Rename project to metaboblend

.travis.yml

@@ -18,8 +18,8 @@ install:
   - pip install .
 
 script:
-  - metaboverse --help
-  - pytest --cov=metaboverse tests/
+  - metaboblend --help
+  - pytest --cov=metaboblend tests/
 
 after_script:
   - codecov

README.rst

@@ -1,30 +1,30 @@
-MetaboVerse
+MetaboBlend
 ===========
 |Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |binder|
 
 Python package for *de novo* structural elucidation of small molecules in mass spectrometry-based Metabolomics
 
-- **Documentation:** https://metaboverse.readthedocs.io/en/latest
-- **Source:** https://github.com/computational-metabolomics/metaboverse
-- **Bug reports:** https://github.com/computational-metabolomics/metaboverse/issues
+- **Documentation:** https://metaboblend.readthedocs.io/en/latest
+- **Source:** https://github.com/computational-metabolomics/metaboblend
+- **Bug reports:** https://github.com/computational-metabolomics/metaboblend/issues
 
 Installation
 ------------
-See the `Installation page <https://metaboverse.readthedocs.io/en/latest/introduction.html#installation>`__ of
-the `online documentation <https://computational-metabolomics.github.io/metaboverse/>`__.
+See the `Installation page <https://metaboblend.readthedocs.io/en/latest/introduction.html#installation>`__ of
+the `online documentation <https://computational-metabolomics.github.io/metaboblend/>`__.
 
 
 Command line
 ------------
 ::
 
-    $ metaboverse --help
+    $ metaboblend --help
 
 
 Bugs
 ----
-Please report any bugs that you find `here <https://github.com/computational-metabolomics/metaboverse/issues>`_.
-Or fork the repository on `GitHub <https://github.com/computational-metabolomics/metaboverse/>`_
+Please report any bugs that you find `here <https://github.com/computational-metabolomics/metaboblend/issues>`_.
+Or fork the repository on `GitHub <https://github.com/computational-metabolomics/metaboblend/>`_
 and create a pull request (PR). We welcome all contributions, and we
 will help you to make the PR if you are new to `git`.
 
@@ -37,36 +37,36 @@ Developers & Contributors
 
 Licenses
 --------
-MetaboVerse is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboverse/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber
+MetaboBlend is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber
 
 
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/metaboverse.svg?style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/metaboverse
+.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/metaboblend.svg?style=flat&maxAge=3600&label=Travis-CI
+   :target: https://travis-ci.com/computational-metabolomics/metaboblend
 
-.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/metaboverse.svg?style=flat&maxAge=3600&label=AppVeyor
-   :target: https://ci.appveyor.com/project/RJMW/metaboverse/branch/master
+.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/metaboblend.svg?style=flat&maxAge=3600&label=AppVeyor
+   :target: https://ci.appveyor.com/project/RJMW/metaboblend/branch/master
 
-.. |Py versions| image:: https://img.shields.io/pypi/pyversions/metaboverse.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/metaboverse/
+.. |Py versions| image:: https://img.shields.io/pypi/pyversions/metaboblend.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/metaboblend/
 
-.. |Version| image:: https://img.shields.io/pypi/v/metaboverse.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/metaboverse/
+.. |Version| image:: https://img.shields.io/pypi/v/metaboblend.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/metaboblend/
 
 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
-   :target: https://github.com/computational-metabolomics/metaboverse
+   :target: https://github.com/computational-metabolomics/metaboblend
 
 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
-   :target: http://bioconda.github.io/recipes/metaboverse/README.html
+   :target: http://bioconda.github.io/recipes/metaboblend/README.html
 
-.. |License| image:: https://img.shields.io/pypi/l/metaboverse.svg?style=flat&maxAge=3600
+.. |License| image:: https://img.shields.io/pypi/l/metaboblend.svg?style=flat&maxAge=3600
    :target: https://www.gnu.org/licenses/gpl-3.0.html
 
 .. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=3600
-   :target: https://metaboverse.readthedocs.io/en/latest/
+   :target: https://metaboblend.readthedocs.io/en/latest/
 
-.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/metaboverse/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/computational-metabolomics/metaboverse
+.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/metaboblend/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/computational-metabolomics/metaboblend
 
 .. |binder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/computational-metabolomics/metaboverse/master?filepath=notebooks%2Fworkflow.ipynb
+   :target: https://mybinder.org/v2/gh/computational-metabolomics/metaboblend/master?filepath=notebooks%2Fworkflow.ipynb
 

appveyor.yml

@@ -19,5 +19,5 @@ install:
   - pip install .
 
 test_script:
-  - metaboverse --help
+  - metaboblend --help
   - pytest

docs/source/bugs_and_issues.rst

@@ -1,7 +1,7 @@
 Bugs and Issues
 ===============
 TODO: change package name
-Please report any bugs that you find `here <https://github.com/computational-metabolomics/metaboverse/issues>`_.
-Or fork the repository on `GitHub <https://github.com/computational-metabolomics/metaboverse/>`_
+Please report any bugs that you find `here <https://github.com/computational-metabolomics/metaboblend/issues>`_.
+Or fork the repository on `GitHub <https://github.com/computational-metabolomics/metaboblend/>`_
 and create a pull request (PR). We welcome all contributions, and we will help you to make
 the PR if you are new to `git`.

docs/source/changelog.rst

@@ -1,6 +1,6 @@
 Changelog
 =========
 TODO: change package name
-Noteable changes made to the project will be recorded here. See `the commit history on github <https://github.com/computational-metabolomics/metaboverse>`_ for further details.
+Noteable changes made to the project will be recorded here. See `the commit history on github <https://github.com/computational-metabolomics/metaboblend>`_ for further details.
 
