Merge fixed espresso (#159)

.github/workflows/gen_gallery_scripts.yml

@@ -0,0 +1,61 @@
+name: Generate sphinx-gallery scripts from notebooks
+
+on:
+ workflow_dispatch:
+# push:
+# branches: main
+# paths:
+# - 'examples/**'
+# schedule:
+# - cron: '54 13 * * *'
+
+
+jobs:
+ generate_scripts:
+ name: Generate scripts
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout repo
+ uses: actions/checkout@v2
+
+ - name: Install Python 3.9
+ uses: actions/setup-python@v2
+ with:
+ python-version: 3.9
+
+ - name: Install dependencies
+ run: |
+ sudo apt-get install pandoc
+ pip install pypandoc
+ 
+ - name: Add/Update badges
+ uses: trsvchn/colab-badge-action@v4
+ with:
+ verbose: true
+
+ - name: Run _ipynb_to_gallery.py
+ run: |
+ python tools/sphinx_gallery/ipynb_to_gallery.py all
+ 
+ - name: Set git config
+ continue-on-error: true
+ run: |
+ git config --global user.name "github-actions[bot]"
+ git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+ 
+ - name: Commit changes to notebooks
+ continue-on-error: true
+ run: |
+ git add examples/*
+ git commit -m "chore: added badges to colab in examples/"
+
+ - name: Commit changes to scripts
+ continue-on-error: true
+ run: |
+ git add tools/sphinx_gallery/scripts/*
+ git commit -m "chore: update scripts/"
+ 
+ - name: Push back to repo
+ run: |
+ git status
+ git push

.github/workflows/test_all_scripts.yml

@@ -0,0 +1,43 @@
+name: Check all Python examples work
+
+on:
+ workflow_dispatch:
+ # pull_request:
+ # types:
+ # - ready_for_review
+ # paths:
+ # - 'examples/**'
+ # push:
+ # branches: main
+ # paths:
+ # - 'examples/**'
+
+jobs:
+ test:
+ name: Test running all example scripts
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout repo
+ uses: actions/checkout@v2
+
+ - name: Install Python 3.9
+ uses: actions/setup-python@v2
+ with:
+ python-version: 3.9
+
+ - name: Set up Python env
+ run: |
+ python -m pip install matplotlib
+
+ - name: Install CoFI
+ run: |
+ python -m pip install cofi
+
+ - name: Run script
+ run: |
+ python tools/validation/test_all_notebooks_scripts.py
+
+ - name: Upload artifact
+ uses: actions/upload-artifact@v2
+ with:
+ path: ./debug.log

.gitignore

@@ -1,6 +1,6 @@
-# Editor temporary/working/backup files #
-#########################################
-.vscode/
+# Editor / OS related
+.vscode
+.DS_Store
 
 # Packaging tmp stuff #
 #######################
@@ -47,9 +47,17 @@ src/espresso/_version.py
 .pytest_cache
 *__pycache__
 .ipynb_checkpoints
+.cache/*
+*__pycache__/
 *.pyc
 .report.json
 
-# OS generated files #
-######################
-*.DS_Store*
+# # Generated by sphinx-gallery
+# tools/sphinx_gallery/generated/
+
+# Custom testing files
+tools/validation/_output/
+debug.log
+
+# Temporary data files
+examples/pygimli_dcip/transform-2020-simpeg

contrib/fmm_tomography/fmm_tomography.py

@@ -339,6 +339,7 @@ def get_gauss_model(extent,nx,ny): # build two gaussian anomaly velocity model
  gauss1,gauss2 = rv1.pdf(pos),rv2.pdf(pos)
  return 2000.*np.ones([nx,ny]) + (vc1-vb)*gauss1/np.max(gauss1) + (vc2-vb)*gauss2/np.max(gauss2)
 
+
 # build test velocity models
 # read vtx format velocity model and source receivers files
 def read_vtxmodel(filename, with_line_breaks=True):
@@ -391,3 +392,7 @@ def read_receivers(filename):
  recs[i,1],recs[i,0] = float(columns[0]),float(columns[1])
  f.close()
  return recs
+
+
+# 37 EARTH SCIENCES -> 3706 Geophysics -> 370609 Seismology and seismic exploration -> Fast Marching Method -> FmmTomography
+# description: The wave front tracker routines solves boundary value ray tracing problems into 2D heterogeneous wavespeed media, defined by continuously varying velocity model calculated by 2D cubic B-splines.

contrib/gravity_inversion/gravity_inversion.py

@@ -619,3 +619,7 @@ def _inject_density(model, x_nodes, y_nodes, z_nodes, x, y, z, value):
  model[ind] = value
 
  return model
+
+
+# 37 EARTH SCIENCES -> 3706 Geophysics -> 370606 Gravimetrics -> 3D gravity -> GravityInversion
+# description: This example implements a simple gravity forward problem. The model represents density within the earth on a 3D Cartesian grid.

