Moved install and reset functions to PlanetProfile/ and updated READM…

…E to detail installation for both branches

PlanetProfile/Main.py

@@ -948,7 +948,7 @@ def RunPPfile(bodyname, fName, Params=None):
             CopyCarefully(default, expected)
         else:
             log.warning(f'{expected} does not exist and no default was found at {default}.')
-    Planet = importlib.import_module(f'{bodyname}.{loadName}')
+    Planet = importlib.import_module(f'{bodyname}.{loadName}').Planet
     Planet, Params = PlanetProfile(Planet, Params)
     return Planet, Params
 

PlanetProfile/__init__.py

@@ -5,9 +5,10 @@ def CopyCarefully(source, destination):
         if os.path.dirname(destination) != '':
             os.makedirs(os.path.dirname(destination), exist_ok=True)
         shutil.copy(source, destination)
-    except OSError:
+    except OSError as err:
         raise OSError(f'Unable to copy from {source} to {destination}. ' +
-                      f'Check that you have write permission for {os.getcwd()}.')
+                      f'Check that you have write permission for {os.getcwd()}. ' +
+                      f'The error reported was:\n{err}')
     else:
         print(f'{destination} was copied from default at {source}.')
 
@@ -19,9 +20,10 @@ def CopyOnlyIfNeeded(source, destination):
             if os.path.dirname(destination) != '':
                 os.makedirs(os.path.dirname(destination), exist_ok=True)
             shutil.copy(source, destination)
-        except OSError:
+        except OSError as err:
             raise OSError(f'Unable to copy from {source} to {destination}. ' +
-                          f'Check that you have write permission for {os.getcwd()}.')
+                          f'Check that you have write permission for {os.getcwd()}. ' +
+                          f'The error reported was:\n{err}')
         else:
             print(f'{destination} was copied from default at {source}.')
 

PlanetProfile/install.py

@@ -0,0 +1,33 @@
+import os, shutil
+from glob import glob
+import logging as log
+from PlanetProfile import _Defaults, configTemplates, configLocals, CopyOnlyIfNeeded
+
+def PPinstall():
+    """ Copies default body files from PlanetProfile/Default/Body/ directories to Body/ directories found here. 
+        The input files found in the Body/PPBody.py files here will override the defaults.
+        Same for config files in this directory--they will override settings found in config files
+        in the PlanetProfile/ directory.
+    """
+
+    print('Copying any Body/PPBody.py, Body/inductionData/*.txt, and config files that aren\'t ' +
+             'in the right places from their defaults.')
+
+    # Copy default profiles
+    Defaults = glob(os.path.join(_Defaults, '*', 'PP*.py'))
+    Copies = [file.split(f'Default{os.sep}')[-1] for file in Defaults]
+    for Body, Destination in zip(Defaults, Copies):
+        CopyOnlyIfNeeded(Body, Destination)
+
+    # Copy inductionData contents
+    inductionFiles = glob(os.path.join(_Defaults, '*', 'inductionData', '*.txt'))
+    copies = [file.split(f'Default{os.sep}')[-1] for file in inductionFiles]
+    for file, copy in zip(inductionFiles, copies):
+        CopyOnlyIfNeeded(file, copy)
+
+    # Copy config files
+    for template, local in zip(configTemplates, configLocals):
+        CopyOnlyIfNeeded(template, local)
+
+if __name__ == '__main__':
+    PPinstall()

