pmagpy-cli 4.3.13__tar.gz → 4.6.0__tar.gz

pmagpy_cli-4.6.0/PKG-INFO

@@ -0,0 +1,111 @@
+Metadata-Version: 2.4
+Name: pmagpy-cli
+Version: 4.6.0
+Summary: Analysis tools for paleo/rock magnetic data
+Home-page: https://github.com/PmagPy/PmagPy
+Author: PmagPy team
+Author-email: ltauxe@ucsd.edu
+License: BSD-3-Clause
+Keywords: geology paleomagnetism
+Classifier: Development Status :: 4 - Beta
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: pmagpy==4.6.0
+Requires-Dist: wxPython
+Requires-Dist: pillow
+Requires-Dist: appdirs
+Provides-Extra: maps
+Requires-Dist: pmagpy[maps]; extra == "maps"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+
+**PmagPy** is a comprehensive set of tools for analyzing paleomagnetic data. It facilitates interpretation of demagnetization data, Thellier-type experimental data and data from other types of rock magnetic experiments. PmagPy can be used to create a wide variety of useful plots and conduct statistical tests. It is designed to work with the MagIC database (https://earthref.org/MagIC), allowing manipulation of downloaded data sets as well as preparation of new contributions for uploading to the MagIC database. Functions within PmagPy can be imported and used in Jupyter notebooks enabling fully documented and nicely illustrated data analysis.
+
+## Citing PmagPy
+
+Users of PmagPy should cite the open access article:
+
+Tauxe, L., R. Shaar, L. Jonestrask, N. L. Swanson-Hysell, R. Minnett, A. A. P. Koppers, C. G. Constable, N. Jarboe, K. Gaastra, and L. Fairchild (2016), PmagPy: Software package for paleomagnetic data analysis and a bridge to the Magnetics Information Consortium (MagIC) Database, Geochem. Geophys. Geosyst., 17, https://doi.org/10.1002/2016GC006307.
+
+## Main features
+
+PmagPy is comprised of:
+  - GUI programs for getting data into MagIC database format (pmag\_gui), analyzing demagnetization data (demag\_gui) and analyzing paleointensity data (thellier\_gui). These GUIs are available as part of the python package pmagpy-cli.  Alternatively, these GUIs are available for download as standalone applications for [macOS](https://github.com/PmagPy/PmagPy-Standalone-OSX/releases/latest) and [Windows](https://github.com/PmagPy/PmagPy-Standalone-Windows/releases/latest).
+  - Command line programs for all sorts of paleomagnetic data analysis and wrangling (contained within the programs folder of the repository and pip installed as pmagpy-cli).
+  - The pmagpy function modules for paleomagnetic data analysis (pmagpy.pmag) and plotting (pmagpy.pmagplotlib) as well as a function module that further enables paleomagnetic data analysis within interactive computing environments such as the Jupyter notebook (pmagpy.ipmag). The functions within these modules are at the heart of the GUI and command line programs. With pmagpy installed ([described below](#how-to-get-it)), these modules can be imported (e.g. `from pmagpy import ipmag`).
+  - A rock magnetism module (pmagpy.rockmag) for processing and interpreting hysteresis, backfield, FORC, low-temperature, thermomagnetic, and anisotropy experiments, demonstrated in the [RockmagPy notebooks](https://pmagpy.github.io/RockmagPy-notebooks).
+  - Example data files that are used in the examples provided in the [PmagPy documentation notebooks](https://pmagpy.github.io/PmagPy-docs/documentation_notebooks/PmagPy_introduction.html)
+
+Use of all these features is described in the [PmagPy documentation](https://pmagpy.github.io/PmagPy-docs/) and the underlying science behind the data and code can be explored in the book [Essentials of Paleomagnetism: Third Web Edition](http://earthref.org/MagIC/books/Tauxe/Essentials/). Example Jupyter notebooks using PmagPy can be found in this [repository](https://github.com/PmagPy/2016_Tauxe-et-al_PmagPy_Notebooks)
+
+## How to get it
+
+Full instructions for installing and using PmagPy are in the [PmagPy documentation](https://pmagpy.github.io/PmagPy-docs/installation/PmagPy_install.html). You don't need a programming background to follow them. In brief:
+
+| I want to... | Do this |
