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rename from Examples/python/simulation/ex06_Reflectometry/RoughnessModel.py
rename to Examples/Python/simulation/ex06_Reflectometry/RoughnessModel.py
diff --git a/Examples/python/simulation/ex06_Reflectometry/SpecularSimulationWithRoughness.py b/Examples/Python/simulation/ex06_Reflectometry/SpecularSimulationWithRoughness.py
similarity index 100%
rename from Examples/python/simulation/ex06_Reflectometry/SpecularSimulationWithRoughness.py
rename to Examples/Python/simulation/ex06_Reflectometry/SpecularSimulationWithRoughness.py
diff --git a/Examples/python/simulation/ex06_Reflectometry/TOFRWithResolution.py b/Examples/Python/simulation/ex06_Reflectometry/TOFRWithResolution.py
similarity index 100%
rename from Examples/python/simulation/ex06_Reflectometry/TOFRWithResolution.py
rename to Examples/Python/simulation/ex06_Reflectometry/TOFRWithResolution.py
diff --git a/Examples/python/simulation/ex06_Reflectometry/TimeOfFlightReflectometry.py b/Examples/Python/simulation/ex06_Reflectometry/TimeOfFlightReflectometry.py
similarity index 100%
rename from Examples/python/simulation/ex06_Reflectometry/TimeOfFlightReflectometry.py
rename to Examples/Python/simulation/ex06_Reflectometry/TimeOfFlightReflectometry.py
diff --git a/Examples/python/simulation/ex06_Reflectometry/genx_angular_divergence.dat.gz b/Examples/Python/simulation/ex06_Reflectometry/genx_angular_divergence.dat.gz
similarity index 100%
rename from Examples/python/simulation/ex06_Reflectometry/genx_angular_divergence.dat.gz
rename to Examples/Python/simulation/ex06_Reflectometry/genx_angular_divergence.dat.gz
diff --git a/Examples/python/simulation/ex07_Miscellaneous/AccessingSimulationResults.py b/Examples/Python/simulation/ex07_Miscellaneous/AccessingSimulationResults.py
similarity index 100%
rename from Examples/python/simulation/ex07_Miscellaneous/AccessingSimulationResults.py
rename to Examples/Python/simulation/ex07_Miscellaneous/AccessingSimulationResults.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/AxesInDifferentUnits.py b/Examples/Python/simulation/ex07_Miscellaneous/AxesInDifferentUnits.py
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rename from Examples/python/simulation/ex07_Miscellaneous/AxesInDifferentUnits.py
rename to Examples/Python/simulation/ex07_Miscellaneous/AxesInDifferentUnits.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/BoxesWithSpecularPeak.py b/Examples/Python/simulation/ex07_Miscellaneous/BoxesWithSpecularPeak.py
similarity index 100%
rename from Examples/python/simulation/ex07_Miscellaneous/BoxesWithSpecularPeak.py
rename to Examples/Python/simulation/ex07_Miscellaneous/BoxesWithSpecularPeak.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/CylindersInAverageLayer.py b/Examples/Python/simulation/ex07_Miscellaneous/CylindersInAverageLayer.py
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rename from Examples/python/simulation/ex07_Miscellaneous/CylindersInAverageLayer.py
rename to Examples/Python/simulation/ex07_Miscellaneous/CylindersInAverageLayer.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/DepthProbe.py b/Examples/Python/simulation/ex07_Miscellaneous/DepthProbe.py
similarity index 100%
rename from Examples/python/simulation/ex07_Miscellaneous/DepthProbe.py
rename to Examples/Python/simulation/ex07_Miscellaneous/DepthProbe.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/FindPeaks.py b/Examples/Python/simulation/ex07_Miscellaneous/FindPeaks.py