PlanetProfile/reset.py

@@ -0,0 +1,40 @@
+import os, shutil
+from glob import glob
+import logging as log
+from PlanetProfile import _Defaults, configTemplates, configLocals, CopyCarefully
+
+def PPreset():
+    """ Copies default body files from PlanetProfile/Default/Body/ directories to Body/ directories found here.
+        The input files found in the Body/PPBody.py files here will override the defaults.
+        Same for config files in this directory--they will override settings found in config files
+        in the PlanetProfile/ directory.
+    """
+
+    print('WARNING: This will reset all Body/PPBody.py, Body/inductionData/*.txt, and config files to their defaults.')
+    answer = input('Continue? (y/n) ')
+
+    if answer in ['y', 'Y', 'yes', 'Yes', 'YES']:
+        # Copy default profiles
+        Defaults = glob(os.path.join(_Defaults, '*', 'PP*.py'))
+        Copies = [file.split(f'Default{os.sep}')[-1] for file in Defaults]
+        for Body, Destination in zip(Defaults, Copies):
+            CopyCarefully(Body, Destination)
+
+        # Copy inductionData contents
+        inductionFiles = glob(os.path.join(_Defaults, '*', 'inductionData', '*.txt'))
+        copies = [file.split(f'Default{os.sep}')[-1] for file in inductionFiles]
+        for file, copy in zip(inductionFiles, copies):
+            CopyCarefully(file, copy)
+
+        # Copy config files
+        for template, local in zip(configTemplates, configLocals):
+            CopyCarefully(template, local)
+
+    elif answer in ['n', 'N', 'no', 'No', 'NO']:
+        print('Aborting.')
+        exit(0)
+    else:
+        raise ValueError(f'Response "{answer}" not recognized.')
+
+if __name__ == '__main__':
+    PPreset()

README.md

@@ -1,93 +1,89 @@
 # PlanetProfile v2.0.0
-Python software for constructing 1D interior structure models based on planetary properties. Self-consistent thermodynamics are used for fluid, rock, and mineral phases. Sound speeds, attenuation, and electrical conductivities are computed as outputs. The main code is called from an input file containing all the planetary data. Ideally, no tweaks to the main code are needed in order to change the outputs of the model.
+Software framework for constructing 1D interior structure models based on planetary properties. Self-consistent thermodynamics are used for fluid, rock, and mineral phases. Sound speeds, attenuation, and electrical conductivities are computed as outputs. The main code is called from an input file containing all the planetary data.
 
 ## Acknowledging PlanetProfile
 We want to hear about your work with PlanetProfile! Please consider sending us a message alerting us to your work (svance@jpl.caltech.edu). Suggested acknowledgement in publications: "Data used in this work were generated using the open source PlanetProfile software hosted on GitHub."
 
+## Getting started
+PlanetProfile is available in Python and Matlab.
+
+*For Python,* the recommended way to install is with with pip:
+1. (Recommended) Install all dependencies listed in the next section before proceeding.
+1. At a terminal:
+`python -m pip install PlanetProfile`
+Python 3.8 or higher is required. Pip will install dependencies, but a conda environment with the prerequisites listed below is recommended.
+1. Create a directory where you'd like to store configurations and have folders for each body.
+1. Navigate into the new directory.
+1. At a terminal:
+`python -m PlanetProfile.install PPinstall`
+This will copy files from their defaults to the current directory.
+1. Run the software with, for example:
+`python -m PlanetProfile.Main Europa`
+or
+`python -m PlanetProfile.Main path/to/PPBody.py`
+or in a Python script with
+`from PlanetProfile.Main import RunPPfile
+RunPPfile('Europa', 'PPEuropa.py')`
+
+*For Matlab:*
+  1. Download or clone this repository.
+  1. Install prerequisites below.
+  1. At a terminal: 
+  `make install`
+  Or, add everything in the top-level directory except the PlanetProfile sub-folder to the Matlab path.
+  1. In Matlab, set the current directory to the top-level directory of the downloaded repository (top PlanetProfile folder).
+  1. Run the software with `PPEuropa` in the Matlab command prompt, or by opening and running one of the files located at Body/PPBody.m (e.g. Titan/PPTitan.m).
+
 ## Prerequisites
-* SeaFreeze -- see https://github.com/Bjournaux/SeaFreeze, installed with pip
-* MoonMag -- see https://github.com/itsmoosh/MoonMag, installed with pip
-* TEOS-10 Gibbs Seawater for python -- installed with conda
-* ObsPy (optional) -- installed with conda
+A simple list with install commands for Python is in the next section.
+* SeaFreeze -- see https://github.com/Bjournaux/SeaFreeze
+  * Python: Installed with pip: `pip install SeaFreeze`
+  * Matlab: Download the repository to Thermodynamics/SeaFreeze and add the contents to the Matlab path.
+* MoonMag -- see https://github.com/itsmoosh/MoonMag
+  * Python only -- Installed with pip: `pip install MoonMag`
+  * In Matlab, magnetic induction calculations are performed numerically and cannot incorporate lateral asymmetry in conducting layers.
+* Gibbs Seawater toolbox of TEOS-10 -- see https://www.teos-10.org/
+  * Python: Installed with conda via conda-forge: `conda install -c conda-forge gsw` 
+  * Matlab: Already packaged into the PlanetProfile repository along with the original license.
+* Perple_X -- see http://www.perplex.ethz.ch/
+  * For both Python and Matlab, Perple_X outputs are currently hosted as part of the installation, in Thermodynamics/Perple_X for Matlab and in PlanetProfile/Thermodynamics/EOSdata/Perple_X for Python. The files we use were generated with Perple_X v6.7.9.
+* TauP/ObsPy (optional) -- see https://www.seis.sc.edu/taup/
+  * Python: Installed with conda via conda-forge: `conda install -c conda-forge obspy`
+  * Matlab: Already packaged into the PlanetProfile repository along with the original license.
 * A working TeX/LaTeX distribution (such as TeXlive) is recommended for optimum plot labels. TeXlive is available at: https://tug.org/texlive/acquire-netinstall.html
-* Python 3.8+ installed, preferably via Anaconda. Required modules:
-  * Standard Anaconda (for miniconda, install with conda install <packageName1> <packagename2> etc.):
-    * numpy
-    * scipy
-    * matplotlib
-    * mpmath
-  * Conda-forge (install with conda install -c conda-forge <packageName>):
-    * gsw
-    * obspy
-    * spiceypy
-    * cmasher
-* Some magnetic field features require use of the [SPICE toolkit through Mice](https://naif.jpl.nasa.gov/pub/naif/toolkit_docs/MATLAB/index.html). To install Mice:
-  * Navigate to https://naif.jpl.nasa.gov/naif/toolkit_MATLAB.html, follow the link for your operating system, download the .zip or .tar.Z file to PlanetProfile/Utilities/spice/, and unpack the archive (into PlanetProfile/spice/mice/).
-* Refprop is required for NH3 solutions: https://www.nist.gov/refprop
-  * Due to various complications it is not currently implemented.
 
