diff --git a/transcript_sequence_extractor/.gitignore b/.gitignore similarity index 98% rename from transcript_sequence_extractor/.gitignore rename to .gitignore index a9524a1..ad4a1f1 100644 --- a/transcript_sequence_extractor/.gitignore +++ b/.gitignore @@ -1,5 +1,3 @@ -.DS_Store - # Created by https://www.toptal.com/developers/gitignore/api/python # Edit at https://www.toptal.com/developers/gitignore?templates=python @@ -169,5 +167,10 @@ cython_debug/ # Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration poetry.toml +# ruff +.ruff_cache/ + +# LSP config files +pyrightconfig.json # End of https://www.toptal.com/developers/gitignore/api/python diff --git a/terminal_fragment_selector/LICENSE b/LICENSE similarity index 94% rename from terminal_fragment_selector/LICENSE rename to LICENSE index edb8749..86aa0ce 100644 --- a/terminal_fragment_selector/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022 zavolan_group / tools +Copyright (c) 2022 Zavolan Lab, Biozentrum, University of Basel Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/cdna_generator/.gitignore b/cdna_generator/.gitignore deleted file mode 100644 index 767b802..0000000 --- a/cdna_generator/.gitignore +++ /dev/null @@ -1,165 +0,0 @@ -.ipynb* - -Untitled.ipynb - -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -#pdm.lock -# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it -# in version control. -# https://pdm.fming.dev/#use-with-ide -.pdm.toml - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -.idea/ - diff --git a/cdna_generator/LICENSE b/cdna_generator/LICENSE deleted file mode 100644 index 4ca67a6..0000000 --- a/cdna_generator/LICENSE +++ /dev/null @@ -1,11 +0,0 @@ - The MIT License (MIT) - -Copyright © 2022 Samuel Mondal - -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. - - diff --git a/environment.yml b/environment.yml index bb7989a..709fe3b 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: scrna-seq-sim +name: scrnasim channels: - defaults - bioconda diff --git a/priming_site_predictor/.gitignore b/priming_site_predictor/.gitignore deleted file mode 100644 index a43cb67..0000000 --- a/priming_site_predictor/.gitignore +++ /dev/null @@ -1,166 +0,0 @@ -# Created by https://www.toptal.com/developers/gitignore/api/python -# Edit at https://www.toptal.com/developers/gitignore?templates=python - -### Python ### -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -#pdm.lock -# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it -# in version control. -# https://pdm.fming.dev/#use-with-ide -.pdm.toml - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -#.idea/ - -# End of https://www.toptal.com/developers/gitignore/api/python \ No newline at end of file diff --git a/priming_site_predictor/LICENSE b/priming_site_predictor/LICENSE deleted file mode 100644 index 504d7a6..0000000 --- a/priming_site_predictor/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) [2022] [University of Basel] - -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. \ No newline at end of file diff --git a/read_sequencer/.gitignore b/read_sequencer/.gitignore deleted file mode 100644 index 83c7b50..0000000 --- a/read_sequencer/.gitignore +++ /dev/null @@ -1,175 +0,0 @@ -.DS_Store -.idea/ -read_sequencer.egg-info -readsequencer.egg-info -# Created by https://www.toptal.com/developers/gitignore/api/python -# Edit at https://www.toptal.com/developers/gitignore?templates=python - -### Python ### -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv - For a library or package, you might want to ignore these files since the code is - intended to run in multiple environments; otherwise, check them in: -.python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -Pipfile.