home/home_node.html
-    :alt: Abteilung TSA
-    :align: center
-
-We are the `Institute of Energy and Climate Research: Techno-Economic Energy Systems Analysis (IEK-3)
-<https://www.fz-juelich.de/iek/iek-3/DE/Home/home_node.html>`_ belonging to the Forschungszentrum Jülich.
-Our interdisciplinary department's research is focusing on energy-related process and systems analyses. Data searches and
-system simulations are used to determine energy and mass balances, as well as to evaluate performance, emissions and
-costs of energy systems. The results are used for performing comparative assessment studies between the various systems.
-Our current priorities include the development of energy strategies, in accordance with the German Federal Government’s
-greenhouse gas reduction targets, by designing new infrastructures for sustainable and secure energy supply chains and
-by conducting cost analysis studies for integrating new technologies into future energy market frameworks.
-
-**Contributions and Users**
-
-Within the BMWi funded project `METIS <http://www.metis-platform.net/>`_ we develop together with the RWTH-Aachen
-`(Prof. Aaron Praktiknjo) <http://www.wiwi.rwth-aachen.de/cms/Wirtschaftswissenschaften/Die-Fakultaet/Institute-und-Lehrstuehle/Professoren/~jgfr/Praktiknjo-Aaron/?allou=1&lidx=1>`_,
-the EDOM Team at FAU `(PD Lars Schewe) <http://www.mso.math.fau.de/de/edom/team/schewe-lars/dr-lars-schewe>`_ and the
-`Jülich Supercomputing Centre (JSC) <http://www.fz-juelich.de/ias/jsc/DE/Home/home_node.html>`_ energy system models
-on both, global and national scales, and new methods for effectively solving them.
-
-.. image:: http://www.metis-platform.net/metis-platform/DE/_Documents/Pictures/projectTeamAtKickOffMeeting_640x338.jpg?__blob=normal
-    :target: http://www.metis-platform.net
-    :alt: METIS Team
-    :align: center
-
-Dr. Martin Robinius is teaching a `course <https://www.campus-elgouna.tu-berlin.de/energy/v_menu/msc_business_engineering_energy/modules_and_curricula/project_market_coupling/>`_
-at TU Berlin in which he is introducing tsam to students.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -38,6 +38,7 @@ The authors of both, the program and the publications, **kindly request you to c
     newsDoc
     integratedSoftwareDoc
     legalNoticeDoc
+    aboutUsDoc
     furtherReadingDoc
 
 * :ref:`genindex`

diff --git a/docs/source/newsDoc.rst b/docs/source/newsDoc.rst
@@ -2,8 +2,7 @@
 tsam's Change Log
 #################
 
-In tsam's latest release (1.1.0) the following functionalities were included:
+In tsam's latest release (1.1.1) the following functionalities were included:
 
-* Segmentation - the clustering of adjacent time steps - according to `Pineda et al. (2018) <https://ieeexplore.ieee.org/abstract/document/8369128>`_
-* k-MILP - an extension of the MILP-based k-medoids clustering that allows automatic identification of extreme periods according to `Zatti et al. (2019) <https://www.sciencedirect.com/science/article/abs/pii/S0360544219309077>`_
-* The option to dynamically choose whether to clusters found should be represented by their centroid or medoid.
+* Significantly increased test coverage 
+* Separation between clustering and representation, i.e. for clustering algorithms like Ward’s hierarchical clustering algorithm the representation by medoids or centroids can now freely be chosen.
diff --git a/docs/source/periodAggregationDoc.rst b/docs/source/periodAggregationDoc.rst
@@ -0,0 +1,15 @@
+#############################
+The Aggregation Functionality
+#############################
+
+.. |br| raw:: html
+
+   <br />
+
+Descriptions of the basic functions are given below.
+
+**Function descriptions:**
+
+.. automodule:: periodAggregation
+   :members:
+   :member-order: bysource
diff --git a/docs/source/representationsDoc.rst b/docs/source/representationsDoc.rst
@@ -0,0 +1,15 @@
+################################
+The Representation Functionality
+################################
+
+.. |br| raw:: html
+
+   <br />
+
+Descriptions of the basic functions are given below.
+
+**Function descriptions:**
+
+.. automodule:: representations
+   :members:
+   :member-order: bysource
diff --git a/docs/source/structureOfTsamDoc.rst b/docs/source/structureOfTsamDoc.rst
@@ -15,6 +15,8 @@ clustering of adjacent time steps called segmentation.
    :maxdepth: 2
 
    timeseriesaggregationDoc
+   periodAggregationDoc
+   representationsDoc
 
 **Submodules including exact k-medoids and segmentation**
 

diff --git a/docs/source/timeseriesaggregationDoc.rst b/docs/source/timeseriesaggregationDoc.rst
@@ -11,7 +11,7 @@ Descriptions of the basic functions are given below.
 **Function descriptions:**
 
 .. automodule:: timeseriesaggregation
-   :members: unstackToPeriods, aggregatePeriods, medoidRepresentation, meanRepresentation
+   :members: unstackToPeriods
    :member-order: bysource
 
    .. autoclass:: TimeSeriesAggregation