chore: synchronize changes between main and dev (#34)

* release: Merge into main and create tag as v1.0.3 (sandialabs#72) * build: update to create a standalone executable (sandialabs#66) * ci: add executable to release workflow * ci: modify semantic-release pr requests to choose between release and chore * docs: update readme to show standalone version is available Signed-off-by: David Hart <[email protected]> * ci: create reusable testing workflow Signed-off-by: David Hart <[email protected]> --------- Signed-off-by: David Hart <[email protected]> * refactor(cpp): abstract out a BaseModel class for API clarity (sandialabs#71) * refactor: change the way logging is done, make output directories more explicit (not enforced yet) * refactor: modify logging output formats * refactor: move certain elements out of Model into a BaseModel * ci: Check output of a continuous release process * ci: modify semantic-release pr requests to choose between release and chore * refactor(version): move location of version number to avoid circular imports * refactor(test): fix test to match refactor of license and copyright text names * ci(test): Test using re-usable workflow for testing * ci(test): update test workflows to use same reusable workflow underneath * ci(test): create separate tests for each of the OSes * ci(testsuite): change titles of os-specific workflows for brevity * release: 1.0.3 Automatically generated by python-semantic-release --------- Signed-off-by: David Hart <[email protected]> Co-authored-by: David Hart <[email protected]> Co-authored-by: github-actions <[email protected]>
dbhart · Oct 29, 2024 · 83f85ed · 83f85ed
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diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -9,6 +9,11 @@ name: "CodeQL Advanced"
 on:
   push:
     branches: [ "main" ]
+    paths:
+      - '.github/workflows/codeql.yml'
+      - '**/*.py'
+      - '**/*.cpp'
+      - '**/*.hpp'
   pull_request:
     branches: [ "main" ]
   schedule:
@@ -61,11 +66,11 @@ jobs:
           uploads.github.com:443
 
     - name: Checkout repository
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@f779452ac5af1c261dce0346a8f964149f49322b # v3.26.13
+      uses: github/codeql-action/init@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
       with:
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
@@ -89,6 +94,6 @@ jobs:
         python3 setup.py build_ext
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@f779452ac5af1c261dce0346a8f964149f49322b # v3.26.13
+      uses: github/codeql-action/analyze@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml
@@ -22,7 +22,7 @@ jobs:
       matrix:
         version: ["3.9", "3.10", "3.11", "3.12"]
         os: [windows-latest, macOS-13, macOS-latest, ubuntu-latest]
-    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@951ebbd277e18b0a5b88a4e67535e262bc59f979
+    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@7952e59342a8c8d1c8ad833121049bac58277167
     with:
       version: ${{ matrix.version }}
       os: ${{ matrix.os }}

diff --git a/.github/workflows/continuous-release.yml b/.github/workflows/continuous-release.yml
@@ -3,9 +3,7 @@
 name: Check release
 
 on:
-  push:
   pull_request:
-  workflow_dispatch:
 
 permissions:
   contents: read
@@ -17,7 +15,6 @@ jobs:
 
     permissions:
       id-token: write
-      contents: write
       pull-requests: write
 
     steps:
@@ -27,7 +24,7 @@ jobs:
         egress-policy: audit
 
     - name: Setup | Checkout Repository at workflow sha
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       with:
         fetch-depth: 0
         ref: ${{ github.sha }}
@@ -39,10 +36,11 @@ jobs:
     - name: Action | Semantic Version
       id: check
       # Adjust tag with desired version if applicable.
-      uses: python-semantic-release/python-semantic-release@657118d28ae4a74d8a387bedf5db2bb7bac0cb33 # v9.11.1
+      uses: python-semantic-release/python-semantic-release@c1bcfdbb994243ac7cf419365d5894d6bfb2950e # v9.12.0
       with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
         build: false
-        changelog: false
+        changelog: true
         commit: false
         push: false
         tag: false
@@ -51,9 +49,9 @@ jobs:
     - name: Action | Comment on PR with new version
       run: |
         echo "## The results of python-semantic-release are below." | tee -a "$GITHUB_STEP_SUMMARY"
-        echo "* released: ${{ github.check.outputs.released }}" | tee -a "$GITHUB_STEP_SUMMARY"
-        echo "* is_prerelease: ${{ github.check.outputs.is_prerelease }}" | tee -a "$GITHUB_STEP_SUMMARY"
-        echo "* version: ${{ github.check.outputs.version }}" | tee -a "$GITHUB_STEP_SUMMARY"
-        echo "* tag: ${{ github.check.outputs.tag }}" | tee -a "$GITHUB_STEP_SUMMARY"
-        # echo "The release number should be ${{ github.check.outputs.version }}" >> release.md
-        # gh pr comment ${{ github.event.pull_request.number }} --body "This PR should include a release: ${{ steps.check.outputs.released }}\n"
+        echo "* released: ${{ steps.check.outputs.released }}" | tee -a "$GITHUB_STEP_SUMMARY"
+        echo "* is_prerelease: ${{ steps.check.outputs.is_prerelease }}" | tee -a "$GITHUB_STEP_SUMMARY"
+        echo "* version: ${{ steps.check.outputs.version }}" | tee -a "$GITHUB_STEP_SUMMARY"
+        echo "* tag: ${{ steps.check.outputs.tag }}" | tee -a "$GITHUB_STEP_SUMMARY"
+        # echo "The release number should be ${{ steps.check.outputs.version }}" >> release.md
+        gh pr comment ${{ github.event.pull_request.number }} --body "This PR should include a release: ${{ steps.check.outputs.released }}\n"
diff --git a/.github/workflows/continuous-testing.yml b/.github/workflows/continuous-testing.yml
@@ -14,7 +14,7 @@ permissions:
 