contrib/magnetotelluric_1D/magnetotelluric_1D.py

@@ -333,4 +333,5 @@ def load_data(filename, error_floor = 0.05, subsampling = 3):
  return freqs, dobs, derr
 
 
-
+# 37 EARTH SCIENCES -> 3706 Geophysics -> 370602 Electrical and electromagnetic methods in geophysics -> Magnetotelluric -> Magnetotelluric1D
+# description: Compute the MT response of a 1D resistivty model.

contrib/pumping_test/pumping_test.py

@@ -297,3 +297,7 @@ def log_prior(self, model):
  180.846000, 183.214000, 185.583000, 186.208000])
 
 #yp5 = np.array([])
+
+
+# 37 EARTH SCIENCES -> 3707 Hydrology -> 370703 Groundwater hydrology -> Pumping Test -> PumpingTest
+# description: This example involves the matching of an appropriate forward model to time-drawdown data obtained from a two-well constant rate discharge test.

contrib/receiver_function_inversion/receiver_function_inversion.py

@@ -210,3 +210,7 @@ def log_prior(self, model):
  if depths_in_0_60 and veloc_in_3_7 and params_increasing:
  return np.log(1/60).item()
  return float("-inf")
+
+
+# 37 EARTH SCIENCES -> 3706 Geophysics -> 370609 Seismology and seismic exploration -> Receiver function -> ReceiverFunctionInversion
+# description: 'Receiver functions' are a class of seismic data used to study discontinuities (layering) in the Earth's crust.

contrib/simple_regression/simple_regression.py

@@ -279,3 +279,7 @@ def curveFittingJac(xpts,nModelParameters, basis='polynomial',domainLength=1.):
  else:
  raise ValueError("Unsupported basis")
  return G
+
+
+# 49 MATHEMATICAL SCIENCES -> 4905 Statistics -> 490501 Applied statistics -> Curve fitting -> SimpleRegression
+# description: This example includes various small 1D regression (curve-fitting) problems. Several different forms of basis function are supported: polynomial, Fourier and discrete.

contrib/slug_test/slug_test.py

@@ -226,3 +226,7 @@ def log_prior(self, model):
  0.0323345, 0.0311248, 0.0299604, 0.0288395, 0.0277606,
  0.0267220, 0.0257223, 0.0247600, 0.0238337, 0.0229421,
  0.0220838])
+
+
+# 37 EARTH SCIENCES -> 3707 Hydrology -> 370703 Groundwater hydrology -> Slug test -> SlugTest
+# description: This example involves the matching of an appropriate forward model to time-displacement data obtained from a traditional single well slug test.

contrib/surface_wave_tomography/surface_wave_tomography.py

@@ -9,8 +9,6 @@
 import cartopy.crs as ccrs
 
 
-
-
 class SurfaceWaveTomography(EspressoProblem):
  """Forward simulation class"""
 
@@ -159,10 +157,5 @@ def log_prior(self, model):
  raise NotImplementedError # optional
 
 
-
-
-
-
-
-
-
+# 37 EARTH SCIENCES -> 3706 Geophysics -> 370609 Seismology and seismic exploration -> Ambient noise -> SurfaceWaveTomography
+# description: Mapping lateral variations in surface-wave velocity at continental (USA -- example 1) and global (example 2) scale. Here, the problem is linearized, meaning that we assume that surface waves travel along the great-circle path connecting two points on the Earth surface.

contrib/xray_tomography/xray_tomography.py

@@ -1,3 +1,4 @@
+from espresso import EspressoProblem
 import numpy as np
 from espresso import EspressoProblem
 from espresso.exceptions import InvalidExampleError
@@ -7,7 +8,6 @@
 import tqdm
 
 
-
 class XrayTomography(EspressoProblem):
  """Forward simulation class
  """
@@ -301,4 +301,8 @@ def pngToModel(pngfile,nx,ny,bg=1.,sc=1.):
  model = sc*(bg+np.asarray(png.convert('L').resize((nx,ny)).transpose(Image.Transpose.ROTATE_270))/255.)
  except:
  model = sc*(bg+np.asarray(png.convert('L').resize((nx,ny)).transpose(Image.ROTATE_270))/255.) 
- return model
+ return model
+
+
+# 37 EARTH SCIENCES -> 3706 Geophysics -> 370609 Seismology And Seismic Exploration -> Xray Tracer -> Xray tomography
+# description: We assume that the x-rays travel at the same speed regardless of the medium through which they are passing, and so their paths are straight lines between source and receiver.