Updated copyrights and .gitignore

VermaLab · Jun 3, 2025 · 0e8b74e · 0e8b74e
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diff --git a/.gitignore b/.gitignore
@@ -3,160 +3,9 @@ __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/latest/usage/project/#working-with-version-control
-.pdm.toml
-.pdm-python
-.pdm-build/
-
-# 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/DigitalAssays/DigitalAnalysis.ipynb b/DigitalAssays/DigitalAnalysis.ipynb
@@ -9,7 +9,7 @@
     "This folder is meant to serve as an example of how to call and interact with the `DigitalAssayAnalysis` module. \n",
     "\n",
     "## License\n",
-    "Copyright (C) 2024 Purdue Research Foundation. This work is protected under GNU Affero General Public License Version 3 with Commons Clause. Please see the `LICENSE` file for more information."
+    "Copyright (C) 2025 Purdue Research Foundation. This work is protected under GNU Affero General Public License Version 3 with Commons Clause. Please see the `LICENSE` file for more information."
    ]
   },
   {

diff --git a/DigitalAssays/DigitalAssayAnalysis.py b/DigitalAssays/DigitalAssayAnalysis.py
@@ -7,7 +7,7 @@
 __email__ = 'msverma@purdue.edu'
 __version__ = '1.0.0'
 __status__ = 'Development'
-__copyright__ = "Copyright (C) 2024 Purdue Research Foundation"
+__copyright__ = "Copyright (C) 2025 Purdue Research Foundation"
 __license__ = "GNU Affero General Public License Version 3 with Commons Clause"
 
 #### BEGIN IMPORTS

diff --git a/DigitalAssays/README.md b/DigitalAssays/README.md
@@ -93,4 +93,4 @@ $C_{avg, 95\\%} = \left( \frac{C_{avg, sample} - t_{crit}\cdot\sigma (C)}{\sqrt{
 
 Averages for copies per reaction are calcualted the same way, except replacing $C_{cps/\mu L}$ with $C_{cps/rxn}$.
 
-<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><span property="dct:title">&copy; 2024 - Purdue Research Foundation. Reaction Analysis Library Documentation</span> by <span property="cc:attributionName">Josiah Davidson</span> is licensed under <a href="https://creativecommons.org/licenses/by-nc/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1" alt=""></a></p>
+<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><span property="dct:title">&copy; 2025 - Purdue Research Foundation. Reaction Analysis Library Documentation</span> by <span property="cc:attributionName">Josiah Davidson</span> is licensed under <a href="https://creativecommons.org/licenses/by-nc/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1" alt=""></a></p>
diff --git a/README.md b/README.md
@@ -4,4 +4,4 @@ This repo contains a variety of scripts used by the Verma lab for evaluation and
 
 - [DigitalAssays](https://github.itap.purdue.edu/VermaLab/ReactionAnalysisLibrary/tree/main/DigitalAssays)
 
-<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><span property="dct:title">&copy; 2024 - Purdue Research Foundation. Primer Analysis Documentation</span> by <span property="cc:attributionName">Josiah Davidson</span> is licensed under <a href="https://creativecommons.org/licenses/by-nc/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1" alt=""></a></p>
+<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><span property="dct:title">&copy; 2025 - Purdue Research Foundation. Primer Analysis Documentation</span> by <span property="cc:attributionName">Josiah Davidson</span> is licensed under <a href="https://creativecommons.org/licenses/by-nc/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1" alt=""></a></p>