Testing updates (#62)

* try updating ci to use mamba * try again with micromamba * indentation error * update environment file * install geoscilabs in test environment * updates to fix deprecating plotImage, SimPEG, discretize deprication fixes * make running test verbose * update extractCoreMesh --> extract_core_mesh * remove the mamba activate command * split up tests into matrix * simplify some of the environment file * have environment file follow dev environment file * update the VMD code to fix deprications
geoscixyz · Aug 15, 2023 · 26ce0a8 · 26ce0a8
1 parent bea6b88
commit 26ce0a8
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -9,38 +9,29 @@ on:
       - '*'
 jobs:
   setup-build:
-    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
+    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }}, ${{ matrix.test-file }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        python-version: [3.7, "3.10"]
+        test-file: ["tests/test_dcip.py", "tests/test_em.py", "tests/test_gpr.py tests/test_seismic.py", "tests/test_inversion.py", "tests/test_gravity.py tests/test_mag.py"]
 
     steps:
     - uses: actions/checkout@v2
-    - name: Setup Conda
-      uses: s-weigand/setup-conda@v1
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        update-conda: true
-        conda-channels: conda-forge
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install Env
-      shell: bash
-      run: |
-        python --version
-        conda env create -f environment-dev.yml
-
-    - name: Install Our Package
-      shell: bash
-      run: |
-        source activate geosci-labs-dev
-        pip install -e .
-        conda list
-
+        environment-file: environment-dev.yml
+        init-shell: >-
+          bash
+          powershell
+        create-args: >-
+          python=${{ matrix.python-version }}
+        cache-environment: true
+        post-cleanup: 'all'
     - name: Run Tests
-      shell: bash
+      shell: micromamba-shell {0}
       run: |
-        source activate geosci-labs-dev
-        pytest .
+        pip install -e . --no-deps
+        pytest ${{ matrix.test-file }} -v
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -2,24 +2,17 @@ name: geosci-labs-dev
 
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - cvxopt
   - deepdish
   - discretize
-  - empymod
   - ipywidgets>=0.6.0
   - jupyter
   - matplotlib=3.4.3
-  - mkl>=2021.3.0
-  - numpy=1.21
   - Pillow
   - pip
   - pymatsolver
-  - python=3.10
   - requests
-  - scipy>=1.7
-  - scikit-learn<1.0
   - SimPEG
   - pytest
   - flake8

diff --git a/environment.yml b/environment.yml
@@ -6,18 +6,14 @@ dependencies:
   - cvxopt
   - deepdish
   - discretize
-  - empymod=2.0.0
   - ipywidgets>=0.6.0
   - jupyter
   - matplotlib<3.5
-  - mkl>=2021.3.0
-  - numpy
   - Pillow
   - pip
   - pymatsolver
   - python=3.10
   - requests
-  - scipy
   - SimPEG
   - pip:
     - git+https://github.com/geoscixyz/geosci-labs
diff --git a/geoscilabs/dcip/DCIP_overburden_PseudoSection.py b/geoscilabs/dcip/DCIP_overburden_PseudoSection.py
@@ -26,7 +26,7 @@
 from discretize import TensorMesh
 
 from SimPEG import maps, SolverLU, utils
-from SimPEG.utils import ExtractCoreMesh
+from SimPEG.utils import extract_core_mesh
 from SimPEG.electromagnetics.static import resistivity as DC
 from SimPEG.electromagnetics.static import induced_polarization as IP
 from pymatsolver import Pardiso
@@ -50,7 +50,7 @@
 xr = np.arange(xmin, xmax + 1.0, dx)
 dxr = np.diff(xr)
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -855,7 +855,7 @@ def DCIP2Dfwdfun(
         u = np.ma.masked_where(mdctrue <= np.log(1e-8), mtrue)
     else:
         u = np.ma.masked_where(mtrue <= np.log(1e-8), np.log10(1.0 / (mapping * mtrue)))
-    dat1 = mesh.plotImage(
+    dat1 = mesh.plot_image(
         u,
         ax=ax1,
         clim=(u.min(), u.max()),

diff --git a/geoscilabs/dcip/DCWidgetPlate2_5D.py b/geoscilabs/dcip/DCWidgetPlate2_5D.py
@@ -16,7 +16,7 @@
 
 from discretize import TensorMesh
 from SimPEG import maps, SolverLU, utils
-from SimPEG.utils import ExtractCoreMesh
+from SimPEG.utils import extract_core_mesh
 from SimPEG.electromagnetics.static import resistivity as DC
 from ..base import widgetify
 
