Merge branch 'dev' into fix_ndarray_qois

UCL-CCS · Dec 4, 2024 · 8b23495 · 8b23495
2 parents 58a213f + d607845
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diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -12,12 +12,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -24,18 +24,18 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           category: "/language:${{ matrix.language }}"
diff --git a/.github/workflows/coveralls.yml b/.github/workflows/coveralls.yml
@@ -15,21 +15,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.10']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py develop
-        python setup.py build_cannonsim
+        python -m pip install --editable .
+        cd tests/cannonsim/src; make; cd ../../..
         pip install pytest-cov
         pip install coveralls
     - name: Create coverage report

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -6,7 +6,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Copy Dockerfile
       run: |
         cp tutorials/kubernetes/Dockerfile .

diff --git a/.github/workflows/pdocs.yml b/.github/workflows/pdocs.yml
@@ -13,22 +13,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py develop
-        python setup.py build_cannonsim
+        python -m pip install --editable .
+        cd tests/cannonsim/src; make; cd ../../.. 
         pip install pdoc
     - name: Checkout
-      uses: actions/checkout@v2.3.1
+      uses: actions/checkout@v3
     - name: Build
       run: |
+        export PDOC_ALLOW_EXEC=1
         pdoc -d numpy -o ./pdocs easyvvuq
     - name: Publish generated content to GitHub Pages
       uses: JamesIves/[email protected]

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -15,29 +15,29 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py develop
-        python setup.py build_cannonsim
+        python -m pip install --editable .
+        cd tests/cannonsim/src; make; cd ../../..
         pip install pytest-cov
         pip install coveralls
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         pytest --benchmark-skip tests/
diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml
@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/.gitignore b/.gitignore
@@ -21,4 +21,3 @@ pep.sh
 *.csv
 env/
 .ipynb_checkpoints/
-fusion_pce.*/
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt
diff --git a/README.md b/README.md
@@ -34,6 +34,8 @@ Available analysis and sampling methods:
 
 * Polynomial Chaos Expansion
 * Stochastic Collocation
+* Dimension-adaptive Stochastic Collocation for high-dimensional inputs (incl notebook in `./tutorials` and [theoretical tutorial](https://www.researchgate.net/publication/359296270_Adaptive_sparse-grid_tutorial))
+* Simplex Stochastic Collocation for irregular outputs (incl notebook in `./tutorials` and [article](https://doi.org/10.1016/J.JCP.2015.12.034))
 * Monte Carlo Sensitivity Analysis
 * Markov-Chain Monte Carlo
 
@@ -87,16 +89,11 @@ git clone https://github.com/UCL-CCS/EasyVVUQ.git
 
 Note: As above, you need to be sure you are installing for Python 3 - if necessary replace `pip` with `pip3` and `python` with `python3` in the commands below.
 
-We are trying to keep dependencies at a minimum but a few are inevitable, to install them use:
+We are trying to keep dependencies at a minimum but a few are inevitable, to install these, install the EasyVVUQ library itself and build a test case use:
 ```
 cd EasyVVUQ/
 
-pip install --use-feature=2020-resolver -r requirements.txt
-```
-
-Then the library can be installed using:
-```buildoutcfg
-python setup.py install
+bash install_EasyVVUQ.sh
 ```
 
