Merge everest into ert

equinor · Sep 12, 2024 · 897a5b6 · 897a5b6
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diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -132,7 +132,7 @@ jobs:
 
     - name: Test docs
       run: |
-        sphinx-build -n -v -E -W ./docs ./tmp/ert_docs
+        sphinx-build -n -v -E -W ./docs/ert ./tmp/ert_docs
 
   publish:
     name: Publish to PyPI

diff --git a/.github/workflows/mac-run-tests-build-docs.yml b/.github/workflows/mac-run-tests-build-docs.yml
@@ -0,0 +1,79 @@
+name: macos-run-tests-build-docs
+
+on:
+  pull_request:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    tags: "*"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+env:
+  NO_PROJECT_RES: 1
+
+jobs:
+  tests:
+    if: github.ref_type == 'tag' # only build for mac when tags
+    name: "py-${{ matrix.python-version }}_${{ matrix.test_type }}_${{ matrix.os }}"
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.12']
+        os: ['macos-13', 'macos-14', 'macos-14-large']
+        # https://github.com/actions/runner-images/tree/main?tab=readme-ov-file#available-images
+        exclude:
+          - os: 'macos-14'
+            python-version: '3.8'
+          - os: 'macos-14-large'
+            python-version: '3.8'
+          - os: 'macos-13'
+            python-version: '3.12'
+
+        test_type: ['doc', 'test', 'integration-test', 'everest-models-test']
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: "pip"
+        cache-dependency-path: |
+          pyproject.toml
+
+    - name: Install HDF5 source files
+      run: brew install hdf5
+
+    - name: Install Everest and dependencies
+      run: |
+        pip install .[dev, everest]
+
+    - name: Run Tests
+      if: matrix.test_type == 'test'
+      run: |
+        python -m pytest tests/everest -n 4 -m "not ui_test and not integration_test and not fails_on_macos_github_workflow" --dist loadgroup
+
+    - name: Run Integration Tests
+      if: matrix.test_type == 'integration-test'
+      run: |
+        python -m pytest tests/everest -n 4 -m "integration_test and not fails_on_macos_github_workflow" --dist loadgroup
+
+#    - name: Build Documentation
+#      if: matrix.test_type == 'doc'
+#      run: |
+#        pip install git+https://github.com/equinor/everest-models.git
+#        mkdir tmp
+#        sphinx-build -W -b html -d tmp/doctrees docs/source {envtmpdir}/html
+
+    - name: Run tests requiring everest-models
+      if: matrix.test_type == 'everest-models-test'
+      run: |
+        pip install git+https://github.com/equinor/everest-models.git
+        python -m pytest tests/everest -n 4 -m everest_models_test --dist loadgroup
diff --git a/.github/workflows/run-tests-build-docs.yml b/.github/workflows/run-tests-build-docs.yml
@@ -0,0 +1,71 @@
+name: run-tests-build-docs
+
+on:
+  pull_request:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    tags: "*"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+env:
+  NO_PROJECT_RES: 1
+
+jobs:
+  tests:
+    name: "py_${{ matrix.python-version }}_${{ matrix.test_type }}"
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.11', '3.12']
+        os: [ubuntu-22.04]
+        test_type: ['doc', 'ui-test', 'test', 'integration-test', 'everest-models-test']
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: "pip"
+
+    - name: Install Everest and dependencies
+      run: |
+        pip install .[dev,everest]
+
+    - name: Run Tests
+      if: matrix.test_type == 'test'
+      run: |
+        pytest tests/everest -n 4 -m "not ui_test and not integration_test" --dist loadgroup -sv
+
+    - name: Run Integration Tests
+      if: matrix.test_type == 'integration-test'
+      run: |
+        pytest tests -n 4 -m "integration_test" --dist loadgroup
+
+    - name: Run UI Tests
+      if: matrix.test_type == 'ui-test'
+      env:
+        QT_QPA_PLATFORM: 'minimal'
+      run: |
+        python -m pytest tests/everest -m "ui_test"
+
+    - name: Build Documentation
+      if: matrix.test_type == 'doc'
+      run: |
+        pip install git+https://github.com/equinor/everest-models.git
+        mkdir tmp
+        sphinx-build -W -b html -d tmp/everest/doctrees docs/everest/source {envtmpdir}/html
+
+    - name: Run tests requiring everest-models
+      if: matrix.test_type == 'everest-models-test'
+      run: |
+        pip install git+https://github.com/equinor/everest-models.git
+        python -m pytest tests -n 4 -m everest_models_test --dist loadgroup
diff --git a/.github/workflows/test_ert.yml b/.github/workflows/test_ert.yml
@@ -45,17 +45,17 @@ jobs:
     - name: Test GUI
       if: inputs.test-type == 'gui-test'
       run: |
-        pytest tests --junit-xml=junit.xml -v --mpl -m "requires_window_manager" --benchmark-disable
+        pytest tests --junit-xml=junit.xml -v --mpl -m "requires_window_manager" --benchmark-disable --ignore=tests/everest
 
