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lheagylheagy
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Update environment (#141)
* update environment * update dev environment * revert renaming of environment * roll back simpeg to 0.23 * roll back simpeg * update environment * update environment * update environment * try unpinning matplotlib dep * try removing qt from matplotlib dependency * update environment * remove matplotlib version pin * update testing * SimPEG --> simpeg * update environment file * update testing * update python version * update testing * restart and clear outputs from all notebooks * update testing
1 parent 24d2a22 commit 4b514ba

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-514
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‎.github/workflows/tests.yml‎

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

‎environment-dev.yml‎

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This file was deleted.

‎environment.yml‎

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

‎notebooks/dcip/DC_SurveyDataInversion.ipynb‎

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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/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",
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" warnings.warn(\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"import warnings\n",
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"warnings.filterwarnings(\"ignore\")\n",
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "04569e8a845b4a32bc77d043b2950dd3",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"MyApp(children=(ToggleButtons(description='survey', options=('Dipole-Dipole', 'Dipole-Pole', 'Pole-Dipole', 'P…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"cylinder_app()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "d1384e6efce843ca873e1a2f8571cc74",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"MyApp(children=(FloatSlider(value=-30.0, continuous_update=False, description='A', max=40.0, min=-40.0, step=1…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"plot_layer_potentials_app()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "d645ed44e78b485a93927aa419e818e8",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"MyApp(children=(IntSlider(value=0, description='i', max=17), Output()), layout=Layout(align_items='stretch', d…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"MidpointPseudoSectionWidget()"
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]
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},
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {
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"scrolled": false
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},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "6a25181275ec473a99eb1e64715b50d2",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"interactive(children=(BoundedFloatText(value=1000.0, description='$\\\\rho_1$', max=1000.0, min=10.0), BoundedFl…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"DC2DPseudoWidget()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "79e1c6477a08484db56eb9cd47a1916a",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"MyApp(children=(BoundedFloatText(value=1000.0, description='$\\\\rho_1$', max=1000.0, min=10.0), BoundedFloatTex…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"DC2DfwdWidget()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.13"
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"version": "3.11.10"
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},
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"widgets": {
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"state": {
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
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}

‎notebooks/em/EM_EM31.ipynb‎

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

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