+|---|---|
+| Use Pmag GUI, Demag GUI, or Thellier GUI, and nothing else | Download the standalone application for [macOS](https://github.com/PmagPy/PmagPy-Standalone-OSX/releases/latest) or [Windows](https://github.com/PmagPy/PmagPy-Standalone-Windows/releases/latest) (no Python needed) |
+| Try PmagPy without installing anything | Use the [EarthRef JupyterHub](https://pmagpy.github.io/PmagPy-docs/installation/PmagPy_install.html#using-pmagpy-online), or run `%pip install pmagpy` in a Google Colab notebook |
+| Use PmagPy in Jupyter notebooks, run the command-line programs, or run the GUIs on Linux | [Install PmagPy on your computer](https://pmagpy.github.io/PmagPy-docs/installation/pip_install.html) with conda and pip |
+| Contribute to PmagPy, or use changes before they are released | Do a [developer install](https://pmagpy.github.io/PmagPy-docs/installation/developer_install.html) |
+
+### Install on your computer
+
+The recommended approach uses [Miniforge](https://github.com/conda-forge/miniforge) to create a conda environment with the scientific Python packages, and then pip to install PmagPy. With Miniforge installed, run these commands in a terminal (on Windows, in Miniforge Prompt):
+
+```
+conda create -n pmagpy -c conda-forge python=3.12 numpy scipy matplotlib pandas cartopy shapely wxpython pyqt jupyterlab pip
+conda activate pmagpy
+pip install --upgrade pmagpy pmagpy-cli
+```
+
+`pmagpy` contains the function modules used in Jupyter notebooks and your own code; `pmagpy-cli` adds the command-line programs and the GUIs. To update later, activate the environment and rerun the last command. The [installation guide](https://pmagpy.github.io/PmagPy-docs/installation/pip_install.html) explains each step, and the [troubleshooting page](https://pmagpy.github.io/PmagPy-docs/installation/troubleshooting.html) covers common problems.
+
+### Developer install
+
+To work from the source code (the master branch or your own fork) rather than a release, clone the repository, create an environment from its `environment.yml`, and install it in editable mode:
+
+```
+git clone https://github.com/PmagPy/PmagPy.git
+cd PmagPy
+conda env create -f environment.yml -n pmagpy-dev
+conda activate pmagpy-dev
+pip install -e ".[maps]"
+```
+
+Edits to the code, and `git pull`, take effect immediately without reinstalling. The command-line programs and GUIs can be run from the `programs` directory (for example, `python pmag_gui.py`), or installed from the released `pmagpy-cli` package alongside the editable library. Full details are in the [developer install instructions](https://pmagpy.github.io/PmagPy-docs/installation/developer_install.html).
+
+
+## Background and support
+
+The code base for the PmagPy project has been built up over many years by Lisa Tauxe (Professor Emerita at the Scripps Institution of Oceanography) supported by grants from the National Science Foundation. Substantial contributions to the project have been made by Nick Swanson-Hysell (Associate Professor at the University of Minnesota), Ron Shaar (Associate Professor at the Hebrew University of Jerusalem), Lori Jonestrask and Kevin Gaastra as well as others.
+
+## Contributing
+
+If you want to get involved with the project - whether that means reporting a bug, requesting a feature, or adding significant code - please check out the project's [Contribution guidelines](https://github.com/PmagPy/PmagPy/blob/master/CONTRIBUTING.md).
+
+## More information
+
+This code and the [PmagPy documentation](https://pmagpy.github.io/PmagPy-docs/) are companions to the the book Essentials of Paleomagnetism: Third Web Edition (http://earthref.org/MagIC/books/Tauxe/Essentials/) written by Lisa Tauxe with contributions from Subir K. Banerjee, Robert F. Butler and Rob van der Voo. The printed version of the book came out in January, 2010 from University of California Press (http://www.ucpress.edu/book.php?isbn=9780520260313).
+
+## Licensing
+
+This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/PmagPy/PmagPy/blob/master/license.txt) for details.