-## Setup
-1. Install SeaFreeze and MoonMag with pip using the command: pip3 install SeaFreeze MoonMag
-  1. Note: This step should be completed only after all necessary prerequisites are installed for your conda environment.
-1. If TauP functionality is desired in Matlab, download ~~matTaup (https://github.com/g2e/seizmo/) and add mattaup, misc, and models to Utilities folder~~.
-1. Install magnetic induction data by downloading all .mat files from https://zenodo.org/record/5057572 into the MagneticInduction/FTdata folder.
+## Installation of prerequisites
+### Python 
+1. Python version 3.8+ must be installed, preferably via Anaconda. Required modules can be installed in Miniconda with the following command:
+  1. `conda install numpy scipy matplotlib mpmath`
+1. Conda-forge modules can be installed in Anaconda or Miniconda with the following command:
+  1. `conda install -c conda-forge gsw obspy spiceypy cmasher cartopy`
+1. AFTER the above modules have been installed with conda, install SeaFreeze and MoonMag with the following command:
+  1. `pip install SeaFreeze MoonMag`
+  1. Finally, install PlanetProfile with `pip install PlanetProfile`
+Note that although MoonMag supports use of SPICE kernels with SpiceyPy, their use is not yet implemented in PlanetProfile. 
+
+### Matlab
+1. Download PlanetProfile repository.
+1. Download SeaFreeze repository to PlanetProfile/Thermodynamics/SeaFreeze/ (NOT PlanetProfile/PlanetProfile/Thermodynamics).
+1. Add SeaFreeze folder and sub-folders to Matlab path.
+Some magnetic field features require use of the [SPICE toolkit through Mice](https://naif.jpl.nasa.gov/pub/naif/toolkit_docs/MATLAB/index.html). To install Mice:
+1. Navigate to https://naif.jpl.nasa.gov/naif/toolkit_MATLAB.html
+1. Follow the link for your operating system and download the .zip or .tar.Z file to PlanetProfile/Utilities/spice/
+1. Unpack the archive (into PlanetProfile/spice/mice/)
+1. Add PlanetProfile/Utilities/spice/mice/src/mice/ and PlanetProfile/Utilities/spice/mice/lib/ to your Matlab path.
 1. Install necessary SPICE kernels by downloading them from https://naif.jpl.nasa.gov/pub/naif/generic_kernels/ and placing them in PlanetProfile/Utilities/spice/. The planetary constants kernel (PCK) and leap-seconds kernel (TLS) are saved in this repository, but the generic ephemeris kernels (SPK, .bsp files) are too large for us to save here. There is one for each planet's satellites, located at https://naif.jpl.nasa.gov/pub/naif/generic_kernels/spk/satellites/. Currently in use are:
   1. jup365.bsp
   1. sat427.bsp
   1. ura111.bsp
   1. nep095.bsp
-  1. Add PlanetProfile/Utilities/spice/mice/src/mice/ and PlanetProfile/Utilities/spice/mice/lib/ to your Matlab path.
-1. Open a Terminal and navigate to the PlanetProfile directory.
-1. Run PlanetProfile with the command: python PlanetProfile.py
 
