Merge branch 'dev'

CHANGELOG

@@ -3,17 +3,26 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
-## [Unreleased]
+## [1.1.1] - 2021-04-17
 ### Added
 - Version number is defined within `VelocityConversion/__init__.py` and is being
-  read when building the documentation.
+  read when building the documentation and installing via `pip`.
+- Added support for pipenv.
 - The density for the simple pressure calculation can now be defined by
   declaring the variable `SimpleRho`.
-- Function `Convert()` for convenience when using VelocityConversion as a Python
-  module.
+- Function `Convert()` for convenience when using VelocityConversion as a
+  Python module.
+- Added `UnavailableMethodError` when user want to use pressure- and
+  temperature-dependent expansion coefficient (`-AlphaPT`), since this method
+  is currently buggy.
 
 ### Changed
 - Enhanced the documentation.
+- Use getter and setter for `UseAlpha` variable.
+
+### Fixed
+- Fixed a bug where the csv tables were not copied when using `pip install .`.
+- Fixed an issue where pressure would not be computed with the simple method.
 
 ## [1.1.0] - 2019-07-16
 ### Added

Pipfile

@@ -0,0 +1,22 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+numpy = "*"
+
+[dev-packages]
+flake8 = "*"
+pydocstyle = "*"
+ipython = "*"
+pep8 = "*"
+sphinx = "*"
+sphinx-rtd-theme = "*"
+doc8 = "*"
+coverage = "*"
+matplotlib = "*"
+m2r2 = "*"
+
+[requires]
+python_version = "3.9"

README.md

@@ -2,16 +2,16 @@
 
 [![DOI](https://zenodo.org/badge/87794116.svg)](https://zenodo.org/badge/latestdoi/87794116)
 
-- [VelocityConversion](#VelocityConversion)
-  - [Introduction](#Introduction)
-  - [Recommended citation for VelocityConversion](#Recommended-citation-for-VelocityConversion)
-  - [Prerequisites](#Prerequisites)
-  - [How to get started](#How-to-get-started)
-    - [Usage as command line tool](#Usage-as-command-line-tool)
-    - [Usage as a Python module](#Usage-as-a-Python-module)
-  - [Modifying physical properties of the minerals](#Modifying-physical-properties-of-the-minerals)
-  - [References](#References)
-  - [Licence](#Licence)
+- [VelocityConversion](#velocityconversion)
+  - [Introduction](#introduction)
+  - [Recommended citation for VelocityConversion](#recommended-citation-for-velocityconversion)
+  - [Prerequisites](#prerequisites)
+  - [How to get started](#how-to-get-started)
+    - [Usage as command line tool](#usage-as-command-line-tool)
+    - [Usage as a Python module](#usage-as-a-python-module)
+  - [Modifying physical properties of the minerals](#modifying-physical-properties-of-the-minerals)
+  - [References](#references)
+  - [Licence](#licence)
 
 ## Introduction
 
@@ -40,6 +40,19 @@ If you use this code, please consider citing it as
 This code requires an installation of Python 3.x and numpy.
 Building the documentation furthermore requires sphinx and m2r.
 
+You can use [`pipenv`](https://pypi.org/project/pipenv/) to create an
+environment:
+
+```bash
+pipenv install
+```
+
+ctivate the environment via
+
+```bash
+pipenv shell
+```
+
 ## How to get started
 
 The code can be used either as a command line tool or as a module within
@@ -50,6 +63,13 @@ repository:
 git clone https://github.com/cmeessen/VelocityConversion.git
 ```
 
+or, if you haven an [SSH key](https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent)
+associated to your account:
+
+```bash
+git clone [email protected]:cmeessen/VelocityConversion.git
+```
+
 To check whether everything is working run the tests
 
 ```bash
@@ -76,7 +96,7 @@ In order to use the code as command line tool, add the `./Examples` directory
 to your `PATH`, e.g. in your bash profile:
 
 ```bash
-export PATH=/path/to/VelocityConversion/Examples
+export PATH=/path/to/VelocityConversion/Examples:$PATH
 ```
 
 Alternatively you can move the bash script
@@ -147,6 +167,12 @@ For a more complete documentation on how to use `VelocityConversion` as a Python
 module please visit the
 [documentation](https://cmeessen.github.io/VelocityConversion/).
 
+To uninstall `VelocityConversion`, run
+
+```bash
+pip uninstall velocityconversion-cmeessen
+```
+
 ## Modifying physical properties of the minerals
 
 The database that contains the physical properties of the individual mineral

VelocityConversion/__init__.py

@@ -16,26 +16,6 @@
 #     You should have received a copy of the GNU General Public License       #
 #  along with VelocityConversion. If not, see <http://www.gnu.org/licenses/>. #
 ###############################################################################
-"""
-This code is a python implementation of the p- and s-wave velocity to density
-conversion approach after Goes et al. (2000)
-
-Recommended citation
-====================
-
-> Meeßen, Christian (2017): VelocityConversion. V. v1.0.1. GFZ Data Services.
-> http://doi.org/10.5880/GFZ.6.1.2017.001
-
-Contact
-=======
-
-For questions or suggestions please contact
-
-| Christian Meeßen
-| Section 4.5 Basin Modelling
-| GFZ Potsdam
-| [email protected]
-"""
 
 from __future__ import print_function, unicode_literals
 import numpy as np
@@ -47,7 +27,12 @@
 from warnings import warn
 import __main__
 
-__version__ = '1.1.1-rc1'
+__version__ = '1.1.1'
+
+
+class UnavailableMethodError(Exception):
+    """Raise when trying to use AlphaPT"""
+    pass
 
 
 class MantleConversion:
@@ -73,7 +58,7 @@ def __init__(self):
         self.Verbose = False
         self.SimpleP = False
         self.NN = False
-        self.UseAlpha = 'Alpha'
+        self._UseAlpha = 'Alpha'
         self.VelType = None
         self.scaleV = 1.
 