-**Metaboverse v0.1.0**
+**MetaboBlend v0.1.0**

docs/source/citation.rst

@@ -1,6 +1,6 @@
 Citation
 ========
 TODO: change package name
-To cite *Metaboverse* please use the following publication.
+To cite *MetaboBlend* please use the following publication.
 
     Manuscript in preparation

docs/source/conf.py

@@ -15,11 +15,11 @@
 
 sys.path.insert(0, os.path.abspath('..'))
 sys.path.insert(0, os.path.abspath('../..'))
-sys.path.insert(0, os.path.abspath('../../metaboverse'))
+sys.path.insert(0, os.path.abspath('../../metaboblend'))
 
 # -- Project information -----------------------------------------------------
 
-project = 'Metaboverse'
+project = 'MetaboBlend'
 copyright = '2020, Ralf Weber'
 author = 'Jack Gisby, Ralf Weber'
 

docs/source/index.rst

@@ -1,4 +1,4 @@
-Welcome to Metaboverse's documentation!
+Welcome to MetaboBlend's documentation!
 =======================================
 TODO: change package name
 |Version| |Py versions| |Git| |Bioconda| |Build Status (Travis)| |Build Status (AppVeyor)| |License| |RTD doc| |codecov| |binder|
@@ -17,41 +17,41 @@ Python package for *de novo* structural elucidation of small molecules in mass s
 
 .. toctree::
    :maxdepth: 2
-   :caption: Metaboverse:
+   :caption: MetaboBlend:
 
-   metaboverse.auxiliary
-   metaboverse.build_structures
-   metaboverse.databases
+   metaboblend.auxiliary
+   metaboblend.build_structures
+   metaboblend.databases
 
-.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/metaboverse.svg?style=flat&maxAge=3600&label=Travis-CI
-   :target: https://travis-ci.com/computational-metabolomics/metaboverse
+.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/metaboblend.svg?style=flat&maxAge=3600&label=Travis-CI
+   :target: https://travis-ci.com/computational-metabolomics/metaboblend
 
-.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/metaboverse.svg?style=flat&maxAge=3600&label=AppVeyor
-   :target: https://ci.appveyor.com/project/RJMW/metaboverse/branch/master
+.. |Build Status (AppVeyor)| image:: https://img.shields.io/appveyor/ci/RJMW/metaboblend.svg?style=flat&maxAge=3600&label=AppVeyor
+   :target: https://ci.appveyor.com/project/RJMW/metaboblend/branch/master
 
-.. |Py versions| image:: https://img.shields.io/pypi/pyversions/metaboverse.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/metaboverse/
+.. |Py versions| image:: https://img.shields.io/pypi/pyversions/metaboblend.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/metaboblend/
 
-.. |Version| image:: https://img.shields.io/pypi/v/metaboverse.svg?style=flat&maxAge=3600
-   :target: https://pypi.python.org/pypi/metaboverse/
+.. |Version| image:: https://img.shields.io/pypi/v/metaboblend.svg?style=flat&maxAge=3600
+   :target: https://pypi.python.org/pypi/metaboblend/
 
 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
-   :target: https://github.com/computational-metabolomics/metaboverse
+   :target: https://github.com/computational-metabolomics/metaboblend
 
 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
-   :target: http://bioconda.github.io/recipes/metaboverse/README.html
+   :target: http://bioconda.github.io/recipes/metaboblend/README.html
 
-.. |License| image:: https://img.shields.io/pypi/l/metaboverse.svg?style=flat&maxAge=3600
+.. |License| image:: https://img.shields.io/pypi/l/metaboblend.svg?style=flat&maxAge=3600
    :target: https://www.gnu.org/licenses/gpl-3.0.html
 
 .. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=3600
-   :target: https://metaboverse.readthedocs.io/en/latest/
+   :target: https://metaboblend.readthedocs.io/en/latest/
 
-.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/metaboverse/branch/master/graph/badge.svg
-   :target: https://codecov.io/gh/computational-metabolomics/metaboverse
+.. |codecov| image:: https://codecov.io/gh/computational-metabolomics/metaboblend/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/computational-metabolomics/metaboblend
 
 .. |binder| image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/computational-metabolomics/metaboverse/master?filepath=notebooks%2Fworkflow.ipynb
+   :target: https://mybinder.org/v2/gh/computational-metabolomics/metaboblend/master?filepath=notebooks%2Fworkflow.ipynb
 