pmagpy_cli-4.6.0/README.md

@@ -0,0 +1,87 @@
+# PmagPy: tools for paleomagnetic data analysis
+
+<table>
+<tr>
+  <td>Latest Release</td>
+  <td><img src="https://img.shields.io/pypi/v/pmagpy.svg" alt="latest release" /></td>
+</tr>
+<tr>
+  <td>License</td>
+  <td><img src="https://img.shields.io/pypi/l/pmagpy.svg" alt="license" /></td>
+</tr>
+</table>
+
+## What is it
+
+**PmagPy** is a comprehensive set of tools for analyzing paleomagnetic data. It facilitates interpretation of demagnetization data, Thellier-type experimental data and data from other types of rock magnetic experiments. PmagPy can be used to create a wide variety of useful plots and conduct statistical tests. It is designed to work with the MagIC database (https://earthref.org/MagIC), allowing manipulation of downloaded data sets as well as preparation of new contributions for uploading to the MagIC database. Functions within PmagPy can be imported and used in Jupyter notebooks enabling fully documented and nicely illustrated data analysis.
+
+## Citing PmagPy
+
+Users of PmagPy should cite the open access article:
+
+Tauxe, L., R. Shaar, L. Jonestrask, N. L. Swanson-Hysell, R. Minnett, A. A. P. Koppers, C. G. Constable, N. Jarboe, K. Gaastra, and L. Fairchild (2016), PmagPy: Software package for paleomagnetic data analysis and a bridge to the Magnetics Information Consortium (MagIC) Database, Geochem. Geophys. Geosyst., 17, https://doi.org/10.1002/2016GC006307.
+
+## Main features
+
+PmagPy is comprised of:
+  - GUI programs for getting data into MagIC database format (pmag\_gui), analyzing demagnetization data (demag\_gui) and analyzing paleointensity data (thellier\_gui). These GUIs are available as part of the python package pmagpy-cli.  Alternatively, these GUIs are available for download as standalone applications for [macOS](https://github.com/PmagPy/PmagPy-Standalone-OSX/releases/latest) and [Windows](https://github.com/PmagPy/PmagPy-Standalone-Windows/releases/latest).
+  - Command line programs for all sorts of paleomagnetic data analysis and wrangling (contained within the programs folder of the repository and pip installed as pmagpy-cli).
+  - The pmagpy function modules for paleomagnetic data analysis (pmagpy.pmag) and plotting (pmagpy.pmagplotlib) as well as a function module that further enables paleomagnetic data analysis within interactive computing environments such as the Jupyter notebook (pmagpy.ipmag). The functions within these modules are at the heart of the GUI and command line programs. With pmagpy installed ([described below](#how-to-get-it)), these modules can be imported (e.g. `from pmagpy import ipmag`).
+  - A rock magnetism module (pmagpy.rockmag) for processing and interpreting hysteresis, backfield, FORC, low-temperature, thermomagnetic, and anisotropy experiments, demonstrated in the [RockmagPy notebooks](https://pmagpy.github.io/RockmagPy-notebooks).
+  - Example data files that are used in the examples provided in the [PmagPy documentation notebooks](https://pmagpy.github.io/PmagPy-docs/documentation_notebooks/PmagPy_introduction.html)
+
+Use of all these features is described in the [PmagPy documentation](https://pmagpy.github.io/PmagPy-docs/) and the underlying science behind the data and code can be explored in the book [Essentials of Paleomagnetism: Third Web Edition](http://earthref.org/MagIC/books/Tauxe/Essentials/). Example Jupyter notebooks using PmagPy can be found in this [repository](https://github.com/PmagPy/2016_Tauxe-et-al_PmagPy_Notebooks)
+
+## How to get it
+
+Full instructions for installing and using PmagPy are in the [PmagPy documentation](https://pmagpy.github.io/PmagPy-docs/installation/PmagPy_install.html). You don't need a programming background to follow them. In brief:
+
+| I want to... | Do this |
+|---|---|
+| Use Pmag GUI, Demag GUI, or Thellier GUI, and nothing else | Download the standalone application for [macOS](https://github.com/PmagPy/PmagPy-Standalone-OSX/releases/latest) or [Windows](https://github.com/PmagPy/PmagPy-Standalone-Windows/releases/latest) (no Python needed) |
+| Try PmagPy without installing anything | Use the [EarthRef JupyterHub](https://pmagpy.github.io/PmagPy-docs/installation/PmagPy_install.html#using-pmagpy-online), or run `%pip install pmagpy` in a Google Colab notebook |
+| Use PmagPy in Jupyter notebooks, run the command-line programs, or run the GUIs on Linux | [Install PmagPy on your computer](https://pmagpy.github.io/PmagPy-docs/installation/pip_install.html) with conda and pip |
+| Contribute to PmagPy, or use changes before they are released | Do a [developer install](https://pmagpy.github.io/PmagPy-docs/installation/developer_install.html) |
+
+### Install on your computer
+
+The recommended approach uses [Miniforge](https://github.com/conda-forge/miniforge) to create a conda environment with the scientific Python packages, and then pip to install PmagPy. With Miniforge installed, run these commands in a terminal (on Windows, in Miniforge Prompt):
+
+```
+conda create -n pmagpy -c conda-forge python=3.12 numpy scipy matplotlib pandas cartopy shapely wxpython pyqt jupyterlab pip
+conda activate pmagpy
+pip install --upgrade pmagpy pmagpy-cli
+```
+
+`pmagpy` contains the function modules used in Jupyter notebooks and your own code; `pmagpy-cli` adds the command-line programs and the GUIs. To update later, activate the environment and rerun the last command. The [installation guide](https://pmagpy.github.io/PmagPy-docs/installation/pip_install.html) explains each step, and the [troubleshooting page](https://pmagpy.github.io/PmagPy-docs/installation/troubleshooting.html) covers common problems.
+
+### Developer install
+
+To work from the source code (the master branch or your own fork) rather than a release, clone the repository, create an environment from its `environment.yml`, and install it in editable mode:
+
+```
+git clone https://github.com/PmagPy/PmagPy.git
+cd PmagPy
+conda env create -f environment.yml -n pmagpy-dev
+conda activate pmagpy-dev
+pip install -e ".[maps]"
+```
+
+Edits to the code, and `git pull`, take effect immediately without reinstalling. The command-line programs and GUIs can be run from the `programs` directory (for example, `python pmag_gui.py`), or installed from the released `pmagpy-cli` package alongside the editable library. Full details are in the [developer install instructions](https://pmagpy.github.io/PmagPy-docs/installation/developer_install.html).
+
+
+## Background and support
+
+The code base for the PmagPy project has been built up over many years by Lisa Tauxe (Professor Emerita at the Scripps Institution of Oceanography) supported by grants from the National Science Foundation. Substantial contributions to the project have been made by Nick Swanson-Hysell (Associate Professor at the University of Minnesota), Ron Shaar (Associate Professor at the Hebrew University of Jerusalem), Lori Jonestrask and Kevin Gaastra as well as others.
+
+## Contributing
+
+If you want to get involved with the project - whether that means reporting a bug, requesting a feature, or adding significant code - please check out the project's [Contribution guidelines](https://github.com/PmagPy/PmagPy/blob/master/CONTRIBUTING.md).
+
+## More information
+
+This code and the [PmagPy documentation](https://pmagpy.github.io/PmagPy-docs/) are companions to the the book Essentials of Paleomagnetism: Third Web Edition (http://earthref.org/MagIC/books/Tauxe/Essentials/) written by Lisa Tauxe with contributions from Subir K. Banerjee, Robert F. Butler and Rob van der Voo. The printed version of the book came out in January, 2010 from University of California Press (http://www.ucpress.edu/book.php?isbn=9780520260313).
+
+## Licensing
+
+This code can be freely used, modified, and shared. It is licensed under a 3-clause BSD license. See [license.txt](https://github.com/PmagPy/PmagPy/blob/master/license.txt) for details.