     - name: Unit Test
       if: inputs.test-type == 'unit-tests'
       run: |
-        pytest tests --junit-xml=junit.xml -n logical --show-capture=stderr -v -m "not integration_test and not requires_window_manager" --benchmark-disable --dist loadgroup
+        pytest tests --junit-xml=junit.xml -n logical --show-capture=stderr -v -m "not integration_test and not requires_window_manager" --benchmark-disable --dist loadgroup --ignore=tests/everest
 
     - name: Integration Test
       if: inputs.test-type == 'integration-tests'
       run: |
-        pytest tests --junit-xml=junit.xml -n logical --show-capture=stderr -v -m "integration_test and not requires_window_manager" --benchmark-disable
+        pytest tests --junit-xml=junit.xml -n logical --show-capture=stderr -v -m "integration_test and not requires_window_manager" --benchmark-disable --ignore=tests/everest
 
     - name: Test for a clean repository
       run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,6 +5,7 @@ repos:
     -   id: no-commit-to-branch
     -   id: check-json
     -   id: check-yaml
+        exclude: tests/everest/test_data/valid_config_file/invalid_yaml_config.yml # Invalid yml needed for testing
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
         exclude: test-data/eclipse/parse/ERROR.PRT # exact format is needed for testing

diff --git a/docs/_ext/ert_jobs.py → docs/ert/_ext/ert_jobs.py b/docs/_ext/ert_jobs.py → docs/ert/_ext/ert_jobs.py
diff --git a/docs/_templates/breadcrumbs.html → docs/ert/_templates/breadcrumbs.html b/docs/_templates/breadcrumbs.html → docs/ert/_templates/breadcrumbs.html
diff --git a/docs/_templates/ert_narratives.tmpl → docs/ert/_templates/ert_narratives.tmpl b/docs/_templates/ert_narratives.tmpl → docs/ert/_templates/ert_narratives.tmpl
diff --git a/docs/about/click-on-stderr.png → docs/ert/about/click-on-stderr.png b/docs/about/click-on-stderr.png → docs/ert/about/click-on-stderr.png
diff --git a/docs/about/click-show-details.png → docs/ert/about/click-show-details.png b/docs/about/click-show-details.png → docs/ert/about/click-show-details.png
diff --git a/docs/about/index.rst → docs/ert/about/index.rst b/docs/about/index.rst → docs/ert/about/index.rst
diff --git a/docs/about/license-retry.png → docs/ert/about/license-retry.png b/docs/about/license-retry.png → docs/ert/about/license-retry.png
diff --git a/docs/about/release_notes.rst → docs/ert/about/release_notes.rst b/docs/about/release_notes.rst → docs/ert/about/release_notes.rst
diff --git a/docs/about/v10_manage_experiments.png → docs/ert/about/v10_manage_experiments.png b/docs/about/v10_manage_experiments.png → docs/ert/about/v10_manage_experiments.png
diff --git a/docs/about/v9_auto_scale.png → docs/ert/about/v9_auto_scale.png b/docs/about/v9_auto_scale.png → docs/ert/about/v9_auto_scale.png
diff --git a/docs/about/v9_update_param.png → docs/ert/about/v9_update_param.png b/docs/about/v9_update_param.png → docs/ert/about/v9_update_param.png
diff --git a/docs/about/version-8.0-delete-runpath.gif → .../ert/about/version-8.0-delete-runpath.gif b/docs/about/version-8.0-delete-runpath.gif → .../ert/about/version-8.0-delete-runpath.gif
diff --git a/docs/about/version-8.0-localization.gif → docs/ert/about/version-8.0-localization.gif b/docs/about/version-8.0-localization.gif → docs/ert/about/version-8.0-localization.gif
diff --git a/docs/about/version-8.0-suggestor.png → docs/ert/about/version-8.0-suggestor.png b/docs/about/version-8.0-suggestor.png → docs/ert/about/version-8.0-suggestor.png
diff --git a/docs/about/version-8.0-update.gif → docs/ert/about/version-8.0-update.gif b/docs/about/version-8.0-update.gif → docs/ert/about/version-8.0-update.gif
diff --git a/docs/conf.py → docs/ert/conf.py b/docs/conf.py → docs/ert/conf.py
@@ -16,7 +16,7 @@
 import sys
 from importlib import metadata
 
-sys.path.append(os.path.abspath("./_ext"))
+sys.path.append(os.path.abspath("_ext"))
 
 # -- Project information -----------------------------------------------------
 

diff --git a/docs/developer_documentation/concepts.rst → .../ert/developer_documentation/concepts.rst b/docs/developer_documentation/concepts.rst → .../ert/developer_documentation/concepts.rst
diff --git a/.../developer_documentation/dev-strategy.rst → .../developer_documentation/dev-strategy.rst b/.../developer_documentation/dev-strategy.rst → .../developer_documentation/dev-strategy.rst
diff --git a/...developer_documentation/forward_model.rst → ...developer_documentation/forward_model.rst b/...developer_documentation/forward_model.rst → ...developer_documentation/forward_model.rst
diff --git a/docs/developer_documentation/qt.rst → docs/ert/developer_documentation/qt.rst b/docs/developer_documentation/qt.rst → docs/ert/developer_documentation/qt.rst
diff --git a/docs/developer_documentation/roadmap.rst → docs/ert/developer_documentation/roadmap.rst b/docs/developer_documentation/roadmap.rst → docs/ert/developer_documentation/roadmap.rst
diff --git a/..._started/configuration/poly_new/guide.rst → ..._started/configuration/poly_new/guide.rst b/..._started/configuration/poly_new/guide.rst → ..._started/configuration/poly_new/guide.rst
diff --git a/.../configuration/poly_new/minimal/POLY_EVAL → .../configuration/poly_new/minimal/POLY_EVAL b/.../configuration/poly_new/minimal/POLY_EVAL → .../configuration/poly_new/minimal/POLY_EVAL
diff --git a/...ed/configuration/poly_new/minimal/ert.png → ...ed/configuration/poly_new/minimal/ert.png b/...ed/configuration/poly_new/minimal/ert.png → ...ed/configuration/poly_new/minimal/ert.png
diff --git a/...d/configuration/poly_new/minimal/poly.ert → ...d/configuration/poly_new/minimal/poly.ert b/...d/configuration/poly_new/minimal/poly.ert → ...d/configuration/poly_new/minimal/poly.ert
diff --git a/...guration/poly_new/minimal/simulations.png → ...guration/poly_new/minimal/simulations.png b/...guration/poly_new/minimal/simulations.png → ...guration/poly_new/minimal/simulations.png
diff --git a/...guration/poly_new/minimal/startdialog.png → ...guration/poly_new/minimal/startdialog.png b/...guration/poly_new/minimal/startdialog.png → ...guration/poly_new/minimal/startdialog.png
diff --git a/...onfiguration/poly_new/minimal/warning.png → ...onfiguration/poly_new/minimal/warning.png b/...onfiguration/poly_new/minimal/warning.png → ...onfiguration/poly_new/minimal/warning.png
diff --git a/...poly_new/with_more_observations/POLY_EVAL → ...poly_new/with_more_observations/POLY_EVAL b/...poly_new/with_more_observations/POLY_EVAL → ...poly_new/with_more_observations/POLY_EVAL
diff --git a/...ly_new/with_more_observations/coeff_b.png → ...ly_new/with_more_observations/coeff_b.png b/...ly_new/with_more_observations/coeff_b.png → ...ly_new/with_more_observations/coeff_b.png
diff --git a/...y_new/with_more_observations/coeff_priors → ...y_new/with_more_observations/coeff_priors b/...y_new/with_more_observations/coeff_priors → ...y_new/with_more_observations/coeff_priors
diff --git a/...ations/generate_synthetic_observations.py → ...ations/generate_synthetic_observations.py b/...ations/generate_synthetic_observations.py → ...ations/generate_synthetic_observations.py
diff --git a/...y_new/with_more_observations/observations → ...y_new/with_more_observations/observations b/...y_new/with_more_observations/observations → ...y_new/with_more_observations/observations
diff --git a/...y_new/with_more_observations/poly_eval.py → ...y_new/with_more_observations/poly_eval.py b/...y_new/with_more_observations/poly_eval.py → ...y_new/with_more_observations/poly_eval.py
diff --git a/...new/with_more_observations/poly_final.ert → ...new/with_more_observations/poly_final.ert b/...new/with_more_observations/poly_final.ert → ...new/with_more_observations/poly_final.ert
diff --git a/.../with_more_observations/poly_obs_data.txt → .../with_more_observations/poly_obs_data.txt b/.../with_more_observations/poly_obs_data.txt → .../with_more_observations/poly_obs_data.txt
diff --git a/...tion/poly_new/with_observations/POLY_EVAL → ...tion/poly_new/with_observations/POLY_EVAL b/...tion/poly_new/with_observations/POLY_EVAL → ...tion/poly_new/with_observations/POLY_EVAL
diff --git a/...on/poly_new/with_observations/coeff_a.png → ...on/poly_new/with_observations/coeff_a.png b/...on/poly_new/with_observations/coeff_a.png → ...on/poly_new/with_observations/coeff_a.png
diff --git a/...on/poly_new/with_observations/coeff_b.png → ...on/poly_new/with_observations/coeff_b.png b/...on/poly_new/with_observations/coeff_b.png → ...on/poly_new/with_observations/coeff_b.png
diff --git a/...on/poly_new/with_observations/coeff_c.png → ...on/poly_new/with_observations/coeff_c.png b/...on/poly_new/with_observations/coeff_c.png → ...on/poly_new/with_observations/coeff_c.png
diff --git a/...n/poly_new/with_observations/coeff_priors → ...n/poly_new/with_observations/coeff_priors b/...n/poly_new/with_observations/coeff_priors → ...n/poly_new/with_observations/coeff_priors
diff --git a/...ations/generate_synthetic_observations.py → ...ations/generate_synthetic_observations.py b/...ations/generate_synthetic_observations.py → ...ations/generate_synthetic_observations.py
diff --git a/...n/poly_new/with_observations/observations → ...n/poly_new/with_observations/observations b/...n/poly_new/with_observations/observations → ...n/poly_new/with_observations/observations
diff --git a/...n/poly_new/with_observations/plot_obs.png → ...n/poly_new/with_observations/plot_obs.png b/...n/poly_new/with_observations/plot_obs.png → ...n/poly_new/with_observations/plot_obs.png
diff --git a/...n/poly_new/with_observations/poly_eval.py → ...n/poly_new/with_observations/poly_eval.py b/...n/poly_new/with_observations/poly_eval.py → ...n/poly_new/with_observations/poly_eval.py
diff --git a/...poly_new/with_observations/poly_final.ert → ...poly_new/with_observations/poly_final.ert b/...poly_new/with_observations/poly_final.ert → ...poly_new/with_observations/poly_final.ert
diff --git a/...y_new/with_observations/poly_obs_data.txt → ...y_new/with_observations/poly_obs_data.txt b/...y_new/with_observations/poly_obs_data.txt → ...y_new/with_observations/poly_obs_data.txt
diff --git a/...iguration/poly_new/with_results/POLY_EVAL → ...iguration/poly_new/with_results/POLY_EVAL b/...iguration/poly_new/with_results/POLY_EVAL → ...iguration/poly_new/with_results/POLY_EVAL
diff --git a/...ration/poly_new/with_results/coeff_priors → ...ration/poly_new/with_results/coeff_priors b/...ration/poly_new/with_results/coeff_priors → ...ration/poly_new/with_results/coeff_priors
diff --git a/...iguration/poly_new/with_results/plots.png → ...iguration/poly_new/with_results/plots.png b/...iguration/poly_new/with_results/plots.png → ...iguration/poly_new/with_results/plots.png
diff --git a/...figuration/poly_new/with_results/poly.ert → ...figuration/poly_new/with_results/poly.ert b/...figuration/poly_new/with_results/poly.ert → ...figuration/poly_new/with_results/poly.ert
diff --git a/...ration/poly_new/with_results/poly_eval.py → ...ration/poly_new/with_results/poly_eval.py b/...ration/poly_new/with_results/poly_eval.py → ...ration/poly_new/with_results/poly_eval.py
diff --git a/...ation/poly_new/with_results/poly_plot.png → ...ation/poly_new/with_results/poly_plot.png b/...ation/poly_new/with_results/poly_plot.png → ...ation/poly_new/with_results/poly_plot.png
diff --git a/...ion/poly_new/with_simple_script/POLY_EVAL → ...ion/poly_new/with_simple_script/POLY_EVAL b/...ion/poly_new/with_simple_script/POLY_EVAL → ...ion/poly_new/with_simple_script/POLY_EVAL
diff --git a/...ation/poly_new/with_simple_script/ert.png → ...ation/poly_new/with_simple_script/ert.png b/...ation/poly_new/with_simple_script/ert.png → ...ation/poly_new/with_simple_script/ert.png
diff --git a/...tion/poly_new/with_simple_script/poly.ert → ...tion/poly_new/with_simple_script/poly.ert b/...tion/poly_new/with_simple_script/poly.ert → ...tion/poly_new/with_simple_script/poly.ert
diff --git a/.../poly_new/with_simple_script/poly_eval.py → .../poly_new/with_simple_script/poly_eval.py b/.../poly_new/with_simple_script/poly_eval.py → .../poly_new/with_simple_script/poly_eval.py
diff --git a/...started/howto/adaptive_localization.ipynb → ...started/howto/adaptive_localization.ipynb b/...started/howto/adaptive_localization.ipynb → ...started/howto/adaptive_localization.ipynb
diff --git a/...ted/howto/ert_screenshot_adaptive_loc.png → ...ted/howto/ert_screenshot_adaptive_loc.png b/...ted/howto/ert_screenshot_adaptive_loc.png → ...ted/howto/ert_screenshot_adaptive_loc.png
diff --git a/docs/getting_started/howto/esmda_restart.rst → ...t/getting_started/howto/esmda_restart.rst b/docs/getting_started/howto/esmda_restart.rst → ...t/getting_started/howto/esmda_restart.rst
diff --git a/docs/getting_started/howto/plugin_system.rst → ...t/getting_started/howto/plugin_system.rst b/docs/getting_started/howto/plugin_system.rst → ...t/getting_started/howto/plugin_system.rst
@@ -128,7 +128,7 @@ The configuration file needed to use the ``installable_workflow_jobs`` hook must
 and specify its arguments.
 The built-in internal ``CSV_EXPORT`` workflow job is shown as an example:
 
-.. literalinclude:: ../../../src/ert/resources/workflows/jobs/internal-gui/config/CSV_EXPORT
+.. literalinclude:: ../../../../src/ert/resources/workflows/jobs/internal-gui/config/CSV_EXPORT
 
 Implement the hook specification as follows to register the workflow job ``CSV_EXPORT``:
 
@@ -149,7 +149,7 @@ Implement the hook specification as follows to register the workflow job ``CSV_E
 The second approach does not require creating a workflow job configuration file up-front,
 and allows adding documentation.
 
-.. literalinclude:: ../../../src/ert/plugins/hook_specifications/jobs.py
+.. literalinclude:: ../../../../src/ert/plugins/hook_specifications/jobs.py
    :pyobject: legacy_ertscript_workflow
 
 Minimal example:

diff --git a/.../getting_started/howto/restart-es-mda.png → .../getting_started/howto/restart-es-mda.png b/.../getting_started/howto/restart-es-mda.png → .../getting_started/howto/restart-es-mda.png
diff --git a/docs/getting_started/setup.rst → docs/ert/getting_started/setup.rst b/docs/getting_started/setup.rst → docs/ert/getting_started/setup.rst
diff --git a/...ting_parameters/fig/evaluate_ensemble.gif → ...ting_parameters/fig/evaluate_ensemble.gif b/...ting_parameters/fig/evaluate_ensemble.gif → ...ting_parameters/fig/evaluate_ensemble.gif
diff --git a/.../updating_parameters/fig/prior_params.png → .../updating_parameters/fig/prior_params.png b/.../updating_parameters/fig/prior_params.png → .../updating_parameters/fig/prior_params.png
diff --git a/...pdating_parameters/fig/prior_response.png → ...pdating_parameters/fig/prior_response.png b/...pdating_parameters/fig/prior_response.png → ...pdating_parameters/fig/prior_response.png
diff --git a/...pdating_parameters/fig/restart_es_mda.gif → ...pdating_parameters/fig/restart_es_mda.gif b/...pdating_parameters/fig/restart_es_mda.gif → ...pdating_parameters/fig/restart_es_mda.gif
diff --git a/.../updating_parameters/fig/sample_prior.gif → .../updating_parameters/fig/sample_prior.gif b/.../updating_parameters/fig/sample_prior.gif → .../updating_parameters/fig/sample_prior.gif
diff --git a/...updating_parameters/fig/update_report.png → ...updating_parameters/fig/update_report.png b/...updating_parameters/fig/update_report.png → ...updating_parameters/fig/update_report.png
diff --git a/...ing_started/updating_parameters/index.rst → ...ing_started/updating_parameters/index.rst b/...ing_started/updating_parameters/index.rst → ...ing_started/updating_parameters/index.rst
diff --git a/...updating_parameters/update_parameters.rst → ...updating_parameters/update_parameters.rst b/...updating_parameters/update_parameters.rst → ...updating_parameters/update_parameters.rst
diff --git a/...arted/webviz-ert/observation_analyzer.gif → ...arted/webviz-ert/observation_analyzer.gif b/...arted/webviz-ert/observation_analyzer.gif → ...arted/webviz-ert/observation_analyzer.gif
diff --git a/...arted/webviz-ert/parameter_comparison.gif → ...arted/webviz-ert/parameter_comparison.gif b/...arted/webviz-ert/parameter_comparison.gif → ...arted/webviz-ert/parameter_comparison.gif
diff --git a/...etting_started/webviz-ert/plot_viewer.gif → ...etting_started/webviz-ert/plot_viewer.gif b/...etting_started/webviz-ert/plot_viewer.gif → ...etting_started/webviz-ert/plot_viewer.gif
diff --git a/...arted/webviz-ert/response_correlation.gif → ...arted/webviz-ert/response_correlation.gif b/...arted/webviz-ert/response_correlation.gif → ...arted/webviz-ert/response_correlation.gif
diff --git a/docs/getting_started/webviz-ert/start_up.gif → ...t/getting_started/webviz-ert/start_up.gif b/docs/getting_started/webviz-ert/start_up.gif → ...t/getting_started/webviz-ert/start_up.gif
diff --git a/...getting_started/webviz-ert/webviz-ert.rst → ...getting_started/webviz-ert/webviz-ert.rst b/...getting_started/webviz-ert/webviz-ert.rst → ...getting_started/webviz-ert/webviz-ert.rst
diff --git a/docs/img/logo.png → docs/ert/img/logo.png b/docs/img/logo.png → docs/ert/img/logo.png
diff --git a/docs/index.rst → docs/ert/index.rst b/docs/index.rst → docs/ert/index.rst
@@ -1,4 +1,4 @@
-.. image:: ../src/ert/gui/resources/gui/img/ert_icon.svg
+.. image:: ../../src/ert/gui/resources/gui/img/ert_icon.svg
    :align: center
    :scale: 50%
 