 ## Contributing
 PlanetProfile is open source software. Please see the [LICENSE](https://github.com/vancesteven/PlanetProfile/blob/master/LICENSE) file and read the guidelines for contrbuting in [CONTRIBUTING.md](https://github.com/vancesteven/PlanetProfile/blob/master/CONTRIBUTING.md) if you are interested in joining the project. Also see our community guidelines in [CODE_OF_CONDUCT.md](https://github.com/vancesteven/PlanetProfile/blob/master/CODE_OF_CONDUCT.md).
 
 ## Notes
+* With the PlanetProfile 2.0 release, both Python and Matlab are available. The two branches do not have the same functionality yet with this release--some features exist in each that are not yet found in the other. A later release will align their functionality as much as possible. For now, the Python version is recommended.
 * As of 2020-09-28, PlanetProfile v1.1.0 was released along with code for making calculations regarding magnetic induction. The development (master) branch of PlanetProfile is set up to generate profiles from minimal inputs. Output profiles that may be used along with the induction calculations may be found in the v1.1.0 release.
 * The default settings include a recalculation of all parameters. It is recommended to recalculate all parameters whenever PlanetProfile is updated and any time a change in input parameters may affect layer thicknesses or other intermediate variables.
-* To re-use data from past profiles, which dramatically speeds up runtime, set the CALC_NEW flags in the config.m input file to 0. If you are using git, use the following command to avoid editing the repository version of the config file:
-> git update-index --assume-unchanged config.m
-
-Some calculations use parallel computing with the multiprocessing builtin module. There are known cross-platform compatibility issues yet to be resolved. By default, multiprocessing is disasbled; enable it by setting DO_PARALLEL = True in config.py.
-
-Calculations with seawater solutions use the Gibbs Seawater package: https://teos-10.github.io/GSW-Python/
-
-Calculations with NH3 solutions use REFPROP and require a compiled dynamic library based on the REFPROP source code (see below for placement of files).  The source can be obtained from the National Institute of Standards and Technology https://www.nist.gov/refprop
-Access to REFPROP functions is through python 3 using librefprop.so: https://github.com/jowr/librefprop.so
-Python capabilities are employed using the included matlab code refproppy.m
-REFPROP version 10, expected in October 2017, will provide matlab functions and Mac modules, which may eliminate the need for the above workarounds.
-Instructions for installing Python 3 on a Mac can be found at http://docs.python-guide.org/en/latest/starting/install3/osx/
-
-Rock properties are from Perple_X: http://www.perplex.ethz.ch/
-Input files were developed by Fabio Cammarano. Version 6.7.9 is currently being used.
-
-
-## To-dos:
-Modularization is not complete. 
-Further equations of state are under development
-Update to work with REFPROP V10
-
-The source files and library for REFPROP should be placed in the top-level directory under /opt, as per below
-$ls /opt
-librefprop.dylib refprop/
-
-$ls /opt/refprop
-fluids   mixtures
-
-$ls /opt/refprop/fluids
-1BUTENE.FLD  C1CC6.FLD    COS.FLD      D6.FLD       ETHYLENE.FLD HYDROGEN.FLD MD3M.FLD     MOLEATE.FLD  NITROGEN.FLD PENTANE.FLD  R115.FLD     R124.FLD     R152A.FLD    R236FA.FLD   RE143A.FLD   WATER.FLD
-ACETONE.FLD  C2BUTENE.FLD CYCLOHEX.FLD DECANE.FLD   FLUORINE.FLD IBUTENE.FLD  MD4M.FLD     MPALMITA.FLD NONANE.FLD   PROPANE.FLD  R116.FLD     R125.FLD     R161.FLD     R245CA.FLD   RE245CB2.FLD XENON.FLD
-AMMONIA.FLD  C3CC6.FLD    CYCLOPEN.FLD DEE.FLD      H2S.FLD      IHEXANE.FLD  MDM.FLD      MSTEARAT.FLD NOVEC649.FLD PROPYLEN.FLD R12.FLD      R13.FLD      R21.FLD      R245FA.FLD   RE245FA2.FLD
-ARGON.FLD    C4F10.FLD    CYCLOPRO.FLD DMC.FLD      HCL.FLD      IOCTANE.FLD  METHANE.FLD  MXYLENE.FLD  OCTANE.FLD   PROPYNE.FLD  R1216.FLD    R134A.FLD    R218.FLD     R32.FLD      RE347MCC.FLD
-BENZENE.FLD  C5F12.FLD    D2.FLD       DME.FLD      HELIUM.FLD   IPENTANE.FLD METHANOL.FLD N2O.FLD      ORTHOHYD.FLD PXYLENE.FLD  R123.FLD     R14.FLD      R22.FLD      R365MFC.FLD  SF6.FLD
-BUTANE.FLD   CF3I.FLD     D2O.FLD      EBENZENE.FLD HEPTANE.FLD  ISOBUTAN.FLD MLINOLEA.FLD NEON.FLD     OXYGEN.FLD   R11.FLD      R1233ZD.FLD  R141B.FLD    R227EA.FLD   R40.FLD      SO2.FLD
-C11.FLD      CO.FLD       D4.FLD       ETHANE.FLD   HEXANE.FLD   KRYPTON.FLD  MLINOLEN.FLD NEOPENTN.FLD OXYLENE.FLD  R113.FLD     R1234YF.FLD  R142B.FLD    R23.FLD      R41.FLD      T2BUTENE.FLD
-C12.FLD      CO2.FLD      D5.FLD       ETHANOL.FLD  HMX.BNC      MD2M.FLD     MM.FLD       NF3.FLD      PARAHYD.FLD  R114.FLD     R1234ZE.FLD  R143A.FLD    R236EA.FLD   RC318.FLD    TOLUENE.FLD
 
