Merge pull request #243 from rmodrak/master

Updated installation instructions
uafgeotools · Jan 19, 2024 · 3730282 · 3730282
2 parents d7d53e3 + 0b26033
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diff --git a/docs/install/arm64.rst b/docs/install/arm64.rst
@@ -1,6 +1,16 @@
 
-Installation on ARM64 systems
-=============================
+.. warning::
+
+   With newer versions of MTUQ, the same installation procedure works for Macs
+   as for other computers. Thus, the following modified procedure may no longer 
+   be necessary (though it should still continue to work).
+
+
+
+Modified installation procedure for Apple M1 and Apple M2 Macs
+==============================================================
+
+Newer Mac computers use proprietary Apple processors based on the ARM64 architecture.
 
 To install MTUQ on ARM64 systems, create a conda virtual environment:
 
@@ -37,16 +47,16 @@ Finally, install PyGMT:
 
 .. code::
 
-    conda install 'pygmt>=0.9'
+    conda install 'pygmt=0.9'
 
 
 .. note::
 
-    Users may receive the following Instaseis warning message:
+    Users may receive the following Instaseis warning:
 
     `UserWarning: Please don't install from a tarball. Use the proper pypi release or install from git.`
 
-    Now that Instaseis PyPI releases are no longer maintained, the above message can be ignored.
+    In fact, env_arm64.yaml does install Instaseis from git, and the above message can be ignored.
 
 
 .. note::

diff --git a/docs/install/index.rst b/docs/install/index.rst
@@ -1,14 +1,14 @@
 Installation
 ============
 
-We recommend installing MTUQ under Anaconda or Miniconda, which if not already present can be obtained following `these instructions <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_.
+We recommend installing MTUQ under Miniconda, which can be obtained following `these instructions <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_.
 
 
 To install MTUQ, create a conda virtual environment:
 
 .. code::
 
-   conda create -n mtuq python=3
+   conda create -n mtuq
 
 
 Download the MTUQ source code:
@@ -43,7 +43,7 @@ Finally, install PyGMT:
 
 .. note::
 
-    PyGMT installation has been finicky at times, so we include it as a separate step after the main env.yaml-based installation. 
+    PyGMT installation has been finicky at times, so we include it as a separate step after the main env.yaml-based installation. Most MTUQ functions will continue to work without PyGMT. (`See here <https://uafgeotools.github.io/mtuq/install/issues.html#pygmt-installation>`_ for more information.)
 
 
 **Troubleshooting**

diff --git a/docs/install/issues.rst b/docs/install/issues.rst
@@ -1,51 +1,50 @@
 
+Troubleshooting
+===============
 
-Installation on Apple M1 and Apple M2 Macs
-------------------------------------------
 
-Newer Mac computers use proprietary Apple processors based on the ARM64 architecture.  On these and other ARM64 systems, a modified `conda env` command is necessary
+PyGMT installation
+------------------
 
-.. code::
+MTUQ uses full moment tensor plotting functions from the PyGMT graphics library.
 
-   conda env update --file env_arm64.yaml
+To avoid a known issue with PyGMT installation under conda, it is necessary to specify a minimum PyGMT version as follows:
+
+.. code::
 
-but otherwise users can follow the normal installation procedure.
+    conda install 'pygmt>=0.9'
 
-For more information, please see:
 
-`MTUQ installation on ARM64 systems <https://uafgeotools.github.io/mtuq/install/arm64.html>`_
+A more conservative approach, which avoids possible issues with PyGMT 0.10 releases, is to specify the more stable PyGMT 0.9 version:
 
+.. code::
 
-Installation under virutalenv
------------------------------
+    conda install 'pygmt=0.9'
 
-For most users, we recommend installing MTUQ under conda.  However, in rare cases it seems that MTUQ can be more easily installed under virtualenv.
 
-For more information, please see:
+If PyGMT installation fails, most MTUQ functions will still work, but some plotting functions will fall back to GMT or ObsPy.  
 
-`MTUQ installation under virtualenv <https://uafgeotools.github.io/mtuq/install/virtualenv.html>`_
+We note that some versions of GMT and ObsPy do not plot `full moment tensors <https://github.com/obspy/obspy/issues/2388>`_ correctly.
 
 
-Troubleshooting PyGMT installation
-----------------------------------
 
-MTUQ uses full moment tensor plotting functions from the PyGMT graphics library.
+Speeding up conda installs
+--------------------------
 
-To avoid a known issue with PyGMT installation under conda, it is necessary to specify a minimum PyGMT version as follows:
+Sometimes the conda package manager can be very slow. To speed it up, older conda installations can be updated, making libmamba the default dependency solver:
 
 .. code::
 
-    conda install 'pygmt>=0.9'
-
+    conda update -n base conda
 
-A more conservative approach, which avoids suspected problems with PyGMT 0.10 releases, is to specify the more stable PyGMT 0.9 version:
 
-.. code::
 
-    conda install 'pygmt=0.9'
+MTUQ installation on Apple M1 and Apple M2 Macs
+-----------------------------------------------
 
+Installation on Apple M1 and Apple M2 Macs is now possible using the default installation procedure.
 
-If PyGMT installation fails, most MTUQ functions will still work, but some plotting functions will fall back to GMT or ObsPy.  
+For older versions of MTUQ, a modified installation procedure may stil be necessary.  For more information, please see:
 
-We note that some versions of GMT and ObsPy do not plot `full moment tensors <https://github.com/obspy/obspy/issues/2388>`_ correctly.
+`MTUQ installation on ARM64 systems <https://uafgeotools.github.io/mtuq/install/arm64.html>`_
 
diff --git a/docs/install/virtualenv.rst b/docs/install/virtualenv.rst
@@ -1,7 +1,7 @@
 Installation under virtualenv
 =============================
 
-Install `virtualenv`, if not already present, following these `instructions <https://virtualenv.pypa.io/en/latest/installation.html>`_.
+Install virtualenv, if not already present, following these `instructions <https://virtualenv.pypa.io/en/latest/installation.html>`_.
 
 Create a virtual environment:
 
@@ -28,7 +28,7 @@ Install MTUQ:
    pip install -e .
 
 
-If `instaseis` installation fails, try:
+If Instaseis installation fails, try:
 
 .. code::
 

diff --git a/docs/user_guide/03.rst b/docs/user_guide/03.rst
@@ -54,7 +54,7 @@ To open an AxiSEM database client in MTUQ:
    db = open_db(path_to_NetCDF_file, format="AxiSEM")
 
 
-`FK <https://www.eas.slu.edu/People/LZhu/home.html>`_ simulates wave propagation in horizontally-layered elastic media using a frequency-wavenumber method.   FK  simulations create SAC files in a directory tree organized by model, event depth, and event distance.  Each SAC file represents a vertical, radial, or transverse velocity time series in units of 10^-20*cm*(dyne-cm)^-1 s^-1.
+`FK <https://www.eas.slu.edu/People/LZhu/home.html>`_ simulates wave propagation in horizontally-layered elastic media using a frequency-wavenumber integration method.   FK  simulations create SAC files in a directory tree organized by model, event depth, and event distance.  Each SAC file represents a vertical, radial, or transverse velocity time series in units of 10^-20*cm*(dyne-cm)^-1 s^-1.
 
 
 To open an FK database client in MTUQ:

diff --git a/docs/user_guide/06/custom_backends.rst b/docs/user_guide/06/custom_backends.rst
@@ -31,7 +31,7 @@ Note that the backend function contains hardcoded settings that improve the appe
       fig.basemap(
           region=gmt_region,
           projection=gmt_projection,
-          frame=["xa5", "ya2"],
+          frame=gmt_frame,
           )
 
       fig.coast(

diff --git a/env_arm64.yaml b/env_arm64.yaml
@@ -1,8 +1,7 @@
-# for installation on ARM64 systems, including Apple M1 and Apple M2
 
 channels:
-  - defaults
   - conda-forge
+  - defaults
 
 dependencies:
   - conda-build
@@ -21,9 +20,8 @@ dependencies:
   - pytest
   - pip
   - pip:
-    - git+https://github.com/sstaehler/instaseis.git
+    - git+https://github.com/rmodrak/instaseis.git
     - tables
     - seisgen
     - seishmc
     - -e .
-
diff --git a/env_default.yaml b/env_default.yaml
@@ -1,15 +1,14 @@
 
 channels:
-  - defaults
   - conda-forge
+  - defaults
 
 dependencies:
   - conda-build
   - python=3
   - numpy 
   - scipy 
   - obspy 
-  - instaseis 
   - pandas 
   - xarray 
   - netCDF4
@@ -21,6 +20,7 @@ dependencies:
   - pytest
   - pip
   - pip:
+    - git+https://github.com/rmodrak/instaseis.git
     - tables
     - seisgen
     - seishmc

diff --git a/examples/DetailedAnalysis.py b/examples/DetailedAnalysis.py
@@ -497,11 +497,11 @@
         # save processed waveforms as binary files
         os.makedirs(event_id+'FMT_waveforms', exist_ok=True)
 
-        data_bw.write(event_id+'FMT_waveforms/dat_bw.p')
-        data_sw.write(event_id+'FMT_waveforms/dat_sw.p')
+        data_bw.write(event_id+'FMT_waveforms/dat_bw')
+        data_sw.write(event_id+'FMT_waveforms/dat_sw')
 
-        synthetics_bw.write(event_id+'FMT_waveforms/syn_bw.p')
-        synthetics_sw.write(event_id+'FMT_waveforms/syn_sw.p')
+        synthetics_bw.write(event_id+'FMT_waveforms/syn_bw')
+        synthetics_sw.write(event_id+'FMT_waveforms/syn_sw')
 
 
         # save misfit surfaces as netCDF files

diff --git a/mtuq/dataset.py b/mtuq/dataset.py
@@ -1,5 +1,6 @@
 
 import obspy
+import os
 import numpy as np
 import pickle
 
@@ -268,9 +269,25 @@ def __copy__(self):
         return new_ds
 
 
-    def write(self, filename):
+    def write(self, path, format='sac'):
         """ Writes a Python pickle of current dataset
         """
-        with open(filename, "wb") as file:
-           pickle.dump(self, file)
+        if format.lower() == 'pickle':
+
+            with open(filename, "wb") as file:
+               pickle.dump(self, path)
+
+        elif format.lower() == 'sac':
+
+            os.makedirs(path, exist_ok=True)
+            for stream in self:
+                for trace in stream:
+
+                    keys = ('network','station','location','channel')
+                    filename = '.'.join([trace.stats[key] for key in keys])
+
+                    fullpath = '%s/%s.%s' % (path,filename,'sac')
+                    trace.write(fullpath, format='sac')
+
+
 
diff --git a/mtuq/graphics/uq/_gmt/plot_depth b/mtuq/graphics/uq/_gmt/plot_depth
@@ -7,7 +7,7 @@
 #
 
 
-# add mtuq/graphics/_gmt to the path
+# add mtuq/graphics/uq/_gmt to the path
 export PATH=${PATH:+${PATH}:}$(dirname ${BASH_SOURCE[0]})
 source _gmt_functions
 

diff --git a/mtuq/graphics/uq/_gmt/plot_force b/mtuq/graphics/uq/_gmt/plot_force
@@ -4,7 +4,7 @@
 # PLOT_FORCE
 #
 
-# add mtuq/graphics/_gmt to the path
+# add mtuq/graphics/uq/_gmt to the path
 export PATH=${PATH:+${PATH}:}$(dirname ${BASH_SOURCE[0]})
 source _gmt_functions
 

diff --git a/mtuq/graphics/uq/_gmt/plot_latlon b/mtuq/graphics/uq/_gmt/plot_latlon
@@ -1,12 +1,11 @@
 #!/bin/bash -e
 
-
-# USAGE
-#   plot_mt_xy out filetype mt_file mw_file xmin xmax ymin ymax xlabel ylabel [title] [subtitle]
+#
+# PLOT_LATLON
 #
 
 
-# add mtuq/graphics/_gmt to the path
+# add mtuq/graphics/uq/_gmt to the path
 export PATH=${PATH:+${PATH}:}$(dirname ${BASH_SOURCE[0]})
 source _gmt_functions
 

diff --git a/mtuq/graphics/uq/_gmt/plot_lune b/mtuq/graphics/uq/_gmt/plot_lune
@@ -6,7 +6,7 @@
 #
 
 
-# add mtuq/graphics/_gmt to the path
+# add mtuq/graphics/uq/_gmt to the path
 export PATH=${PATH:+${PATH}:}$(dirname ${BASH_SOURCE[0]})
 source _gmt_functions
 

diff --git a/mtuq/graphics/uq/_gmt/plot_vw b/mtuq/graphics/uq/_gmt/plot_vw
@@ -1,12 +1,12 @@
 #!/bin/bash -e
 
 #
-# PLOT_LUNE
-#    plots values from ASCII file on eigenvalue lune
+# PLOT_VW
+#    plots values from ASCII file on vw rectangle
 #
 
 
-# add mtuq/graphics/_gmt to the path
+# add mtuq/graphics/uq/_gmt to the path
 export PATH=${PATH:+${PATH}:}$(dirname ${BASH_SOURCE[0]})
 source _gmt_functions
 

diff --git a/setup/code_generator.py b/setup/code_generator.py
@@ -1299,11 +1299,11 @@
         # save processed waveforms as binary files
         os.makedirs(event_id+'FMT_waveforms', exist_ok=True)
 
-        data_bw.write(event_id+'FMT_waveforms/dat_bw.p')
-        data_sw.write(event_id+'FMT_waveforms/dat_sw.p')
+        data_bw.write(event_id+'FMT_waveforms/dat_bw')
+        data_sw.write(event_id+'FMT_waveforms/dat_sw')
 
-        synthetics_bw.write(event_id+'FMT_waveforms/syn_bw.p')
-        synthetics_sw.write(event_id+'FMT_waveforms/syn_sw.p')
+        synthetics_bw.write(event_id+'FMT_waveforms/syn_bw')
+        synthetics_sw.write(event_id+'FMT_waveforms/syn_sw')
 
 
         # save misfit surfaces as netCDF files