created structure

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-ENTER_YOUR_EMAIL_ADDRESS.
+[email protected].
 
 All complaints will be reviewed and investigated promptly and fairly.
 

CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# template-python-repository pull request guidelines
+# eeg_research pull request guidelines
 
-Pull requests are always welcome, and we appreciate any help you give. Note that a code of conduct applies to all spaces managed by the template-python-repository project, including issues and pull requests. Please see the [Code of Conduct](CODE_OF_CONDUCT.md) for details.
+Pull requests are always welcome, and we appreciate any help you give. Note that a code of conduct applies to all spaces managed by the eeg_research project, including issues and pull requests. Please see the [Code of Conduct](CODE_OF_CONDUCT.md) for details.
 
 When submitting a pull request, we ask you to check the following:
 

LICENSE

@@ -1,21 +1,165 @@
-MIT License
-
-Copyright (c) 2023 Child Mind Institute
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

README.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/657341621.svg)](https://zenodo.org/doi/10.5281/zenodo.10383685)
 # Todo
 
-- [ ] Run `setup_template.py` to initialize the repository.
+- [x] Run `setup_template.py` to initialize the repository.
 - [ ] Replace the content of this `README.md` with details specific to your project.
 - [ ] Install the `pre-commit` hooks to ensure code quality on each commit.
 - [ ] Revise SECURITY.md to reflect supported versions or remove it if not applicable.
@@ -12,12 +12,12 @@
 
 # EEG research
 
-[![Build](https://github.com/childmindresearch/template-python-repository/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/template-python-repository/actions/workflows/test.yaml?query=branch%3Amain)
-[![codecov](https://codecov.io/gh/childmindresearch/template-python-repository/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/template-python-repository)
+[![Build](https://github.com/childmindresearch/eeg_research/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/eeg_research/actions/workflows/test.yaml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/childmindresearch/eeg_research/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/eeg_research)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![stability-stable](https://img.shields.io/badge/stability-experimental-red.svg)
-[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/childmindresearch/template-python-repository/blob/main/LICENSE)
-[![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/template-python-repository)
+[![LGPL--3.0 License](https://img.shields.io/badge/license-LGPL--3.0-blue.svg)](https://github.com/childmindresearch/eeg_research/blob/main/LICENSE)
+[![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/eeg_research)
 
 The purpose of this monorepository is to group all software tools and pipelines related to EEG (experiment, cleaning, analysis etc.)
 

SECURITY.md

@@ -15,6 +15,6 @@ Note which version(s) will receive security updates. For example:
 
 ## Reporting Vulnerabilities
 
-To report security vulnerabilities, please do NOT use our issues page. Instead, kindly email us at ENTER_YOUR_EMAIL_ADDRESS. Please refrain from using other communication channels.
+To report security vulnerabilities, please do NOT use our issues page. Instead, kindly email us at [email protected]. Please refrain from using other communication channels.
 
 For non-security-related issues, we welcome your input and feedback on our issues page. Feel free to share your ideas and suggestions to help us improve our services.

pyproject.toml

@@ -1,11 +1,11 @@
 [tool.poetry]
-name = "app-name"
+name = "eeg_research"
 version = "0.1.0"
-description = "A beautiful description."
-authors = ["Reinder Vos de Wael <[email protected]>"]
+description = "All tools and pipelines developed for eeg research"
+authors = ["Samuel Louviot <[email protected]>"]
 license = "LGPL-2.1"
 readme = "README.md"
-packages = [{include = "APP_NAME", from = "src"}]
+packages = [{include = "eeg_research", from = "src"}]
 
 [tool.poetry.dependencies]
 python = "~3.11"