Preparations for first pypi release

.circleci/config.yml

@@ -10,7 +10,7 @@ default_job: &default_job
     - checkout
     - run:
         name: Install Python dependencies
-        command: python3.8 -m pip install -r requirements.txt
+        command: python3.8 -m pip install -r requirements/dev.txt
     - run:
         name: Configure
         command: |
@@ -89,7 +89,7 @@ jobs:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.8 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements/dev.txt
       - run:
           name: Configure
           command: |
@@ -119,7 +119,7 @@ jobs:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.8 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements/dev.txt
       - run:
           name: Configure
           command: |
@@ -138,7 +138,7 @@ jobs:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.8 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements/dev.txt
       - run:
           name: Configure
           command: |
@@ -160,7 +160,7 @@ jobs:
       - run:
           name: Install Python dependencies
           command: |
-            python3.8 -m pip install -r requirements.txt
+            python3.8 -m pip install -r requirements/dev.txt
             python3.8 -m pip install codecov coverage
       - run:
           name: Configure
@@ -199,7 +199,7 @@ jobs:
       - checkout
       - run:
           name: Install Python dependencies
-          command: python3.8 -m pip install -r requirements.txt
+          command: python3.8 -m pip install -r requirements/common.txt -r requirements/tests.txt
       - run:
           name: Configure
           command: |

AUTHORS.txt

@@ -0,0 +1,16 @@
+Michele Ceriotti
+Félix Musil
+Max Veit
+Alexander Goscinski
+Guillaume Fraux
+Michael J. Willatt
+Markus Stricker
+Till Junge
+Klim Goldshtein
+Chiheb B. Mahmoud
+Federico Giberti
+Andrea Grisafi
+Rose K. Cersonsky
+Lorenzo Gigli
+Jigyasa Nigam
+Kevin K. Huguenin-Dumittan

MANIFEST.in

@@ -1,4 +1,4 @@
-include README.rst requirements_pip.txt CMakeLists.txt pyproject.toml
+include README.rst AUTHORS.txt requirements/minimal.txt CMakeLists.txt pyproject.toml
 recursive-include  src *
 recursive-include  bindings *
 recursive-include  cmake *

README.rst

@@ -35,31 +35,15 @@ For more information, have a look at the documentation_!
 Development
 -----------
 
-The code is currently in the alpha development phase; it is not yet
-suitable for public use. Nevertheless, there is a significant amount of
-functionality (including two tutorials) currently working and available
-to test if you’re feeling adventurous. Feedback and bug reports are
-welcome, as long as you keep the above in mind.
+The code is currently in the beta development phase, therefore we cannot guarantee that the interface and data formats will not change, but it has been in use for at least a year.
+Feedback and bug reports are welcome, as long as you keep the above in mind.
 
 .. end-intro
 
 See `Helpers for Developers`_ below for some essential tools if you want to help
-develop libRascal.  Be sure to also read `CONTRIBUTING.rst <CONTRIBUTING.rst>`_
+develop librascal.  Be sure to also read `CONTRIBUTING.rst <https://github.com/cosmo-epfl/librascal/blob/master/CONTRIBUTING.rst>`_
 if you plan on making a contribution.
 
