From 8da2adddcc916c695a315e791ce3d9a890814f45 Mon Sep 17 00:00:00 2001 From: Surag Nair <10693069+suragnair@users.noreply.github.com> Date: Thu, 23 Feb 2023 18:56:14 -0800 Subject: [PATCH] removed accessory files --- src/basepairmodels/.gitignore | 70 ------------------------- src/basepairmodels/LICENSE | 21 -------- src/basepairmodels/requirements.txt | 21 -------- src/genomicsdlarchsandlosses/.gitignore | 69 ------------------------ src/genomicsdlarchsandlosses/LICENSE | 21 -------- src/mseqgen/.gitignore | 8 --- src/mseqgen/LICENSE | 21 -------- 7 files changed, 231 deletions(-) delete mode 100755 src/basepairmodels/.gitignore delete mode 100755 src/basepairmodels/LICENSE delete mode 100755 src/basepairmodels/requirements.txt delete mode 100755 src/genomicsdlarchsandlosses/.gitignore delete mode 100755 src/genomicsdlarchsandlosses/LICENSE delete mode 100755 src/mseqgen/.gitignore delete mode 100755 src/mseqgen/LICENSE diff --git a/src/basepairmodels/.gitignore b/src/basepairmodels/.gitignore deleted file mode 100755 index 42966c1..0000000 --- a/src/basepairmodels/.gitignore +++ /dev/null @@ -1,70 +0,0 @@ -# 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/ -*.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 -tests/ -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -.hypothesis/ -.pytest_cache/ - - -# Sphinx documentation -docs-build/* -_build/ - -# Jupyter Notebook -.ipynb_checkpoints - -# pyenv -.python-version - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - diff --git a/src/basepairmodels/LICENSE b/src/basepairmodels/LICENSE deleted file mode 100755 index d4590a2..0000000 --- a/src/basepairmodels/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2020 Kundaje Lab - -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/src/basepairmodels/requirements.txt b/src/basepairmodels/requirements.txt deleted file mode 100755 index 60c0816..0000000 --- a/src/basepairmodels/requirements.txt +++ /dev/null @@ -1,21 +0,0 @@ -tensorflow-gpu==1.14 -tensorflow-probability==0.7 -keras==2.2.4 -scikit-learn -scipy -scikit-image -deepdish -h5py -numpy==1.16.4 -pandas -matplotlib -plotly -deeptools -pyfaidx -modisco -deeplift -tqdm -pycodestyle -pytest -pandas - diff --git a/src/genomicsdlarchsandlosses/.gitignore b/src/genomicsdlarchsandlosses/.gitignore deleted file mode 100755 index d389c9e..0000000 --- a/src/genomicsdlarchsandlosses/.gitignore +++ /dev/null @@ -1,69 +0,0 @@ -# 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/ -*.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/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -.hypothesis/ -.pytest_cache/ - - -# Sphinx documentation -docs-build/* -_build/ - -# Jupyter Notebook -.ipynb_checkpoints - -# pyenv -.python-version - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - diff --git a/src/genomicsdlarchsandlosses/LICENSE b/src/genomicsdlarchsandlosses/LICENSE deleted file mode 100755 index 05d6173..0000000 --- a/src/genomicsdlarchsandlosses/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2021 Kundaje Lab - -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/src/mseqgen/.gitignore b/src/mseqgen/.gitignore deleted file mode 100755 index 3da9ad1..0000000 --- a/src/mseqgen/.gitignore +++ /dev/null @@ -1,8 +0,0 @@ -build/ -docs-build/ -*.egg-info/ -*.egg -.ipynb_checkpoints -__pycache__/ -*.py[cod] -*$py.class diff --git a/src/mseqgen/LICENSE b/src/mseqgen/LICENSE deleted file mode 100755 index 24836b2..0000000 --- a/src/mseqgen/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2019 Kundaje Lab - -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.