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -#pdm.lock -# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it -# in version control. -# https://pdm.fming.dev/#use-with-ide -.pdm.toml - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -#.idea/ - -### Python Patch ### -# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration -poetry.toml - - -# End of https://www.toptal.com/developers/gitignore/api/python diff --git a/read_sequencer/LICENSE.txt b/read_sequencer/LICENSE.txt deleted file mode 100644 index 9ae3ad4..0000000 --- a/read_sequencer/LICENSE.txt +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2022 Clara Serger, Michael Sandholzer and Christoph Harmel - -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. \ No newline at end of file diff --git a/cdna_generator/.DS_Store b/scRNAsim_toolz/cdna_generator/.DS_Store similarity index 100% rename from cdna_generator/.DS_Store rename to scRNAsim_toolz/cdna_generator/.DS_Store diff --git a/cdna_generator/.gitlab-ci.yml b/scRNAsim_toolz/cdna_generator/.gitlab-ci.yml similarity index 100% rename from cdna_generator/.gitlab-ci.yml rename to scRNAsim_toolz/cdna_generator/.gitlab-ci.yml diff --git a/cdna_generator/Dockerfile b/scRNAsim_toolz/cdna_generator/Dockerfile similarity index 100% rename from cdna_generator/Dockerfile rename to scRNAsim_toolz/cdna_generator/Dockerfile diff --git a/cdna_generator/README.md b/scRNAsim_toolz/cdna_generator/README.md similarity index 100% rename from cdna_generator/README.md rename to scRNAsim_toolz/cdna_generator/README.md diff --git a/cdna_generator/cdna/__init__.py b/scRNAsim_toolz/cdna_generator/__init__.py similarity index 100% rename from cdna_generator/cdna/__init__.py rename to scRNAsim_toolz/cdna_generator/__init__.py diff --git a/cdna_generator/cdna/cdna.py b/scRNAsim_toolz/cdna_generator/cdna.py similarity index 100% rename from cdna_generator/cdna/cdna.py rename to scRNAsim_toolz/cdna_generator/cdna.py diff --git a/cdna_generator/cdna/cli.py b/scRNAsim_toolz/cdna_generator/cli.py similarity index 100% rename from cdna_generator/cdna/cli.py rename to scRNAsim_toolz/cdna_generator/cli.py diff --git a/cdna_generator/requirements.txt b/scRNAsim_toolz/cdna_generator/requirements.txt similarity index 100% rename from cdna_generator/requirements.txt rename to scRNAsim_toolz/cdna_generator/requirements.txt diff --git a/cdna_generator/requirements_dev.txt b/scRNAsim_toolz/cdna_generator/requirements_dev.txt similarity index 100% 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a/priming_site_predictor/primingsitepredictor/__init__.py b/scRNAsim_toolz/priming_site_predictor/__init__.py similarity index 100% rename from priming_site_predictor/primingsitepredictor/__init__.py rename to scRNAsim_toolz/priming_site_predictor/__init__.py diff --git a/priming_site_predictor/primingsitepredictor/cli.py b/scRNAsim_toolz/priming_site_predictor/cli.py similarity index 100% rename from priming_site_predictor/primingsitepredictor/cli.py rename to scRNAsim_toolz/priming_site_predictor/cli.py diff --git a/priming_site_predictor/primingsitepredictor/psp.py b/scRNAsim_toolz/priming_site_predictor/psp.py similarity index 100% rename from priming_site_predictor/primingsitepredictor/psp.py rename to scRNAsim_toolz/priming_site_predictor/psp.py diff --git a/priming_site_predictor/requirements.txt b/scRNAsim_toolz/priming_site_predictor/requirements.txt similarity index 100% rename from priming_site_predictor/requirements.txt rename to scRNAsim_toolz/priming_site_predictor/requirements.txt diff --git a/priming_site_predictor/requirements_dev.txt b/scRNAsim_toolz/priming_site_predictor/requirements_dev.txt similarity index 100% rename from priming_site_predictor/requirements_dev.txt rename to scRNAsim_toolz/priming_site_predictor/requirements_dev.txt diff --git a/priming_site_predictor/setup.py b/scRNAsim_toolz/priming_site_predictor/setup.py similarity index 100% rename from priming_site_predictor/setup.py rename to scRNAsim_toolz/priming_site_predictor/setup.py diff --git a/read_sequencer/.gitlab-ci.yml b/scRNAsim_toolz/read_sequencer/.gitlab-ci.yml similarity index 100% rename from read_sequencer/.gitlab-ci.yml rename to scRNAsim_toolz/read_sequencer/.gitlab-ci.yml diff --git a/read_sequencer/README.md b/scRNAsim_toolz/read_sequencer/README.md similarity index 100% rename from read_sequencer/README.md rename to scRNAsim_toolz/read_sequencer/README.md diff --git a/read_sequencer/readsequencer/__init__.py 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read_sequencer/requirements.txt rename to scRNAsim_toolz/read_sequencer/requirements.txt diff --git a/read_sequencer/setup.py b/scRNAsim_toolz/read_sequencer/setup.py similarity index 100% rename from read_sequencer/setup.py rename to scRNAsim_toolz/read_sequencer/setup.py diff --git a/terminal_fragment_selector/.gitlab-ci.yml b/scRNAsim_toolz/terminal_fragment_selector/.gitlab-ci.yml similarity index 100% rename from terminal_fragment_selector/.gitlab-ci.yml rename to scRNAsim_toolz/terminal_fragment_selector/.gitlab-ci.yml diff --git a/terminal_fragment_selector/README.md b/scRNAsim_toolz/terminal_fragment_selector/README.md similarity index 100% rename from terminal_fragment_selector/README.md rename to scRNAsim_toolz/terminal_fragment_selector/README.md diff --git a/terminal_fragment_selector/term_frag_sel/__init__.py b/scRNAsim_toolz/terminal_fragment_selector/__init__.py similarity index 100% rename from terminal_fragment_selector/term_frag_sel/__init__.py rename to scRNAsim_toolz/terminal_fragment_selector/__init__.py diff --git a/terminal_fragment_selector/term_frag_sel/cli.py b/scRNAsim_toolz/terminal_fragment_selector/cli.py similarity index 100% rename from terminal_fragment_selector/term_frag_sel/cli.py rename to scRNAsim_toolz/terminal_fragment_selector/cli.py diff --git a/terminal_fragment_selector/term_frag_sel/fragmentation.py b/scRNAsim_toolz/terminal_fragment_selector/fragmentation.py similarity index 100% rename from terminal_fragment_selector/term_frag_sel/fragmentation.py rename to scRNAsim_toolz/terminal_fragment_selector/fragmentation.py diff --git a/terminal_fragment_selector/requirements.txt b/scRNAsim_toolz/terminal_fragment_selector/requirements.txt similarity index 100% rename from terminal_fragment_selector/requirements.txt rename to scRNAsim_toolz/terminal_fragment_selector/requirements.txt diff --git a/terminal_fragment_selector/requirements_dev.txt b/scRNAsim_toolz/terminal_fragment_selector/requirements_dev.txt similarity index 100% rename from terminal_fragment_selector/requirements_dev.txt rename to scRNAsim_toolz/terminal_fragment_selector/requirements_dev.txt diff --git a/terminal_fragment_selector/setup.py b/scRNAsim_toolz/terminal_fragment_selector/setup.py similarity index 100% rename from terminal_fragment_selector/setup.py rename to scRNAsim_toolz/terminal_fragment_selector/setup.py diff --git a/terminal_fragment_selector/term_frag_sel/utils.py b/scRNAsim_toolz/terminal_fragment_selector/utils.py similarity index 100% rename from terminal_fragment_selector/term_frag_sel/utils.py rename to scRNAsim_toolz/terminal_fragment_selector/utils.py diff --git a/scRNAsim_toolz/transcript_sampler/.gitignore b/scRNAsim_toolz/transcript_sampler/.gitignore deleted file mode 100644 index e6b679b..0000000 --- a/scRNAsim_toolz/transcript_sampler/.gitignore +++ /dev/null @@ -1,67 +0,0 @@ -# Created by https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode -# Edit at https://www.toptal.com/developers/gitignore?templates=macos,visualstudiocode - -### macOS ### -# General -.DS_Store -.AppleDouble -.LSOverride - -# Icon must end with two \r -Icon - - -# Thumbnails -._* - -# Files that might appear in the root of a volume -.DocumentRevisions-V100 -.fseventsd -.Spotlight-V100 -.TemporaryItems -.Trashes -.VolumeIcon.icns -.com.apple.timemachine.donotpresent - -# Directories potentially created on remote AFP share -.AppleDB -.AppleDesktop -Network Trash Folder -Temporary Items -.apdisk - -### macOS Patch ### -# iCloud generated files -*.icloud - -### VisualStudioCode ### -.vscode/* -!.vscode/settings.json -!.vscode/tasks.json -!.vscode/launch.json -!.vscode/extensions.json -!.vscode/*.code-snippets - -# Local History for Visual Studio Code -.history/ - -# Built Visual Studio Code Extensions -*.vsix - -### VisualStudioCode Patch ### -# Ignore all local history of files -.history -.ionide -.vscode - -# End of https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode - -__pycache__/ -*_cache -*egg-info/ -.coverage -build/ -*/play.py -*.log -temp/ -output_files diff --git a/scRNAsim_toolz/transcript_sampler/LICENSE b/scRNAsim_toolz/transcript_sampler/LICENSE deleted file mode 100644 index edb8749..0000000 --- a/scRNAsim_toolz/transcript_sampler/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2022 zavolan_group / tools - -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. diff --git a/transcript_sequence_extractor/.gitlab-ci.yml b/scRNAsim_toolz/transcript_sequence_extractor/.gitlab-ci.yml similarity index 100% rename from transcript_sequence_extractor/.gitlab-ci.yml rename to scRNAsim_toolz/transcript_sequence_extractor/.gitlab-ci.yml diff --git a/transcript_sequence_extractor/README.md b/scRNAsim_toolz/transcript_sequence_extractor/README.md similarity index 100% rename from transcript_sequence_extractor/README.md rename to scRNAsim_toolz/transcript_sequence_extractor/README.md diff --git a/transcript_sequence_extractor/sequence_extractor/__init__.py b/scRNAsim_toolz/transcript_sequence_extractor/__init__.py similarity index 100% rename from transcript_sequence_extractor/sequence_extractor/__init__.py rename to scRNAsim_toolz/transcript_sequence_extractor/__init__.py diff --git a/transcript_sequence_extractor/sequence_extractor/cli.py b/scRNAsim_toolz/transcript_sequence_extractor/cli.py similarity index 100% rename from transcript_sequence_extractor/sequence_extractor/cli.py rename to scRNAsim_toolz/transcript_sequence_extractor/cli.py diff --git a/transcript_sequence_extractor/sequence_extractor/exon_concatenation.py b/scRNAsim_toolz/transcript_sequence_extractor/exon_concatenation.py similarity index 100% rename from transcript_sequence_extractor/sequence_extractor/exon_concatenation.py rename to scRNAsim_toolz/transcript_sequence_extractor/exon_concatenation.py diff --git a/transcript_sequence_extractor/sequence_extractor/poly_a.py b/scRNAsim_toolz/transcript_sequence_extractor/poly_a.py similarity index 100% rename from transcript_sequence_extractor/sequence_extractor/poly_a.py rename to scRNAsim_toolz/transcript_sequence_extractor/poly_a.py diff --git a/transcript_sequence_extractor/sequence_extractor/pre_bedtools.py b/scRNAsim_toolz/transcript_sequence_extractor/pre_bedtools.py similarity index 100% rename from transcript_sequence_extractor/sequence_extractor/pre_bedtools.py rename to scRNAsim_toolz/transcript_sequence_extractor/pre_bedtools.py diff --git a/transcript_sequence_extractor/requirements.txt b/scRNAsim_toolz/transcript_sequence_extractor/requirements.txt similarity index 100% rename from transcript_sequence_extractor/requirements.txt rename to scRNAsim_toolz/transcript_sequence_extractor/requirements.txt diff --git a/transcript_sequence_extractor/requirements_dev.txt b/scRNAsim_toolz/transcript_sequence_extractor/requirements_dev.txt similarity index 100% rename from transcript_sequence_extractor/requirements_dev.txt rename to scRNAsim_toolz/transcript_sequence_extractor/requirements_dev.txt diff --git a/transcript_sequence_extractor/setup.py b/scRNAsim_toolz/transcript_sequence_extractor/setup.py similarity index 100% rename from transcript_sequence_extractor/setup.py rename to scRNAsim_toolz/transcript_sequence_extractor/setup.py diff --git a/transcript_structure_generator/.gitlab-ci.yml b/scRNAsim_toolz/transcript_structure_generator/.gitlab-ci.yml similarity index 100% rename from transcript_structure_generator/.gitlab-ci.yml rename to scRNAsim_toolz/transcript_structure_generator/.gitlab-ci.yml diff --git a/transcript_structure_generator/README.md b/scRNAsim_toolz/transcript_structure_generator/README.md similarity index 100% rename from transcript_structure_generator/README.md rename to scRNAsim_toolz/transcript_structure_generator/README.md diff --git a/transcript_structure_generator/tsg/__init__.py b/scRNAsim_toolz/transcript_structure_generator/__init__.py similarity index 100% rename from transcript_structure_generator/tsg/__init__.py rename to scRNAsim_toolz/transcript_structure_generator/__init__.py diff --git a/transcript_structure_generator/tsg/__main__.py b/scRNAsim_toolz/transcript_structure_generator/__main__.py similarity index 100% rename from transcript_structure_generator/tsg/__main__.py rename to scRNAsim_toolz/transcript_structure_generator/__main__.py diff --git a/transcript_structure_generator/tsg/cli.py b/scRNAsim_toolz/transcript_structure_generator/cli.py similarity index 100% rename from transcript_structure_generator/tsg/cli.py rename to scRNAsim_toolz/transcript_structure_generator/cli.py diff --git a/transcript_structure_generator/tsg/main.py b/scRNAsim_toolz/transcript_structure_generator/main.py similarity index 100% rename from transcript_structure_generator/tsg/main.py rename to scRNAsim_toolz/transcript_structure_generator/main.py diff --git a/transcript_structure_generator/requirements.txt b/scRNAsim_toolz/transcript_structure_generator/requirements.txt similarity index 100% rename from transcript_structure_generator/requirements.txt rename to scRNAsim_toolz/transcript_structure_generator/requirements.txt diff --git a/transcript_structure_generator/requirements_dev.txt b/scRNAsim_toolz/transcript_structure_generator/requirements_dev.txt similarity index 100% rename from transcript_structure_generator/requirements_dev.txt rename to scRNAsim_toolz/transcript_structure_generator/requirements_dev.txt diff --git a/transcript_structure_generator/setup.py b/scRNAsim_toolz/transcript_structure_generator/setup.py similarity index 100% rename from transcript_structure_generator/setup.py rename to scRNAsim_toolz/transcript_structure_generator/setup.py diff --git a/terminal_fragment_selector/.gitignore b/terminal_fragment_selector/.gitignore deleted file mode 100644 index 20d1246..0000000 --- a/terminal_fragment_selector/.gitignore +++ /dev/null @@ -1,64 +0,0 @@ -# Created by https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode -# Edit at https://www.toptal.com/developers/gitignore?templates=macos,visualstudiocode - -### macOS ### -# General -.DS_Store -.AppleDouble -.LSOverride - -# Icon must end with two \r -Icon - - -# Thumbnails -._* - -# Files that might appear in the root of a volume -.DocumentRevisions-V100 -.fseventsd -.Spotlight-V100 -.TemporaryItems -.Trashes -.VolumeIcon.icns -.com.apple.timemachine.donotpresent - -# Directories potentially created on remote AFP share -.AppleDB -.AppleDesktop -Network Trash Folder -Temporary Items -.apdisk - -### macOS Patch ### -# iCloud generated files -*.icloud - -### VisualStudioCode ### -.vscode/* -!.vscode/settings.json -!.vscode/tasks.json -!.vscode/launch.json -!.vscode/extensions.json -!.vscode/*.code-snippets - -# Local History for Visual Studio Code -.history/ - -# Built Visual Studio Code Extensions -*.vsix - -### VisualStudioCode Patch ### -# Ignore all local history of files -.history -.ionide -.vscode - -# End of https://www.toptal.com/developers/gitignore/api/macos,visualstudiocode - -__pycache__/ -*_cache -*egg-info/ -.coverage -build/ -*/play.py \ No newline at end of file diff --git a/cdna_generator/tests/.gitkeep b/tests/cdna_generator/.gitkeep similarity index 100% rename from cdna_generator/tests/.gitkeep rename to tests/cdna_generator/.gitkeep diff --git a/cdna_generator/tests/__init__.py b/tests/cdna_generator/__init__.py similarity index 100% rename from cdna_generator/tests/__init__.py rename to tests/cdna_generator/__init__.py diff --git a/cdna_generator/tests/test_cdna.py b/tests/cdna_generator/test_cdna.py similarity index 100% rename from cdna_generator/tests/test_cdna.py rename to tests/cdna_generator/test_cdna.py diff --git a/cdna_generator/tests/test_files/.gitkeep b/tests/cdna_generator/test_files/.gitkeep similarity index 100% rename from cdna_generator/tests/test_files/.gitkeep rename to tests/cdna_generator/test_files/.gitkeep diff --git a/cdna_generator/tests/test_files/Example_GTF_Input.GTF b/tests/cdna_generator/test_files/Example_GTF_Input.GTF similarity index 100% rename from cdna_generator/tests/test_files/Example_GTF_Input.GTF rename to tests/cdna_generator/test_files/Example_GTF_Input.GTF diff --git a/cdna_generator/tests/test_files/cDNA.csv b/tests/cdna_generator/test_files/cDNA.csv similarity index 100% rename from cdna_generator/tests/test_files/cDNA.csv rename to tests/cdna_generator/test_files/cDNA.csv diff --git a/cdna_generator/tests/test_files/cDNA.fasta b/tests/cdna_generator/test_files/cDNA.fasta similarity index 100% rename from cdna_generator/tests/test_files/cDNA.fasta rename to tests/cdna_generator/test_files/cDNA.fasta diff --git a/cdna_generator/tests/test_files/copy_number_file.csv b/tests/cdna_generator/test_files/copy_number_file.csv similarity index 100% rename from cdna_generator/tests/test_files/copy_number_file.csv rename to tests/cdna_generator/test_files/copy_number_file.csv diff --git a/cdna_generator/tests/test_files/copy_number_input.csv b/tests/cdna_generator/test_files/copy_number_input.csv similarity index 100% rename from cdna_generator/tests/test_files/copy_number_input.csv rename to tests/cdna_generator/test_files/copy_number_input.csv diff --git a/cdna_generator/tests/test_files/transcript.fasta b/tests/cdna_generator/test_files/transcript.fasta similarity index 100% rename from cdna_generator/tests/test_files/transcript.fasta rename to tests/cdna_generator/test_files/transcript.fasta diff --git a/cdna_generator/tests/test_files/yeast_example.fa b/tests/cdna_generator/test_files/yeast_example.fa similarity index 100% rename from cdna_generator/tests/test_files/yeast_example.fa rename to tests/cdna_generator/test_files/yeast_example.fa diff --git a/priming_site_predictor/tests/__init__.py b/tests/priming_site_predictor/__init__.py similarity index 100% rename from priming_site_predictor/tests/__init__.py rename to tests/priming_site_predictor/__init__.py diff --git a/priming_site_predictor/tests/test_cli.py b/tests/priming_site_predictor/test_cli.py similarity index 100% rename from priming_site_predictor/tests/test_cli.py rename to tests/priming_site_predictor/test_cli.py diff --git a/priming_site_predictor/tests/test_files/RIBlast_output_example.txt b/tests/priming_site_predictor/test_files/RIBlast_output_example.txt similarity index 100% rename from priming_site_predictor/tests/test_files/RIBlast_output_example.txt rename to tests/priming_site_predictor/test_files/RIBlast_output_example.txt diff --git a/priming_site_predictor/tests/test_files/output_transcripts_df.gtf b/tests/priming_site_predictor/test_files/output_transcripts_df.gtf similarity index 100% rename from priming_site_predictor/tests/test_files/output_transcripts_df.gtf rename to tests/priming_site_predictor/test_files/output_transcripts_df.gtf diff --git a/priming_site_predictor/tests/test_files/primer1.fasta b/tests/priming_site_predictor/test_files/primer1.fasta similarity index 100% rename from priming_site_predictor/tests/test_files/primer1.fasta rename to tests/priming_site_predictor/test_files/primer1.fasta diff --git a/priming_site_predictor/tests/test_files/test_fasta.fasta b/tests/priming_site_predictor/test_files/test_fasta.fasta similarity index 100% rename from priming_site_predictor/tests/test_files/test_fasta.fasta rename to tests/priming_site_predictor/test_files/test_fasta.fasta diff --git a/priming_site_predictor/tests/test_files/yeast_test_files/dbRNA_test.fa b/tests/priming_site_predictor/test_files/yeast_test_files/dbRNA_test.fa similarity index 100% rename from priming_site_predictor/tests/test_files/yeast_test_files/dbRNA_test.fa rename to tests/priming_site_predictor/test_files/yeast_test_files/dbRNA_test.fa diff --git a/priming_site_predictor/tests/test_files/yeast_test_files/queryRNA_test.fa b/tests/priming_site_predictor/test_files/yeast_test_files/queryRNA_test.fa similarity index 100% rename from priming_site_predictor/tests/test_files/yeast_test_files/queryRNA_test.fa rename to tests/priming_site_predictor/test_files/yeast_test_files/queryRNA_test.fa diff --git a/priming_site_predictor/tests/test_psp.py b/tests/priming_site_predictor/test_psp.py similarity index 100% rename from priming_site_predictor/tests/test_psp.py rename to tests/priming_site_predictor/test_psp.py diff --git a/read_sequencer/tests/__init__.py b/tests/read_sequencer/__init__.py similarity index 100% rename from read_sequencer/tests/__init__.py