Rename library to giotto-tda (#198)

* Bump library to 0.1.4, globally rename giotto module to gtda

* Populated RELEASE.rst with past release info and new release

* Globally rename glearn -> gtda

* Add tracking for gudhi-devel and ripser

.coveragerc

@@ -1,13 +1,13 @@
 [run]
 omit =
-    */giotto/externals/*
+    */gtda/externals/*
     **/setup.py
 
-    */giotto/compose/*
-    */giotto/datasets/*
-    */giotto/images/*
-    */giotto/neural_network/*
-    */giotto/model_selection/*
+    */gtda/compose/*
+    */gtda/datasets/*
+    */gtda/images/*
+    */gtda/neural_network/*
+    */gtda/model_selection/*
 
     **/base.py
     **/pipeline.py

.gitignore

@@ -24,7 +24,7 @@ doc/build
 doc/generated
 
 # Pybind11
-giotto/externals/pybind11
+gtda/externals/pybind11
 
 # Output files
 *.out
@@ -40,4 +40,4 @@ giotto/externals/pybind11
 .hypothesis/
 
 # development
-giotto/mapper/scratch/*
+gtda/mapper/scratch/*

.gitmodules

@@ -1,7 +1,7 @@
-[submodule "giotto/externals/ripser"]
-	path = giotto/externals/ripser
+[submodule "gtda/externals/ripser"]
+	path = gtda/externals/ripser
 	url = https://github.com/scikit-tda/ripser.py.git
-[submodule "giotto/externals/gudhi-devel"]
-	path = giotto/externals/gudhi-devel
-	url = https://github.com/giotto-learn/gudhi-devel
+[submodule "gtda/externals/gudhi-devel"]
+	path = gtda/externals/gudhi-devel
+	url = https://github.com/giotto-ai/gudhi-devel
 	branch = giotto

CMakeLists.txt

@@ -1,8 +1,8 @@
 cmake_minimum_required(VERSION 3.9)
 project(giotto_bindings LANGUAGES CXX)
 
-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/giotto/externals/pybind11)
-set(BINDINGS_DIR "giotto/externals/bindings")
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/gtda/externals/pybind11)
+set(BINDINGS_DIR "gtda/externals/bindings")
 
 find_package(Boost 1.56 REQUIRED)
 include_directories(${Boost_INCLUDE_DIR})
@@ -46,7 +46,7 @@ target_compile_options(giotto_bottleneck PUBLIC -Wall -O3)
 target_compile_options(giotto_bottleneck PUBLIC $<$<CONFIG:DEBUG>:-O2 -ggdb -D_GLIBCXX_DEBUG>)
 target_compile_definitions(giotto_bottleneck PRIVATE BOOST_RESULT_OF_USE_DECLTYPE=1 BOOST_ALL_NO_LIB=1 BOOST_SYSTEM_NO_DEPRECATED=1)
 
-set(GUDHI_SRC_DIR "giotto/externals/gudhi-devel/src")
+set(GUDHI_SRC_DIR "gtda/externals/gudhi-devel/src")
 
 #######################################################################
 #                           Cubical Complex                           #

CODE_AUTHORS

@@ -1,5 +1,5 @@
-# The following is the list of the code authors of the giotto-learn python
-# package. Where component authors are known, add them here. 
+# The following is the list of the code authors of the giotto-tda python
+# package. Where component authors are known, add them here.
 
 Guillaume Tauzin, [email protected]
 Umberto Lupo, [email protected]

CODE_OWNERS

@@ -1,5 +1,5 @@
 
-# The following is the list of the code owners of the giotto-learn python
+# The following is the list of the code owners of the giotto-tda python
 # package.
 