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/leastsq_jacobian.py

@@ -1,5 +1,3 @@
-from builtins import map
-from builtins import range
 import numpy
 from scipy import optimize
 
@@ -97,7 +95,7 @@ def do_circlefit(x, y):
 def get_SSE(a,b,r,x,y):
     """
     input: a, b, r, x, y.  circle center, radius, xpts, ypts
-    output: SSE
+    output: SSE (sum of squared errors)
     """
     SSE = 0
     X = numpy.array(x)

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/lib_IZZI_MD.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from builtins import range
 from numpy import *
 
 

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/lib_arai_plot_statistics.py

@@ -1,7 +1,5 @@
 #! /usr/bin/env python
 
-#from scipy import *
-from builtins import range
 import numpy
 
 

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/lib_curvature.py

@@ -1,8 +1,5 @@
 #!/usr/bin/env python 
 
-from builtins import zip
-from builtins import map
-from builtins import range
 import numpy
 from numpy import *
 

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/lib_directional_statistics.py

@@ -1,6 +1,5 @@
 #! /usr/bin/env python
 
-from builtins import range
 import numpy
 import math
 
@@ -111,7 +110,7 @@ def cart2dir(cart):
     try:
         Decs=(numpy.arctan2(Ys,Xs) / rad)%360. # calculate declination taking care of correct quadrants (arctan2) and making modulo 360.
         Incs = numpy.arcsin(Zs / Rs) / rad # calculate inclination (converting to degrees) #
-    except:
+    except Exception:
         print('trouble in cart2dir') # most likely division by zero somewhere
         return numpy.zeros(3)
     return numpy.array([Decs,Incs,Rs]).transpose() # return the directions list

