Update environment

.github/workflows/tests.yml

@@ -2,11 +2,10 @@ name: Testing
 
 on:
   push:
-    branches:
-      - '*'
+    branches: ['*']
   pull_request:
-    branches:
-      - '*'
+    branches: ['*']
+
 jobs:
   setup-build:
     name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
@@ -18,26 +17,53 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
-        test_file: ["tests/test_dcip.py", "tests/test_em.py", "tests/test_gpr.py", "tests/test_mag.py", "tests/test_seismic.py"]
+        python-version: ["3.11"]
+        test_file: [
+          "tests/test_dcip.py",
+          "tests/test_em.py",
+          "tests/test_gpr.py tests/test_seismic.py",
+          "tests/test_mag.py"
+        ]
+    env:
+      PYTEST_DISABLE_PLUGIN_AUTOLOAD: "1"
+      MPLBACKEND: Agg        # avoid GUI backends import cost
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        auto-update-conda: true
-        activate-environment: geosci-labs
-        channels: conda-forge
-        environment-file: environment.yml
-        python-version: ${{ matrix.python-version }}
-    - name: Install Env
-      run: |
-        conda info
-        conda config --show
-        conda install -y pytest
-        pip install testipynb
-        conda list
-    - name: Run Tests
-      run: |
-        pytest -v ${{ matrix.test_file }}
+      - uses: actions/checkout@v4
+
+      # Use Miniforge3 (not "latest" to avoid 404s) + mamba, strict conda-forge
+      - name: Setup Conda (Miniforge3 + mamba)
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          miniforge-version: "24.11.0-0"     # pin to avoid 'latest' asset 404s
+          python-version: ${{ matrix.python-version }}
+          activate-environment: geosci-labs
+          environment-file: environment.yml
+          use-mamba: true
+          auto-update-conda: false
+          auto-activate-base: false
+          channels: conda-forge
+          channel-priority: strict
+          condarc: |
+            channels:
+              - conda-forge
+            channel_priority: strict
+
+      - name: Show environment info
+        run: |
+          conda info
+          conda list
+
+      - name: Install test dependencies (pytest + testipynb)
+        run: |
+          n=0
+          until [ $n -ge 3 ]; do
+            mamba install -y pytest && pip install -U testipynb && break
+            n=$((n+1))
+            echo "Retry $n/3 after transient fetch error..."
+            sleep 10
+          done
+
+      - name: Run tests
+        run: pytest -v ${{ matrix.test_file }}

environment.yml

@@ -3,17 +3,20 @@ name: geosci-labs
 channels:
   - conda-forge
 dependencies:
-  - cvxopt
-  - deepdish
-  - discretize
-  - ipywidgets>=0.6.0
-  - jupyter
-  - matplotlib<3.5
-  - Pillow
-  - pip
-  - pymatsolver
-  - python=3.10
+  - python=3.11
+  - numpy
+  - scipy
+  - pydiso
+  - matplotlib
+  - ipywidgets
+  - jupyterlab
+  - pillow
   - requests
+  - discretize
   - simpeg
+  - pymatsolver
+  - deepdish
+  - cvxopt
+  - pip
   - pip:
     - git+https://github.com/geoscixyz/geosci-labs

notebooks/dcip/DC_SurveyDataInversion.ipynb

@@ -2,18 +2,9 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/syckdog/opt/anaconda3/envs/e350_notebook/lib/python3.9/site-packages/discretize/utils/code_utils.py:247: FutureWarning: ExtractCoreMesh has been deprecated, please use extract_core_mesh. It will be removed in version 1.0.0 of discretize.\n",
-      "  warnings.warn(\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import warnings\n",
     "warnings.filterwarnings(\"ignore\")\n",
@@ -54,24 +45,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "04569e8a845b4a32bc77d043b2950dd3",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "MyApp(children=(ToggleButtons(description='survey', options=('Dipole-Dipole', 'Dipole-Pole', 'Pole-Dipole', 'P…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "cylinder_app()"
    ]
@@ -139,24 +115,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d1384e6efce843ca873e1a2f8571cc74",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "MyApp(children=(FloatSlider(value=-30.0, continuous_update=False, description='A', max=40.0, min=-40.0, step=1…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "plot_layer_potentials_app()"
    ]
@@ -198,24 +159,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d645ed44e78b485a93927aa419e818e8",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "MyApp(children=(IntSlider(value=0, description='i', max=17), Output()), layout=Layout(align_items='stretch', d…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "MidpointPseudoSectionWidget()"
    ]
@@ -242,26 +188,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6a25181275ec473a99eb1e64715b50d2",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "interactive(children=(BoundedFloatText(value=1000.0, description='$\\\\rho_1$', max=1000.0, min=10.0), BoundedFl…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "DC2DPseudoWidget()"
    ]
@@ -296,34 +225,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "79e1c6477a08484db56eb9cd47a1916a",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "MyApp(children=(BoundedFloatText(value=1000.0, description='$\\\\rho_1$', max=1000.0, min=10.0), BoundedFloatTex…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "DC2DfwdWidget()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -343,7 +250,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.10"
   },
   "widgets": {
    "state": {
@@ -366,5 +273,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

notebooks/em/EM_EM31.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -65,34 +65,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f1ca2def4ff64fd59de24c86ec4ed65f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "interactive(children=(FloatSlider(value=0.0, continuous_update=False, description='$h_{boom}$', max=2.0), Floa…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "interactive_responseFct()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -111,9 +89,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }