first attempt at getting website to rebuild

.github/workflows/python-app.yml

@@ -0,0 +1,62 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: EM Website Build
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        pip install -r requirements.txt
+    - name: Test with pytest
+      run: |
+        pytest -s -v tests
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: test
+    if: github.ref == 'refs/heads/main'
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Build pages
+      run: |
+        python _ext/build_contrib_case.py
+        make html
+        python copy_images
+
+    - name: GitHub Pages
+      uses: crazy-max/ghaction-github-pages@v2.5.0
+      with:
+        build_dir: _build/html
+        fqdn: em.geosci.xyz
+        jekyll: false
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

_ext/autodoc.py → _ext/build_contrib_case.py

@@ -1,4 +1,3 @@
-import shutil
 import os
 import json
 import io
@@ -8,10 +7,10 @@
 CONTRIB_INFO = ['affiliation', 'location', 'email', 'url', 'ORCID']
 CASEHISTORY_INFO = ['citations', 'contributors', 'tags']
 
-ORCID_URL = u'http://orcid.org/'
+ORCID_URL = 'http://orcid.org/'
 
 THIS_IS_AUTOGENERATED = (
-    u".. --------------------------------- ..\n"
+    ".. --------------------------------- ..\n"
     "..                                   ..\n"
     "..    THIS FILE IS AUTO GENEREATED   ..\n"
     "..                                   ..\n"
@@ -21,48 +20,6 @@
 )
 
 
-def make_formula_sheet():
-
-    # Create the examples dir in the docs folder.
-
-    EquationSheetDir = os.path.sep.join(
-        fName.split(os.path.sep)[:-2] + ['content', 'equation_bank']
-    )
-    files = os.listdir(EquationSheetDir)
-
-    rst = os.path.sep.join(
-        (fName.split(os.path.sep)[:-2] + ['content', 'equation_bank' + '.rst'])
-    )
-
-    out = u""".. _equation_bank:
-
-{}
-
-
-Equation Bank
-=============
-
-""".format(THIS_IS_AUTOGENERATED)
-
-    print('\nCreating: equation_bank.rst')
-    f = open(rst, 'w')
-    f.write(out)
-
-    for name in files:
-        out = """
-
- - {}
-
-    .. include:: equation_bank/{}
-
-        """.format(name.rstrip('.rst'), name)
-        f.write(out)
-
-    f.close()
-
-    print('Done writing equation_bank.rst\n')
-
-
 def make_contributorslist(fpath='contributors.json',
                           fout='contributors.rst',
                           contrib_info=CONTRIB_INFO):
@@ -335,28 +292,10 @@ def make_case_histories(fpath='content/case_histories/case_histories.json',
     print('Done writing case_histories.rst')
 
 
-# .. raw:: html
-
-#     <span id="{uid}"></span><h3><a class="referance internal" href="{source}/index.html" title="Go to the case history">{title}</a></h3>
-#     <div class="row">
-#     <div class="col-md-6">
-#     <a class="reference internal image-reference" href="../../_images/{thumbnail}"><img alt="../../_images/{thumbnail}" class="align-left" src="../../_images/{thumbnail}" style="width: 250px;" /></a>
-#     </div>
-#     <div class="col-md-6">
-#     <ul>
-#     {info_block}
-#     </ul>
-#     </div>
-#     <br>
-#     <br>
-#     </div>
-
-
 if __name__ == '__main__':
     """
         Run the following to create the formula sheet.
     """
 
-    make_formula_sheet()
     make_contributorslist()
     make_case_histories()

_ext/copyImages.py → _ext/copy_images.py

@@ -1,7 +1,8 @@
 import os
 import shutil
 
-def copyImages():
+
+def copy_images():
     # get relevant directories
     cwd = os.getcwd()
     contentdir = os.path.sep.join(cwd.split(os.path.sep) + ['content'])
@@ -27,9 +28,13 @@ def copyImages():
         if root.endswith('images'):
             for filename in fileList:
                 if filename not in imnames:
-                    shutil.copy(os.path.join(root, filename),buildimagesdir)
-    return
+                    print(f'copying in {filename}')
+                    shutil.copy(os.path.join(root, filename), buildimagesdir)
+
 
+if __name__ == '__main__':
+    """
+        Run the following to create the formula sheet.
+    """
 
-if __name__ == "__main__":
-    copyImages()
+    copy_images()

content/geophysical_surveys/dcr/images/EMGeosci_DCR_3DFwr_Sphere_Example.py

@@ -17,6 +17,9 @@
 
 """
 
+# This script was used to create the static images in dcr.
+# It is not needed to be run to build the decomentation.
+
 
 #%%
 from SimPEG import *

content/maxwell3_fdem/circuitmodel_for_eminduction/derive_response_function.rst

@@ -103,13 +103,10 @@ Below figure shows real and imaginary component of :math:`Q`.
 