diff --git a/docs/reference/configuration/data_types.rst → ...rt/reference/configuration/data_types.rst b/docs/reference/configuration/data_types.rst → ...rt/reference/configuration/data_types.rst
diff --git a/docs/reference/configuration/fig/README.md → ...ert/reference/configuration/fig/README.md b/docs/reference/configuration/fig/README.md → ...ert/reference/configuration/fig/README.md
diff --git a/docs/reference/configuration/fig/config.ert → ...rt/reference/configuration/fig/config.ert b/docs/reference/configuration/fig/config.ert → ...rt/reference/configuration/fig/config.ert
diff --git a/docs/reference/configuration/fig/const.png → ...ert/reference/configuration/fig/const.png b/docs/reference/configuration/fig/const.png → ...ert/reference/configuration/fig/const.png
diff --git a/.../configuration/fig/derrf_right_skewed.png → .../configuration/fig/derrf_right_skewed.png b/.../configuration/fig/derrf_right_skewed.png → .../configuration/fig/derrf_right_skewed.png
diff --git a/...iguration/fig/derrf_symmetric_uniform.png → ...iguration/fig/derrf_symmetric_uniform.png b/...iguration/fig/derrf_symmetric_uniform.png → ...iguration/fig/derrf_symmetric_uniform.png
diff --git a/docs/reference/configuration/fig/dunif.png → ...ert/reference/configuration/fig/dunif.png b/docs/reference/configuration/fig/dunif.png → ...ert/reference/configuration/fig/dunif.png
diff --git a/...ration/fig/errf_right_skewed_unimodal.png → ...ration/fig/errf_right_skewed_unimodal.png b/...ration/fig/errf_right_skewed_unimodal.png → ...ration/fig/errf_right_skewed_unimodal.png
diff --git a/...figuration/fig/errf_symmetric_uniform.png → ...figuration/fig/errf_symmetric_uniform.png b/...figuration/fig/errf_symmetric_uniform.png → ...figuration/fig/errf_symmetric_uniform.png
diff --git a/...reference/configuration/fig/lognormal.png → ...reference/configuration/fig/lognormal.png b/...reference/configuration/fig/lognormal.png → ...reference/configuration/fig/lognormal.png
diff --git a/...eference/configuration/fig/loguniform.png → ...eference/configuration/fig/loguniform.png b/...eference/configuration/fig/loguniform.png → ...eference/configuration/fig/loguniform.png
diff --git a/docs/reference/configuration/fig/normal.png → ...rt/reference/configuration/fig/normal.png b/docs/reference/configuration/fig/normal.png → ...rt/reference/configuration/fig/normal.png
diff --git a/docs/reference/configuration/fig/priors.txt → ...rt/reference/configuration/fig/priors.txt b/docs/reference/configuration/fig/priors.txt → ...rt/reference/configuration/fig/priors.txt
diff --git a/...eference/configuration/fig/triangular.png → ...eference/configuration/fig/triangular.png b/...eference/configuration/fig/triangular.png → ...eference/configuration/fig/triangular.png
diff --git a/...erence/configuration/fig/truncated_ok.png → ...erence/configuration/fig/truncated_ok.png b/...erence/configuration/fig/truncated_ok.png → ...erence/configuration/fig/truncated_ok.png
diff --git a/docs/reference/configuration/fig/uniform.png → ...t/reference/configuration/fig/uniform.png b/docs/reference/configuration/fig/uniform.png → ...t/reference/configuration/fig/uniform.png
diff --git a/...reference/configuration/forward_model.rst → ...reference/configuration/forward_model.rst b/...reference/configuration/forward_model.rst → ...reference/configuration/forward_model.rst
