Merge pull request #1 from IPESE/develop_cedric

Develop cedric

.gitignore

@@ -312,7 +312,11 @@ reho/data/QBuildings/*
 documentation/_build
 documentation/sections/_autosummary
 
+# Test
+reho/test/data/*
+reho/test/figures/*
+reho/test/results/*
+
 # Scripts
 scripts/*
 !scripts/examples/
-!scripts/test/

documentation/conf.py

@@ -28,6 +28,7 @@
               'sphinx_design',
               'sphinx_copybutton',
               'nbsphinx']
+source_suffix = [".rst", ".md"]
 exclude_patterns = ['LICENSE']
 # autosummary_generate = True  # Turn on sphinx.ext.autosummary
 
@@ -49,7 +50,7 @@
   'github_url': 'https://github.com/IPESE/REHO',
   'header_links_before_dropdown': 7,
   'navbar_align': 'left',
-  "external_links": [{"name": "REHO-fm", "url": "https://ipese-test.epfl.ch/reho-fm/"}],
+  # "external_links": [{"name": "REHO-fm", "url": "https://ipese-test.epfl.ch/reho-fm/"}],
   "icon_links": [{"name": "IPESE",
                   "url": "https://ipese-web.epfl.ch/ipese-blog/",
                   "icon": "https://github.com/IPESE/REHO/blob/documentation/documentation/images/logos/ipese_square.png?raw=true",
@@ -67,34 +68,32 @@
 
 # ------------ Autodoc ------------------------------------
 autodoc_member_order = 'bysource'
-autodoc_mock_imports = ['amplpy',
-                        'pandas',
-                        'openpyxl',
-                        'numpy',
-                        'scipy',
-                        'scikit-learn',
-                        'scikit-learn-extra',
-                        'sqlalchemy',
-                        'psycopg2',
-                        'geopandas',
-                        'matplotlib',
-                        'plotly',
-                        'kaleido',
-                        'dotenv',
-                        'requests',
-                        'coloredlogs',
-                        'SALib',
-                        'qmcpy',
-                        'pvlib',
-                        'pyproj',
-                        'shapely',
-                        'pytest']
-sys.modules['scikit-learn'] = MagicMock()
-sys.modules['sklearn'] = MagicMock()
-sys.modules['sklearn.metrics'] = MagicMock()
-sys.modules['scikit-learn-extra'] = MagicMock()
-sys.modules['sklearn_extra'] = MagicMock()
-sys.modules['sklearn_extra.cluster'] = MagicMock()
-sys.modules['sqlalchemy'] = MagicMock()
+autodoc_mock_imports = [
+    "amplpy",
+    "ampl_module_base",
+    "ampl_module_highs",
+    "coloredlogs",
+    "geopandas",
+    "kaleido",
+    "matplotlib",
+    "numpy",
+    "openpyxl",
+    "pandas<2.0.0",
+    "plotly",
+    "psycopg2",
+    "pvlib",
+    "pyclustering"
+    "pyproj",
+    "python-dotenv",
+    "pytest",
+    "qmcpy",
+    "requests",
+    "SALib",
+    "scipy",
+    "setuptools",
+    "shapely",
+    "sqlalchemy",
+    "urllib3",
+]
 sys.modules['sqlalchemy.dialects'] = MagicMock()
 sys.modules['sqlalchemy.exc'] = MagicMock()

documentation/sections/4_Package_structure.rst

@@ -45,7 +45,6 @@ Directory for data-related files.
 - ``QBuildings/``
 - ``SIA/``
 - ``skydome/``
-- ``weather/``
 
 **model/**
 ==================

documentation/sections/5_Getting_started.rst

@@ -101,7 +101,7 @@ Entry points allow to verify the proper intallation of REHO. Select the desired
     reho-examples-test
 
 
-These commands will download files from the ``scripts/test/`` and ``scripts/examples/`` folders from the `repository <https://github.com/IPESE/REHO/tree/main/scripts/examples>`__, copy them locally and execute them.
+These commands will download files from the ``reho/test/`` and ``scripts/examples/`` folders from the `repository <https://github.com/IPESE/REHO/tree/main/scripts/examples>`__, copy them locally and execute them.
 
 
 If your installation is correct, you should:
@@ -117,6 +117,13 @@ If your installation is correct, you should:
 
    Sankey diagram resulting from a basic REHO single-optimization.
 
+.. figure:: ../images/performance.png
+   :width: 1000
+   :align: center
+   :name: sankey
+
+   Economical performance resulting from a REHO multi-objective optimization (Pareto).
+
 From source
 ------------------
 
@@ -181,7 +188,7 @@ Please include a ``venv`` at the project root folder and install dependencies wi
 Checking proper installation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Run ``scripts/test/run.py``, ``scripts/test/plot.py`` or any of the files in ``scripts/examples/``.
+Run ``reho/test/test_run.py``, ``reho/test/test_plot.py`` or any of the files in ``scripts/examples/``.
 
 If your installation is correct, each run should end with *“Process finished with exit code 0”*.
 Some files will also render some results in your web browser and open different tabs showing the outcome of your optimization.
@@ -193,7 +200,7 @@ Some files will also render some results in your web browser and open different
 Git tracking
 ~~~~~~~~~~~~~
 
-You will also see some files appear in some newly created subfolders such as ``data/clustering/``, ``results/`` and ``figures/``. These are not git-tracked. But all the other Python files in ``scripts/examples/`` and ``scripts/test/`` are git-tracked.
+You will also see some files appear in some newly created subfolders such as ``data/clustering/``, ``results/`` and ``figures/``. These are not git-tracked. But all the other Python files in ``scripts/examples/`` are git-tracked.
 
 You should then be careful to not modify the content of these files.
 
@@ -203,12 +210,12 @@ However, for your future work and own case-studies with REHO, you can create any
 Running REHO
 ================
 
-The following paragraphs describe the content of ``scripts/test/run.py`` and ``scripts/test/plot.py``. These latter should allow you to get started with the tool and conduct your first optimizations.
+The following paragraphs describe the content of ``reho/test/test_run.py`` and ``reho/test/test_plot.py``. These latter should allow you to get started with the tool and conduct your first optimizations.
 
-.. literalinclude:: ../../scripts/test/run.py
+.. literalinclude:: ../../reho/test/test_run.py
    :language: python
 
-.. literalinclude:: ../../scripts/test/plot.py
+.. literalinclude:: ../../reho/test/test_plot.py
    :language: python
 
 Set building parameters
@@ -574,7 +581,7 @@ These results can be saved as a `.pickle` or `.xlsx` file with:
 
 .. code-block:: python
 
-    reho.save_results(format=['pickle', 'xlsx'], filename='my_case_study')
+    reho.save_results(format=['pickle', 'xlsx'], filename='test_results')
 
 
 Read results
@@ -584,7 +591,7 @@ Saved results can be accessed with:
 
 .. code-block:: python
 
-    results = pd.read_pickle('my_case_study.pickle')
+    results = pd.read_pickle('test_results.pickle')
 
 And browsing through ``Scn_ID`` and ``Pareto_ID`` with: