Merge pull request #48 from MTgeophysics/updates

Check for Pardiso import

Author: kujaku11

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.8
+current_version = 2.0.9
 files = setup.py mtpy/__init__.py README.md docs/source/conf.py
 commit = True
 tag = True

.github/workflows/testing_pip_import.yml

@@ -0,0 +1,60 @@
+name: TestingInConda
+
+on:
+  push:
+    branches:
+      - 'main'
+
+jobs:
+  setup-build:
+    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup Conda
+      uses: s-weigand/setup-conda@v1
+      with:
+        update-conda: false
+        conda-channels: conda-forge
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Packages
+      shell: bash
+      run: |
+        python --version
+        conda create -n mtpy-v2-test python=--version
+        source activate mtpy-v2-test
+        pip install mtpy-v2
+        conda install pytest
+        conda install pytest-subtests
+        conda install pytest-cov
+        git clone https://github.com/kujaku11/mt_metadata.git
+        git clone install git+https://github.com/kujaku11/mth5.git
+        git clone git+https://github.com/simpeg/aurora
+        git clone https://github.com/MTgeophysics/mtpy_data.git
+        cd mtpy_data
+        pip install -e .
+        cd ..
+        conda list
+        
+    - name: Run Tests
+      shell: bash
+      run: |
+        source activate mtpy-v2-test
+        pytest -rA --cov=./ --cov-report=xml --cov=mtpy
+        
+    - name: "Upload coverage to Codecov"
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      with:
+        fail_ci_if_error: false
+        verbose: true
+        flags: tests
+        

README.md

@@ -7,12 +7,14 @@
 [![Documentation Status](https://readthedocs.org/projects/mtpy-v2/badge/?version=latest)](https://mtpy-v2.readthedocs.io/en/latest/?badge=latest)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/MTgeophysics/mtpy-v2/main)
 
-## Version 2.0.8
+## Version 2.0.9
 
 # Description
 
 `mtpy` provides tools for working with magnetotelluric (MT) data.  MTpy-v2 is an updated version of [mtpy](https://github.com/MTgeophysics/mtpy). Many things have changed under the hood and usage is different from mtpy v1. The main difference is that there is a central data type that can hold transfer functions and then read/write to your modeling program, plot, and analyze your data.  No longer will you need a directory of EDI files and then read them in everytime you want to do something.  You only need to build a project once and save it to an MTH5 file and you are ready to go. All metadata uses [mt-metadata](https://github.com/kujaku11/mt-metadata).
 
+
+
 # Installation
 
 ## Using Pip
@@ -22,7 +24,32 @@
 ## Using conda
 
 `> conda install -c conda-forge mtpy-v2`
-  
+
+### Pardiso Solver
+
+`mtpy-v2` now include some tools to model and invert using `simpeg`. If you want to use the Pardiso solver you will need to install it separately. See the https://github.com/simpeg/pydiso for more information.  Below is a snippet from their recommendations. 
+
+#### Installing from source
+
+The wrapper is written in cython and links to the mkl libraries dynamically. Therefore,
+it needs to find the necessary header files associated with the MKL installation to compile.
+The meson build backend uses pkg-config to identify the locations of the mkl header files
+and library dynamic libraries. Most development installations of MKL should provide the
+necessary pkg-config files for this. For example, conda users can be install the necessary
+configuration information with `mkl-devel` package that is available on the default channel,
+conda-forge channel, the intel channel, or others, e.g.
+
+`conda install mkl-devel`
+
+If you have installed the configuration files to a non-standard location, you will need to set
+`PKG_CONFIG_PATH` to point to that location.
+
+After the necessary MKL files are accessible, you should be able to install by running
+
+`pip install .`
+
+in the installation directory. 
+
 
 # Functionality
 

docs/source/conf.py

@@ -67,9 +67,9 @@
 #
 
 # The short X.Y version.
-version = "2.0.8"
+version = "2.0.9"
 # The full version, including alpha/beta/rc tags.
-release = "2.0.8"
+release = "2.0.9"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

mtpy/__init__.py

@@ -18,7 +18,7 @@
 from mtpy.imaging.mtcolors import MT_CMAP_DICT, register_cmaps
 
