examples: Update latex-mathjax for tutorials and py38

ci: Re-balance test worklfows

.github/workflows/examples.yml

@@ -86,7 +86,7 @@ jobs:
         python examples/cfd/example_diffusion.py
 
     - name: Upload coverage to Codecov
-      if: matrix.name != 'pytest-docker-py38-gcc-omp'
+      if: matrix.name != 'pytest-docker-py39-gcc-omp'
       uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pytest-core-nompi.yml

@@ -31,15 +31,14 @@ jobs:
       matrix:
         name: [
            pytest-ubuntu-py39-gcc11-noomp,
-           pytest-ubuntu-py311-gcc12-omp,
-           pytest-ubuntu-py39-gcc7-omp,
+           pytest-ubuntu-py38-gcc12-omp,
+           pytest-ubuntu-py37-gcc7-omp,
            pytest-ubuntu-py310-gcc10-noomp,
            pytest-ubuntu-py38-gcc8-omp,
            pytest-ubuntu-py39-gcc9-omp,
-           pytest-osx-py38-clang-omp,
-           pytest-docker-py38-gcc-omp,
-           pytest-docker-py38-icc-omp,
-           pytest-docker-py38-icx-omp
+           pytest-osx-py37-clang-omp,
+           pytest-docker-py39-gcc-omp,
+           pytest-docker-py39-icx-omp
         ]
         set: [base, adjoint]
         include:
@@ -50,15 +49,15 @@ jobs:
           language: "C"
           sympy: "1.11"
 
-        - name: pytest-ubuntu-py311-gcc12-omp
-          python-version: '3.11'
+        - name: pytest-ubuntu-py38-gcc12-omp
+          python-version: '3.8'
           os: ubuntu-22.04
           arch: "gcc-12"
           language: "openmp"
           sympy: "1.10"
 
-        - name: pytest-ubuntu-py39-gcc7-omp
-          python-version: '3.9'
+        - name: pytest-ubuntu-py37-gcc7-omp
+          python-version: '3.7'
           os: ubuntu-20.04
           arch: "gcc-7"
           language: "openmp"
@@ -85,29 +84,22 @@ jobs:
           language: "openmp"
           sympy: "1.9"
 
-        - name: pytest-osx-py38-clang-omp
-          python-version: '3.8'
+        - name: pytest-osx-py37-clang-omp
+          python-version: '3.7'
           os: macos-latest
           arch: "clang"
           language: "C"
           sympy: "1.9"
 
-        - name: pytest-docker-py38-gcc-omp
-          python-version: '3.8'
+        - name: pytest-docker-py39-gcc-omp
+          python-version: '3.9'
           os: ubuntu-latest
           arch: "gcc"
           language: "openmp"
           sympy: "1.12"
 
-        - name: pytest-docker-py38-icc-omp
-          python-version: '3.8'
-          os: ubuntu-22.04
-          arch: "icc"
-          language: "openmp"
-          sympy: "1.11"
-
-        - name: pytest-docker-py38-icx-omp
-          python-version: '3.8'
+        - name: pytest-docker-py39-icx-omp
+          python-version: '3.9'
           os: ubuntu-22.04
           arch: "icx"
           language: "openmp"
@@ -120,7 +112,7 @@ jobs:
           test-set: 'adjoint'
 
         exclude:
-        - name: pytest-osx-py38-clang-omp
+        - name: pytest-osx-py37-clang-omp
           set: adjoint
 
     steps:

.github/workflows/tutorials.yml

@@ -22,7 +22,7 @@ jobs:
     env:
       DEVITO_ARCH: "${{ matrix.compiler }}"
       DEVITO_LANGUAGE: ${{ matrix.language }}
-      PYTHON_VERSION: "3.8"
+      PYTHON_VERSION: "3.9"
 
     strategy:
       # Prevent all build to stop if a single one fails
@@ -36,17 +36,17 @@ jobs:
           ]
 
         include:
-          - name: tutos-ubuntu-gcc-py37
+          - name: tutos-ubuntu-gcc-py39
             os: ubuntu-latest
             compiler: gcc
             language: "openmp"
 
-          - name: tutos-osx-gcc-py37
+          - name: tutos-osx-gcc-py39
             os: macos-latest
             compiler: gcc-11
             language: "openmp"
 