@@ -37,7 +37,7 @@
 ymin = -40.0
 ymax = 8.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -638,7 +638,7 @@ def PLOT(
         eps = 1e-16
     else:
         eps = 0.0
-    dat = meshcore.plotImage(
+    dat = meshcore.plot_image(
         u[ind] + eps,
         v_type=xtype,
         ax=ax[1],

diff --git a/geoscilabs/dcip/DCWidgetPlate_2D.py b/geoscilabs/dcip/DCWidgetPlate_2D.py
@@ -15,7 +15,7 @@
 
 from discretize import TensorMesh
 from SimPEG import maps, SolverLU, utils
-from SimPEG.utils import ExtractCoreMesh
+from SimPEG.utils import extract_core_mesh
 from SimPEG.electromagnetics.static import resistivity as DC
 
 from ..base import widgetify
@@ -37,7 +37,7 @@
 ymin = -40.0
 ymax = 8.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -639,7 +639,7 @@ def plot_Surface_Potentials(
         eps = 1e-16
     else:
         eps = 0.0
-    dat = meshcore.plotImage(
+    dat = meshcore.plot_image(
         u[ind] + eps,
         v_type=xtype,
         ax=ax[1],

diff --git a/geoscilabs/dcip/DCWidgetResLayer2D.py b/geoscilabs/dcip/DCWidgetResLayer2D.py
@@ -1,6 +1,6 @@
 from discretize import TensorMesh
 from SimPEG import maps, SolverLU, utils
-from SimPEG.utils import ExtractCoreMesh
+from SimPEG.utils import extract_core_mesh
 import numpy as np
 from SimPEG.electromagnetics.static import resistivity as DC
 import matplotlib
@@ -34,7 +34,7 @@
 ymin = -40.0
 ymax = 8.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -668,7 +668,7 @@ def plot_Surface_Potentials(
         eps = 1e-16
     else:
         eps = 0.0
-    dat = meshcore.plotImage(
+    dat = meshcore.plot_image(
         u[ind] + eps,
         v_type=xtype,
         ax=ax[1],

diff --git a/geoscilabs/dcip/DCWidgetResLayer2_5D.py b/geoscilabs/dcip/DCWidgetResLayer2_5D.py
@@ -11,7 +11,7 @@
 import matplotlib.patches as patches
 
 from SimPEG import maps, SolverLU, utils
-from SimPEG.utils import ExtractCoreMesh
+from SimPEG.utils import extract_core_mesh
 from SimPEG.electromagnetics.static import resistivity as DC
 from pymatsolver import Pardiso
 
@@ -40,7 +40,7 @@
 ymin = -40.0
 ymax = 8.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -674,7 +674,7 @@ def PLOT(
         eps = 1e-16
     else:
         eps = 0.0
-    dat = meshcore.plotImage(
+    dat = meshcore.plot_image(
         u[ind] + eps,
         v_type=xtype,
         ax=ax[1],

diff --git a/geoscilabs/dcip/DCWidget_Overburden_2_5D.py b/geoscilabs/dcip/DCWidget_Overburden_2_5D.py
@@ -22,7 +22,7 @@
 
 from discretize import TensorMesh
 from SimPEG import maps, utils
-from SimPEG.utils import ExtractCoreMesh
+from SimPEG.utils import extract_core_mesh
 from SimPEG.electromagnetics.static import resistivity as DC
 
 from pymatsolver import Pardiso
@@ -43,7 +43,7 @@
 ymin = -1000.0
 ymax = 100.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -679,7 +679,7 @@ def PLOT(
     # print ind.shape
     # print u.shape
     # print xtype
-    dat = meshcore.plotImage(
+    dat = meshcore.plot_image(
         u[ind] + eps,
         v_type=xtype,
         ax=ax[1],

diff --git a/geoscilabs/dcip/DC_Pseudosections.py b/geoscilabs/dcip/DC_Pseudosections.py
@@ -74,7 +74,7 @@ def _transform(self, m):
 ymin = -40.0
 ymax = 5.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = utils.ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = utils.extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -536,7 +536,7 @@ def DC2Dfwdfun(
         ax1 = plt.subplot(211)
         ax2 = plt.subplot(212)
 
-        dat1 = mesh.plotImage(
+        dat1 = mesh.plot_image(
             np.log10(1.0 / (mapping * mtrue)),
             ax=ax1,
             clim=(1, 3),
@@ -576,7 +576,7 @@ def DC2Dfwdfun(
         obs = griddata(xzlocs, appresobs, (xi, yi), method="linear")
         plt.figure(figsize=(12, 9))
         ax1 = plt.subplot(311)
-        dat1 = mesh.plotImage(
+        dat1 = mesh.plot_image(
             np.log10(1.0 / (mapping * mtrue)),
             ax=ax1,
             clim=(1, 3),

diff --git a/geoscilabs/dcip/DC_cylinder.py b/geoscilabs/dcip/DC_cylinder.py
@@ -11,7 +11,7 @@
 from discretize import TensorMesh
 
 from SimPEG import maps, utils
-from SimPEG.utils import ExtractCoreMesh, mkvc
+from SimPEG.utils import extract_core_mesh, mkvc
 from SimPEG.electromagnetics.static import resistivity as DC
 
 from ipywidgets import interact, IntSlider, FloatSlider, FloatText, ToggleButtons, BoundedFloatText
@@ -37,7 +37,7 @@
 ymin = -40.0
 ymax = 8.0
 xylim = np.c_[[xmin, ymin], [xmax, ymax]]
-indCC, meshcore = ExtractCoreMesh(xylim, mesh)
+indCC, meshcore = extract_core_mesh(xylim, mesh)
 indx = (
     (mesh.gridFx[:, 0] >= xmin)
     & (mesh.gridFx[:, 0] <= xmax)
@@ -518,7 +518,7 @@ def plot_Surface_Potentials(
         eps = 1e-16
     else:
         eps = 0.0
-    dat = meshcore.plotImage(
+    dat = meshcore.plot_image(
         u[ind] + eps,
         v_type=xtype,
         ax=ax[1],