Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
PyleoTUPS: Automated Paleoclimate Data Extraction and Processing
================================================================

PyleoTUPS is a Python package developed by LinkedEarth to simplify access to paleoclimate datasets from major public repositories. It provides a unified interface for searching, retrieving, and processing data from `NOAA NCEI for Paleoclimatology <https://www.ncei.noaa.gov/products/paleoclimatology>`_ and `PANGAEA <https://www.pangaea.de>`_, two repositories that differ substantially in structure, metadata organization, search syntax, and file formats.
PyleoTUPS is a Python package developed by `LinkedEarth <https://www.linked.earth>`_ to simplify access to paleoclimate datasets from major public repositories. It provides a unified interface for searching, retrieving, and processing data from `NOAA NCEI for Paleoclimatology <https://www.ncei.noaa.gov/products/paleoclimatology>`_ and `PANGAEA <https://www.pangaea.de>`_, two repositories that differ substantially in structure, metadata organization, search syntax, and file formats.

The package is designed to reduce a common bottleneck in paleoclimate research: manually locating datasets, navigating repository-specific APIs, downloading files, parsing legacy formats, and reshaping results for analysis. PyleoTUPS handles these steps through a consistent Python API and returns results as pandas DataFrames with associated metadata.

Expand Down
60 changes: 59 additions & 1 deletion docs/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,71 @@

.. note::

PyleoTUPS requires the use of Python 3.11 or above
PyleoTUPS requires the use of Python 3.11 or above. We recommend using Python 3.12 to work with `Pyleoclim <https://pyleoclim-util.readthedocs.io/en/latest/>`_.

Installing PyleoTUPS
====================

PyleoTUPS can be easily installed through `PyPI <https://pypi.org/project/pyleotups/>`_. We recommend using a dedicated Anaconda or Miniconda environment to manage dependencies.

Creating an environment and installing PyleoTUPS
------------------------------------------------

Before installing PyleoTUPS, we recommend creating a dedicated conda environment:

.. code-block:: bash

conda create --name pyleotups python=3.12
conda activate pyleotups

Install PyleoTUPS through PyPI, which contains the most stable version of PyleoTUPS:

.. code-block:: bash

pip install pyleotups

This will install the latest official release of PyleoTUPS. To install the development version, use:

.. code-block:: bash

pip install git+https://github.com/LinkedEarth/pyleotups.git

This version may contain bugs not caught by our continuous integration test suite; if so, please report them via `github issues <https://github.com/LinkedEarth/pyleotups/issues>`_.

If you wish to contribute to PyLiPD, see our `contributing guide <https://pyleotups.readthedocs.io/en/latest/contribution_guide.html>`_ for complete instructions on building from the git source tree.

To remove the conda environment:

.. code-block:: bash

conda remove --name pyleotups --all

More information about managing conda environments can be found `here <https://docs.conda.io/en/latest/user-guide/tasks/manage-environments.html>`_.

Running the test suite
======================

PyleoTUPS comes with a set of unit tests. To run these, you need to install `pytest` in the same environment as PyleoTUPS via `pip install pytest`. To run the tests from a Python terminal, navigate to the tests folder on your computer and run:

.. code-block:: bash

pytest

Dependencies
============

PyleoTUPS depends on several Python packages:
* pandas
* numpy
* requests
* pybtex
* tqdm
* nbstripout
* xlrd
* openpyxl
* pangaeapy
* bibtextparser
* doi2bib

These dependencies will be automatically installed when you install PyleoTUPS.

Loading