-Installation
-------------
-
-.. start-install
-
-The installation of the library for python use can be done simply with:
-
-.. code:: bash
-
-   pip install .
-
-assuming that `python` 3.5 (or higher) and `gcc` or `clang` are available.
-
 Dependencies
 ~~~~~~~~~~~~
 
@@ -77,65 +61,44 @@ following packages installed:
 +-------------+--------------------+
 | python      | 3.6 or higher      |
 +-------------+--------------------+
-| numpy       | 1.13 or higher     |
-+-------------+--------------------+
-| scipy       | 1.4.0 or higher    |
-+-------------+--------------------+
-| ASE         | 3.18 or higher     |
-+-------------+--------------------+
 
-Other necessary packages (such as Eigen and PyBind11) are downloaded
-automatically when compiling Rascal.
+Other necessary packages Eigen, PyBind11 and wigxjpf are downloaded
+automatically when compiling librascal.
+
 
-The following packages are required for some optional features:
+Installation
+------------
+
+.. start-install
+
+When the dependencies are met, the python package can be installed with:
+
+.. code:: bash
+
+   pip install librascal
+
+For optional features of librascal the following python packages are required:
 
 +--------------------------+-------------+--------------------+
-| Feature                  | Package     | Required version   |
+| Librascal feature        | Package     | Required version   |
 +==========================+=============+====================+
 | Feature compression      | skcosmo     | 0.1.0 or later     |
 +--------------------------+-------------+--------------------+
 | Rotational algebra       | sympy       | 1.4 or later       |
 | (Clebsch-Gordan coeffs.) |             |                    |
 +--------------------------+-------------+--------------------+
-| Building documentation   | pandoc      | (latest)           |
-+--------------------------+-------------+--------------------+
-|                          | sphinx      | 2.1.2 or later     |
-+--------------------------+-------------+--------------------+
-|                          | breathe     | 4.14.1 or later    |
-+--------------------------+-------------+--------------------+
-|                          | nbsphinx    | 0.8.1 or later     |
-+--------------------------+-------------+--------------------+
-
-Compiling
-~~~~~~~~~
-
-To compile the code it is necessary to have CMake 3.0 and a C++ compiler
-supporting C++14. During the configuration, it will automatically try to
-download the external libraries on which it depends:
-
--  Eigen
--  Pybind11
--  Boost (only the unit test framework library)
--  Python3
-
-And the following libraries to build the documentation:
-
--  Doxygen
--  Sphinx
--  Breathe
 
-Beware, Python3 is mandatory. The code won’t work with a Python version
-older than 3.
-
-You can then use pip to install all python packages required for the usage
-and development of rascal:
+The dependencies for the optional features and the `introductive examples <https://cosmo-epfl.github.io/librascal/examples/examples.html>`_ can be installed with
 
 .. code:: bash
 
-    pip install -r requirements.txt
+   pip install -r requirements/common.txt
+
+Compiling
+~~~~~~~~~
 
-To configure and compile the code with the default options, on \*nix
-systems (Windows is not supported):
+To compile the code it is necessary to have CMake 3.0 and a C++ compiler
+supporting C++14. To configure and compile the code with the default options, on \*nix systems (Windows is not supported):
 
 .. code:: shell
 
@@ -176,7 +139,7 @@ for formatting compliance with clang-format 8.0 or higher and black packages
 .. code:: shell
 
    sudo apt-get install clang-format-8
-   pip3 install black
+   pip install -r requirements/testing.txt
 
 Build Type
 ^^^^^^^^^^
@@ -209,7 +172,7 @@ packages. To install them on ubuntu:
 
 .. code:: shell
 
-  pip3 install sphinx sphinx_rtd_theme breathe nbsphinx
+  pip install -r requirements/doc.txt
   sudo apt-get install pandoc doxygen graphviz
 
 Then to build the documentation run:
@@ -220,7 +183,7 @@ Then to build the documentation run:
   cmake -DBUILD_DOC=ON ..
   make doc
 
-and open :file:`build/docs/html/index.html` in a browser.
+and open `build/docs/html/index.html` in a browser.
 
 Bindings
 ^^^^^^^^
@@ -235,28 +198,24 @@ build only the c++ library:
    cmake -DBUILD_BINDINGS=OFF ..
    make
 
-Installing rascal
-^^^^^^^^^^^^^^^^^
-To install the python library with c++ bindings:
+Helpers for Developers
