Metadata-Version: 1.1
Name: ela
Version: 0.6.4
Summary: A Python package for exploratory lithology analysis
Home-page: https://github.com/jmp75/pyela
Author: Jean-Michel Perraud, Juan Castilla
Author-email: per202@csiro.au
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/jmp75/pyela/issues
Project-URL: Source, https://github.com/jmp75/pyela
Description: ela
        ===
        
        Exploratory Lithology Analysis
        ------------------------------
        
        `license <https://github.com/jmp75/pyela/blob/devel/LICENSE.txt>`__
        |status| master: `build <https://travis-ci.org/jmp75/pyela>`__
        `coverage <https://coveralls.io/github/jmp75/pyela?branch=master>`__
        
        `Getting started tutorial - Bungendore 3D
        lithology <https://github.com/jmp75/pyela-doc/blob/master/tutorials/getting_started.ipynb>`__
        
        Analysing driller’s logs is a tedious and repetitive task in many
        groundwater modelling projects. Automating the process of extracting
        useful information from driller’s logs allows spending less time on
        manual data wrangling, more time on its interpretation, and enhances the
        reproducibility of the analysis.
        
        This package combines features to:
        
        -  perform natural language processing on lithology descriptions in the
           logs, to detect primary and secondary lithologies
        -  apply supervised machine learning to interpolate lithologies across a
           3D grid
        -  visualise interactively the 3D data
        
        License
        -------
        
        MIT (see
        `License.txt <https://github.com/jmp75/pyela/blob/master/LICENSE.txt>`__)
        
        Documentation
        -------------
        
        Tutorials are hosted `in a separate github
        repo <https://github.com/jmp75/pyela-doc>`__
        
        Get a `quick tour of the visualisation part of
        ‘ela’ <https://github.com/jmp75/pyela/blob/master/docs/visual_tour.md>`__.
        
        Installation
        ------------
        
        As of January 2019 `ela is on pypi <https://pypi.org/project/ela/>`__.
        Before installing you may want to skim the “Installation details”
        section thereafter to think of context (e.g. conda env) but otherwhse
        ``pip install ela`` should install the required dependencies.
        
        .. code:: bash
        
           pip search ela
           pip install ela
        
        Alternatively, from source:
        
        .. code:: bash
        
           pip install -r requirements.txt
           python setup.py install
        
        Installation details
        --------------------
        
        ‘ela’ relies on several external packages, and some can be fiddly to
        install depending on the version of Python and these external packages.
        This section thus has fairly prescriptive instructions, given in the
        hope of limiting the risk of issues.
        
        The first part of this section is focused on Linux.
        
        Debian packages for spatial projections
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        ``cartopy`` and possibly other python packages require ``proj4`` version
        4.9+ to be installed (libproj-dev). If your debian/ubuntu repo does not
        suffice (older versions) you may try:
        
        .. code:: bash
        
           sudo apt-get install -y libc6  
           wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/proj-data_4.9.3-2_all.deb
           sudo dpkg -i proj-data_4.9.3-2_all.deb
           wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj12_4.9.3-2_amd64.deb
           sudo dpkg -i libproj12_4.9.3-2_amd64.deb
           wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/proj-bin_4.9.3-2_amd64.deb
           sudo dpkg -i proj-bin_4.9.3-2_amd64.deb
           wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj9_4.9.2-2_amd64.deb 
           sudo dpkg -i libproj9_4.9.2-2_amd64.deb
           wget http://en.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj-dev_4.9.3-2_amd64.deb
           sudo dpkg -i libproj-dev_4.9.3-2_amd64.deb
        
        Installation of python packages dependencies
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        You may want to install
        `Anaconda <http://docs.continuum.io/anaconda/install>`__ to install
        dependencies. Note that I recommend to **not** let anaconda change your
        startup file and change the ``PATH`` environment. To activate Anaconda
        you first need: ``source ~/anaconda3/bin/activate``. Then choose a conda
        environment name.
        
        Optionally you may want to do ``conda update -n base conda`` and
        ``conda update -n base anaconda-navigator``
        
        .. code:: bash
        
           my_env_name=ELA
        
        .. code:: bash
        
           conda create --name ${my_env_name} python=3.6
           conda activate  ${my_env_name}
           conda install --name ${my_env_name} rasterio cartopy geopandas pandas nltk scikit-learn scikit-image matplotlib vtk
        
        As of writing (2018-08) conda does not have pyqt5, and a suitable
        version of mayavi for python3. We use ``pip``
        
        .. code:: bash
        
           pip install --upgrade pip
        
        For Python 3.x one needs to install pyqt5 for mayavi, as per `these
        instructions <https://docs.enthought.com/mayavi/mayavi/installation.html>`__.
        As of Jan 2019 be aware that there is a `known issue in mayavi visual
        rendering with pyqt5 as a
        backend <https://github.com/enthought/mayavi/issues/656>`__ and ‘ela’ is
        affected by this. Nevertheless this is not a commplete blocker for most
        ‘ela’ features so installation instructions are kept here.
        
        .. code:: bash
        
           pip search pyqt5 | sort -g
           pip search mayavi
        
        .. code:: bash
        
           pip install pyqt5
           pip install mayavi
        
        Windows
        ~~~~~~~
        
        Placeholder section. As of Sept 2018 it may be possible to install upon
        Python 3.6+ with Anaconda 3, and then including mayavi from pip.
        
        Related Geoscience packages
        ---------------------------
        
        ‘ela’ aims to complement other Python packages for geoscience, in
        particular for handling bore data . It depends on the package
        `‘striplog’ <https://github.com/agile-geoscience/striplog>`__ and is
        likely to depend on `‘lasio’ <https://github.com/kinverarity1/lasio>`__
        in the future.
        
        Known issues
        ------------
        
        3D interactive visualisation: As of 2018-08, using mayavi 4.6 on python
        3.6 may be `visually
        buggy <https://github.com/enthought/mayavi/issues/656>`__, though users
        reported success on 2019-03. Python 2.7 with mayavi 4.5 via Anaconda2 is
        known to work.
        
        Troubleshooting
        ---------------
        
        If in a conda environment trying to use ``pip`` you get:
        
        .. code:: text
        
           ModuleNotFoundError: No module named 'pip._internal'
        
        consider:
        
        .. code:: bash
        
           curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
           python3 get-pip.py --force-reinstall
        
        .. |status| image:: https://img.shields.io/badge/status-alpha-blue.svg
        
        
Keywords: lithology geophysics groundwater data-mining
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
