Merge branch 'dev' into code_scanning_alerts

.github/workflows/benchmark.yml

@@ -15,18 +15,15 @@ jobs:
         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 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py develop
-        pip install pytest-benchmark
+        python -m pip install .[tests]
     - name: Benchmark with pytest
       run: |
         pytest tests/test_db_benchmark.py --benchmark-json output.json

.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 }}"

.github/workflows/coveralls.yml

@@ -18,17 +18,16 @@ jobs:
         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 -m pip install --editable .
+        python -m pip install flake8
+        python -m pip install --editable .[tests]
         cd tests/cannonsim/src; make; cd ../../..
         pip install pytest-cov
         pip install coveralls

.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 .

.github/workflows/pdocs.yml

@@ -13,20 +13,20 @@ 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 setuptools
+        python -m pip install --editable .[docs]
+        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

.github/workflows/python-package.yml

@@ -18,17 +18,16 @@ jobs:
         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 -m pip install --editable .
+        python -m pip install flake8
+        python -m pip install --editable .[tests]
         cd tests/cannonsim/src; make; cd ../../..
         pip install pytest-cov
         pip install coveralls

.github/workflows/pythonpublish.yml

@@ -13,19 +13,22 @@ 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
-        pip install setuptools wheel twine
+        pip install build twine
+    - name: Build package
+      run: python -m build --sdist --wheel
+    - name: Check package
+      run: python -m twine check dist/*
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
         twine upload dist/*

.gitignore

@@ -21,3 +21,4 @@ pep.sh
 *.csv
 env/
 .ipynb_checkpoints/
+easyvvuq/_version.py

.readthedocs.yaml

@@ -27,9 +27,9 @@ sphinx:
 #    - 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
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

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>`.

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 -----------------------------------------------------
 

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`

easyvvuq/__init__.py

@@ -11,9 +11,14 @@
 from . import analysis
 from . import comparison
 
-# First make sure python version is 3.6+
-assert sys.version_info >= (3, 6), (f"Python version must be >= 3.6,"
-                                    f"found {sys.version_info}")
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("easyvvuq")
+except PackageNotFoundError:
+    from setuptools_scm import get_version  # type: ignore[import]
+
+    __version__ = get_version(root="..", relative_to=__file__)
 
 __copyright__ = """
 
@@ -36,6 +41,3 @@
 
 """
 __license__ = "LGPL"
-
-from . import _version
-__version__ = _version.get_versions()['version']