 .. plot::
 
-    from em_examples.EMcircuit import Qfun
-    import numpy as np
-    import matplotlib.pyplot as plt
     L = 1.
     R = 2000.
     alpha = np.logspace(-3, 3, 100)
-    alpha, Q = Qfun(R, L, None, alpha=alpha)
+    Q = (alpha ** 2 + 1j * alpha) / (1 + alpha ** 2)
     fig = plt.figure(figsize=(5, 3))
     ax1 = plt.subplot(111)
     ax1.semilogx(alpha, Q.real, 'k', lw=3)

content/maxwell3_fdem/circuitmodel_for_eminduction/index.rst

@@ -72,13 +72,10 @@ is the induction number.
 
 .. plot::
 
-    from em_examples.EMcircuit import Qfun
-    import numpy as np
-    import matplotlib.pyplot as plt
     L = 1.
     R = 2000.
     alpha = np.logspace(-3, 3, 100)
-    alpha, Q = Qfun(R, L, None, alpha=alpha)
+    Q = (alpha ** 2 + 1j * alpha) / (1 + alpha ** 2)
     fig = plt.figure(figsize=(5, 3))
     ax1 = plt.subplot(111)
     ax1.semilogx(alpha, Q.real, 'k', lw=3)
@@ -126,6 +123,3 @@ In the following pages we illustrate
     derive_response_function
     understanding_harmonicEMresponse
     understanding_response_widget
-
-
-

content/maxwell3_fdem/circuitmodel_for_eminduction/understanding_harmonicEMresponse.rst

@@ -120,9 +120,7 @@ Computed coupling coefficient along the line is shown below:
 
 .. plot::
 
-    from em_examples.EMcircuit import Mijfun, Cfun, Qfun
-    import numpy as np
-    import matplotlib.pyplot as plt
+    from scipy.constants import mu_0
     L = 1.
     R = 2000.
     xc = 0.
@@ -140,9 +138,41 @@ Computed coupling coefficient along the line is shown below:
     yp = xp.copy()
     zp = np.r_[-ht]
     xyz_profile = np.c_[xp, np.zeros_like(xp), np.ones_like(xp)*ht]
-    c_profile, m12_profile, m23_profile, m13_profile = Cfun(L,R,xc,yc,zc,incl,decl,S,ht,f,xyz_profile)
+    tx_loc = xyz_profile - [S/2, 0, 0]
+    rx_loc = xyz_profile + [S/2, 0, 0]
+
+    def Mij(loc_i, loc_j, dir_i, dir_j, area_i=1, area_j=1):
+        di=dir_i[0]*np.pi/180
+        dd=dir_i[1]*np.pi/180
+
+        m_i = area_i * np.array([
+            np.cos(di)*np.cos(dd),
+            np.cos(di)*np.sin(dd),
+            np.sin(di)
+        ])
+
+        ai=dir_j[0]*np.pi/180
+        ad=dir_j[1]*np.pi/180
+
+        m_j = area_j * np.array([
+            np.cos(ai)*np.cos(ad),
+            np.cos(ai)*np.sin(ad),
+            np.sin(ai)
+        ])
+
+        dr = loc_i - loc_j
+        r = np.linalg.norm(dr, axis=-1)[:, None]
+        B = mu_0 / (4*np.pi) * (3 * dr * dr.dot(m_i)[:, None] / r**5 - m_i/r**3)
+        return B.dot(m_j)
+
+    M13 = Mij(tx_loc, rx_loc, (90, 0), (90, 0))
+    M12 = Mij(tx_loc, [xc, yc, zc], (90, 0), (incl, decl), area_j=3.0)
+    M23 = Mij([xc, yc, zc], rx_loc, (incl, decl), (90, 0), area_i=3.0)
+    C = -M12*M23/(M13*L)
+
+
     fig = plt.figure(figsize=(5,3))
-    plt.plot(xp, c_profile, 'k', lw=2)
+    plt.plot(xp, C, 'k', lw=2)
     plt.plot(xp, np.zeros_like(xp), 'k--', lw=1)
     plt.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
     plt.xlabel("Mid point between Tx and Rx (m)")
@@ -169,13 +199,10 @@ imaginary or ampliutde and phase.
 
 .. plot::
 
-    from em_examples.EMcircuit  import Qfun
-    import numpy as np
-    import matplotlib.pyplot as plt
     L = 1.
     R = 2000.
     alpha = np.logspace(-3, 3, 100)
-    alpha, Q = Qfun(R, L, None, alpha=alpha)
+    Q = (alpha ** 2 + 1j * alpha) / (1 + alpha ** 2)
     fig = plt.figure(figsize=(10, 3))
     ax1 = plt.subplot(121)
     ax2 = plt.subplot(122)
@@ -309,5 +336,3 @@ In frequency domain EM survey:
 
 - the 90 :math:`^\circ` out-of-phase fraction of :math:`H^s_3` is called the
   **Imaginary**, **Out-of-phase**, or **Quadrature** component.
-
-

requirements.txt

@@ -1,15 +1,6 @@
-numpy
-scipy
-ipython
-ipywidgets
-flask
 sphinx
-docutils
-matplotlib
-properties[math]
 sphinxcontrib-bibtex
 sphinx_rtd_theme
-Pillow
-em_examples
-SimPEG
 pytest
+matplotlib
+geoana