From 9e182dd44c0db3aaef8880db0c08ef068fe9a94b Mon Sep 17 00:00:00 2001 From: RJMW Date: Thu, 28 May 2020 16:35:26 +0100 Subject: [PATCH] Replace all --- .travis.yml | 4 +- README.rst | 50 +++++++++---------- appveyor.yml | 2 +- databases/README.md | 0 databases/pkls/README.md | 0 docs/source/bugs_and_issues.rst | 4 +- docs/source/changelog.rst | 4 +- docs/source/citation.rst | 2 +- docs/source/conf.py | 4 +- docs/source/index.rst | 40 +++++++-------- docs/source/installation.rst | 38 +++++++------- docs/source/license.rst | 2 +- docs/source/metaboverse.auxiliary.rst | 2 +- docs/source/metaboverse.build_structures.rst | 2 +- docs/source/metaboverse.databases.rst | 2 +- environment.yml | 2 +- {metaboverse => metaboblend}/__init__.py | 8 +-- {metaboverse => metaboblend}/__main__.py | 12 ++--- {metaboverse => metaboblend}/auxiliary.py | 22 ++++---- .../build_structures.py | 44 ++++++++-------- {metaboverse => metaboblend}/databases.py | 32 ++++++------ scripts/run.py | 4 +- setup.py | 18 +++---- tests/__init__.py | 8 +-- tests/test_auxiliary.py | 10 ++-- tests/test_build_structures.py | 12 ++--- tests/test_databases.py | 10 ++-- tests/test_isomorphism_database.py | 10 ++-- tests/test_substructure_database.py | 10 ++-- tests/test_suite_auxiliary.py | 8 +-- tests/test_suite_build_structures.py | 8 +-- tests/test_suite_databases.py | 8 +-- 32 files changed, 191 insertions(+), 191 deletions(-) delete mode 100644 databases/README.md delete mode 100644 databases/pkls/README.md rename {metaboverse => metaboblend}/__init__.py (74%) rename {metaboverse => metaboblend}/__main__.py (79%) rename {metaboverse => metaboblend}/auxiliary.py (91%) rename {metaboverse => metaboblend}/build_structures.py (94%) rename {metaboverse => metaboblend}/databases.py (98%) diff --git a/.travis.yml b/.travis.yml index a6b850c..8276aae 100644 --- a/.travis.yml +++ b/.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 diff --git a/README.rst b/README.rst index 3c04b95..5356149 100644 --- a/README.rst +++ b/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 `__ of -the `online documentation `__. +See the `Installation page `__ of +the `online documentation `__. Command line ------------ :: - $ metaboverse --help + $ metaboblend --help Bugs ---- -Please report any bugs that you find `here `_. -Or fork the repository on `GitHub `_ +Please report any bugs that you find `here `_. +Or fork the repository on `GitHub `_ 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 `_ for licensing information). Copyright © 2019 - 2020 Ralf Weber +MetaboBlend is licensed under the GNU General Public License v3.0 (see `LICENSE file `_ 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 diff --git a/appveyor.yml b/appveyor.yml index 14aa8df..19ac424 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -19,5 +19,5 @@ install: - pip install . test_script: - - metaboverse --help + - metaboblend --help - pytest diff --git a/databases/README.md b/databases/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/databases/pkls/README.md b/databases/pkls/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/docs/source/bugs_and_issues.rst b/docs/source/bugs_and_issues.rst index dd90edd..629c829 100644 --- a/docs/source/bugs_and_issues.rst +++ b/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 `_. -Or fork the repository on `GitHub `_ +Please report any bugs that you find `here `_. +Or fork the repository on `GitHub `_ 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`. diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 3d86905..f40c1e7 100644 --- a/docs/source/changelog.rst +++ b/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 `_ for further details. +Noteable changes made to the project will be recorded here. See `the commit history on github `_ for further details. -**Metaboverse v0.1.0** +**MetaboBlend v0.1.0** diff --git a/docs/source/citation.rst b/docs/source/citation.rst index e7639ff..7737282 100644 --- a/docs/source/citation.rst +++ b/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 diff --git a/docs/source/conf.py b/docs/source/conf.py index ffd6141..562abf6 100644 --- a/docs/source/conf.py +++ b/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' diff --git a/docs/source/index.rst b/docs/source/index.rst index b2d4041..496ac89 100644 --- a/docs/source/index.rst +++ b/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 ------------------ diff --git a/docs/source/installation.rst b/docs/source/installation.rst index ee132a6..0cd0741 100644 --- a/docs/source/installation.rst +++ b/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:: @@ -25,24 +25,24 @@ 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 @@ -50,9 +50,9 @@ Close and deactivate the ``metaboverse`` environment when you’re done:: PyPi ---- -Install the current release of ``metaboverse`` with ``pip``:: +Install the current release of ``metaboblend`` with ``pip``:: - $ pip install metaboverse + $ pip install metaboblend .. note:: @@ -60,16 +60,16 @@ Install the current release of ``metaboverse`` with ``pip``:: 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 `_ or -`PyPI `_. +Alternatively, you can manually download ``metaboblend`` from +`GitHub `_ or +`PyPI `_. To install one of these versions, unpack it and run the following from the top-level source directory using the Terminal:: @@ -77,4 +77,4 @@ top-level source directory using the Terminal:: Testing ------- -*Metaboverse* uses the Python ``unittest`` testing package. \ No newline at end of file +*MetaboBlend* uses the Python ``unittest`` testing package. \ No newline at end of file diff --git a/docs/source/license.rst b/docs/source/license.rst index 1529349..f9f1639 100644 --- a/docs/source/license.rst +++ b/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 `_ for licensing information). Copyright © 2019 - 2020 Ralf Weber +*MetaboBlend* is licensed under the GNU General Public License v3.0 (see `LICENSE file `_ for licensing information). Copyright © 2019 - 2020 Ralf Weber diff --git a/docs/source/metaboverse.auxiliary.rst b/docs/source/metaboverse.auxiliary.rst index 22b24f4..e68fd6f 100644 --- a/docs/source/metaboverse.auxiliary.rst +++ b/docs/source/metaboverse.auxiliary.rst @@ -1,7 +1,7 @@ Auxiliary ========= -.. automodule:: metaboverse.auxiliary +.. automodule:: metaboblend.auxiliary :members: :undoc-members: :show-inheritance: diff --git a/docs/source/metaboverse.build_structures.rst b/docs/source/metaboverse.build_structures.rst index 52939ef..22e9a03 100644 --- a/docs/source/metaboverse.build_structures.rst +++ b/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: diff --git a/docs/source/metaboverse.databases.rst b/docs/source/metaboverse.databases.rst index 91d9511..ba89a6a 100644 --- a/docs/source/metaboverse.databases.rst +++ b/docs/source/metaboverse.databases.rst @@ -1,7 +1,7 @@ Databases ========= -.. automodule:: metaboverse.databases +.. automodule:: metaboblend.databases :members: :undoc-members: :show-inheritance: diff --git a/environment.yml b/environment.yml index 25975e6..908931b 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: metaboverse +name: metaboblend channels: - conda-forge - bioconda diff --git a/metaboverse/__init__.py b/metaboblend/__init__.py similarity index 74% rename from metaboverse/__init__.py rename to metaboblend/__init__.py index 485bdd4..1bcae72 100644 --- a/metaboverse/__init__.py +++ b/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 . +# along with MetaboBlend. If not, see . # __author__ = 'Ralf Weber (r.j.weber@bham.ac.uk)' diff --git a/metaboverse/__main__.py b/metaboblend/__main__.py similarity index 79% rename from metaboverse/__main__.py rename to metaboblend/__main__.py index 3f9bc61..65d2945 100644 --- a/metaboverse/__main__.py +++ b/metaboblend/__main__.py @@ -3,26 +3,26 @@ # # 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 . +# along with MetaboBlend. If not, see . # import argparse import os -from metaboverse import __version__ +from metaboblend import __version__ from . import databases from . import build_structures @@ -30,7 +30,7 @@ def main(): # pragma: no cover - print(("Executing metaboverse version %s." % __version__)) + print(("Executing metaboblend version %s." % __version__)) parser = argparse.ArgumentParser(description='Python package for de novo structural elucidation of small molecules in mass spectrometry-based Metabolomics', formatter_class=argparse.ArgumentDefaultsHelpFormatter) diff --git a/metaboverse/auxiliary.py b/metaboblend/auxiliary.py similarity index 91% rename from metaboverse/auxiliary.py rename to metaboblend/auxiliary.py index 9dfba2c..f8c65c3 100644 --- a/metaboverse/auxiliary.py +++ b/metaboblend/auxiliary.