diff --git a/docs/reference/configuration/index.rst → docs/ert/reference/configuration/index.rst b/docs/reference/configuration/index.rst → docs/ert/reference/configuration/index.rst
diff --git a/docs/reference/configuration/keywords.rst → .../ert/reference/configuration/keywords.rst b/docs/reference/configuration/keywords.rst → .../ert/reference/configuration/keywords.rst
diff --git a/...reference/configuration/magic_strings.rst → ...reference/configuration/magic_strings.rst b/...reference/configuration/magic_strings.rst → ...reference/configuration/magic_strings.rst
diff --git a/.../reference/configuration/observations.rst → .../reference/configuration/observations.rst b/.../reference/configuration/observations.rst → .../reference/configuration/observations.rst
diff --git a/docs/reference/configuration/queue.rst → docs/ert/reference/configuration/queue.rst b/docs/reference/configuration/queue.rst → docs/ert/reference/configuration/queue.rst
diff --git a/docs/reference/configuration/site_wide.rst → ...ert/reference/configuration/site_wide.rst b/docs/reference/configuration/site_wide.rst → ...ert/reference/configuration/site_wide.rst
diff --git a/docs/reference/queue/QUEUE_TEST → docs/ert/reference/queue/QUEUE_TEST b/docs/reference/queue/QUEUE_TEST → docs/ert/reference/queue/QUEUE_TEST
diff --git a/docs/reference/queue/local_queue.ert → docs/ert/reference/queue/local_queue.ert b/docs/reference/queue/local_queue.ert → docs/ert/reference/queue/local_queue.ert
diff --git a/docs/reference/queue/lsf_queue.ert → docs/ert/reference/queue/lsf_queue.ert b/docs/reference/queue/lsf_queue.ert → docs/ert/reference/queue/lsf_queue.ert
diff --git a/...ference/queue/queue_test_forward_model.py → ...ference/queue/queue_test_forward_model.py b/...ference/queue/queue_test_forward_model.py → ...ference/queue/queue_test_forward_model.py
diff --git a/docs/reference/running_ert.rst → docs/ert/reference/running_ert.rst b/docs/reference/running_ert.rst → docs/ert/reference/running_ert.rst
diff --git a/...ference/workflows/added_workflow_jobs.rst → ...ference/workflows/added_workflow_jobs.rst b/...ference/workflows/added_workflow_jobs.rst → ...ference/workflows/added_workflow_jobs.rst
diff --git a/...eference/workflows/complete_workflows.rst → ...eference/workflows/complete_workflows.rst b/...eference/workflows/complete_workflows.rst → ...eference/workflows/complete_workflows.rst
diff --git a/.../reference/workflows/configuring_jobs.rst → .../reference/workflows/configuring_jobs.rst b/.../reference/workflows/configuring_jobs.rst → .../reference/workflows/configuring_jobs.rst
diff --git a/docs/reference/workflows/index.rst → docs/ert/reference/workflows/index.rst b/docs/reference/workflows/index.rst → docs/ert/reference/workflows/index.rst
diff --git a/docs/reference/workflows/workflows.rst → docs/ert/reference/workflows/workflows.rst b/docs/reference/workflows/workflows.rst → docs/ert/reference/workflows/workflows.rst
diff --git a/docs/static_html/Oscillator.html → docs/ert/static_html/Oscillator.html b/docs/static_html/Oscillator.html → docs/ert/static_html/Oscillator.html
@@ -26,7 +26,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="&lt;no title&gt;" href="../about/index.html" />
+    <link rel="next" title="&lt;no title&gt;" href="../ert/about/index.html" />
     <link rel="prev" title="Example: Polynomial function" href="Polynomial.html" />
 </head>
 