rename to tests/read_sequencer/__init__.py diff --git a/read_sequencer/tests/fasta_testfile/50_seqs_50_1000_bp.fasta b/tests/read_sequencer/fasta_testfile/50_seqs_50_1000_bp.fasta similarity index 100% rename from read_sequencer/tests/fasta_testfile/50_seqs_50_1000_bp.fasta rename to tests/read_sequencer/fasta_testfile/50_seqs_50_1000_bp.fasta diff --git a/read_sequencer/tests/test_cli.py b/tests/read_sequencer/test_cli.py similarity index 100% rename from read_sequencer/tests/test_cli.py rename to tests/read_sequencer/test_cli.py diff --git a/read_sequencer/tests/test_read_sequencer.py b/tests/read_sequencer/test_read_sequencer.py similarity index 100% rename from read_sequencer/tests/test_read_sequencer.py rename to tests/read_sequencer/test_read_sequencer.py diff --git a/terminal_fragment_selector/tests/__init__.py b/tests/terminal_fragment_selector/__init__.py similarity index 100% rename from terminal_fragment_selector/tests/__init__.py rename to tests/terminal_fragment_selector/__init__.py diff --git a/terminal_fragment_selector/tests/test_cli.py b/tests/terminal_fragment_selector/test_cli.py similarity index 100% rename from terminal_fragment_selector/tests/test_cli.py rename to tests/terminal_fragment_selector/test_cli.py diff --git a/terminal_fragment_selector/tests/test_files/test.csv b/tests/terminal_fragment_selector/test_files/test.csv similarity index 100% rename from terminal_fragment_selector/tests/test_files/test.csv rename to tests/terminal_fragment_selector/test_files/test.csv diff --git a/terminal_fragment_selector/tests/test_files/test.fasta b/tests/terminal_fragment_selector/test_files/test.fasta similarity index 100% rename from terminal_fragment_selector/tests/test_files/test.fasta rename to tests/terminal_fragment_selector/test_files/test.fasta diff --git a/terminal_fragment_selector/tests/test_files/test_tab.csv b/tests/terminal_fragment_selector/test_files/test_tab.csv similarity index 100% rename from terminal_fragment_selector/tests/test_files/test_tab.csv rename to tests/terminal_fragment_selector/test_files/test_tab.csv diff --git a/terminal_fragment_selector/tests/test_frag.py b/tests/terminal_fragment_selector/test_frag.py similarity index 100% rename from terminal_fragment_selector/tests/test_frag.py rename to tests/terminal_fragment_selector/test_frag.py diff --git a/terminal_fragment_selector/tests/test_utils.py b/tests/terminal_fragment_selector/test_utils.py similarity index 100% rename from terminal_fragment_selector/tests/test_utils.py rename to tests/terminal_fragment_selector/test_utils.py diff --git a/transcript_sequence_extractor/tests/__init__.py b/tests/transcript_sequence_extractor/__init__.py similarity index 100% rename from transcript_sequence_extractor/tests/__init__.py rename to tests/transcript_sequence_extractor/__init__.py diff --git a/transcript_sequence_extractor/tests/test_exon_concatenation.py b/tests/transcript_sequence_extractor/test_exon_concatenation.py similarity index 100% rename from transcript_sequence_extractor/tests/test_exon_concatenation.py rename to tests/transcript_sequence_extractor/test_exon_concatenation.py diff --git a/transcript_sequence_extractor/tests/test_files/post_bedtools_test.fa b/tests/transcript_sequence_extractor/test_files/post_bedtools_test.fa similarity index 100% rename from transcript_sequence_extractor/tests/test_files/post_bedtools_test.fa rename to tests/transcript_sequence_extractor/test_files/post_bedtools_test.fa diff --git a/transcript_sequence_extractor/tests/test_files/test.bed b/tests/transcript_sequence_extractor/test_files/test.bed similarity index 100% rename from transcript_sequence_extractor/tests/test_files/test.bed rename to tests/transcript_sequence_extractor/test_files/test.bed diff --git a/transcript_sequence_extractor/tests/test_files/test.gtf b/tests/transcript_sequence_extractor/test_files/test.gtf similarity index 100% rename from transcript_sequence_extractor/tests/test_files/test.gtf rename to tests/transcript_sequence_extractor/test_files/test.gtf diff --git a/transcript_sequence_extractor/tests/test_files/test_1.fa