 L2F SA

CONTRIBUTING.rst

@@ -5,9 +5,9 @@ Pull Request Checklist
 ----------------------
 
 Before sending your pull requests, make sure you followed this list.
-  - Read the `contributing guidelines <https://github.com/giotto-learn/giotto-learn/blob/master/GOVERNANCE.rst>`_.
-  - Read the `code of conduct <https://github.com/giotto-learn/giotto-learn/blob/master/CODE_OF_CONDUCT.rst>`_.
-  - Ensure you have signed the `contributor license agreement (CLA) <https://cla-assistant.io/giotto-learn/giotto-learn>`_.
+  - Read the `contributing guidelines <https://github.com/giotto-ai/giotto-tda/blob/master/GOVERNANCE.rst>`_.
+  - Read the `code of conduct <https://github.com/giotto-ai/giotto-tda/blob/master/CODE_OF_CONDUCT.rst>`_.
+  - Ensure you have signed the `contributor license agreement (CLA) <https://cla-assistant.io/giotto-ai/giotto-tda>`_.
   - Check if the changes are consistent with the guidelines.
   - Changes are consistent with the Coding Style.
   - Run Unit Tests.
@@ -18,21 +18,21 @@ How to become a contributor and submit your own code
 Contributor License Agreements
 ------------------------------
 
-In order to become a contributor of Giotto, the first step is to sign the
-`contributor license agreement (CLA) <https://cla-assistant.io/giotto-learn/giotto-learn>`_.
+In order to become a contributor of giotto-tda, the first step is to sign the
+`contributor license agreement (CLA) <https://cla-assistant.io/giotto-ai/giotto-tda>`_.
 **NOTE**: Only original source code from you and other people that have signed
 the CLA can be accepted into the main repository.
 
 Contributing code
 -----------------
 
-If you have improvements to Giotto, do not hesitate to send us pull requests!
+If you have improvements to giotto-tda, do not hesitate to send us pull requests!
 Please follow the Github how to (https://help.github.com/articles/using-pull-requests/).
-The Giotto Team will review your pull requests. Once the pull requests are approved and pass continuous integration checks, the
-Giotto team will work on getting your pull request submitted to our GitHub
+The giotto-tda team will review your pull requests. Once the pull requests are approved and pass continuous integration checks, the
+giotto-tda team will work on getting your pull request submitted to our GitHub
 repository. Eventually, your pull request will be merged automatically on GitHub.
-If you want to contribute, start working through the Giotto codebase,
-navigate to the `GitHub issue tab <https://github.com/giotto-learn/giotto-learn/issues>`_
+If you want to contribute, start working through the giotto-tda codebase,
+navigate to the `GitHub issue tab <https://github.com/giotto-ai/giotto-tda/issues>`_
 and start looking through interesting issues. These are issues that we believe
 are particularly well suited for outside contributions, often because we
 probably won't get to them right now. If you decide to start on an issue, leave
@@ -53,17 +53,17 @@ General guidelines and philosophy for contribution
   b) guard against future breaking changes to lower the maintenance cost.
 * Bug fixes also generally require unit tests, because the presence of bugs
   usually indicates insufficient test coverage.
-* Keep API compatibility in mind when you change code in core Giotto.
+* Keep API compatibility in mind when you change code in core giotto-tda.
 * Clearly define your exceptions using the utils functions and test the exceptions.
-* When you contribute a new feature to Giotto, the maintenance burden is   
-  (by default) transferred to the Giotto team. This means that the benefit   
+* When you contribute a new feature to giotto-tda, the maintenance burden is   
+  (by default) transferred to the giotto-tda team. This means that the benefit   
   of the contribution must be compared against the cost of maintaining the   
   feature.
 
 C++ coding style
 ----------------
 
-Changes to Giotto C/C++ code should conform to `Google C++ Style Guide <https://google.github.io/styleguide/cppguide.html>`_.
+Changes to giotto-tda's C/C++ code should conform to `Google C++ Style Guide <https://google.github.io/styleguide/cppguide.html>`_.
 Use `clang-tidy` to check your C/C++ changes. To install `clang-tidy` on
 ubuntu:16.04, do:
 
@@ -81,7 +81,7 @@ You can check a C/C++ file by doing:
 Python coding style
 -------------------
 
-Changes to Giotto Python code should conform to PEP8 directives.
+Changes to giotto-tda's Python code should conform to PEP8 directives.
 Use `flake8` to check your Python changes. To install `flake8` just do
 
 .. code-block:: python
@@ -106,7 +106,7 @@ We provide a pre-commit git hook to prevent accidental commits to the master bra
 Running unit tests
 ------------------
 
-There are two ways to run Giotto unit tests.
+There are two ways to run unit tests for giotto-tda.
 
