Update doc and relicense

.gitlab-ci.yml

-# This software is based on https://gitlab.com/singularityhub/gitlab-ci,
-# with DOI: https://doi.org/10.5281/zenodo.3834833
-# provided under the following license:
-
-### BSD 3-Clause License
-###
-### Copyright (c) 2018, Vanessa Sochat
-### All rights reserved.
-###
-### Redistribution and use in source and binary forms, with or without
-### modification, are permitted provided that the following conditions are met:
-###
-### * Redistributions of source code must retain the above copyright notice, this
-###   list of conditions and the following disclaimer.
-###
-### * Redistributions in binary form must reproduce the above copyright notice,
-###   this list of conditions and the following disclaimer in the documentation
-###   and/or other materials provided with the distribution.
-###
-### * Neither the name of the copyright holder nor the names of its
-###   contributors may be used to endorse or promote products derived from
-###   this software without specific prior written permission.
-###
-### THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-### AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-### IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-### DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-### FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-### DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-### SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-### CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-### OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-### OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-###
-
 stages:
  - test
  - build

.gitlabci/LICENSE-gitlabci

+BSD 3-Clause License
+
+Copyright (c) 2018, Vanessa Sochat
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

.gitlabci/README-gitlabci.md

 # .gitlabci
 
-## Building Singularity Containers using the continuous integration in GitLab 
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3834833.svg)](https://doi.org/10.5281/zenodo.3834833)
 
 **PLEASE HAVE A LOOK TO THE LICENSING SECTION BELOW BEFORE IMPLEMENTING ANY PART OF THIS CODE INTO YOURS !!**
 
+## Building Singularity Containers using the continuous integration in GitLab 
 
 The source code contained in this folder is based on the following 
-[gitlab-ci repository](https://gitlab.com/singularityhub/gitlab-ci). You can  find a very didactic **tutorial** of how 
+[GitLab-CI repository](https://gitlab.com/singularityhub/gitlab-ci). You can  find a very didactic **tutorial** of how 
 to implement this code [here](https://vsoch.github.io/2018/gitlab-singularity-ci/).
 
-This software (composed of the files within this directory **AND** the `gitlab-ci.yml` file in the
-root directory) provide the necessary tools to:
- - Use a Singularity image stored in the SingularityHub to create a Singularity Container of your repository 
+This software (composed of the files within this directory **AND** part of the the `.gitlab-ci.yml` file in the
+root directory - the `build_image` stage) provide the necessary tools to:
+ - Use a Singularity image stored in the DockerHub site to create a Singularity Container of your repository 
  (thus no need of having installed the Singularity program), and uploaded it directly to your GitLab repository.
  - The Singularity receipt must be provided, of course.
  - In case the container is too large (10 Gb total storage limit for a single GitLab project), you must pass 
  through a cloud service (various examples of different services are shown in the tutorial and the original repository). 
 
-## License of the repository
-The license of the 'parent' repository is `BSD 3-Clause License` ("BSD License 2.0", "Revised BSD License", "New BSD 
-License", or "Modified BSD License"). Before implementing anything from the current or the original repository 
-**please check that the license of the project in which you are going to implement these source files is compatible 
-with BSD 3-Clause**.
-
-If this is the case, each file (based on or modified from its original) MUST contain the license below:  
-
-> BSD 3-Clause License
-> 
-> Copyright (c) 2018, Vanessa Sochat
-> All rights reserved.
-> 
-> Redistribution and use in source and binary forms, with or without
-> modification, are permitted provided that the following conditions are met:
-> 
-> * Redistributions of source code must retain the above copyright notice, this
->   list of conditions and the following disclaimer.
-> 
-> * Redistributions in binary form must reproduce the above copyright notice,
->   this list of conditions and the following disclaimer in the documentation
->   and/or other materials provided with the distribution.
-> 
-> * Neither the name of the copyright holder nor the names of its
-> contributors may be used to endorse or promote products derived from
-> this software without specific prior written permission.
-> 
-> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-> AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-> IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-> DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-> FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-> DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-> SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-> CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-> OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-> OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-### Specific case of the `template_project_repository`:
+## License of the `template_project_repository`:
 The `template_project_repository` contains code from different projects. This 'mixing' can be done because:
  - Both 'parent' projects are Open Source.
- - Both licenses, `BSD 3-Clause` and `GPLv3`, are [compatible](
- https://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean); this means that source code distributed with a BSD 
- 3-Clause license can be included within a project with a GPLv3 license:
-    - Note however that the GNU General Public License v3 is 'copyleft', meaning that the resulting project from the use
-     of any code licensed with GPLv3, must be distributed with the same license, thus GPLv3.
- 
-This are the reasons why the  `template_project_repository` is distributed with the GNU General Public License Version 
-3 and some files contain a BSD-3 Clause license.
+ - None of the original licenses are copy-left.
+ - Both `BSD 3-Clause` and `MIT`, are permissive licenses. All of these points mean that source code distributed with 
+ a BSD 3-Clause license can be included in a project with a MIT license - and of course be re-distributed under `MIT`:
+    - Note however, that the **original licenses** must be included in the resulting project and mentioned in the 
+    LICENSE/documentation files.  
 