 Indices and tables
 ------------------

docs/source/installation.rst

@@ -1,6 +1,6 @@
 Installation
 ============
-TODO: Metaboverse is not yet released on conda/pypi
+TODO: MetaboBlend is not yet released on conda/pypi
 TODO: change package name
 
 Conda (recommended)
@@ -13,10 +13,10 @@ Start the ``conda prompt``
 * Windows: Open the ``Anaconda Prompt`` via the Start menu
 * macOS or Linux: Open a ``Terminal``
 
-Create a metaboverse specific ``conda`` environment.
-This will install a the dependencies required to run ``metaboverse``::
+Create a metaboblend specific ``conda`` environment.
+This will install a the dependencies required to run ``metaboblend``::
 
-    $ conda create --yes --name metaboverse -c conda-forge -c bioconda -c computational-metabolomics
+    $ conda create --yes --name metaboblend -c conda-forge -c bioconda -c computational-metabolomics
 
 .. note::
 
@@ -25,56 +25,56 @@ This will install a the dependencies required to run ``metaboverse``::
 
     You can use the following command to remove a conda environment::
 
-        $ conda env remove -y --name metaboverse
+        $ conda env remove -y --name metaboblend
 
     This is only required if something has gone wrong in the previous step.
 
-Activate the ``metaboverse`` environment::
+Activate the ``metaboblend`` environment::
 
-    $ conda activate metaboverse
+    $ conda activate metaboblend
 
-To test your ``metaboverse`` installation, in your Conda Prompt, run the command::
+To test your ``metaboblend`` installation, in your Conda Prompt, run the command::
 
-    $ metaboverse --help
+    $ metaboblend --help
 
 or::
 
     $ python
-    import metaboverse
+    import metaboblend
 
-Close and deactivate the ``metaboverse`` environment when you’re done::
+Close and deactivate the ``metaboblend`` environment when you’re done::
 
     $ conda deactivate
 
 
 PyPi
 ----
 
-Install the current release of ``metaboverse`` with ``pip``::
+Install the current release of ``metaboblend`` with ``pip``::
 
-    $ pip install metaboverse
+    $ pip install metaboblend
 
 .. note::
 
     * The installation process will take a few minutes.
 
 To upgrade to a newer release use the ``--upgrade`` flag::
 
-    $ pip install --upgrade metaboverse
+    $ pip install --upgrade metaboblend
 
 If you do not have permission to install software systemwide, you can
 install into your user directory using the ``--user`` flag::
 
-    $ pip install --user metaboverse
+    $ pip install --user metaboblend
 
-Alternatively, you can manually download ``metaboverse`` from
-`GitHub <https://github.com/computational-metabolomics/metaboverse/releases>`_  or
-`PyPI <https://pypi.python.org/pypi/metaboverse>`_.
+Alternatively, you can manually download ``metaboblend`` from
+`GitHub <https://github.com/computational-metabolomics/metaboblend/releases>`_  or
+`PyPI <https://pypi.python.org/pypi/metaboblend>`_.
 To install one of these versions, unpack it and run the following from the
 top-level source directory using the Terminal::
 
     $ pip install .
 
 Testing
 -------
-*Metaboverse* uses the Python ``unittest`` testing package.
+*MetaboBlend* uses the Python ``unittest`` testing package.

docs/source/license.rst

@@ -1,4 +1,4 @@
 License
 -------
 TODO: change package name
-*Metaboverse* is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboverse/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber
+*MetaboBlend* is licensed under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/metaboblend/blob/master/LICENSE>`_ for licensing information). Copyright © 2019 - 2020 Ralf Weber

docs/source/metaboverse.auxiliary.rst

@@ -1,7 +1,7 @@
 Auxiliary
 =========
 
-.. automodule:: metaboverse.auxiliary
+.. automodule:: metaboblend.auxiliary
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/metaboverse.build_structures.rst

@@ -1,7 +1,7 @@
 Build Structures
 ================
 
-.. automodule:: metaboverse.build_structures
+.. automodule:: metaboblend.build_structures
     :members:
     :undoc-members:
     :show-inheritance:

docs/source/metaboverse.databases.rst

@@ -1,7 +1,7 @@
 Databases
 =========
 
-.. automodule:: metaboverse.databases
+.. automodule:: metaboblend.databases
     :members:
     :undoc-members:
     :show-inheritance:

environment.yml

@@ -1,4 +1,4 @@
-name: metaboverse
+name: metaboblend
 channels:
   - conda-forge
   - bioconda

metaboverse/__init__.py → metaboblend/__init__.py

@@ -3,20 +3,20 @@
 #
 # Copyright © 2019-2020 Ralf Weber
 #
-# This file is part of MetaboVerse.
+# This file is part of MetaboBlend.
 #
-# MetaboVerse is free software: you can redistribute it and/or modify
+# MetaboBlend 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.
 #
-# MetaboVerse is distributed in the hope that it will be useful,
+# MetaboBlend 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 MetaboVerse.  If not, see <https://www.gnu.org/licenses/>.
+# along with MetaboBlend.  If not, see <https://www.gnu.org/licenses/>.
 #
 
 __author__ = 'Ralf Weber (r.j.weber@bham.ac.uk)'