 1. Using tools and libraries installed directly on your system. The election tool is `pytest`. To install `pytest` just do
 
@@ -120,4 +120,4 @@ You can use `pytest` on your python code via the following instructions:
 
     pytest name_of_your_script.py
 
-2. Using Azure (azure-pipelines.yml) and Giotto's CI scripts.
+2. Using Azure (azure-pipelines.yml) and giotto-tda's CI scripts.

GOVERNANCE.rst

@@ -1,4 +1,4 @@
-This file describe the governance of the Giotto project.
+This file describe the governance of the giotto-tda project.
 
 Project owner:
 --------------
@@ -8,10 +8,10 @@ Project owner:
 Authors:
 --------
 
-- Please refer to the `authors <https://github.com/giotto-learn/giotto-learn/blob/master/CODE_AUTHORS>`_ file
+- Please refer to the `authors <https://github.com/giotto-ai/giotto-tda/blob/master/CODE_AUTHORS>`_ file
 
-Giotto Project Team:
---------------------
+Giotto-tda Project Team:
+------------------------
 
 - Umberto Lupo [email protected] (Maintainer)
 - Lewis Tunstall [email protected] (Maintainer)
@@ -20,4 +20,4 @@ Giotto Project Team:
 Former Project Team Members:
 ----------------------------
 
-- Philippe Nguyen [email protected] (Developer)
+- Philippe Nguyen [email protected] (Developer)

ISSUE_TEMPLATE.md

@@ -1,7 +1,7 @@
-<!-- Instructions For Filing a Bug: https://github.com/giotto-learn/giotto-learn/blob/master/CONTRIBUTING.rst -->
+<!-- Instructions For Filing a Bug: https://github.com/giotto-ai/giotto-tda/blob/master/CONTRIBUTING.rst -->
 
 #### Description
-<!-- Example: Joblib Error thrown when calling fit on VietorisRipsPersistence 
+<!-- Example: Joblib Error thrown when calling fit on VietorisRipsPersistence
 -->
 
 #### Steps/Code to Reproduce
@@ -23,9 +23,9 @@ import platform; print(platform.platform())
 import sys; print("Python", sys.version)
 import numpy; print("NumPy", numpy.__version__)
 import scipy; print("SciPy", scipy.__version__)
-import joblib; print("joblib", joblib.__version__)
-import sklearn; print("Scikit-Learn", sklearn.__version__)
-import giotto; print("giotto-Learn", giotto.__version__)
+import joblib; print("Joblib", joblib.__version__)
+import sklearn; print("Scikit-learn", sklearn.__version__)
+import gtda; print("Giotto-tda", gtda.__version__)
 -->
 
 

PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 <!--
 Thanks for contributing a pull request! Please ensure you have taken a look at
-the contribution guidelines: https://github.com/giotto-learn/giotto-learn/blob/master/CONTRIBUTING.md#pull-request-checklist
+the contribution guidelines: https://github.com/giotto-ai/giotto-tda/blob/master/CONTRIBUTING.md#pull-request-checklist
 -->
 
 #### Reference Issues/PRs

README.rst

@@ -3,7 +3,7 @@
 
 |Azure|_ |Azure-cov|_ |Azure-test|_ |binder|_
 
-.. |Azure| image:: https://dev.azure.com/maintainers/Giotto/_apis/build/status/giotto-ai.giotto-learn?branchName=master
+.. |Azure| image:: https://dev.azure.com/maintainers/Giotto/_apis/build/status/giotto-ai.giotto-tda?branchName=master
 .. _Azure: https://dev.azure.com/maintainers/Giotto/_build/latest?definitionId=2&branchName=master
 
 .. |Azure-cov| image:: https://img.shields.io/badge/Coverage-93%25-passed
@@ -13,14 +13,14 @@
 .. _Azure-test: https://dev.azure.com/maintainers/Giotto/_build/results?buildId=6&view=ms.vss-test-web.build-test-results-tab
 
 .. |binder| image:: https://mybinder.org/badge_logo.svg
-.. _binder: https://mybinder.org/v2/gh/giotto-ai/giotto-learn/master?filepath=examples
+.. _binder: https://mybinder.org/v2/gh/giotto-ai/giotto-tda/master?filepath=examples
 
 
-giotto-learn
-============
+giotto-tda
+==========
 
 
-giotto-learn is a high performance topological machine learning toolbox in Python built on top of
+giotto-tda is a high performance topological machine learning toolbox in Python built on top of
 scikit-learn and is distributed under the GNU AGPLv3 license. It is part of the `Giotto <https://github.com/giotto-ai>`_ family of open-source projects.
 