@@ -204,6 +189,25 @@ def __check_mineralogy__(self):
         self.Mineralogy = np.sort(self.Mineralogy, order='phase')
         self.n_Phases = len(self.Mineralogy['phase'])
 
+    @property
+    def UseAlpha(self):
+        """Property that defines how Alpha is computed"""
+        return self._UseAlpha
+
+    @UseAlpha.setter
+    def UseAlpha(self, mode):
+        valid_modes = {
+            'const': 'Alpha',
+            'T': 'AlphaT',
+        #    'PT': 'AlphaPT'  # Deactivate due to unsolved issues
+        }
+        try:
+            self._UseAlpha = valid_modes[mode]
+        except KeyError:
+            raise UnavailableMethodError(
+                f"This method for computation of Alpha is not available: {mode}"
+        )
+
     def AK135(self, depth, simple=False):
         """
         Return Pressure at given depth based on AK135 model.
@@ -478,7 +482,7 @@ def CalcVRho(self, z, T):
             Array contining V and Rho according for specified z and T
         """
         # Calculate P
-        P = self.AK135(z)
+        P = self.AK135(z, self.SimpleP)
         if self.Verbose:
             print('> z='+str(z)+'km; P='+str(P)+'Pa')
 
@@ -913,9 +917,9 @@ def ReadArgs(self):
         i = 2
         while i < n_args:
             if sys.argv[i] == '-AlphaT':
-                self.UseAlpha = 'AlphaT'
+                self.UseAlpha = 'T'
             elif sys.argv[i] == '-AlphaPT':
-                self.UseAlpha = 'AlphaPT'
+                self.UseAlpha = 'PT'
             elif sys.argv[i] == '-comp':
                 self.LoadMineralogy(sys.argv[i+1])
                 i += 1
@@ -1016,12 +1020,7 @@ def SetAlpha(self, mode):
         mode : str
             Valid modes are `const`, `T` and `PT`
         """
-        valid_modes = {
-            'const': 'Alpha',
-            'T': 'AlphaT',
-            'PT': 'AlphaPT'
-        }
-        self.UseAlpha = valid_modes[mode]
+        self.UseAlpha = mode
 
     def SetMineralogy(self, assemblage):
         """Define the mineralogical assemblage

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: d81aaa56fef58c3b9148eedab21e9f9d
+config: eff9231dd2a1754c818508a98793b04c
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_sources/installation.rst.txt

@@ -7,23 +7,31 @@ Prerequisites
 -------------
 
 :mod:`VelocityConversion` requires Python 2.7 or 3, and a few modules.
-I recommend to use Python 3 and `Anaconda <https://continuum.io>`_.
+I recommend to use Python 3 and `Pipenv <https://github.com/pypa/pipenv>`_.
 
-With Anaconda
-~~~~~~~~~~~~~
+With pipenv
+~~~~~~~~~~~
 
-Install the required modules with Anaconda:
+The advantage of pipenv is, that all dependencies and their versions are
+specified in the ``Pipfile.lock``. Pipenv will create an environment where all
+necessary packages will be installed. To install dependencies with pipenv,
+navigate to the project root folder, and run
 
 .. code-block:: bash
 
-    conda install -c conda-forge numpy
+    pipenv install
 
-To be able to build the documentation from source, further packages are
-required:
+To install other dependencies required to compile the documentation, run:
 
 .. code-block:: bash
 
-    conda install -c conda-forge ipython sphinx m2r sphinx_rtd_theme
+    pipenv install --dev
+
+Enter the environment in the terminal by running
+
+.. code-block:: bash
+
+    pipenv shell
 
 With pip
 ~~~~~~~~~
@@ -40,9 +48,24 @@ and to be able to compile the documentation:
 
     pip install sphinx m2r sphinx_rtd_theme
 
+With Anaconda
+~~~~~~~~~~~~~
+
+Install the required modules with Anaconda:
+
+.. code-block:: bash
+
+    conda install -c conda-forge numpy
+
+To be able to build the documentation from source, further packages are
+required:
+
+.. code-block:: bash
 
-Installing
-----------
+    conda install -c conda-forge ipython sphinx m2r sphinx_rtd_theme
+
+Installation
+------------
 
 :mod:`VelocityConversion` can be used both as a command line tool and as a
 Python module. In both cases, the first step is to create a clone or download
@@ -54,10 +77,18 @@ the repository.
 
 and install it with
 
-.. code-block::
+.. code-block:: bash
 
     pip install .
 
+You can also use :mod:`VelocityConversion` without installing it. In this case,
+you need to add the path of the ``./VelocityConversion`` folder to the system
+path when importing the module:
+
+.. code-block:: python
+
+    import sys
+    sys.path.append('../path/to/gitrepo')
 
 Run tests
 ~~~~~~~~~~