@@ -54,11 +54,11 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/setup.html">Setup</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/key_concepts.html">Key concepts (todo)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/configuration/poly_new/guide.html">Configuration Guide</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/launch.html">Launching ERT</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/gui/gui.html">Graphical User Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/setup.html">Setup</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/key_concepts.html">Key concepts (todo)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/configuration/poly_new/guide.html">Configuration Guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/launch.html">Launching ERT</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/gui/gui.html">Graphical User Interface</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Reference</span></p>
 <ul>
@@ -84,12 +84,12 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Developer Documentation</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/roadmap.html">Roadmap</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/dev-strategy.html">Development strategy</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/milestones.html">Milestones</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/concepts.html">Concepts</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/forward_model.html">The forward model</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/communication_protocol.html">Communication Protocol</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/roadmap.html">Roadmap</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/dev-strategy.html">Development strategy</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/milestones.html">Milestones</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/concepts.html">Concepts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/forward_model.html">The forward model</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/communication_protocol.html">Communication Protocol</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API Reference</span></p>
 <ul>
@@ -116,7 +116,7 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">About</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../about/release_notes.html">Release Notes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/about/release_notes.html">Release Notes</a></li>
 </ul>
 
         </div>
@@ -342,7 +342,7 @@ <h1>Example: Oscillator<a class="headerlink" href="#example-oscillator" title="P
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="Polynomial.html" class="btn btn-neutral float-left" title="Example: Polynomial function" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="../about/index.html" class="btn btn-neutral float-right" title="&lt;no title&gt;" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="../ert/about/index.html" class="btn btn-neutral float-right" title="&lt;no title&gt;" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

diff --git a/docs/static_html/Polynomial.html → docs/ert/static_html/Polynomial.html b/docs/static_html/Polynomial.html → docs/ert/static_html/Polynomial.html
@@ -54,11 +54,11 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/setup.html">Setup</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/key_concepts.html">Key concepts (todo)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/configuration/poly_new/guide.html">Configuration Guide</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/launch.html">Launching ERT</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../getting_started/gui/gui.html">Graphical User Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/setup.html">Setup</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/key_concepts.html">Key concepts (todo)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/configuration/poly_new/guide.html">Configuration Guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/launch.html">Launching ERT</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/getting_started/gui/gui.html">Graphical User Interface</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Reference</span></p>
 <ul>
@@ -84,12 +84,12 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Developer Documentation</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/roadmap.html">Roadmap</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/dev-strategy.html">Development strategy</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/milestones.html">Milestones</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/concepts.html">Concepts</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/forward_model.html">The forward model</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../developer_documentation/communication_protocol.html">Communication Protocol</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/roadmap.html">Roadmap</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/dev-strategy.html">Development strategy</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/milestones.html">Milestones</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/concepts.html">Concepts</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/forward_model.html">The forward model</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/developer_documentation/communication_protocol.html">Communication Protocol</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">API Reference</span></p>
 <ul>
@@ -116,7 +116,7 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">About</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../about/release_notes.html">Release Notes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../ert/about/release_notes.html">Release Notes</a></li>
 </ul>
 
         </div>

diff --git a/docs/static_html/README.txt → docs/ert/static_html/README.txt b/docs/static_html/README.txt → docs/ert/static_html/README.txt
diff --git a/docs/static_html/css/narratives.css → docs/ert/static_html/css/narratives.css b/docs/static_html/css/narratives.css → docs/ert/static_html/css/narratives.css
diff --git a/docs/theory/ensemble_based_methods.rst → docs/ert/theory/ensemble_based_methods.rst b/docs/theory/ensemble_based_methods.rst → docs/ert/theory/ensemble_based_methods.rst
diff --git a/docs/theory/images/Bayes_theorem.PNG → docs/ert/theory/images/Bayes_theorem.PNG b/docs/theory/images/Bayes_theorem.PNG → docs/ert/theory/images/Bayes_theorem.PNG
diff --git a/docs/theory/images/bpr.jpg → docs/ert/theory/images/bpr.jpg b/docs/theory/images/bpr.jpg → docs/ert/theory/images/bpr.jpg
diff --git a/docs/theory/images/posterior_path.png → docs/ert/theory/images/posterior_path.png b/docs/theory/images/posterior_path.png → docs/ert/theory/images/posterior_path.png