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/lib_leastsquares.py

@@ -1,8 +1,7 @@
 #!/usr/bin/env python
 
-from builtins import map
 from numpy import *
-from scipy      import optimize
+from scipy import optimize
 
 
 

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/lib_tail_check_statistics.py

@@ -11,7 +11,7 @@ def get_n_tail(tmax, tail_temps):
         return 0
     try:
         t_index = list(tail_temps).index(tmax)
-    except: # finds correct tmax if there was no tail check performed at tmax
+    except Exception: # finds correct tmax if there was no tail check performed at tmax
         for temp in tail_temps:
             if temp <= tmax:
                 adj_tmax = temp

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/lib/new_lib_curvature.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from builtins import range
 import numpy
 from . import lib_curvature as lib_k
 

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/new_lj_thellier_gui_spd.py

@@ -1,14 +1,11 @@
 #============================================================================================
-from builtins import input
-from builtins import range
-from builtins import object
+
 global CURRENT_VRSION
 CURRENT_VRSION = "v.2.03"
-#import matplotlib
+
 
 import numpy
 import sys
-import os
 import math
 #import pylab,scipy
 ##try:
@@ -17,14 +14,8 @@ import math
 ##    pass
 try:
     import thellier_gui_preferences
-except:
+except Exception:
     pass
-#import copy
-#import stat
-#import subprocess
-#import time
-#import random
-#import copy
 
 #from pylab import *  # this stuff is being used, don't know all where
 
@@ -126,7 +117,7 @@ class Arai_GUI(object):
 #{'treatment_ac_field': '0', 'treatment_dc_field_theta': '90', 'measurement_temp': '273', 'er_citation_names': 'This study', 'measurement_magn_moment': '1.98e-09', 'treatment_temp': '373', 'measurement_number': '1', 'measurement_standard': 'u', 'er_site_name': '0238x', 'er_sample_name': '0238x601104', 'treatment_dc_field_phi': '0', 'measurement_inc': '-8.1', 'er_location_name': '238', 'measurement_dec': '255.7', 'magic_experiment_name': '0238x6011043:LP-PI-TRM:LP-PI-ALT-PTRM:LP-PI-BT-MD:LP-PI-BT-IZZI', 'measurement_flag': 'g', 'er_specimen_name': '0238x6011043', 'measurement_csd': '0.7', 'treatment_dc_field': '4e-05', 'magic_method_codes': 'LT-T-I:LP-PI-TRM-IZ:LP-PI-TRM:LP-PI-ALT-PTRM:LP-PI-BT-MD:LP-PI-BT-IZZI'}
 # so, first is a zero field, heated to 273 and measured at 273.  second is infield, heated to 373 but measured at 273.
 # actual measurements: measurement_magn_moment, measurement_inc, measurement_dec, and measurement_csd.  inc == inclination (how a compass would want to point down through the earth to get to the N pole, at least while in northern hemisphere)  magn_moment = "The product of the pole strength of a magnet and the distance between the poles."  dec == declination.
-      except:
+      except Exception:
           print("-E- ERROR: Cant read magic_measurement.txt file. File is corrupted.")
           return {},{}
 
@@ -282,14 +273,14 @@ class Arai_GUI(object):
       try:
           rmag_anis_data,file_type=self.magic_read(self.WD+'/rmag_anisotropy.txt')
           print( "-I- Anisotropy data read  %s/from rmag_anisotropy.txt\n"%self.WD)
-      except:
+      except Exception:
           print("-W- WARNING cant find rmag_anisotropy in working directory\n")
 
       try:
           results_anis_data,file_type=self.magic_read(self.WD+'/rmag_results.txt')
           print( "-I- Anisotropy data read  %s/from rmag_anisotropy.txt\n"%self.WD)
 
-      except:
+      except Exception:
           print("-W- WARNING cant find rmag_anisotropy in working directory\n")
 
 
@@ -512,7 +503,7 @@ class Arai_GUI(object):
               try:
                   ancient_cooling_rate=float(self.Data_info["er_samples"][sample]['sample_cooling_rate'])
                   ancient_cooling_rate = ancient_cooling_rate / (1e6*365*24*60) # change to K/minute
-              except:
+              except Exception:
                   print("-W- Cant find ancient cooling rate estimation for sample %s"%sample)
                   continue
               self.Data_info["er_samples"]
@@ -787,7 +778,7 @@ class Arai_GUI(object):
                         x_ptrm_check.append(ptrm_checks[k][3] / NRM)
                         y_ptrm_check.append(zerofields[index_zerofield][3] / NRM)
                         ptrm_checks_temperatures.append(ptrm_checks[k][0])
-                    except:
+                    except Exception:
                         pass
 