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rename from Examples/python/simulation/ex07_Miscellaneous/FindPeaks.py
rename to Examples/Python/simulation/ex07_Miscellaneous/FindPeaks.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/HalfSpheresInAverageTopLayer.py b/Examples/Python/simulation/ex07_Miscellaneous/HalfSpheresInAverageTopLayer.py
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rename from Examples/python/simulation/ex07_Miscellaneous/HalfSpheresInAverageTopLayer.py
rename to Examples/Python/simulation/ex07_Miscellaneous/HalfSpheresInAverageTopLayer.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/MagneticSpheres.py b/Examples/Python/simulation/ex07_Miscellaneous/MagneticSpheres.py
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rename from Examples/python/simulation/ex07_Miscellaneous/MagneticSpheres.py
rename to Examples/Python/simulation/ex07_Miscellaneous/MagneticSpheres.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/PolarizedSANS.py b/Examples/Python/simulation/ex07_Miscellaneous/PolarizedSANS.py
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rename from Examples/python/simulation/ex07_Miscellaneous/PolarizedSANS.py
rename to Examples/Python/simulation/ex07_Miscellaneous/PolarizedSANS.py
diff --git a/Examples/python/simulation/ex07_Miscellaneous/SimulationParameters.py b/Examples/Python/simulation/ex07_Miscellaneous/SimulationParameters.py
similarity index 100%
rename from Examples/python/simulation/ex07_Miscellaneous/SimulationParameters.py
rename to Examples/Python/simulation/ex07_Miscellaneous/SimulationParameters.py
diff --git a/Examples/python/utils/__init__.py b/Examples/Python/utils/__init__.py
similarity index 100%
rename from Examples/python/utils/__init__.py
rename to Examples/Python/utils/__init__.py
diff --git a/Examples/python/utils/plot_intensity_data.py b/Examples/Python/utils/plot_intensity_data.py
similarity index 100%
rename from Examples/python/utils/plot_intensity_data.py
rename to Examples/Python/utils/plot_intensity_data.py
diff --git a/Examples/python/utils/plot_intensity_data_diff.py b/Examples/Python/utils/plot_intensity_data_diff.py
similarity index 100%
rename from Examples/python/utils/plot_intensity_data_diff.py
rename to Examples/Python/utils/plot_intensity_data_diff.py
diff --git a/Examples/python/utils/show2d.py b/Examples/Python/utils/show2d.py
similarity index 100%
rename from Examples/python/utils/show2d.py
rename to Examples/Python/utils/show2d.py
diff --git a/Examples/python/utils/show2d_root.py b/Examples/Python/utils/show2d_root.py
similarity index 100%
rename from Examples/python/utils/show2d_root.py
rename to Examples/Python/utils/show2d_root.py
diff --git a/Examples/README b/Examples/README.md
similarity index 100%
rename from Examples/README
rename to Examples/README.md
diff --git a/Examples/cpp/CylindersAndPrisms/README b/Examples/cpp/CylindersAndPrisms/README.md
similarity index 100%
rename from Examples/cpp/CylindersAndPrisms/README
rename to Examples/cpp/CylindersAndPrisms/README.md
diff --git a/Examples/cpp/README b/Examples/cpp/README.md
similarity index 100%
rename from Examples/cpp/README
rename to Examples/cpp/README.md
diff --git a/Sample/StandardSamples/SizeDistributionModelsBuilder.h b/Sample/StandardSamples/SizeDistributionModelsBuilder.h
index 7f6e455989fbd975283ab4b3c980bf7234cc7454..ccf5098c1a0d38dd9efa8163ab27109f8a66e189 100644
--- a/Sample/StandardSamples/SizeDistributionModelsBuilder.h
+++ b/Sample/StandardSamples/SizeDistributionModelsBuilder.h
@@ -18,7 +18,7 @@
 #include "Sample/SampleBuilderEngine/ISampleBuilder.h"
 