-          - name: tutos-osx-clang-py37
+          - name: tutos-osx-clang-py39
             os: macos-latest
             compiler: clang
             language: "C"
@@ -60,11 +60,11 @@ jobs:
     - name: Checkout devito
       uses: actions/checkout@v3
 
-    - name: Set up Python 3.8
-      if: matrix.name != 'tutos-docker-gcc-py38'
+    - name: Set up Python 3.9
+      if: "!contains(matrix.name, 'docker')"
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - uses: maxim-lobanov/setup-xcode@v1
       if: runner.os == 'macOS'

devito/tools/utils.py

@@ -299,6 +299,6 @@ def humanbytes(B):
     elif MB <= B < GB:
         return '%d MB' % round(B / MB)
     elif GB <= B < TB:
-        return '%d GB' % round(B / GB)
+        return '%.1f GB' % round(B / GB, 1)
     elif TB <= B:
-        return '%d TB' % round(B / TB)
+        return '%.1f TB' % round(B / TB, 1)

docker/Dockerfile.cpu

@@ -3,11 +3,7 @@
 # This Dockerfile contains the Devito codes and can be built using different base images.
 ##############################################################
 
-<<<<<<< HEAD
 ARG pyversion=python:3.9
-=======
-ARG pyversion=python:3.8
->>>>>>> 66c0b76b5 (ci: Update python versions, end-of-life for python 3.7)
 ARG arch=gcc
 ARG OMPI_BRANCH="v4.1.4"
 

examples/cfd/02_convection_nonlinear.ipynb

@@ -350,7 +350,7 @@
     {
      "data": {
       "text/latex": [
-       "$\\displaystyle \\left[\\begin{matrix}\\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} + \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} + \\frac{\\partial}{\\partial t} \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)}\\\\\\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} + \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} + \\frac{\\partial}{\\partial t} \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)}\\end{matrix}\\right] = 0$"
+       "$\\displaystyle \\left[\\begin{matrix}U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} + U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} + \\frac{\\partial}{\\partial t} U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)}\\\\U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} + U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} + \\frac{\\partial}{\\partial t} U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)}\\end{matrix}\\right] = 0$"
       ],
       "text/plain": [
        "Eq(Vector(U_x(t, x + h_x/2, y)*Derivative(U_x(t, x + h_x/2, y), x) + U_y(t, x, y + h_y/2)*Derivative(U_x(t, x + h_x/2, y), y) + Derivative(U_x(t, x + h_x/2, y), t), U_x(t, x + h_x/2, y)*Derivative(U_y(t, x, y + h_y/2), x) + U_y(t, x, y + h_y/2)*Derivative(U_y(t, x, y + h_y/2), y) + Derivative(U_y(t, x, y + h_y/2), t)), 0)"
@@ -417,7 +417,7 @@
     {
      "data": {
       "text/latex": [
-       "$\\displaystyle \\left[\\begin{matrix}\\operatorname{U_{x}}{\\left(t + dt,x + \\frac{h_{x}}{2},y \\right)}\\\\\\operatorname{U_{y}}{\\left(t + dt,x,y + \\frac{h_{y}}{2} \\right)}\\end{matrix}\\right] = \\left[\\begin{matrix}dt \\left(- \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} - \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} + \\frac{\\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)}}{dt}\\right)\\\\dt \\left(- \\operatorname{U_{x}}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} - \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} \\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} + \\frac{\\operatorname{U_{y}}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)}}{dt}\\right)\\end{matrix}\\right]$"
+       "$\\displaystyle \\left[\\begin{matrix}U_{x}{\\left(t + dt,x + \\frac{h_{x}}{2},y \\right)}\\\\U_{y}{\\left(t + dt,x,y + \\frac{h_{y}}{2} \\right)}\\end{matrix}\\right] = \\left[\\begin{matrix}dt \\left(- U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} - U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} + \\frac{U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)}}{dt}\\right)\\\\dt \\left(- U_{x}{\\left(t,x + \\frac{h_{x}}{2},y \\right)} \\frac{\\partial}{\\partial x} U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} - U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} \\frac{\\partial}{\\partial y} U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)} + \\frac{U_{y}{\\left(t,x,y + \\frac{h_{y}}{2} \\right)}}{dt}\\right)\\end{matrix}\\right]$"
       ],
       "text/plain": [
        "Eq(Vector(U_x(t + dt, x + h_x/2, y), U_y(t + dt, x, y + h_y/2)), Vector(dt*(-U_x(t, x + h_x/2, y)*Derivative(U_x(t, x + h_x/2, y), x) - U_y(t, x, y + h_y/2)*Derivative(U_x(t, x + h_x/2, y), y) + U_x(t, x + h_x/2, y)/dt), dt*(-U_x(t, x + h_x/2, y)*Derivative(U_y(t, x, y + h_y/2), x) - U_y(t, x, y + h_y/2)*Derivative(U_y(t, x, y + h_y/2), y) + U_y(t, x, y + h_y/2)/dt)))"

examples/cfd/08_shallow_water_equation.ipynb

@@ -228,7 +228,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "0.00022222222222222223 13500\n"
+      "dt= 0.00022222222222222223 nt= 13500\n"
      ]
     }
    ],
@@ -246,7 +246,7 @@
     "Tmax  = 3.\n",
     "dt    = 1/4500.\n",
     "nt    = (int)(Tmax/dt)\n",
-    "print(dt, nt)\n",
+    "print(\"dt=\", dt, \"nt=\", nt)\n",
     "\n",
     "x = np.linspace(0.0, Lx, num=nx)\n",
     "y = np.linspace(0.0, Ly, num=ny)\n",
@@ -6802,6 +6802,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# NBVAL_IGNORE_OUTPUT\n",
     "from scipy.ndimage import gaussian_filter\n",
     "\n",
     "# Define constant ocean depth profile h = 30 m\n",

examples/seismic/tutorials/05_staggered_acoustic.ipynb

@@ -122,7 +122,7 @@
     {
      "data": {
       "text/latex": [
-       "$\\displaystyle \\left[\\begin{matrix}\\operatorname{v_{x}}{\\left(t + dt,x + \\frac{h_{x}}{2},z \\right)}\\\\\\operatorname{v_{z}}{\\left(t + dt,x,z + \\frac{h_{z}}{2} \\right)}\\end{matrix}\\right] = \\left[\\begin{matrix}dt \\left(\\frac{\\partial}{\\partial x} p{\\left(t,x,z \\right)} + \\frac{\\operatorname{v_{x}}{\\left(t,x + \\frac{h_{x}}{2},z \\right)}}{dt}\\right)\\\\dt \\left(\\frac{\\partial}{\\partial z} p{\\left(t,x,z \\right)} + \\frac{\\operatorname{v_{z}}{\\left(t,x,z + \\frac{h_{z}}{2} \\right)}}{dt}\\right)\\end{matrix}\\right]$"
+       "$\\displaystyle \\left[\\begin{matrix}v_{x}{\\left(t + dt,x + \\frac{h_{x}}{2},z \\right)}\\\\v_{z}{\\left(t + dt,x,z + \\frac{h_{z}}{2} \\right)}\\end{matrix}\\right] = \\left[\\begin{matrix}dt \\left(\\frac{\\partial}{\\partial x} p{\\left(t,x,z \\right)} + \\frac{v_{x}{\\left(t,x + \\frac{h_{x}}{2},z \\right)}}{dt}\\right)\\\\dt \\left(\\frac{\\partial}{\\partial z} p{\\left(t,x,z \\right)} + \\frac{v_{z}{\\left(t,x,z + \\frac{h_{z}}{2} \\right)}}{dt}\\right)\\end{matrix}\\right]$"
       ],
       "text/plain": [
        "Eq(Vector(v_x(t + dt, x + h_x/2, z), v_z(t + dt, x, z + h_z/2)), Vector(dt*(Derivative(p(t, x, z), x) + v_x(t, x + h_x/2, z)/dt), dt*(Derivative(p(t, x, z), z) + v_z(t, x, z + h_z/2)/dt)))"
@@ -145,7 +145,7 @@
     {
      "data": {
       "text/latex": [
-       "$\\displaystyle p{\\left(t + dt,x,z \\right)} = dt \\left(16.0 \\frac{\\partial}{\\partial x} \\operatorname{v_{x}}{\\left(t + dt,x + \\frac{h_{x}}{2},z \\right)} + 16.0 \\frac{\\partial}{\\partial z} \\operatorname{v_{z}}{\\left(t + dt,x,z + \\frac{h_{z}}{2} \\right)} + \\frac{p{\\left(t,x,z \\right)}}{dt}\\right)$"
+       "$\\displaystyle p{\\left(t + dt,x,z \\right)} = dt \\left(16.0 \\frac{\\partial}{\\partial x} v_{x}{\\left(t + dt,x + \\frac{h_{x}}{2},z \\right)} + 16.0 \\frac{\\partial}{\\partial z} v_{z}{\\left(t + dt,x,z + \\frac{h_{z}}{2} \\right)} + \\frac{p{\\left(t,x,z \\right)}}{dt}\\right)$"
       ],
       "text/plain": [
        "Eq(p(t + dt, x, z), dt*(16.0*Derivative(v_x(t + dt, x + h_x/2, z), x) + 16.0*Derivative(v_z(t + dt, x, z + h_z/2), z) + p(t, x, z)/dt))"