                 # microwave
@@ -804,7 +795,7 @@ class Arai_GUI(object):
                         x_ptrm_check.append(ptrm_checks[k][3] / NRM)
                         y_ptrm_check.append(zerofields[index_zerofield][3] / NRM)
                         ptrm_checks_temperatures.append(ptrm_checks[k][0])
-                    except:
+                    except Exception:
                         pass
 
 
@@ -855,7 +846,7 @@ class Arai_GUI(object):
                         tail_check_temperatures.append(ptrm_tail[k][0])
 
                         break
-                    except:
+                    except Exception:
                         pass
 
 
@@ -938,7 +929,7 @@ class Arai_GUI(object):
                     #print ""
                     #lj
 
-                except:
+                except Exception:
                     pass
 
         x_AC=numpy.array(x_AC)
@@ -1013,20 +1004,20 @@ class Arai_GUI(object):
 
         try:
             data_er_samples=read_magic_file(self.WD+"/er_samples.txt",'er_sample_name')
-        except:
+        except Exception:
             print("-W- Cant find er_sample.txt in project directory\n")
 
         try:
             data_er_sites=read_magic_file(self.WD+"/er_sites.txt",'er_site_name')
-        except:
+        except Exception:
             print ("-W- Cant find er_sites.txt in project directory\n")
 
         try:
             data_er_ages=read_magic_file(self.WD+"/er_ages.txt",'er_sample_name')
-        except:
+        except Exception:
             try:
                 data_er_ages=read_magic_file(self.WD+"/er_ages.txt",'er_site_name')
-            except:
+            except Exception:
                 print ("-W- Cant find er_ages in project directory\n")
 
 
@@ -1068,7 +1059,7 @@ class Arai_GUI(object):
         Decs = (numpy.arctan2(Ys,Xs) / rad)%360. # calculate declination taking care of correct quadrants (arctan2) and making modulo 360.
         try:
             Incs = numpy.arcsin(Zs / Rs) / rad # calculate inclination (converting to degrees) #
-        except:
+        except Exception:
             print('trouble in cart2dir') # most likely division by zero somewhere
             return numpy.zeros(3)
 
@@ -1103,7 +1094,7 @@ class Arai_GUI(object):
         hold,magic_data,magic_record,magic_keys=[],[],{},[]
         try:
             f=open(infile,"r")
-        except:
+        except Exception:
             return [],'bad_file'
         d = f.readline()[:-1].strip('\n')
         if d[0]=="s" or d[1]=="s":

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/SPD/spd.py

@@ -14,15 +14,9 @@
 # Initial revision: September 2013:
 #
 #============================================================================================
-
-from builtins import object
 import sys
 import numpy
 import os
-#import pylab
-#import scipy
-#from scipy import *
-#import os
 import SPD.lib.lib_arai_plot_statistics as lib_arai
 #import SPD.lib.lib_curvature as lib_k
 import SPD.lib.leastsq_jacobian as lib_k
@@ -791,7 +785,7 @@ class PintPars(object):
                     try:
                         func(self) # this will work if the function has no dependencies
                         stats_run.append(func.__name__)
-                    except:
+                    except Exception:
                         self.calculate_all_statistics() # if no dependency info can be found, just run all statistics
                         return 0 # since all possible statistics have been run, the function ends
         #print 'stats run: ', stats_run

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/command_line_setup.py

@@ -2,12 +2,13 @@ from setuptools import setup, find_packages
 from pmagpy import version
 from programs_list import programs_list
 
-version_num = version.version.strip('pmagpy-')
+version_num = version.version.removeprefix('pmagpy-')
+shared_version_requirement = f'pmagpy=={version_num}'
 