-$ ls /opt/refprop/mixtures/
-AIR.MIX      HIGHN2.MIX   R402A.MIX    R405A.MIX    R407D.MIX    R409B.MIX    R412A.MIX    R415B.MIX    R420A.MIX    R422C.MIX    R426A.MIX    R431A.mix    R436A.MIX    R442A.MIX    R502.MIX     R508B.MIX
-AMARILLO.MIX NGSAMPLE.MIX R402B.MIX    R406A.MIX    R407E.MIX    R410A.MIX    R413A.MIX    R416A.MIX    R421A.MIX    R422D.MIX    R427A.MIX    R432A.mix    R436B.MIX    R443A.MIX    R503.MIX     R509A.MIX
-EKOFISK.MIX  R401A.MIX    R403A.MIX    R407A.MIX    R407F.MIX    R410B.MIX    R414A.MIX    R417A.MIX    R421B.MIX    R423A.MIX    R428A.MIX    R433A.mix    R437A.MIX    R444A.MIX    R504.MIX     R510A.MIX
-GLFCOAST.MIX R401B.MIX    R403B.MIX    R407B.MIX    R408A.MIX    R411A.MIX    R414B.MIX    R418A.MIX    R422A.MIX    R424A.MIX    R429A.mix    R434A.mix    R438A.mix    R500.MIX     R507A.MIX    R512A.MIX
-HIGHCO2.MIX  R401C.MIX    R404A.MIX    R407C.MIX    R409A.MIX    R411B.MIX    R415A.MIX    R419A.MIX    R422B.MIX    R425A.MIX    R430A.mix    R435A.MIX    R441A.MIX    R501.MIX     R508A.MIX  
+Some calculations in Python use parallel computing with the multiprocessing builtin module. There are sometimes cross-platform compatibility issues that crop up. By default, multiprocessing is enabled; disable it by setting Params.DO_PARALLEL = False in configPP.py.