 
-__version__ = "2.0.8"
+__version__ = "2.0.9"
 __all__ = ["MT", "MTData", "MTCollection"]
 
 # =============================================================================

mtpy/modeling/simpeg/recipes/inversion_2d.py

@@ -16,6 +16,7 @@
 import warnings
 import numpy as np
 
+
 import matplotlib.pyplot as plt
 from matplotlib.colors import LogNorm
 
@@ -29,7 +30,16 @@
     data_misfit,
     regularization,
 )
-from pymatsolver import Pardiso
+
+try:
+    from pymatsolver import Pardiso
+
+    pardiso_imported = True
+except ImportError:
+    warnings.warn(
+        "Pardiso not installed see https://github.com/simpeg/pydiso/blob/main/README.md."
+    )
+    pardiso_imported = False
 
 # from dask.distributed import Client, LocalCluster
 from mtpy.modeling.simpeg.data_2d import Simpeg2DData
@@ -58,9 +68,13 @@ def __init__(self, dataframe, data_kwargs={}, mesh_kwargs={}, **kwargs):
         self.ax = self.make_mesh()
         self.air_conductivity = 1e-8
         self.initial_conductivity = 1e-2
-        self.solver = "pardiso"
+        if pardiso_imported:
+            self.solver = "pardiso"
+            self._solvers_dict = {"pardiso": Pardiso}
 
-        self._solvers_dict = {"pardiso": Pardiso}
+        else:
+            self.solver = None
+            self._solvers_dict = {}
 
         # regularization parameters
         self.alpha_s = 1e-5
@@ -175,31 +189,54 @@ def conductivity_map(self):
         """
         return self.exponent_map * self.active_map
 
+    def _get_solver(self):
+        """
+        get solver
+        """
+        try:
+            return self._solvers_dict[self.solver]
+        except KeyError:
+            return None
+
     @property
     def tm_simulation(self):
         """
         Simulation for TE Mode
         """
-
-        return nsem.simulation.Simulation2DElectricField(
-            self.quad_tree.mesh,
-            survey=self.data.tm_survey,
-            sigmaMap=self.conductivity_map,
-            solver=self._solvers_dict[self.solver],
-        )
+        solver = self._get_solver()
+        if solver is not None:
+            return nsem.simulation.Simulation2DElectricField(
+                self.quad_tree.mesh,
+                survey=self.data.tm_survey,
+                sigmaMap=self.conductivity_map,
+                solver=solver,
+            )
+        else:
+            return nsem.simulation.Simulation2DElectricField(
+                self.quad_tree.mesh,
+                survey=self.data.tm_survey,
+                sigmaMap=self.conductivity_map,
+            )
 
     @property
     def te_simulation(self):
         """
         Simulation for TE Mode
         """
-
-        return nsem.simulation.Simulation2DMagneticField(
-            self.quad_tree.mesh,
-            survey=self.data.te_survey,
-            sigmaMap=self.conductivity_map,
-            solver=self._solvers_dict[self.solver],
-        )
+        solver = self._get_solver()
+        if solver is not None:
+            return nsem.simulation.Simulation2DMagneticField(
+                self.quad_tree.mesh,
+                survey=self.data.te_survey,
+                sigmaMap=self.conductivity_map,
+                solver=solver,
+            )
+        else:
+            nsem.simulation.Simulation2DMagneticField(
+                self.quad_tree.mesh,
+                survey=self.data.te_survey,
+                sigmaMap=self.conductivity_map,
+            )
 
     @property
     def te_data_misfit(self):

setup.py

@@ -66,7 +66,7 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/MTgeophysics/mtpy-v2",
-    version="2.0.8",
+    version="2.0.9",
     zip_safe=False,
     package_data={"": []},
 )