primacore 0.1.4__tar.gz

primacore-0.1.4/LICENSE

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+MIT License
+
+Copyright (c) 2025 Jordan
+
+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.

primacore-0.1.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: primacore
+Version: 0.1.4
+Author-email: Jordi Sassoon <jordisassoon@gmail.com>
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: uvicorn
+Requires-Dist: scikit-learn
+Requires-Dist: tqdm
+Requires-Dist: lightgbm
+Dynamic: license-file

primacore-0.1.4/README.md

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+# 🌿 PRIMA: A tool for Palaeoclimatic Reconstruction through Interactive Modelling & Analysis 
+
+PRIAM is an interactive tool for proxy-based climate reconstruction and analysis. It allows users to import palaeoecological proxy data—such as fossil pollen, sediments, or other biological indicators—and apply multiple statistical and machine learning methods to reconstruct past climate conditions. The app provides instant model training, validation, and visualization, offering insights into model performance, feature importance, and uncertainty. Users can explore reconstructed climate variables through dynamic plots, comparative analyses, and summary statistics, making it a comprehensive platform for both research and teaching in palaeoclimatology.
+
+This project implements multiple methods for quantitative palaeoclimate reconstruction from fossil pollen data, including:
+
+* **Modern Analogue Technique (MAT)**
+* **Boosted Regression Trees (BRT)**
+* **Weighted Averaging Partial Least Squares (WA-PLS)**
+* **Random Forest (RF)**
+
+It also provides a **web-based interface** using [Streamlit](https://streamlit.io).
+
+## 📦 Installation
+
+### 1. Clone this repository
+
+```bash
+git clone https://github.com/yourusername/PyLae.git
+cd pollen-recon
+```
+
+### 2. Create and activate a conda environment
+
+```bash
+conda env create -f environment.yml
+conda activate pylaeo
+```
+
+## ⚙️ Command-Line Usage
+
+The main pipeline is in `main.py`.
+It trains models on **training climate + pollen data** and predicts for **fossil pollen samples**.
+
+### Example
+
+```bash
+python main.py \
+  --train_climate ./data/train/AMPD_cl_worldclim2.csv \
+  --train_pollen ./data/train/AMPD_po.csv \
+  --test_pollen ./data/test/scrubbed_SAR.csv \
+  --model RF \
+  --target TANN \
+  --output_csv ./out/predictions.csv
+```
+
+Arguments:
+
+* `--train_climate`: CSV with climate variables (targets).
+* `--train_pollen`: CSV with modern pollen counts.
+* `--test_pollen`: CSV with fossil pollen data.
+* `--model`: Model choice (`MAT`, `BRT`, `WA-PLS`, `RF`).
+* `--target`: Target variable to reconstruct (e.g., `TANN`).
+* `--output_csv`: Where to save predictions.
+
+## 📊 Visualization
+
+Once predictions are saved, you can plot them with:
+
+```bash
+python visuals/plot.py \
+  --predictions_csv ./out/predictions.csv \
+  --output_file ./out/predictions.png \
+  --title "Reconstructed TANN"
+```
+
+## 🌐 Streamlit Web App
+
+For an interactive interface:
+
+```bash
+streamlit run app.py
+```
+
+This will launch a web UI at [http://localhost:8501](http://localhost:8501).
+
+Features:
+
+* Upload training and fossil pollen CSVs.
+* Choose model + target variable.
+* Run predictions interactively.
+* View results as a table and time-series plot.
+* Download predictions as CSV.
+
+## 📂 Project Structure
+
+```
+├── app.py                # Streamlit web app
+├── main.py               # CLI pipeline
+├── models/               # Model classes (MAT, BRT, WA-PLS, RF)
+├── utils/dataloader.py   # Data loading + preprocessing
+├── visuals/plot.py       # Visualization script
+├── data/                 # Example datasets
+├── out/                  # Output predictions + plots
+├── requirements.txt      # Dependencies
+└── README.md             # This file
+```
+
+## 🧑‍💻 Development Notes
+
+* Datasets are aligned automatically (non-overlapping taxa filled with zeros).
+* Predictions are saved with column name `Predicted_<target>`.
+* Tested on Linux (Python 3.10).
+
+## 👩‍🔬 Authors
+
+Dael Sassoon
+ — Palaeoecologist and Marie Curie Research Fellow (GEO3BCN-CSIC, Barcelona).
+Specialising in tropical palaeoecology and quantitative reconstruction of past climates. Developer of PRIAM, integrating palaeoecological data with statistical and machine learning models for climate reconstruction.
+
+Jordan Sassoon
+ — Computer Scientist. 
+Focused on applied AI, data systems, and scientific visualization. Lead developer of the PRIAM interface, integrating backend modelling pipelines with an interactive analytical framework.
+
+## 🧠 Citation
+
+If you use PRIAM in your research, please cite as:
+
+Sassoon, D., & Sassoon, J. (2025). PRIAM: A tool for Palaeoclimatic Reconstruction through Interactive Analysis & Modelling. GitHub repository: https://github.com/jordisassoon/PRIAM

primacore-0.1.4/primacore.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: primacore
+Version: 0.1.4
+Author-email: Jordi Sassoon <jordisassoon@gmail.com>
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: uvicorn
+Requires-Dist: scikit-learn
+Requires-Dist: tqdm
+Requires-Dist: lightgbm
+Dynamic: license-file

primacore-0.1.4/primacore.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+primacore.egg-info/PKG-INFO
+primacore.egg-info/SOURCES.txt
+primacore.egg-info/dependency_links.txt
+primacore.egg-info/requires.txt
+primacore.egg-info/top_level.txt
+primapy/__init__.py

primacore-0.1.4/primacore.egg-info/dependency_links.txt

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+

primacore-0.1.4/primacore.egg-info/requires.txt

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+numpy
+pandas
+uvicorn
+scikit-learn
+tqdm
+lightgbm

primacore-0.1.4/primacore.egg-info/top_level.txt

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+primapy

primacore-0.1.4/pyproject.toml

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+[project]
+name = "primacore"
+version = "0.1.4"
+authors = [{ name = "Jordi Sassoon", email = "jordisassoon@gmail.com" }]
+requires-python = ">=3.10"
+dependencies = [
+  "numpy",
+  "pandas",
+  "uvicorn",
+  "scikit-learn",
+  "tqdm",
+  "lightgbm",
+]
+
+[dependency-groups]
+dev = [
+    "mypy>=1.18.2",
+    "pytest>=8.4.2",
+    "pytest-timeout>=2.4.0",
+    "pytest-vcr>=1.0.2",
+    "python-dotenv>=1.2.1",
+    "ruff>=0.14.3",
+    "shellcheck-py>=0.11.0.1",
+    "ty>=0.0.14",
+    "types-requests>=2.32.4.20260107",
+]
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+include = ["primapy"]
+
+[tool.uv]
+package = true

primacore-0.1.4/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+