Initialize repo with license and informative files.

.gitignore

@@ -0,0 +1,178 @@
+# 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/
+
+# Mac system
+.DS_Store

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Imageomics Institute
+
+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.

README.md

@@ -0,0 +1,31 @@
+# Tree of Life 10M EDA Repo
+
+This repo contains the analysis of the TreeOfLife10M dataset as it's being crafted and refined.
+
+### Data
+
+The `data` folder contains
+ - `v1-dev-names.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the 
+associated taxa information for the image.
+ - `taxa_counts.csv`: count of distinct lower taxa within each higher taxon from `kingdom` down to 
+`genus`, though the genus count was interrupted and therefore is incomplete.
+ - `avg_std_byClass.csv`: average and standard distribution of images given by class. This is for both all 
+images, and images that have labels. Note that kingdoms have not been merged and no standardization has 
+been performed on the taxonomic hierarchy prior to creation of this file.
+
+### Notebooks
+
+The `notebooks` folder contains
+ - `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `v1-dev-names.csv`, generates 
+`taxa_counts.csv`.
+ - `BioCLIP_taxa_viz_bySource.ipynb`: generates data visualizations, in particular, the generation of 
+visualizations in visuals and some histograms. The treemaps produced in the notebook are interactive.
+ - `ToL_EDA.ipynb`: more full EDA of TreeOfLife10M dataset. Explores the labeling inconsistencies for 
+direction of standardization efforts.
+
+Note: run `pip install -r requirements.txt` before starting the notebooks.
+
+### Visuals
+
+Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M. 
+There is also one for just the iNat21 data included.

requirements.txt

@@ -0,0 +1,9 @@
+pandas==2.0.3
+scikit-learn==1.3.1
+seaborn==0.12.2
+matplotlib==3.7.3
+scikit-image==0.21.0
+plotly==5.17.0
+jupyter==1.0.0
+notebook==7.0.4
+kaleido==0.2.1