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 . +# along with MetaboBlend. If not, see . # import itertools @@ -86,7 +86,7 @@ def draw_subgraph(edges, vn): :param edges: Tuple containing tuple of integers representing edges of the connectivity subgraph. :param vn: String containing the degrees (number of atoms available for bonding) of the subgraph's substructures - (nodes), as generated by :py:meth:`metaboverse.auxiliary.get_degrees`. + (nodes), as generated by :py:meth:`metaboblend.auxiliary.get_degrees`. :return: A tuple containing :py:meth:`pylab.plt` and :py:meth:`networkx.Graph` objects based on the connectivity subgraph. @@ -125,10 +125,10 @@ def graph_to_ri(graph: nx.Graph, name): """ Converts a :py:meth:`networkx.Graph` to gfu format to be read by RI. Allows for calculation of mappings by RI which relate the output of geng to the complete multipartite graphs generated by - :py:meth:`metaboverse.auxiliary.calculate_complete_multipartite_graphs`. + :py:meth:`metaboblend.auxiliary.calculate_complete_multipartite_graphs`. :param graph: Graph generated by networkx (e.g. one generated by - :py:meth:`metaboverse.auxiliary.calculate_complete_multipartite_graphs` or geng). + :py:meth:`metaboblend.auxiliary.calculate_complete_multipartite_graphs` or geng). :param name: String containing the graph's name for identification. @@ -154,10 +154,10 @@ def graph_info(p, sG, mappings): Generates and sorts valence and edge information. :param p: String containing a connectivity subgraph configuration generated by - :py:meth:`metaboverse.auxiliary.calculate_complete_multipartite_graphs`. + :py:meth:`metaboblend.auxiliary.calculate_complete_multipartite_graphs`. :param sG: A :py:meth:`networkx.Graph` connectivity subgraph generated by geng based on the output of - :py:meth:`metaboverse.auxiliary.calculate_complete_multipartite_graphs`. + :py:meth:`metaboblend.auxiliary.calculate_complete_multipartite_graphs`. :param mappings: Mappings calculated by RI for the relabelling of a subgraph generated by geng. Used by get_valences in order to calculate bond degrees. @@ -186,12 +186,12 @@ def graph_info(p, sG, mappings): def sort_subgraphs(subgraphs): """ - Sorts a lists of edges for a given connectivity subgraph, provided by :py:meth:`metaboverse.auxiliary.graph_info`, + Sorts a lists of edges for a given connectivity subgraph, provided by :py:meth:`metaboblend.auxiliary.graph_info`, to allow duplicate sets of edges to be removed; the order of the edges is sorted for each substructure (node) before the order of the substructures is sorted, so that all non-unique subgraphs are identical. :param subgraphs: A list of lists containing a tuple of the possible sets of edges between substructures in a - connectivity graph, created by :py:meth:`metaboverse.auxiliary.graph_info`. + connectivity graph, created by :py:meth:`metaboblend.auxiliary.graph_info`. :return: The same list of subgraphs given as input, ordered by both the tuple of edges for each substructure in the subgraphs and the list of these tuples. diff --git a/metaboverse/build_structures.py b/metaboblend/build_structures.py similarity index 94% rename from metaboverse/build_structures.py rename to metaboblend/build_structures.py index c78ee44..33944ca 100644 --- a/metaboverse/build_structures.py +++ b/metaboblend/build_structures.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 . +# along with MetaboBlend. If not, see . # import os @@ -116,13 +116,13 @@ def subset_sum(l, mass, max_subset_length=3): def combine_ecs(ss2_grp, db, table_name, accuracy, ppm=None): """ - A wrapper for :py:meth:`metaboverse.databases.select_ecs` that instead takes a group of subsets, as generated by - the second stage of :py:meth:`metaboverse.build_structres.subset_sum` in - :py:meth:`metaboverse.build_structres.build`. + A wrapper for :py:meth:`metaboblend.databases.select_ecs` that instead takes a group of subsets, as generated by + the second stage of :py:meth:`metaboblend.build_structres.subset_sum` in + :py:meth:`metaboblend.build_structres.build`. :param ss2_grp: A list containing the masses of substructures identified by subset_sum. - :param db: The :py:meth:`metaboverse.databases.SubstructureDb` in which to search for elemental compositions. + :param db: The :py:meth:`metaboblend.databases.SubstructureDb` in which to search