 Website: https://giotto.ai
@@ -29,7 +29,7 @@ Website: https://giotto.ai
 Project genesis
 ---------------
 
-giotto-learn is the result of a collaborative effort between `L2F SA
+giotto-tda is the result of a collaborative effort between `L2F SA
 <https://www.l2f.ch/>`_, the `Laboratory for Topology and Neuroscience
 <https://www.epfl.ch/labs/hessbellwald-lab/>`_ at EPFL, and the `Institute of Reconfigurable & Embedded Digital Systems (REDS)
 <https://heig-vd.ch/en/research/reds>`_ of HEIG-VD.
@@ -40,7 +40,7 @@ Installation
 Dependencies
 ~~~~~~~~~~~~
 
-The latest stable version of giotto-learn requires:
+The latest stable version of giotto-tda requires:
 
 - Python (>= 3.5)
 - NumPy (>= 1.17.0)
@@ -61,19 +61,19 @@ To run the examples, jupyter is required.
 User installation
 ~~~~~~~~~~~~~~~~~
 
-The simplest way to install giotto-learn is using ``pip``   ::
+The simplest way to install giotto-tda is using ``pip``   ::
 
-    pip install -U giotto-learn
+    pip install -U giotto-tda
 
 Note: the above may fail on old versions of ``pip``. We recommend upgrading ``pip``
 to a recent version.
 
 Pre-release, experimental builds containing recently added features and/or
 bug fixes can be installed by running   ::
 
-    pip install -U giotto-learn-nightly
+    pip install -U giotto-tda-nightly
 
-The main difference between ``giotto-learn-nightly`` and the developer
+The main difference between ``giotto-tda-nightly`` and the developer
 installation (see below) is that the former is shipped with pre-compiled wheels
 (similarly to the stable release) and hence does not require any C++ dependencies.
 
@@ -87,13 +87,13 @@ Contributing
 
 We welcome new contributors of all experience levels. The Giotto
 community goals are to be helpful, welcoming, and effective. To learn more about
-making a contribution to giotto-learn, please see the `CONTRIBUTING.rst
-<https://github.com/giotto-ai/giotto-learn/blob/master/CONTRIBUTING.rst>`_ file.
+making a contribution to giotto-tda, please see the `CONTRIBUTING.rst
+<https://github.com/giotto-ai/giotto-tda/blob/master/CONTRIBUTING.rst>`_ file.
 
 Developer installation
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Installing both the PyPI release and source of giotto-learn in the same environment is not recommended since it is
+Installing both the PyPI release and source of giotto-tda in the same environment is not recommended since it is
 known to cause conflicts with the C++ bindings.
 
 C++ dependencies:
@@ -136,15 +136,15 @@ Source code
 
 You can check the latest sources with the command::
 
-    git clone https://github.com/giotto-ai/giotto-learn.git
+    git clone https://github.com/giotto-ai/giotto-tda.git
 
 
 To install:
 '''''''''''
 
 .. code-block:: bash
 
-   cd giotto-learn
+   cd giotto-tda
    pip install -e ".[tests, doc]"
 
 This way, you can pull the library's latest changes and make them immediately available on your machine.
@@ -162,15 +162,15 @@ source directory::
 Changelog
 ---------
 
-See the `RELEASE.rst <https://github.com/giotto-ai/giotto-learn/blob/master/RELEASE.rst>`__ file
-for a history of notable changes to giotto-learn.
+See the `RELEASE.rst <https://github.com/giotto-ai/giotto-tda/blob/master/RELEASE.rst>`__ file
+for a history of notable changes to giotto-tda.
 
 Important links
 ~~~~~~~~~~~~~~~
 
-- Official source code repo: https://github.com/giotto-ai/giotto-learn
-- Download releases: https://pypi.org/project/giotto-learn/
-- Issue tracker: https://github.com/giotto-ai/giotto-learn/issues
+- Official source code repo: https://github.com/giotto-ai/giotto-tda
+- Download releases: https://pypi.org/project/giotto-tda/
+- Issue tracker: https://github.com/giotto-ai/giotto-tda/issues
 
 Community
 ---------