Merge pull request #2 from jpvantassel/dev

In preparation for v0.1.1
jpvantassel · Apr 25, 2022 · a9fdd0f · a9fdd0f
2 parents d7ea1e7 + fe0b434
commit a9fdd0f
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -16,14 +16,17 @@ workflows:
       - test-38:
           context:
             - docker
-      # - test-39:
-      #     context:
-      #       - docker
+      - test-39:
+          context:
+            - docker
+      - test-310:
+          context:
+            - docker
 
 jobs:
   test-36: &test-template
     docker:
-      - image: circleci/python:3.6.9
+      - image: cimg/python:3.6.9
         auth:
           username: jpvantassel
           password: $DOCKER_PASS
@@ -75,23 +78,31 @@ jobs:
   test-37:
     <<: *test-template
     docker:
-      - image: circleci/python:3.7.5
+      - image: cimg/python:3.7.5
         auth:
           username: jpvantassel
           password: $DOCKER_PASS
 
   test-38:
     <<: *test-template
     docker:
-      - image: circleci/python:3.8.0
+      - image: cimg/python:3.8.10
         auth:
           username: jpvantassel
           password: $DOCKER_PASS
 
-  # test-39:
-  #   <<: *test-template
-  #   docker:
-  #     - image: circleci/python:3.9.0
-  #       auth:
-  #         username: jpvantassel
-  #         password: $DOCKER_PASS
+  test-39:
+    <<: *test-template
+    docker:
+      - image: cimg/python:3.9.6
+        auth:
+          username: jpvantassel
+          password: $DOCKER_PASS
+
+  test-310:
+    <<: *test-template
+    docker:
+      - image: cimg/python:3.10.2
+        auth:
+          username: jpvantassel
+          password: $DOCKER_PASS
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,5 +1,5 @@
 This license applies to swprocess a Python package for surface wave processing.
-Copyright (C) 2020 Joseph P. Vantassel ([email protected])
+Copyright (C) 2020 Joseph P. Vantassel ([email protected])
 
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 > Joseph P. Vantassel, The University of Texas at Austin
 
 [![DOI](https://zenodo.org/badge/202217252.svg)](https://zenodo.org/badge/latestdoi/202217252)
-[![PyPI - License](https://img.shields.io/pypi/l/swprocess)](https://github.com/jpvantassel/swprocess/blob/master/LICENSE.txt)
+[![PyPI - License](https://img.shields.io/pypi/l/swprocess)](https://github.com/jpvantassel/swprocess/blob/main/LICENSE.txt)
 [![CircleCI](https://circleci.com/gh/jpvantassel/swprocess.svg?style=svg)](https://circleci.com/gh/jpvantassel/swprocess)
 [![Documentation Status](https://readthedocs.org/projects/swprocess/badge/?version=latest)](https://swprocess.readthedocs.io/en/latest/?badge=latest)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/swprocess)
@@ -30,10 +30,9 @@ the following:
 > Vantassel, J. P. (2021). jpvantassel/swprocess: latest (Concept). Zenodo.
 > [https://doi.org/10.5281/zenodo.4584128](https://doi.org/10.5281/zenodo.4584128)
 
-> Vantassel, J. P. & Cox, B. R. (2021). "SWprocess: A workflow for developing robust
-> estimates of surface wave dispersion uncertainty". Submitted to a special edition of the
-> Journal of Seismology organized by the Consortium of Organizations for Strong Motion
-> Observation Systems (COSMOS)
+> Vantassel, J. P. & Cox, B. R. (2022). "SWprocess: a workflow for developing robust
+> estimates of surface wave dispersion uncertainty". Journal of Seismology.
+> [https://doi.org/10.1007/s10950-021-10035-y](https://doi.org/10.1007/s10950-021-10035-y)
 
 _Note: For software, version specific citations should be preferred to
 general concept citations, such as that listed above. To generate a version
@@ -96,7 +95,7 @@ last few lines of the text displayed in the console.
 ### Using _swprocess_
 
 1.  Download the contents of the
-  [examples](https://github.com/jpvantassel/swprocess/tree/master/examples)
+  [examples](https://github.com/jpvantassel/swprocess/tree/main/examples)
   directory to any location of your choice.
 
 2.  Start by processing the provided active-source data using the

diff --git a/benchmarks/model_0/vis_model_0.ipynb b/benchmarks/model_0/vis_model_0.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",

diff --git a/benchmarks/model_1/vis_model_1.ipynb b/benchmarks/model_1/vis_model_1.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",

diff --git a/benchmarks/model_2/vis_model_2.ipynb b/benchmarks/model_2/vis_model_2.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",

diff --git a/benchmarks/model_3/vis_model_3.ipynb b/benchmarks/model_3/vis_model_3.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",

diff --git a/docs/conf.py b/docs/conf.py
@@ -13,12 +13,21 @@
 import os
 import sys
 
-meta = {}
-with open("../swprocess/meta.py") as f:
-    exec(f.read(), meta)
-
 sys.path.insert(0, os.path.abspath('../swprocess'))
 
+
+def parse_meta(path_to_meta):
+    with open(path_to_meta) as f:
+        meta = {}
+        for line in f.readlines():
+            if line.startswith("__version__"):
+                meta["__version__"] = line.split('"')[1]
+    return meta
+
+
+meta = parse_meta("../swprocess/meta.py")
+
+
 # -- Project information -----------------------------------------------------
 project = 'swprocess'
 copyright = '2020, Joseph P. Vantassel'

diff --git a/docs/index.rst b/docs/index.rst
@@ -2,14 +2,23 @@ swprocess Documentation
 =======================
 
 `swprocess` is a Python package for surface wave processing.
-It includes features for performing active-source surface wave
-processing [i.e., mulitchannel analysis of surface wave (MASW)], 
-post-processing passive-wavefield surface wave data
-[i.e., microtremor array measurements (MAM)] processed using
-the open-source software Geopsy, and combining active-source
-and/or passive-wavefield data to calculate rigorous statistics
-on the surface wave dispersion data, which account for epistemic
-and aleatory uncertainty.
+
+`swprocess` supports:
+
+* processing of active-source surface wave data (i.e., MASW),
+* post-processing of passive-wavefield surface wave data (i.e., MAM) processed using Geopsy,
+* combining active-source and/or passive-wavefield dispersion data from different arrays, and
+* calculation of rigorous surface wave dispersion statistics.
+
+If you use `swprocess` in your research or consulting please cite the following:
+
+ * Vantassel, J. P. (2021). jpvantassel/swprocess: latest (Concept). Zenodo. `https://doi.org/10.5281/zenodo.4584128 <https://doi.org/10.5281/zenodo.4584128>`_
+ * Vantassel, J. P. & Cox, B. R. (2022). "SWprocess: a workflow for developing robust estimates of surface wave dispersion uncertainty". Journal of Seismology. `https://doi.org/10.1007/s10950-021-10035-y <https://doi.org/10.1007/s10950-021-10035-y>`_
+
+*Note: For software, version specific citations should be preferred to
+general concept citations, such as that listed above. To generate a version
+specific citation for swprocess, please use the citation tool on the swprocess*
+`archive <https://doi.org/10.5281/zenodo.4584128>`_.
 
 This package is actively being developed, so if you do not see a feature you
 would like it may very well be under development and released in

diff --git a/docs/license.rst b/docs/license.rst
@@ -3,7 +3,7 @@
 License Information
 ===================
 
-   Copyright (C) 2020 Joseph P. Vantassel ([email protected])
+   Copyright (C) 2020 Joseph P. Vantassel ([email protected])
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -16,4 +16,4 @@ License Information
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
-   along with this program.  If not, see <https: //www.gnu.org/licenses/>.
+   along with this program.  If not, see `<https: //www.gnu.org/licenses/> <https: //www.gnu.org/licenses/>`_.
diff --git a/docs/make_html.sh b/docs/make_html.sh
@@ -3,4 +3,3 @@
 sphinx-build -E -b html . html
 cd html
 ls
-/c/Program\ Files/Mozilla\ Firefox/firefox index.html
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/examples/extract/extract.ipynb b/examples/extract/extract.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",
@@ -36,10 +36,9 @@
     "> Vantassel, J. P. (2021). jpvantassel/swprocess: latest (Concept). Zenodo.\n",
     "> [https://doi.org/10.5281/zenodo.4584128](https://doi.org/10.5281/zenodo.4584128)\n",
     "\n",
-    "> Vantassel, J. P. & Cox, B. R. (2021). \"SWprocess: A workflow for developing robust\n",
-    "> estimates of surface wave dispersion uncertainty\". Submitted to a special edition of the\n",
-    "> Journal of Seismology organized by the Consortium of Organizations for Strong Motion\n",
-    "> Observation Systems (COSMOS)\n",
+    "> Vantassel, J. P. & Cox, B. R. (2022). \"SWprocess: a workflow for developing robust\n",
+    "> estimates of surface wave dispersion uncertainty\". Journal of Seismology.\n",
+    "> [https://doi.org/10.1007/s10950-021-10035-y](https://doi.org/10.1007/s10950-021-10035-y)\n",
     "\n",
     "_Note: For software, version specific citations should be preferred to\n",
     "general concept citations, such as that listed above. To generate a version\n",
@@ -96,7 +95,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -110,7 +109,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,

diff --git a/examples/mam/mam_fk.ipynb b/examples/mam/mam_fk.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",
@@ -36,10 +36,9 @@
     "> Vantassel, J. P. (2021). jpvantassel/swprocess: latest (Concept). Zenodo.\n",
     "> [https://doi.org/10.5281/zenodo.4584128](https://doi.org/10.5281/zenodo.4584128)\n",
     "\n",
-    "> Vantassel, J. P. & Cox, B. R. (2021). \"SWprocess: A workflow for developing robust\n",
-    "> estimates of surface wave dispersion uncertainty\". Submitted to a special edition of the\n",
-    "> Journal of Seismology organized by the Consortium of Organizations for Strong Motion\n",
-    "> Observation Systems (COSMOS)\n",
+    "> Vantassel, J. P. & Cox, B. R. (2022). \"SWprocess: a workflow for developing robust\n",
+    "> estimates of surface wave dispersion uncertainty\". Journal of Seismology.\n",
+    "> [https://doi.org/10.1007/s10950-021-10035-y](https://doi.org/10.1007/s10950-021-10035-y)\n",
     "\n",
     "_Note: For software, version specific citations should be preferred to\n",
     "general concept citations, such as that listed above. To generate a version\n",
@@ -244,7 +243,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -258,7 +257,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,

diff --git a/examples/masw/masw.ipynb b/examples/masw/masw.ipynb
diff --git a/examples/stats/stats.ipynb b/examples/stats/stats.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "This file is distributed as part of _swprocess_, a Python package for surface wave processing.\n",
     "\n",
-    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
+    "    Copyright (C) 2020 Joseph P. Vantassel ([email protected])\n",
     "\n",
     "    This program is free software: you can redistribute it and/or modify\n",
     "    it under the terms of the GNU General Public License as published by\n",
@@ -36,10 +36,9 @@
     "> Vantassel, J. P. (2021). jpvantassel/swprocess: latest (Concept). Zenodo.\n",
     "> [https://doi.org/10.5281/zenodo.4584128](https://doi.org/10.5281/zenodo.4584128)\n",
     "\n",
-    "> Vantassel, J. P. & Cox, B. R. (2021). \"SWprocess: A workflow for developing robust\n",
-    "> estimates of surface wave dispersion uncertainty\". Submitted to a special edition of the\n",
-    "> Journal of Seismology organized by the Consortium of Organizations for Strong Motion\n",
-    "> Observation Systems (COSMOS)\n",
+    "> Vantassel, J. P. & Cox, B. R. (2022). \"SWprocess: a workflow for developing robust\n",
+    "> estimates of surface wave dispersion uncertainty\". Journal of Seismology.\n",
+    "> [https://doi.org/10.1007/s10950-021-10035-y](https://doi.org/10.1007/s10950-021-10035-y)\n",
     "\n",
     "_Note: For software, version specific citations should be preferred to\n",
     "general concept citations, such as that listed above. To generate a version\n",
@@ -471,6 +470,15 @@
     "for ax, _xtype, _ytype in zip(axs, xtype, ytype):\n",
     "    if _xtype == xdomain and _ytype == ydomain:\n",
     "        master_suite.plot_statistics(ax=ax, xx=xx, mean=mean, stddev=stddev)\n",
+    "        \n",
+    "# Frequency\n",
+    "ax = axs[0]\n",
+    "ax.set_xlim(50, 100)\n",
+    "ax.set_ylim(800, 1800)\n",
+    "# Wavelength\n",
+    "ax = axs[1]\n",
+    "ax.set_xlim(5, 100)\n",
+    "ax.set_ylim(800, 1800)\n",
     "\n",
     "axs[-1].legend(bbox_to_anchor = (1.1, 0.5), loc=\"center left\")\n",
     "\n",
@@ -606,7 +614,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -620,7 +628,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.5"
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,

diff --git a/requirements.txt b/requirements.txt
@@ -2,7 +2,8 @@ numpy
 scipy
 matplotlib
 obspy
-sigpropy>=0.3.0
+sigpropy>=1.0.0
 pandas
 PyQt5
-coverage
+coverage
+tox