 # skip the html header at the top of README.md
 with open('README.md', encoding='utf-8') as f:
     lines = f.readlines()[14:]
-    long_description = "\n".join(lines)
+    long_description = "".join(lines)
 
 
 setup(
@@ -15,6 +16,7 @@ setup(
     version=version_num,
     description='Analysis tools for paleo/rock magnetic data',
     long_description=long_description,
+    long_description_content_type='text/markdown',
     url='https://github.com/PmagPy/PmagPy',
     author='PmagPy team',
     author_email='ltauxe@ucsd.edu',
@@ -36,10 +38,8 @@ setup(
     python_requires='>=3.9',
 
     install_requires=[
-        'pmagpy',
+        shared_version_requirement,
         'wxPython',
-        'PyQt5',
-        'lmfit',
         'pillow',
         'appdirs',
     ],

pmagpy_cli-4.6.0/dialogs/__init__.py

@@ -0,0 +1,34 @@
+"""GUI dialog package with lazy submodule loading."""
+
+from importlib import import_module
+
+
+_SUBMODULES = {
+    'ErMagicBuilder': 'ErMagicBuilder',
+    'demag_dialogs': 'demag_dialogs',
+    'demag_interpretation_editor': 'demag_interpretation_editor',
+    'grid_frame3': 'grid_frame3',
+    'magic_grid3': 'magic_grid3',
+    'pmag_gui_dialogs': 'pmag_gui_dialogs',
+    'pmag_er_magic_dialogs': 'pmag_er_magic_dialogs',
+    'pmag_menu_dialogs': 'pmag_menu_dialogs',
+    'pmag_widgets': 'pmag_widgets',
+    'thellier_consistency_test': 'thellier_consistency_test',
+    'thellier_gui_dialogs': 'thellier_gui_dialogs',
+    'thellier_gui_lib': 'thellier_gui_lib',
+    'thellier_interpreter': 'thellier_interpreter',
+}
+
+__all__ = list(_SUBMODULES)
+
+
+def __getattr__(name):
+    if name not in _SUBMODULES:
+        raise AttributeError(f"module 'dialogs' has no attribute {name!r}")
+    module = import_module(f'.{_SUBMODULES[name]}', __name__)
+    globals()[name] = module
+    return module
+
+
+def __dir__():
+    return sorted(list(globals()) + __all__)

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/dialogs/demag_dialogs.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+import importlib
 import matplotlib
 import numpy as np
 import wx
@@ -12,15 +13,17 @@ import matplotlib.pyplot as plt
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas
 from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as NavigationToolbar
+from dialogs.plot_export import save_figure
 from pmagpy.demag_gui_utilities import *
 from pmag_env import set_env
 from numpy import vstack,sqrt
 from functools import reduce
 
 has_cartopy, Cartopy = pmag.import_cartopy()
+cfeature = ccrs = None
 if has_cartopy:
-    import cartopy.feature as cfeature
-    import cartopy.crs as ccrs
+    cfeature = importlib.import_module('cartopy.feature')
+    ccrs = importlib.import_module('cartopy.crs')
 
 #============================================================================================
 # LOG HEADER:
@@ -46,7 +49,7 @@ class VGP_Dialog(wx.Frame):
 
     def __init__(self,parent,VGP_Data):
         if set_env.IS_FROZEN and not set_env.IS_WIN:
-            parent.user_warning("This feature is not available in the standalone executable.  If you need to look at VGPs, consider installing Python and PmagPy: https://earthref.org/PmagPy/cookbook/#getting_python");
+            parent.user_warning("This feature is not available in the standalone executable.  If you need to look at VGPs, consider installing Python and PmagPy: https://pmagpy.github.io/PmagPy-docs/installation/pip_install.html");
             self.failed_init=True
             return
         self.failed_init = False
@@ -398,11 +401,9 @@ class SaveMyPlot(wx.Frame):
             return
 
         title=name
-        self.panel = wx.Panel(self)
         self.dpi=300
 
-        canvas_tmp_1 = FigCanvas(self.panel, -1, fig)
-        canvas_tmp_1.print_figure(path, dpi=self.dpi)
+        save_figure(fig, path, dpi=self.dpi)
 
 #--------------------------------------------------------------
 # MagIc results tables dialog
@@ -550,7 +551,7 @@ class user_input(wx.Dialog):
         for i,ctrl in enumerate(self.list_ctrls):
             if hasattr(self.parse_funcs,'__getitem__') and len(self.parse_funcs)>i and hasattr(self.parse_funcs[i],'__call__'):
                 try: return_dict[self.inputs[i]] = self.parse_funcs[i](ctrl.GetValue())
-                except: return_dict[self.inputs[i]] = ctrl.GetValue()
+                except Exception: return_dict[self.inputs[i]] = ctrl.GetValue()
             else:
                 return_dict[self.inputs[i]] = ctrl.GetValue()
         return ('' not in list(return_dict.values()), return_dict)
@@ -1146,7 +1147,7 @@ class convert_generic_files_to_MagIC(wx.Frame):
         self.er_sample_data={}
         try:
             self.er_sample_data=self.read_magic_file(os.path.join(self.WD, "er_samples.txt"), 'er_sample_name')
-        except:
+        except Exception:
             print("-W- WARNING: Cant find er_samples.txt table")
 
         for i in range(self.max_files):