examples/seismic/tutorials/06_elastic.ipynb

@@ -153,7 +153,7 @@
     {
      "data": {
       "text/latex": [
-       "$\\displaystyle \\left[\\begin{matrix}\\operatorname{v_{x}}{\\left(t + dt,x + \\frac{h_{x}}{2},z \\right)}\\\\\\operatorname{v_{z}}{\\left(t + dt,x,z + \\frac{h_{z}}{2} \\right)}\\end{matrix}\\right] = \\left[\\begin{matrix}dt \\left(0.555555555555556 \\frac{\\partial}{\\partial x} \\operatorname{t_{xx}}{\\left(t,x,z \\right)} + 0.555555555555556 \\frac{\\partial}{\\partial z} \\operatorname{t_{xz}}{\\left(t,x + \\frac{h_{x}}{2},z + \\frac{h_{z}}{2} \\right)} + \\frac{\\operatorname{v_{x}}{\\left(t,x + \\frac{h_{x}}{2},z \\right)}}{dt}\\right)\\\\dt \\left(0.555555555555556 \\frac{\\partial}{\\partial x} \\operatorname{t_{xz}}{\\left(t,x + \\frac{h_{x}}{2},z + \\frac{h_{z}}{2} \\right)} + 0.555555555555556 \\frac{\\partial}{\\partial z} \\operatorname{t_{zz}}{\\left(t,x,z \\right)} + \\frac{\\operatorname{v_{z}}{\\left(t,x,z + \\frac{h_{z}}{2} \\right)}}{dt}\\right)\\end{matrix}\\right]$"
+       "$\\displaystyle \\left[\\begin{matrix}v_{x}{\\left(t + dt,x + \\frac{h_{x}}{2},z \\right)}\\\\v_{z}{\\left(t + dt,x,z + \\frac{h_{z}}{2} \\right)}\\end{matrix}\\right] = \\left[\\begin{matrix}dt \\left(0.555555555555556 \\frac{\\partial}{\\partial x} t_{xx}{\\left(t,x,z \\right)} + 0.555555555555556 \\frac{\\partial}{\\partial z} t_{xz}{\\left(t,x + \\frac{h_{x}}{2},z + \\frac{h_{z}}{2} \\right)} + \\frac{v_{x}{\\left(t,x + \\frac{h_{x}}{2},z \\right)}}{dt}\\right)\\\\dt \\left(0.555555555555556 \\frac{\\partial}{\\partial x} t_{xz}{\\left(t,x + \\frac{h_{x}}{2},z + \\frac{h_{z}}{2} \\right)} + 0.555555555555556 \\frac{\\partial}{\\partial z} t_{zz}{\\left(t,x,z \\right)} + \\frac{v_{z}{\\left(t,x,z + \\frac{h_{z}}{2} \\right)}}{dt}\\right)\\end{matrix}\\right]$"
       ],
       "text/plain": [
        "Eq(Vector(v_x(t + dt, x + h_x/2, z), v_z(t + dt, x, z + h_z/2)), Vector(dt*(0.555555555555556*Derivative(t_xx(t, x, z), x) + 0.555555555555556*Derivative(t_xz(t, x + h_x/2, z + h_z/2), z) + v_x(t, x + h_x/2, z)/dt), dt*(0.555555555555556*Derivative(t_xz(t, x + h_x/2, z + h_z/2), x) + 0.555555555555556*Derivative(t_zz(t, x, z), z) + v_z(t, x, z + h_z/2)/dt)))"