+~~~~~~~~~~~~~~~~~~~~~~
 
-.. code:: shell
+All python packages used for development can be installed with:
 
-   pip install .
+.. code:: shell
 
-
-Helpers for Developers
-~~~~~~~~~~~~~~~~~~~~~~
+   pip install -r requirements/dev.txt
 
 Deepclean
 ^^^^^^^^^
 
 To remove all the cmake files/folders except for the external
-library (enable glob and remove):
+libraries (e.g. Eigen):
 
 .. code:: shell
 
-   shopt -s extglob
-   rm -fr -- !(external|third-party)
+   make deepclean
 
 Automatic code formatting
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -272,7 +231,7 @@ tools with:
 
 .. code:: shell
 
-   sudo apt-get install clang-format
+   sudo apt-get install clang-format-8
    pip install black
 
 The automatic formatting of the c++ and python files can be
@@ -336,41 +295,8 @@ noise.)
 
 Nonetheless, it is highly discouraged to contribute code in the form of
 notebooks; even with filters like ``nbstripout`` they're a hassle to use
-in version control.  Use them only for tutorials or *stable* examples that
+in version control.  Use them only for comprehensive tutorials or *stable* examples that
 are either meant to be run *interactively* or are meant to be processed by
 `sphinx` (`nbsphinx <https://nbsphinx.readthedocs.io/en/latest/>`_) for
 inclusion in the
-`tutorials page <https://cosmo-epfl.github.io/librascal/tutorials/tutorials.html>`_.
-
-Miscellaneous Information
--------------------------
-
--  Common cmake flags:
-
-   -  -DCMAKE_CXX_COMPILER
-   -  -DCMAKE_C_COMPILER
-   -  -DCMAKE_BUILD_TYPE
-   -  -DBUILD_BINDINGS
-   -  -DINSTALL_PATH
-   -  -DBUILD_DOC
-   -  -DBUILD_TESTS
-
--  Special flags:
-
-   -  -DBUILD_BINDINGS:
-
-      -  ON (default) -> build python binding
-      -  OFF -> does not build python binding
-
-   -  -DINSTALL_PATH:
-
-      -  empty (default) -> does not install in a custom folder
-      -  custom string -> root path for the installation
-
-
-To build librascal as a docker environment:
-
-.. code:: shell
-
-   sudo docker build -t test -f ./docker/install_env.dockerfile  .
-   sudo docker run -it -v /path/to/repo/:/home/user/  test
+`introductive examples <https://cosmo-epfl.github.io/librascal/examples/examples.html>`_.

bindings/CMakeLists.txt

@@ -80,22 +80,22 @@ set_target_properties(_rascal PROPERTIES INSTALL_RPATH "${BINDNIGS_INSTALL_RPATH
 
 # Normal installation procedure
 # copy rascal folder in the python distribution
-install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/rascal" DESTINATION "${CMAKE_INSTALL_PREFIX}/bindings"
+install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/librascal" DESTINATION "${CMAKE_INSTALL_PREFIX}/bindings"
     PATTERN "*__pycache__" EXCLUDE
     PATTERN "*.pyc" EXCLUDE
     PATTERN "*.so" EXCLUDE
     PATTERN "*.dylib" EXCLUDE
 )
-install(TARGETS _rascal DESTINATION "${CMAKE_INSTALL_PREFIX}/bindings/rascal/lib")
+install(TARGETS _rascal DESTINATION "${CMAKE_INSTALL_PREFIX}/bindings/librascal/lib")
 
 # Copy the python wrappers in the build folder
 # Copy the resulting bindings lib in the python wrapper lib folder
 add_custom_target(copy_python_bindings ALL
-    COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_BINARY_DIR}/rascal
+    COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_BINARY_DIR}/librascal
     COMMAND ${CMAKE_COMMAND} -E copy_directory
-        ${CMAKE_CURRENT_SOURCE_DIR}/rascal ${CMAKE_BINARY_DIR}/rascal
+        ${CMAKE_CURRENT_SOURCE_DIR}/librascal ${CMAKE_BINARY_DIR}/librascal
     COMMAND ${CMAKE_COMMAND} -E copy
-        ${CMAKE_CURRENT_BINARY_DIR}/_rascal.* ${CMAKE_BINARY_DIR}/rascal/lib/
+        ${CMAKE_CURRENT_BINARY_DIR}/_rascal.* ${CMAKE_BINARY_DIR}/librascal/lib/
     DEPENDS _rascal
     COMMENT "Copying python bindings and libraries"
 )

bindings/rascal/__init__.py → bindings/librascal/__init__.py

@@ -1,3 +1,3 @@
 __all__ = ["lib", "representations", "utils", "neighbourlist"]
 
-__version__ = "0.0.0"
+__version__ = "0.1.0"

bindings/rascal/models/kernels.py → bindings/librascal/models/kernels.py

@@ -45,7 +45,7 @@ class Kernel(BaseIO):
     sparse kernels [1]_, we refer to the pseudo points with 'M'. So a
     kernel between the training samples and the pseudo points is
     'KNM'. For more information on sparse kernels see
-    :meth:`rascal.models.krr.train_gap_model`.
+    :meth:`librascal.models.krr.train_gap_model`.
 
     .. [1] Joaquin Quiñonero-Candela, Carl Edward Rasmussen;
             A Unifying View of Sparse Approximate Gaussian Process Regression,