 //! Creates the sample demonstrating size distribution model in decoupling approximation.
-//! Equivalent of Examples/python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
+//! Equivalent of Examples/Python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
 //! @ingroup standard_samples
 
 class SizeDistributionDAModelBuilder : public ISampleBuilder
@@ -28,7 +28,7 @@ public:
 };
 
 //! Creates the sample demonstrating size distribution model in local monodisperse approximation.
-//! Equivalent of Examples/python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
+//! Equivalent of Examples/Python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
 //! @ingroup standard_samples
 
 class SizeDistributionLMAModelBuilder : public ISampleBuilder
@@ -38,7 +38,7 @@ public:
 };
 
 //! Creates the sample demonstrating size distribution model in size space coupling approximation.
-//! Equivalent of Examples/python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
+//! Equivalent of Examples/Python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
 //! @ingroup standard_samples
 
 class SizeDistributionSSCAModelBuilder : public ISampleBuilder
diff --git a/Tests/Functional/Python/PyCore/README b/Tests/Functional/Python/PyCore/README.md
similarity index 100%
rename from Tests/Functional/Python/PyCore/README
rename to Tests/Functional/Python/PyCore/README.md
diff --git a/Tests/Functional/Python/PyEmbedded/README b/Tests/Functional/Python/PyEmbedded/README.md
similarity index 100%
rename from Tests/Functional/Python/PyEmbedded/README
rename to Tests/Functional/Python/PyEmbedded/README.md
diff --git a/Tests/Functional/Python/PyFit/README b/Tests/Functional/Python/PyFit/README.md
similarity index 100%
rename from Tests/Functional/Python/PyFit/README
rename to Tests/Functional/Python/PyFit/README.md
diff --git a/Tests/Functional/README b/Tests/Functional/README.md
similarity index 100%
rename from Tests/Functional/README
rename to Tests/Functional/README.md
diff --git a/Tests/Performance/Python/README b/Tests/Performance/Python/README.md
similarity index 100%
rename from Tests/Performance/Python/README
rename to Tests/Performance/Python/README.md
diff --git a/ThirdParty/Core/tspectrum/README b/ThirdParty/Core/tspectrum/README.md
similarity index 100%
rename from ThirdParty/Core/tspectrum/README
rename to ThirdParty/Core/tspectrum/README.md
diff --git a/Wrap/python/README b/Wrap/Python/README.md
similarity index 100%
rename from Wrap/python/README
rename to Wrap/Python/README.md
diff --git a/Wrap/python/__init__.py.in b/Wrap/Python/__init__.py.in
similarity index 100%
rename from Wrap/python/__init__.py.in
rename to Wrap/Python/__init__.py.in
diff --git a/Wrap/python/bornagain_python_install.py b/Wrap/Python/bornagain_python_install.py
similarity index 100%
rename from Wrap/python/bornagain_python_install.py
rename to Wrap/Python/bornagain_python_install.py
diff --git a/Wrap/python/plot_utils.py b/Wrap/Python/plot_utils.py
similarity index 99%
rename from Wrap/python/plot_utils.py
rename to Wrap/Python/plot_utils.py
index f0161beb3932617d752e82b5c95678dcaae8b078..f21d57b1c379beb7b030a2e39de49a766704944d 100644
--- a/Wrap/python/plot_utils.py
+++ b/Wrap/Python/plot_utils.py
@@ -2,7 +2,7 @@
 '''
 #   BornAgain: simulate and fit scattering at grazing incidence
 #
-#   @file      Wrap/python.plot_utils
+#   @file      Wrap/Python.plot_utils
 #   @brief     Python extensions of the SWIG-generated Python module bornagain.
 #
 #   @homepage  http://apps.jcns.fz-juelich.de/BornAgain
diff --git a/auto/README b/auto/README.md
similarity index 100%
rename from auto/README
rename to auto/README.md
diff --git a/auto/Wrap/doxygenSample.i b/auto/Wrap/doxygenSample.i
index 1e129b4a8c4e862a90da074e661312b87937dbd7..a9dc98b810dc82e331f3cc92ab6905efa533b8bf 100644
--- a/auto/Wrap/doxygenSample.i
+++ b/auto/Wrap/doxygenSample.i
@@ -7073,7 +7073,7 @@ Sets the batch and thread information to be used.
 // File: classSizeDistributionDAModelBuilder.xml
 %feature("docstring") SizeDistributionDAModelBuilder "
 
-Creates the sample demonstrating size distribution model in decoupling approximation. Equivalent of Examples/python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
+Creates the sample demonstrating size distribution model in decoupling approximation. Equivalent of Examples/Python/simulation/ex03_InterferenceFunctions/ApproximationDA.py
 
 C++ includes: SizeDistributionModelsBuilder.h
 ";
@@ -7085,7 +7085,7 @@ C++ includes: SizeDistributionModelsBuilder.h
 // File: classSizeDistributionLMAModelBuilder.xml
 %feature("docstring") SizeDistributionLMAModelBuilder "
 
-Creates the sample demonstrating size distribution model in local monodisperse approximation. Equivalent of Examples/python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
+Creates the sample demonstrating size distribution model in local monodisperse approximation. Equivalent of Examples/Python/simulation/ex03_InterferenceFunctions/ApproximationLMA.py
 
 C++ includes: SizeDistributionModelsBuilder.h
 ";
@@ -7097,7 +7097,7 @@ C++ includes: SizeDistributionModelsBuilder.h
 // File: classSizeDistributionSSCAModelBuilder.xml
 %feature("docstring") SizeDistributionSSCAModelBuilder "
 
-Creates the sample demonstrating size distribution model in size space coupling approximation. Equivalent of Examples/python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
+Creates the sample demonstrating size distribution model in size space coupling approximation. Equivalent of Examples/Python/simulation/ex03_InterferenceFunctions/ApproximationSSCA.py
 