for elemental compositions. :param table_name: The name of the table containing substructures in which to search for elemental compositions. @@ -153,7 +153,7 @@ def combine_ecs(ss2_grp, db, table_name, accuracy, ppm=None): def reindex_atoms(records): """ Parses the libs of groups of substructures that are to be combined; the lib is a dictionary containing details - about the substructure, as generated by :py:meth:`metaboverse.databases.get_substructure`. Combines the + about the substructure, as generated by :py:meth:`metaboblend.databases.get_substructure`. Combines the molecules into a single :py:meth:`rdkit.Chem.Mol` object and obtains details on their bonding properties. :param records: Takes a list of lib dictionaries that contain details on each substructure to be combined. @@ -167,7 +167,7 @@ def reindex_atoms(records): substructures. * **bond_types** A dictionary containing the indices of atoms that are available for bonding as keys and values - detailing their bond types. See :py:meth:`metaboverse.build_structures.add_bonds`. + detailing their bond types. See :py:meth:`metaboblend.build_structures.add_bonds`. """ atoms_available, atoms_to_remove, bond_types = [], [], {} @@ -213,13 +213,13 @@ def reindex_atoms(records): def add_bonds(mols, edges, atoms_available, bond_types, debug=False): """ Takes a set of substructures and attempts to combine them together to generate a final structure. One of the last - steps in the :py:meth:`metaboverse.build_structures.build` workflow. + steps in the :py:meth:`metaboblend.build_structures.build` workflow. :param mols: A :py:meth:`rdkit.Chem.CombineMols` object, that stores all the substructures as a single molecule. :param edges: The edges to use in order to join the substructures together, obtained from the connectivity database - (:py:meth:`metaboverse.databases.create_isomorphism_database`). + (:py:meth:`metaboblend.databases.create_isomorphism_database`). :param atoms_available: A list of the indices of atoms that are available for bonding. @@ -331,13 +331,13 @@ def build(mc, exact_mass, fn_out, heavy_atoms, max_valence, accuracy, max_atoms_ :param max_n_substructures: The maximum number of substructures to be used for building molecules. :param path_db: The path to the SQLite 3 substructure database, as generated by - :py:meth:`metaboverse.databases.SubstructureDb`. + :py:meth:`metaboblend.databases.SubstructureDb`. :param path_db_k_graphs: The path to the SQLite 3 connectivity database, as generated by - :py:meth:`metaboverse.databases.create_isomorphism_database`. + :py:meth:`metaboblend.databases.create_isomorphism_database`. :param path_pkls: The path to the connectivity graphs described by the SQLite 3 connectivity database, as generated - by :py:meth:`metaboverse.databases.create_isomorphism_database`. + by :py:meth:`metaboblend.databases.create_isomorphism_database`. :param fragment_mass: A mass by which to filter results; if not provided, all possible structures will be generated. @@ -444,13 +444,13 @@ def build(mc, exact_mass, fn_out, heavy_atoms, max_valence, accuracy, max_atoms_ def gen_subs_table(db, heavy_atoms, max_valence, max_atoms_available, max_mass, table_name="subset_substructures"): """ Generate a temporary secondary substructure table restricted by a set of parameters. Generated as an initial step - in :py:meth:`metaboverse.build_structures.build` in order to limit the processing overhead as a result of + in :py:meth:`metaboblend.build_structures.build` in order to limit the processing overhead as a result of repeatedly querying the SQLite substructure database. :param max_mass: The maximum allowed mass of substructures in the temporary table; there is no point considering substructures with greater mass than the target mol. - :param db: Connection to a :py:meth:`metaboverse.databases.SubstructureDb` from which to extract substructures. + :param db: Connection to a :py:meth:`metaboblend.databases.SubstructureDb` from which to extract substructures. :param heavy_atoms: List of integers used to limit which substructures are transferred into the temporary table. @@ -486,7 +486,7 @@ def gen_subs_table(db, heavy_atoms, max_valence, max_atoms_available, max_mass, def build_from_subsets(ss2_grp, mc, table_name, db, lls=[], ppm=None, debug=False,): """ - A stage of the :py:meth:`metaboverse.build_structures.build` workflow for generating molecules to a given mass + A stage of the :py:meth:`metaboblend.build_structures.build` workflow for generating molecules to a given mass from substructures. At this stage, mass subsets have been identified in the substructure database. Each of these groups are now filtered further by identifying masses that refer to valid subsets of molecules, before they are built to generate new molecules. @@ -514,8 +514,8 @@ def build_from_subsets(ss2_grp, mc, table_name, db, lls=[], ppm=None, debug=Fals * **False** Hide debug print statements. :param table_name: The name of the table within the substructure database from which to extract substructures. A - prefiltered table based on the parameters specified in :py:meth:`metaboverse.build_structures.build`. See - :py:meth:`metaboverse.build_structures.gen_subs_table`. + prefiltered table based on the parameters specified in :py:meth:`metaboblend.build_structures.build`. See + :py:meth:`metaboblend.build_structures.gen_subs_table`. """ list_ecs = combine_ecs(ss2_grp, db, table_name, "0_0001", ppm) @@ -585,7 +585,7 @@ def isomorphism_graphs(path_pkls, id_pkl): """ Loads a PKL file of a particular ID to build a molecule from a set of substructures. The PKL file contains the set of non-isomorphic graphs for the particular ID, before passing it to - `:py:meth:`metaboverse.databases.SubstructureDb.isomorphism_graphs` to be parsed. + `:py:meth:`metaboblend.databases.SubstructureDb.isomorphism_graphs` to be parsed. :param path_pkls: The directory containing PKL files. @@ -621,7 +621,7 @@ def lll_build(lll, configs_iso, path_pkls, debug): tuples for each substructure; these tuples specify how many bonds each substructure can make. :param path_pkls: The path to the connectivity graphs described by the SQLite 3 connectivity database, as generated - by :py:meth:`metaboverse.databases.create_isomorphism_database`. + by :py:meth:`metaboblend.databases.create_isomorphism_database`. :return: List of smiles representing molecules generated (and the substructures used to generate them). """ diff --git a/metaboverse/databases.py b/metaboblend/databases.py similarity index 98% rename from metaboverse/databases.py rename to metaboblend/databases.py index ecfc674..d04c2e2 100644 --- a/metaboverse/databases.py +++ b/metaboblend/databases.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 . +# along with MetaboBlend. If not, see . # import io @@ -39,7 +39,7 @@ def reformat_xml(source, encoding="utf8"): """ - Reformats HMDB xml files to be compatible with :py:meth:`metaboverse.databases.parse_xml`; some such files do not + Reformats HMDB xml files to be compatible with :py:meth:`metaboblend.databases.parse_xml`; some such files do not contain a `` header. :param source: Path to file to be reformatted. @@ -72,7 +72,7 @@ def parse_xml(source, encoding="utf8", reformat=False): :param encoding: Encoding of source file. - :param reformat: Whether to apply :py:meth:`metaboverse.databases.reformat_xml` to the XML file. Is required for + :param reformat: Whether to apply :py:meth:`metaboblend.databases.reformat_xml` to the XML file. Is required for XML files recording single metabolites. * **True** Add a `` header to the XML file before parsing. @@ -218,11 +218,11 @@ def generate_substructure_network(self, method="default", min_node_weight=2, rem * **default** Generate a standard substructure network using the most time-efficient method. Node weights represent the frequency of substructures in the substructure database whilst edge weights represent the co-occurence of these substructures. See - :py:meth:`metaboverse.databases.default_substructure_network`. + :py:meth:`metaboblend.databases.default_substructure_network`. * **extended** Alternative method for generating substructure networks that generates an intermediate metabolite-substructure linkage network; returns the same network as the **default** method. See - :py:meth:`metaboverse.databases.extended_substructure_network`. + :py:meth:`metaboblend.databases.extended_substructure_network`. * **parent_structure_linkage** Uses the **extended** method and returns the intermediate metabolite-substructure linkage network; instead of weighted edges between substructures being present, @@ -272,11 +272,11 @@ def extended_substructure_network(self, substructure_graph, unique_hmdb_ids, inc