{pmagpy_cli-4.3.13 → pmagpy_cli-4.6.0}/dialogs/demag_interpretation_editor.py

@@ -6,6 +6,7 @@ from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas
 from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg as NavigationToolbar
 from matplotlib.figure import Figure
 import help_files.demag_interpretation_editor_help as dieh
+from dialogs import gui_theme
 from pmagpy.demag_gui_utilities import *
 from pmagpy.Fit import *
 from pmagpy.pmag import get_version
@@ -28,6 +29,7 @@ class InterpretationEditorFrame(wx.Frame):
         #call init of super class
         default_style = wx.MINIMIZE_BOX | wx.MAXIMIZE_BOX | wx.RESIZE_BORDER | wx.SYSTEM_MENU | wx.CAPTION | wx.CLOSE_BOX | wx.CLIP_CHILDREN | wx.NO_FULL_REPAINT_ON_RESIZE | wx.WS_EX_CONTEXTHELP | wx.FRAME_EX_CONTEXTHELP
         wx.Frame.__init__(self, self.parent, title="Interpretation Editor version:%s"%CURRENT_VERSION,style=default_style, size=(675*self.GUI_RESOLUTION,425*self.GUI_RESOLUTION))
+        gui_theme.bind_theme_updates(self)
         self.Bind(wx.EVT_CLOSE, self.on_close_edit_window)
         #setup wx help provider class to give help messages
         provider = wx.SimpleHelpProvider()
@@ -237,8 +239,8 @@ class InterpretationEditorFrame(wx.Frame):
         for parameter in ['mean_type','dec','inc','alpha95','K','R','n_lines','n_planes']:
             COMMAND="self.%s_window=wx.TextCtrl(self.panel,style=wx.TE_CENTER|wx.TE_READONLY,size=(100*self.GUI_RESOLUTION,25))"%parameter
             exec(COMMAND)
-            COMMAND="self.%s_window.SetBackgroundColour(wx.WHITE)"%parameter
-            exec(COMMAND)
+            gui_theme.style_control(
+                getattr(self, "{}_window".format(parameter)))
             COMMAND="self.%s_window.SetFont(font2)"%parameter
             exec(COMMAND)
             COMMAND="self.%s_outer_window = wx.GridSizer(1,2,5*self.GUI_RESOLUTION,15*self.GUI_RESOLUTION)"%parameter
@@ -346,7 +348,7 @@ class InterpretationEditorFrame(wx.Frame):
         m_help = menu_Help.Append(-1, "&Usage and Tips\tCtrl-H", "")
         self.Bind(wx.EVT_MENU, self.on_menu_help, m_help)
 
-        m_cookbook = menu_Help.Append(-1, "&PmagPy Cookbook\tCtrl-Shift-W", "")
+        m_cookbook = menu_Help.Append(-1, "&PmagPy Documentation\tCtrl-Shift-W", "")
         self.Bind(wx.EVT_MENU, self.parent.on_menu_cookbook, m_cookbook)
 
         m_docs = menu_Help.Append(-1, "&Open Docs\tCtrl-Shift-H", "")
@@ -482,7 +484,11 @@ class InterpretationEditorFrame(wx.Frame):
             else: inc = "N/A"
             if 'specimen_mad' in list(pars.keys()): mad = "%.1f"%pars['specimen_mad']
             else: mad = "N/A"
-            if 'specimen_dang' in list(pars.keys()): dang = "%.1f"%pars['specimen_dang']
+            # DANG is not calculated for anchored lines (placeholder of 0), nor
+            # for fits that return -1 (vector and Fisher means)
+            if 'specimen_dang' in list(pars.keys()) and float(pars['specimen_dang']) != -1 \
+                    and pars.get('calculation_type') != 'DE-BFL-A':
+                dang = "%.1f"%pars['specimen_dang']
             else: dang = "N/A"
             if 'specimen_alpha95' in list(pars.keys()): a95 = "%.1f"%pars['specimen_alpha95']
             else: a95 = "N/A"