b/tests/transcript_sequence_extractor/test_files/test_1.fa similarity index 100% rename from transcript_sequence_extractor/tests/test_files/test_1.fa rename to tests/transcript_sequence_extractor/test_files/test_1.fa diff --git a/transcript_sequence_extractor/tests/test_files/test_2.fa b/tests/transcript_sequence_extractor/test_files/test_2.fa similarity index 100% rename from transcript_sequence_extractor/tests/test_files/test_2.fa rename to tests/transcript_sequence_extractor/test_files/test_2.fa diff --git a/transcript_sequence_extractor/tests/test_poly_a.py b/tests/transcript_sequence_extractor/test_poly_a.py similarity index 100% rename from transcript_sequence_extractor/tests/test_poly_a.py rename to tests/transcript_sequence_extractor/test_poly_a.py diff --git a/transcript_structure_generator/tests/__init__.py b/tests/transcript_structure_generator/__init__.py similarity index 100% rename from transcript_structure_generator/tests/__init__.py rename to tests/transcript_structure_generator/__init__.py diff --git a/transcript_structure_generator/tests/resources/Annotation1.gtf b/tests/transcript_structure_generator/resources/Annotation1.gtf similarity index 100% rename from transcript_structure_generator/tests/resources/Annotation1.gtf rename to tests/transcript_structure_generator/resources/Annotation1.gtf diff --git a/transcript_structure_generator/tests/resources/Annotations2.gtf b/tests/transcript_structure_generator/resources/Annotations2.gtf similarity index 100% rename from transcript_structure_generator/tests/resources/Annotations2.gtf rename to tests/transcript_structure_generator/resources/Annotations2.gtf diff --git a/transcript_structure_generator/tests/resources/Transcript1.csv b/tests/transcript_structure_generator/resources/Transcript1.csv similarity index 100% rename from transcript_structure_generator/tests/resources/Transcript1.csv rename to tests/transcript_structure_generator/resources/Transcript1.csv diff --git a/transcript_structure_generator/tests/resources/Transcript2.tsv b/tests/transcript_structure_generator/resources/Transcript2.tsv similarity index 100% rename from transcript_structure_generator/tests/resources/Transcript2.tsv rename to tests/transcript_structure_generator/resources/Transcript2.tsv diff --git a/transcript_structure_generator/tests/test_main.py b/tests/transcript_structure_generator/test_main.py similarity index 100% rename from transcript_structure_generator/tests/test_main.py rename to tests/transcript_structure_generator/test_main.py diff --git a/transcript_sequence_extractor/LICENSE b/transcript_sequence_extractor/LICENSE deleted file mode 100644 index fc46329..0000000 --- a/transcript_sequence_extractor/LICENSE +++ /dev/null @@ -1,9 +0,0 @@ - The MIT License (MIT) - -Copyright © 2022 Samuel Mondal - -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. diff --git a/transcript_structure_generator/.gitignore b/transcript_structure_generator/.gitignore deleted file mode 100644 index dc92f04..0000000 --- a/transcript_structure_generator/.gitignore +++ /dev/null @@ -1,161 +0,0 @@ -# Created by https://www.toptal.com/developers/gitignore/api/python,git -# Edit at https://www.toptal.com/developers/gitignore?templates=python,git - -### Git ### -# Created by git for backups. To disable backups in Git: -# $ git config --global mergetool.keepBackup false -*.orig - -# Created by git when using merge tools for conflicts -*.BACKUP.* -*.BASE.* -*.LOCAL.* -*.REMOTE.* -*_BACKUP_*.txt -*_BASE_*.txt -*_LOCAL_*.txt -*_REMOTE_*.txt - -### Python ### -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# End of https://www.toptal.com/developers/gitignore/api/python,git - -data \ No newline at end of file diff --git a/transcript_structure_generator/LICENSE b/transcript_structure_generator/LICENSE deleted file mode 100644 index 2313fb3..0000000 --- a/transcript_structure_generator/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2021 Zavolan Lab, Biozentrum, University of Basel - -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. \ No newline at end of file