which involves substructure nodes, weighted by frequency, and metabolite nodes; unweighted edges are found between substructures and metabolites, representing the structures from which substructures were generated. This intermediate network can be returned, or it may be transformed into the standard substructure network - generated by :py:meth:`metaboverse.databases.default_substructure_network`. + generated by :py:meth:`metaboblend.databases.default_substructure_network`. :param substructure_graph: A :py:meth:`networkx.Graph` containing substructure nodes, weighted by their frequencies in the substructure database. Can be passed by - :py:meth:`metaboverse.databases.generate_substructure_network`. + :py:meth:`metaboblend.databases.generate_substructure_network`. :param unique_hmdb_ids: A list containing distinct HMDB IDs from the substructure database. @@ -321,7 +321,7 @@ def default_substructure_network(self, substructure_graph, unique_hmdb_ids): :param substructure_graph: A :py:meth:`networkx.Graph` containing substructure nodes, weighted by their frequencies in the substructure database. Can be passed by - :py:meth:`metaboverse.databases.generate_substructure_network`. + :py:meth:`metaboblend.databases.generate_substructure_network`. :param unique_hmdb_ids: A list containing distinct HMDB IDs from the substructure database. @@ -453,7 +453,7 @@ def select_sub_structures(self, l_atoms, table_name): :return: A list of lists containing the libs of the substructures obtained by the query; the lib is a dictionary containing details about the substructure, as generated by - :py:meth:`metaboverse.databases.get_substructure`. + :py:meth:`metaboblend.databases.get_substructure`. """ subsets = [] @@ -589,7 +589,7 @@ def get_substructure(mol, idxs_edges_subgraph, debug=False): * "**mol**": Substructure :py:meth:`rdkit.Chem.Mol` * "**bond_types**": The type of bonds to be formed by dummy atoms - see - :py:meth:`metaboverse.build_structures.add_bonds` and :py:meth:`Chem.rdchem.BondType`. Is a dictionary + :py:meth:`metaboblend.build_structures.add_bonds` and :py:meth:`Chem.rdchem.BondType`. Is a dictionary whose keys are atom indices and values are bond types, as follows: * **1.0** Single @@ -755,7 +755,7 @@ def calculate_exact_mass(mol, exact_mass_elements=None): def filter_records(records): """ - Filters records generated by :py:meth:`parse_xml` to ensure they are compatible with the Metaboverse workflow. + Filters records generated by :py:meth:`parse_xml` to ensure they are compatible with the MetaboBlend workflow. :param records: A dictionary containing information about the molecule, as generated by :py:meth:`parse_xml`. @@ -888,7 +888,7 @@ def get_sgs(record_dict, n_min, n_max, method="exhaustive"): Generates substructures based on an original molecule, which are described by sets of its bond indices. :param record_dict: A dictionary of key information about the original molecule, as generated by - :py:meth:`metaboverse.databases.filter_records`. Includes HMDBID, smiles and the related + :py:meth:`metaboblend.databases.filter_records`. Includes HMDBID, smiles and the related :py:meth:`rdkit.Chem.Mol` representation. :param n_min: The minimum number of bonds (edges) for a valid substructure. @@ -961,7 +961,7 @@ def update_substructure_database(fn_hmdb, fn_db, n_min, n_max, records=None, met :param n_max: The maximum number of bonds (edges) for a valid substructure. :param records: Records of molecules to be fragmented. Must be a list containing dictionaries containing key - information about the molecules, as generated by :py:meth:`metaboverse.databases.parse_xml`; if records + information about the molecules, as generated by :py:meth:`metaboblend.databases.parse_xml`; if records is not supplied, the records will be obtained from the XML at `fn_hmdb`. :param method: The method by which to fragment molecules. Substructures must have an exact substructure match in diff --git a/scripts/run.py b/scripts/run.py index 8a3ed6a..d7fc994 100644 --- a/scripts/run.py +++ b/scripts/run.py @@ -1,5 +1,5 @@ -from metaboverse.databases import * -from metaboverse.build_structures import * +from metaboblend.databases import * +from metaboblend.build_structures import * def build_graph_isomorphism_database(sizes=[1, 2], boxes=3, diff --git a/setup.py b/setup.py index c4e9357..7516238 100644 --- a/setup.py +++ b/setup.py @@ -3,37 +3,37 @@ # # Copyright © 2017-2019 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 . +# along with MetaboBlend. If not, see . # import setuptools import sys -import metaboverse +import metaboblend def main(): - setuptools.setup(name="metaboverse", - version=metaboverse.