 **PLEASE TAKE THE TIME TO CHECK AND VERIFY LICENSES AND THEIR COMPATIBILITIES** 
  
\ No newline at end of file

.zenodoci/LICENSE-zenodoci

+MIT License
+
+Copyright (c) 2020, ZenodoCI developers.
+
+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.

.zenodoci/README_zenodoci.md

@@ -4,81 +4,54 @@
 
 ## Continuous Deployment to Zenodo
 
-The source code contained in this folder is based on the  
-[zenodo-python repository](https://github.com/SiLeBAT/zenodo-python).
+The source code contained in this folder is based on the [ZenodoCI](https://gitlab.in2p3.fr/escape2020/escape/zenodoci) 
+project. The library was developed specifically to perform a deploy stage (to the Zenodo repository) in a GitLab CI 
+pipeline that **could be implemented in any external project**. 
+  
 
-The software (composed of the `zenodolib.py` script) provides a library to handle the upload of a 
-specified file(s) to (sandbox)zenodo. Please **JUST** upload stable versions/releases of source code and/or images
+The library (composed of the scripts within the `.zenodoci` directory) provides a module to handle the upload of 
+specified file(s) to (sandbox)zenodo. Please **JUST** upload stable versions/releases of source code and/or image
  containers!
 
-By using the `zenodolib` library, as well as the created Singularity container (check the `.gitlabci` directory), 
-the second stage of the CI pipeline (see the `.gitlab-ci.yml` file) will:
+The `deploy` stage in the CI pipeline (see the `.gitlab-ci.yml` file) will make use of the `zenodoapi` library and
+ the built Singularity container created in the previous CI stage (check the `.gitlabci` directory too) to:
  - Either upload the desired file(s) to the ESCAPE community in Zenodo.
  - Either upload a new version of an existing entry to Zenodo.
  
-The `repository_information.json` file must be filled up before pushing to the project repository. Also, depending on 
-the case, the corresponding python script (`upload_new_deposit.py` or `upload_new_version_of_deposit.py`) must be 
- adapted and included into the `.gitlab-ci.yml` file with its corresponding arguments.
+The `repository_information.json` file must be filled up before pushing to the GitLab repository. This file will be 
+used to fill up the compulsory information that a Zenodo entry must contain. Also, depending on the case, the 
+corresponding python script (`upload_new_deposit.py` or `upload_new_version_of_deposit.py`) must be adapted and
+ included into the `.gitlab-ci.yml` file with its corresponding arguments (examples are shown in the yml file).
 
 ### Zenodo token & GitLab CI environment variable
 
 To connect the GitLab repository with Zenodo in an autonomous way, a personal access token must be created. This token 
-is assign to a **single** Zenodo account, and it will allow to interact with (sandbox)zenodo through its 
-API. To create the token:
+is assigned to a **single** Zenodo account, and it will allow the interaction with
+ (sandbox.)zenodo through its API. To create the token:
  - Go to (sandbox)zenodo.org
  - Account --> Applications --> Personal access token --> New token. 
  
-This token will be passed later in the continuous deployment stage of the CI/CD pipeline. For not sharing publicly 
-your personal token, you should create an environment variable in your GitLab repository. This way, the token could be used as a variable without
- revealing its value. To create an an environment variable:
+This token will be passed later in the deployment stage of the CI pipeline. For not sharing publicly 
+your personal token, you should create an environment variable in your GitLab repository. This way, the token could be
+ used as a variable without revealing its value. To create an an environment variable:
   - Go to your GitLab repository.
   - Settings --> CI/CD --> Variables --> Add variable --> Fill the fields --> Mask your variable(s) !!
 
 The environment variable will look like this:
 
 ```sh
-    $ python .zenodoci/upload_new_deposit.py -i build/Singularity -t $ZENODO_TOKEN
+    $ python .zenodoci/upload_new_deposit.py -i build -t $ZENODO_TOKEN -s False
 ```
 
-## License of the repository
-
-The license of the 'parent' repository is `GNU GENERAL PUBLIC LICENSE Version 3` ("GNU GPL v3" or "GPLv3"). Before 
-implementing anything from the current or the original repository **please check that the license of the project 
-in which you are going to implement these source files is compatible with the GPLv3 license**.
-
-If this is the case: 
- - The whole resulting project must be distributed with the same license, i.e., `GPLv3` and contain the license
-  and copyright notice (see the LICENSE file of the `template_project_repository`). GPLv3 is copyleft.
- - Changes must be stated (here is an example of the kind of text that must be included in each modified file): 
- 
-> This code is part of https://github.com/SiLeBAT/zenodo-python 
-> 
-> Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
-> This program is free software: you can redistribute it and/or modify
-> it under the terms of the GNU General Public License as published by
-> the Free Software Foundation, either version 3 of the License, or
-> (at your option) any later version.
->
-> This program is distributed in the hope that it will be useful,
-> but WITHOUT ANY WARRANTY; without even the implied warranty of
-> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-> GNU General Public License for more details.
->
-> You should have received a copy of the GNU General Public License
-> along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-
-### Specific case of the `template_project_repository`:
+## License of the `template_project_repository`:
 The `template_project_repository` contains code from different projects. This 'mixing' can be done because:
  - Both 'parent' projects are Open Source.
- - Both licenses, `BSD 3-Clause` and `GPLv3`, are [compatible](
- https://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean); this means that source code distributed with a BSD 
- 3-Clause license can be included within a project with a GPLv3 license:
-    - Note however that the GNU General Public License v3 is 'copyleft', meaning that the resulting project from the use
-     of any code licensed with GPLv3, must be distributed with the same license, thus GPLv3.
- 
-This are the reasons why the  `template_project_repository` is distributed with the GNU General Public License Version 
-3 and some files contain a BSD-3 Clause license.
-
+ - None of the original licenses are copy-left.
+ - Both `BSD 3-Clause` and `MIT`, are permissive licenses. All of these points mean that source code distributed with 
+ a BSD 3-Clause license can be included in a project with a MIT license - and of course be re-distributed under `MIT`:
+    - Note however, that the **original licenses** must be included in the resulting project and mentioned in the 
+    LICENSE/documentation files.  
+     
+     
 **PLEASE TAKE THE TIME TO CHECK AND VERIFY LICENSES AND THEIR COMPATIBILITIES** 
  
\ No newline at end of file

.zenodoci/upload_new_deposit.py

@@ -3,7 +3,7 @@ import os
 import json
 import argparse
 from distutils.util import strtobool
-from .zenodoapi import ZenodoAPI
+from zenodoapi import ZenodoAPI
 
 
 parser = argparse.ArgumentParser(description="Upload new deposit entry to Zenodo")

.zenodoci/upload_new_version_deposit.py

@@ -3,7 +3,7 @@ import os
 import json
 import argparse
 from distutils.util import strtobool
-from .zenodoapi import ZenodoAPI
+from zenodoapi import ZenodoAPI
 
 parser = argparse.ArgumentParser(description="Upload a new version of an existing deposit to Zenodo")
 

README.md

@@ -27,11 +27,11 @@ The repository shows the **basic documentation** that should be included within
 
 It would be highly suitable to include too:
    - A setup file as well as the basic commands to install the library (see below).
-   - A .gitignore file.
+   - A `.gitignore` file.
    - Unitary and integration tests, and ideally a CI pipeline.
    
-**Please feel free to copy / base on / template this project!** (Look to left of the `Clone or download` button in the 
-[GitHub](https://github.com/garciagenrique/template_project_escape) site).
+**Please feel free to clone / fork / template this project!** (For example, look to left of the 
+`Clone or download` button in the [GitHub](https://github.com/garciagenrique/template_project_escape) site).
 
 Take few minutes to check the [ESCAPE repository's guidelines](https://gitlab.in2p3.fr/escape2020/guidelines) too.