 C++ includes: SizeDistributionModelsBuilder.h
 ";
diff --git a/cmake/BornAgain/Config.cmake b/cmake/BornAgain/Config.cmake
index bd48224c063cf03230168482f1e317191908f46e..36a0e80f044cd48756598510a799553fb5dcddf2 100644
--- a/cmake/BornAgain/Config.cmake
+++ b/cmake/BornAgain/Config.cmake
@@ -23,9 +23,9 @@ configure_file(${CONFIGURABLES_DIR}/BABuild.h.in  ${BUILD_INC_DIR}/BABuild.h @ON
 configure_file(${CONFIGURABLES_DIR}/BATesting.h.in  ${BUILD_INC_DIR}/BATesting.h @ONLY)
 string(APPEND CMAKE_CXX_FLAGS " -I${BUILD_INC_DIR}")
 
-configure_file(${CMAKE_SOURCE_DIR}/Examples/python/utils/plot_intensity_data.py
+configure_file(${CMAKE_SOURCE_DIR}/Examples/Python/utils/plot_intensity_data.py
     ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/plot_intensity_data.py COPYONLY)
-configure_file(${CMAKE_SOURCE_DIR}/Examples/python/utils/plot_intensity_data_diff.py
+configure_file(${CMAKE_SOURCE_DIR}/Examples/Python/utils/plot_intensity_data_diff.py
     ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/plot_intensity_data_diff.py COPYONLY)
 
 # -----------------------------------------------------------------------------
diff --git a/cmake/BornAgain/Directories.cmake b/cmake/BornAgain/Directories.cmake
index 064e6ec569fd604386eef5684ce18ab7e54868c0..330836505a5d8bc908abc9862ca0f530d2ed9a36 100644
--- a/cmake/BornAgain/Directories.cmake
+++ b/cmake/BornAgain/Directories.cmake
@@ -4,7 +4,7 @@
 
 set(WRAP_DIR ${CMAKE_SOURCE_DIR}/Wrap)
 set(TEST_REFERENCE_DIR ${CMAKE_SOURCE_DIR}/Tests/ReferenceData)
-set(PY_EXAMPLES_DIR ${CMAKE_SOURCE_DIR}/Examples/python)
+set(PY_EXAMPLES_DIR ${CMAKE_SOURCE_DIR}/Examples/Python)
 
 # -----------------------------------------------------------------------------
 # auto directories (refreshed when CONFIGURE options are set)
diff --git a/cmake/BornAgain/NixInstall.cmake b/cmake/BornAgain/NixInstall.cmake
index 6c7bdfbb5155adf9902b1abb905a88e2d37f4b77..56f8402578de8a0297286c3ab8e1fe1b79f65557 100644
--- a/cmake/BornAgain/NixInstall.cmake
+++ b/cmake/BornAgain/NixInstall.cmake
@@ -29,6 +29,6 @@ if(NOT BORNAGAIN_APPLE_BUNDLE AND NOT BUILD_DEBIAN)
         " COMPONENT Runtime)
 else()
 
-    install(FILES ${WRAP_DIR}/python/bornagain_python_install.py
+    install(FILES ${WRAP_DIR}/Python/bornagain_python_install.py
         DESTINATION ${destination_libexec})
 endif()
diff --git a/cmake/BornAgain/PythonAPI.cmake b/cmake/BornAgain/PythonAPI.cmake
index 1262f810d6d710e97a9dedc8eea6f63b286febb1..1d73ad5299c3cc5fe26715a3abe1876cbd99e3dc 100644
--- a/cmake/BornAgain/PythonAPI.cmake
+++ b/cmake/BornAgain/PythonAPI.cmake
@@ -4,7 +4,7 @@ if(NOT BORNAGAIN_PYTHON)
     message(FATAL_ERROR "PythonAPI included though BORNAGAIN_PYTHON=false")
 endif()
 
-configure_file(${WRAP_DIR}/python/plot_utils.py
+configure_file(${WRAP_DIR}/Python/plot_utils.py
     ${CMAKE_BINARY_DIR}/lib/bornagain/plot_utils.py COPYONLY)
 
 if(WIN32)
@@ -16,7 +16,7 @@ if(BORNAGAIN_APPLE_BUNDLE)
     set(BA_MODULES_IMPORT_PATH
         lib/BornAgain-${BornAgain_VERSION_MAJOR}.${BornAgain_VERSION_MINOR})
 endif()
-configure_file("${WRAP_DIR}/python/__init__.py.in"
+configure_file("${WRAP_DIR}/Python/__init__.py.in"
     "${CMAKE_BINARY_DIR}/lib/bornagain/__init__.py" @ONLY)
 
 if(CONFIGURE_BINDINGS)
diff --git a/devtools/README b/devtools/README.md
similarity index 100%
rename from devtools/README
rename to devtools/README.md
diff --git a/devtools/profiling/README b/devtools/profiling/README.md
similarity index 100%
rename from devtools/profiling/README
rename to devtools/profiling/README.md