 ## API

diff --git a/dask-worker-space/global.lock b/dask-worker-space/global.lock
diff --git a/dask-worker-space/purge.lock b/dask-worker-space/purge.lock
diff --git a/docs/source/old/basic_tutorial.rst → docs/attic/doc/source/old/basic_tutorial.rst b/docs/source/old/basic_tutorial.rst → docs/attic/doc/source/old/basic_tutorial.rst
diff --git a/docs/source/old/cooling_coffee_cup.rst → ...tic/doc/source/old/cooling_coffee_cup.rst b/docs/source/old/cooling_coffee_cup.rst → ...tic/doc/source/old/cooling_coffee_cup.rst
diff --git a/docs/source/old/custom_encoder.rst → docs/attic/doc/source/old/custom_encoder.rst b/docs/source/old/custom_encoder.rst → docs/attic/doc/source/old/custom_encoder.rst
diff --git a/docs/source/old/dask_tutorial.rst → docs/attic/doc/source/old/dask_tutorial.rst b/docs/source/old/dask_tutorial.rst → docs/attic/doc/source/old/dask_tutorial.rst
diff --git a/docs/source/old/fusion_tutorial.rst → .../attic/doc/source/old/fusion_tutorial.rst b/docs/source/old/fusion_tutorial.rst → .../attic/doc/source/old/fusion_tutorial.rst
diff --git a/.../source/old/hier_sparse_grid_tutorial.rst → .../source/old/hier_sparse_grid_tutorial.rst b/.../source/old/hier_sparse_grid_tutorial.rst → .../source/old/hier_sparse_grid_tutorial.rst
diff --git a/docs/source/old/mcmc.rst → docs/attic/doc/source/old/mcmc.rst b/docs/source/old/mcmc.rst → docs/attic/doc/source/old/mcmc.rst
diff --git a/docs/source/old/multiencoder_tutorial.rst → .../doc/source/old/multiencoder_tutorial.rst b/docs/source/old/multiencoder_tutorial.rst → .../doc/source/old/multiencoder_tutorial.rst
diff --git a/docs/source/old/multisampler_tutorial.rst → .../doc/source/old/multisampler_tutorial.rst b/docs/source/old/multisampler_tutorial.rst → .../doc/source/old/multisampler_tutorial.rst
diff --git a/docs/source/old/relocate.rst → docs/attic/doc/source/old/relocate.rst b/docs/source/old/relocate.rst → docs/attic/doc/source/old/relocate.rst
diff --git a/docs/source/old/tutorials.rst → docs/attic/doc/source/old/tutorials.rst b/docs/source/old/tutorials.rst → docs/attic/doc/source/old/tutorials.rst
diff --git a/docs/source/old/validate_similarities.rst → .../doc/source/old/validate_similarities.rst b/docs/source/old/validate_similarities.rst → .../doc/source/old/validate_similarities.rst
diff --git a/docs/source/old/workflow_changes.rst → ...attic/doc/source/old/workflow_changes.rst b/docs/source/old/workflow_changes.rst → ...attic/doc/source/old/workflow_changes.rst
diff --git a/docs/source/concepts.rst b/docs/source/concepts.rst
@@ -62,18 +62,18 @@ central location where all information about your campaign is
 kept. The `Campaign` handles all validation and is transfers
 information between each stage of the workflow.
 
-The `Basic Tutorial <https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/basic_tutorial.ipynb>`_
+The `Basic Tutorial <https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/basic_tutorial.ipynb>`_ (link to repository) or `Basic Tutorial Binder <https://mybinder.org/v2/gh/UCL-CCS/EasyVVUQ/a6852d6c5ba36f15579e601d7a8d074505f31084?filepath=tutorials%2Fbasic_tutorial.ipynb>`_ (link to Binder to directly run the notebook) 
 gives a good hands-on introduction to defining parameters and 
 creating a campaign.
 
+
 Elements
 --------
 
 Within VECMA software components that can be reused in a wide range of
 application scenarios are known as ``Elements``.
 Within EasyVVUQ we provide five classes of ``Elements`` (:ref:`samplers`,
-:ref:`decoders`, :ref:`encoders`, and those providing :ref:`collation`,
-for the aggregation step, and :ref:`analysis` functionality) which we 
+:ref:`decoders`, :ref:`encoders`, and :ref:`analysis` functionality) which we 
 describe below.
 
 .. _samplers:
@@ -89,7 +89,7 @@ They deal with generic information in the sense that all parameters use the
 nomenclature and units provided by the user rather than anything specific to
 any application or workflow.
 
-Detailed information on the Sampler modules is available `here <https://easyvvuq.readthedocs.io/en/dev/_autodoc/easyvvuq.sampling.html>`_.
+Detailed information on the Sampler modules is available :doc:`here <_autodoc/easyvvuq.sampling>`.
 
 .. _encoders:
 
@@ -107,7 +107,7 @@ generic Encoder base class is picked up and may be used.
 This enables EasyVVUQ to be easily extended for new applications by 
 experienced users.
 
-Detailed information on the Encoder modules is available `here <https://easyvvuq.readthedocs.io/en/dev/_autodoc/easyvvuq.encoders.html>`_.
+Detailed information on the Encoder modules is available :doc:`here <_autodoc/easyvvuq.encoders>`.
 
 .. _decoders:
 
@@ -121,7 +121,7 @@ facilitate analysis of a wide range of applications.
 
 The `Encoder-Decoder tutorial <https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/encoder_decoder_tutorial.ipynb>`_
 provides a good introduction to using Encoders and Decoders within EasyVVUQ. Detailed information on the Decoder modules
-themselves is available `here <https://easyvvuq.readthedocs.io/en/dev/_autodoc/easyvvuq.decoders.html>`_.
+themselves is available :doc:`here <_autodoc/easyvvuq.decoders>`.
 
 .. _analysis:
 
@@ -133,5 +133,11 @@ on the simulation output across a range of runs.
 Different types of analysis (for example bootstrapping of multiple runs from
 varied initial conditions) are, or will be,  provided by EasyVVUQ.
 
-Detailed information on the Analysis modules is available `here <https://easyvvuq.readthedocs.io/en/dev/_autodoc/easyvvuq.analysis.html>`_
+Detailed information on the Analysis modules is available :doc:`here <_autodoc/easyvvuq.analysis>`.
+
+.. _execution:
+
+Execution
+---------
 
+Some more information on the use of QCG-Pilothob can be found :doc:`here <QCG-PilotJob-EasyVVUQ>`.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -12,12 +12,12 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../easyvvuq'))
+sys.path.insert(0, os.path.abspath('../..'))
 
 from sphinx.ext.apidoc import main as apidoc_main
 apidoc_main(["--force", "-o", "./_autodoc", "../../easyvvuq"])
 
-autodoc_mock_imports = ['dill']
+autodoc_mock_imports = ['dill', 'SALib', 'cerberus', 'chaospy', 'scipy', 'qcg', 'kubernetes', 'dask', 'sqlalchemy', 'numpoly', 'sklearn']
 
 # -- Project information -----------------------------------------------------
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -11,6 +11,8 @@ and uncertainty quantification (VVUQ) for a wide variety of simulations.
 It was conceived and developed within the EU funded `VECMA <http://www.vecma.eu/>`_ 
 (Verified Exascale Computing for Multiscale Applications) project.
 
+A good introduction can be found in the paper by D. Suleimenova *et al.*, “Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit”, J. Comput. Sci. 53, 101402 (2021), `DOI:10.1016/j.jocs.2021.101402 <https://doi.org/10.1016/j.jocs.2021.101402>`_.
+
 .. _goals:
 
 Goals
@@ -57,3 +59,4 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+* :doc:`_autodoc/modules`
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -6,7 +6,7 @@ EasyVVUQ installation
 Installation
 ------------
 
-.. note:: To use the library you will need Python 3.7+.
+.. note:: To use the library you will need Python 3.8+.
 
 Installation should be straight forward::
 
@@ -21,12 +21,11 @@ Github as follows::
 
     git clone https://github.com/UCL-CCS/EasyVVUQ.git
     cd EasyVVUQ
-    pip install -r requirements.txt
-    python setup.py install
+    bash install_EasyVVUQ.sh
 
-.. note:: The above assumes that your default `python` is Python 3. If 
-          that is not the case replace `python` with `python3` and `pip` 
-          with `pip3`.
+.. note:: The `install_EasyVVUQ.sh` script above assumes that your default `python`
+          is Python 3. If that is not the case replace `python` with `python3` and
+          `pip` with `pip3`.
 
 Depending on your setup you may not have permission to install packages.
 In that case, we recommend creating a virtual environment using  

diff --git a/easyvvuq/__init__.py b/easyvvuq/__init__.py
@@ -37,6 +37,5 @@
 """
 __license__ = "LGPL"
 
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,4 +21,3 @@ pep.sh @@
     *.csv
     env/
     .ipynb_checkpoints/
-    fusion_pce.*/