Foqus cloud

.addheader.yml

@@ -1,5 +1,5 @@
 # Usage:
-# addheader -c addheader.yml
+# addheader -c .addheader.yml -P ""
 root: .
 text: header_text.txt
 patterns:

.github/actions/pylint/action.yml

@@ -15,6 +15,6 @@ runs:
       shell: bash
       run: |
         echo '::group::Output of pylint'
-        pylint --rcfile=.pylint/pylintrc --disable=W,C,R,I foqus_lib/
+        pylint --rcfile=.pylint/pylintrc --disable=all --enable=E --enable=wrong-import-order foqus_lib/
         echo '::endgroup::'
 

.github/actions/setup-foqus/action.yml

@@ -14,14 +14,14 @@ runs:
       # IMPORTANT this requires the Conda env setup to be run before this action
     - name: Update pip and other packaging tools using Conda
       # -l: login shell, needed when using Conda run:
-      shell: bash -l {0}
+      shell: bash -l -eo pipefail {0}
       run: |
         echo '::group::Output of "conda install" command'
-        conda install --yes --quiet -c conda-forge pip pywin32
+        conda install --yes --quiet -c conda-forge pip pywin32=306
         conda list
         echo '::endgroup::'
     - name: Install FOQUS and dependencies using pip
-      shell: bash -l {0}
+      shell: bash -l -eo pipefail {0}
       run: |
         echo '::group::Output of "pip install" command'
         ${{ inputs.pip-install-command }} ${{ inputs.pip-install-target}}
@@ -33,7 +33,7 @@ runs:
         pip show ccsi-foqus PyQt5
         echo '::endgroup::'
     - name: Install psuade-lite using Conda
-      shell: bash -l {0}
+      shell: bash -l -eo pipefail {0}
       run: |
         echo '::group::Output of "conda install psuade-lite"'
         conda install --yes --quiet -c CCSI-Toolset -c conda-forge psuade-lite=1.9

.github/workflows/checks.yml

@@ -21,21 +21,22 @@ on:
 defaults:
   run:
     # the -l flag is needed for the Conda environment to be activated properly
-    shell: bash -l {0}
+    shell: bash -l -eo pipefail {0}
 
 env:
   FOQUS_CONDA_ENV_NAME_DEV: ccsi-foqus-dev
   PYTEST_BASETEMP: .pytest
+  DEFAULT_PYTHON_VERSION: '3.10'
 
 jobs:
   code-formatting:
     name: Code formatting (Black)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: ${{ env.DEFAULT_PYTHON_VERSION }}
       - name: Install Black
         # unlike the other jobs, we don't need to install FOQUS and/or all the dev dependencies,
         # but we still want to specify the Black version to use in requirements-dev.txt for local development
@@ -47,74 +48,117 @@ jobs:
       - name: Run Black to verify that the committed code is formatted
         run: |
           black --check .
+  spell-check:
+    name: Check Spelling
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+      - name: Run Spell Checker
+        uses: crate-ci/typos@master
+        with: 
+          config: .typos.toml
   pytest:
     name: pytest (py${{ matrix.python-version }}/${{ matrix.os }})
-    needs: [code-formatting]
     runs-on: ${{ matrix.os-version }}
     strategy:
       fail-fast: false
       matrix:
         python-version:
-          - '3.7'
           - '3.8'
           - '3.9'
-          # - '3.10'
+          - '3.10'
+          - '3.11'
+          - '3.12'
         os:
           - linux
           - win64
+          - macos-x86_64
           - macos
         include:
+          - os: macos-x86_64
+            os-version: macos-13
           - os: macos
-            os-version: macos-10.15
+            os-version: macos-14
           - os: linux
             os-version: ubuntu-20.04
           - os: win64
             os-version: windows-2019
-          - python-version: "3.8"  # avoid uploading coverage for full matrix
+          - python-version: '3.10'  # avoid uploading coverage for full matrix
             use_coverage: true
-          - python-version: "3.8"  # this is to avoid installing optional dependencies in all environments
-            optional-dependencies: tensorflow sympy torch scikit-learn
+          - python-version: '3.10'  # install ML AI dependencies with coverage run
+            optional-dependencies: -r requirements-mlai.txt
+          - python-version: '3.11'  # install ML AI dependencies with a newer Python version
+            optional-dependencies: -r requirements-mlai.txt
     env:
       # uncomment this to debug Qt initialization errors
       # QT_DEBUG_PLUGINS: '1'
       MPLBACKEND: AGG
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.FOQUS_CONDA_ENV_NAME_DEV }}
           python-version: ${{ matrix.python-version }}
+          miniconda-version: latest
       - name: Set up FOQUS
         uses: ./.github/actions/setup-foqus
         with:
           pip-install-target: -r requirements-dev.txt ${{ matrix.optional-dependencies }}
-      - name: Set common pytest flags
-        run:
-          echo 'PYTEST_ADDOPTS=--pyargs foqus_lib --verbose --color=yes --basetemp "${{ env.PYTEST_BASETEMP }}"' >> $GITHUB_ENV
       - name: Set up GUI test environment (Linux)
         if: contains(matrix.os, 'linux')
         run: |
           echo "QT_QPA_PLATFORM=minimal" >> $GITHUB_ENV
-      - name: Run pytest (default options)
-        if: "! matrix.use_coverage"
-        run: |
-          pytest foqus_lib/
-      - name: Run pytest (coverage)
+      - name: Set common pytest flags
+        run:
+          echo 'PYTEST_ADDOPTS=--pyargs foqus_lib --maxfail=3 --verbose --color=yes --basetemp "${{ env.PYTEST_BASETEMP }}"' >> $GITHUB_ENV
+      - name: Add pytest coverage flags
         if: matrix.use_coverage
+        run:
+          echo "PYTEST_ADDOPTS=$PYTEST_ADDOPTS --cov=./ --cov-report=xml --cov-report=term" >> $GITHUB_ENV
+      - name: Run pytest
         run: |
-          pytest foqus_lib/ --cov=./ --cov-report=xml --cov-report=term
+          pytest foqus_lib/
       - name: Upload pytest artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         if: always()
         with:
           # TODO decide if we need a separate upload for each Python version
           name: pytest-dir-${{ matrix.os }}-py${{ matrix.python-version }}
           path: ${{ env.PYTEST_BASETEMP }}
           retention-days: 7
+      - name: Upload coverage report as job artifact
+        if: always() && matrix.use_coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report-${{ matrix.os }}
+          path: coverage.xml
+          if-no-files-found: error
+
+  upload-coverage:
+    name: Upload coverage report (Codecov)
+    needs: [pytest]
+    runs-on: ubuntu-latest
+    steps:
+      # the checkout step is needed to have access to codecov.yml
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: coverage-report-*
       - name: Upload coverage report to Codecov
-        if: matrix.use_coverage
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          verbose: true
+          # NOTE: secrets are not available for pull_request workflows
+          # However, as of 2024-02-10, Codecov is still allowing tokenless upload from PRs
+          # but does require token for other workflows e.g. merge to `main`
+          # see https://github.com/codecov/codecov-action/issues/1274#issuecomment-1934437359
+          token: ${{ secrets.CODECOV_TOKEN }}
+          # pinning version after v0.7.0 broke tokenless upload
+          # see codecov/codecov-action#1487
+          version: v0.7.2
 
   pylint:
     name: pylint (py${{ matrix.python-version }})
@@ -123,14 +167,15 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - '3.7'
           - '3.8'
           - '3.9'
-          # - '3.10'
+          - '3.10'
+          - '3.11'
+          - '3.12'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.FOQUS_CONDA_ENV_NAME_DEV }}
           python-version: ${{ matrix.python-version }}
@@ -140,15 +185,15 @@ jobs:
           pip-install-target: -r requirements-dev.txt
       - name: Run pylint
         run: |
-          pylint --rcfile=.pylint/pylintrc --disable=W,C,R,I foqus_lib/
+          pylint --rcfile=.pylint/pylintrc --disable=all --enable=E --enable=wrong-import-order foqus_lib/
 
   docs:
     name: Build docs
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: ${{ env.FOQUS_CONDA_ENV_NAME_DEV }}
           python-version: ${{ matrix.python-version }}

.github/workflows/nightlies.yml

@@ -23,9 +23,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - '3.7'
           - '3.8'
-          # - '3.9'
+          - '3.9'
         os:
           - linux
           - win64
@@ -37,7 +36,7 @@ jobs:
           - '3.9.0'
         include:
           - os: macos
-            os-version: macos-10.15
+            os-version: macos-12
           - os: linux
             os-version: ubuntu-20.04
           - os: win64
@@ -59,7 +58,7 @@ jobs:
           pip_install_target: ${{ matrix.pip-install-target }}
         run: |
           echo '::group::Output of conda create/activate/install'
-          conda create --name ccsi-foqus --quiet --yes -c conda-forge python="$py_ver" pywin32
+          conda create --name ccsi-foqus --quiet --yes -c conda-forge python="$py_ver" pywin32=306
           conda activate ccsi-foqus
           conda install --yes -c CCSI-Toolset -c conda-forge psuade-lite=1.9
           echo '::endgroup::'

.gitignore

@@ -24,6 +24,7 @@ eggs/
 *.lib
 *.suo
 *.zip
+Pipfile
 
 # OSX
 *.DS_Store

.pylint/foqus_transform.py

@@ -1,5 +1,5 @@
-###############################################################################
-# FOQUS Copyright (c) 2012 - 2021, by the software owners: Oak Ridge Institute
+#################################################################################
+# FOQUS Copyright (c) 2012 - 2024, by the software owners: Oak Ridge Institute
 # for Science and Education (ORISE), TRIAD National Security, LLC., Lawrence
 # Livermore National Security, LLC., The Regents of the University of
 # California, through Lawrence Berkeley National Laboratory, Battelle Memorial
@@ -11,8 +11,7 @@
 # Please see the file LICENSE.md for full copyright and license information,
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
-#
-###############################################################################
+#################################################################################
 import astroid
 
 

.readthedocs.yaml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# the build.os and build.tools section is mandatory
+build:
+  os: ubuntu-20.04  # for consistency, matches the one used for CI
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
     fail_on_warning: true

.typos.toml

@@ -0,0 +1,46 @@
+[files]
+extend-exclude = [
+    "*.smp",
+    "*.ui",
+    "*.html",
+    "*.css",
+    "*.js",
+    "*.svg",
+    "*.foqus",
+    "*.bkp",
+    "*.acmf",
+    "*.for",
+    "*.his",
+    "*.def",
+    "*.ads",
+    "*.pt",
+    "*.pkl",
+    "*.R",
+    "*.json",
+]
+
+[default.extend-words]
+# Ignore IDAES
+IDAES = "IDAES"
+FO = "FO"  # TODO: probably an abbreviation?
+sur = "sur"  # abbreviation for 'surrogate'
+nd = "nd"  # used as a variable name in sdoeAnalysisDialog
+astroid = "astroid"  # Python package name
+yhat = "yhat"  # used as a variable name in SurrogateParser
+iy = "iy"  # used as a variable name in SurrogateParser
+# proper nouns
+Gess = "Gess"
+# false positives
+strat = "strat"  # abbreviation of "strategy" used by Hypothesis
+arange = "arange"  # from numpy.arange function
+
+[default.extend-identifiers]
+# false positives
+strngComps = "strngComps"  # strng = strongly (connected)
+# true positives that are part of the API
+userInterupt = "userInterupt"
+maxTimeInterupt = "maxTimeInterupt"
+PyCodeInterupt = "PyCodeInterupt"
+simin_nam = "simin_nam"
+simout_nam = "simout_nam"
+displayAvailablityWarning = "displayAvailablityWarning"

LICENSE.md

@@ -1,13 +1,13 @@
 Copyright and License
 =====================
 
-Copyright (c) 2012 - 2023
+Copyright (c) 2012 - 2024
 
 Copyright Notice
 ----------------
 
 Foqus was produced under the DOE Carbon Capture Simulation Initiative (CCSI), and is copyright (c)
-2012 - 2023 by the software owners: Oak Ridge Institute for Science and Education (ORISE), TRIAD
+2012 - 2024 by the software owners: Oak Ridge Institute for Science and Education (ORISE), TRIAD
 National Security, LLC., Lawrence Livermore National Security, LLC., The Regents of the University
 of California, through Lawrence Berkeley National Laboratory, Battelle Memorial Institute, Pacific
 Northwest Division through Pacific Northwest National Laboratory, Carnegie Mellon University, West
@@ -23,7 +23,7 @@ publicly and display publicly, and to permit other to do so.
 License Agreement
 -----------------
 
-Foqus Copyright (c) 2012 - 2023, by the software owners: Oak Ridge Institute for Science and
+Foqus Copyright (c) 2012 - 2024, by the software owners: Oak Ridge Institute for Science and
 Education (ORISE), TRIAD National Security, LLC., Lawrence Livermore National Security, LLC., The
 Regents of the University of California, through Lawrence Berkeley National Laboratory, Battelle
 Memorial Institute, Pacific Northwest Division through Pacific Northwest National Laboratory,