__version__, + setuptools.setup(name="metaboblend", + version=metaboblend.__version__, description="", long_description=open('README.rst').read(), author="Ralf Weber", author_email="r.j.weber@bham.ac.uk", - url="https://github.com/computational-metabolomics/metaboverse", + url="https://github.com/computational-metabolomics/metaboblend", license="GPLv3", platforms=['Windows, UNIX'], keywords=['Metabolomics', 'Lipidomics', 'Mass spectrometry', 'Metabolite Identification'], @@ -53,7 +53,7 @@ def main(): ], entry_points={ 'console_scripts': [ - 'metaboverse = metaboverse.__main__:main' + 'metaboblend = metaboblend.__main__:main' ] } ) diff --git a/tests/__init__.py b/tests/__init__.py index efb191c..1d66a83 100644 --- a/tests/__init__.py +++ b/tests/__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 . +# along with MetaboBlend. If not, see . # diff --git a/tests/test_auxiliary.py b/tests/test_auxiliary.py index d4d8933..1214d38 100644 --- a/tests/test_auxiliary.py +++ b/tests/test_auxiliary.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 . +# along with MetaboBlend. If not, see . # @@ -25,7 +25,7 @@ from io import BytesIO import zipfile import pickle -from metaboverse.auxiliary import * +from metaboblend.auxiliary import * def to_test_result(*args): diff --git a/tests/test_build_structures.py b/tests/test_build_structures.py index d0dc7aa..d9cf6f8 100644 --- a/tests/test_build_structures.py +++ b/tests/test_build_structures.py @@ -3,27 +3,27 @@ # # 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 . +# along with MetaboBlend. If not, see . # import unittest import zipfile -from metaboverse.build_structures import * -from metaboverse.databases import * +from metaboblend.build_structures import * +from metaboblend.databases import * def to_test_result(*args): diff --git a/tests/test_databases.py b/tests/test_databases.py index 8384bf1..57a569b 100644 --- a/tests/test_databases.py +++ b/tests/test_databases.py @@ -3,27 +3,27 @@ # # 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 . +# along with MetaboBlend. If not, see . # import os import unittest import zipfile -from metaboverse.databases import * +from metaboblend.databases import * def to_test_result(*args): diff --git a/tests/test_isomorphism_database.py b/tests/test_isomorphism_database.py index 5ea37a1..e8a89e7 100644 --- a/tests/test_isomorphism_database.py +++ b/tests/test_isomorphism_database.py @@ -3,26 +3,26 @@ # # 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 . +# along with MetaboBlend. If not, see . # import unittest import zipfile -from metaboverse.databases import * +from metaboblend.databases import * def to_test_result(*args): diff --git a/tests/test_substructure_database.py b/tests/test_substructure_database.py index 11c5c30..39b5989 100644 --- a/tests/test_substructure_database.py +++ b/tests/test_substructure_database.py @@ -3,27 +3,27 @@ # # 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 . +# along with MetaboBlend. If not, see . # import unittest import zipfile from shutil import copyfile -from metaboverse.databases import * +from metaboblend.databases import * def to_test_result(*args): diff --git a/tests/test_suite_auxiliary.py b/tests/test_suite_auxiliary.py index 95c7b34..c44171d 100644 --- a/tests/test_suite_auxiliary.py +++ b/tests/test_suite_auxiliary.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 . +# along with MetaboBlend. If not, see . # diff --git a/tests/test_suite_build_structures.py b/tests/test_suite_build_structures.py index 649ef08..48176ba 100644 --- a/tests/test_suite_build_structures.py +++ b/tests/test_suite_build_structures.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 . +# along with MetaboBlend. If not, see . # diff --git a/tests/test_suite_databases.py b/tests/test_suite_databases.py index 0d36504..7f5eb7f 100644 --- a/tests/test_suite_databases.py +++ b/tests/test_suite_databases.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 . +# along with MetaboBlend. If not, see . #