 jobs:
   quick-test:
-    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@951ebbd277e18b0a5b88a4e67535e262bc59f979
+    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@7952e59342a8c8d1c8ad833121049bac58277167
     with:
       version: "3.12"
       os: ubuntu-latest

diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -22,6 +22,6 @@ jobs:
           egress-policy: audit
 
       - name: 'Checkout Repository'
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@5a2ce3f5b92ee19cbb1541a4984c76d921601d7c # v4.3.4
+        uses: actions/dependency-review-action@4081bf99e2866ebe428fc0477b69eb4fcda7220a # v4.4.0
diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
@@ -36,7 +36,7 @@ jobs:
         with:
           egress-policy: audit
 
-      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           fetch-depth: 0
 
@@ -47,7 +47,7 @@ jobs:
           git branch
           git remote -v
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
           python-version: '3.12'
 

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -42,10 +42,10 @@ jobs:
             uploader.codecov.io:443
 
       - name: Check out the commit
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
           python-version: ${{ inputs.version }}
 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -27,12 +27,12 @@ jobs:
 
     steps:
       - name: Setup | Install python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
           python-version: '3.12'
 
       - name: Setup | Checkout Code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Setup | Install Dependencies
         run: |
@@ -77,7 +77,7 @@ jobs:
           egress-policy: audit
 
       - name: Setup | Checkout Code
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Action | Build Wheels
         uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.0
@@ -99,7 +99,7 @@ jobs:
         egress-policy: audit
 
     - name: Setup | Checkout Code
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       with:
         fetch-depth: 0  # Optional, use if you use setuptools_scm
         submodules: true  # Optional, use if you have submodules

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -50,7 +50,7 @@ jobs:
             www.bestpractices.dev:443
 
       - name: "Checkout code"
-        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           persist-credentials: false
 
@@ -86,6 +86,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@f779452ac5af1c261dce0346a8f964149f49322b # v3.26.13
+        uses: github/codeql-action/upload-sarif@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/semantic-release.yml b/.github/workflows/semantic-release.yml
@@ -26,7 +26,7 @@ jobs:
         egress-policy: audit
 
     - name: Setup | Checkout Repository at workflow sha
-      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       with:
         fetch-depth: 0
         ref: ${{ github.sha }}

diff --git a/.github/workflows/test-linux.yml b/.github/workflows/test-linux.yml
@@ -1,4 +1,4 @@
-name: ubuntu // CPython 3.9 — 3.12
+name: '🐧-🐍3.9--3.12'
 
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         version: ["3.9", "3.10", "3.11", "3.12"]
-    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@951ebbd277e18b0a5b88a4e67535e262bc59f979
+    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@7952e59342a8c8d1c8ad833121049bac58277167
     with:
       version: ${{ matrix.version }}
       os: ubuntu-latest

diff --git a/.github/workflows/test-macOS_arm.yml b/.github/workflows/test-macOS_arm.yml
@@ -1,4 +1,4 @@
-name: macOS-14 // CPython 3.9 — 3.12
+name: '🍎-🐍3.9--3.12'
 
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         version: ["3.9", "3.10", "3.11", "3.12"]
-    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@951ebbd277e18b0a5b88a4e67535e262bc59f979
+    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@7952e59342a8c8d1c8ad833121049bac58277167
     with:
       version: ${{ matrix.version }}
       os: macOS-latest

diff --git a/.github/workflows/test-macOS_intel.yml b/.github/workflows/test-macOS_intel.yml
@@ -1,4 +1,4 @@
-name: macOS-13 // CPython 3.9 — 3.12
+name: '🍏-🐍3.9--3.12'
 
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         version: ["3.9", "3.10", "3.11", "3.12"]
-    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@951ebbd277e18b0a5b88a4e67535e262bc59f979
+    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@7952e59342a8c8d1c8ad833121049bac58277167
     with:
       version: ${{ matrix.version }}
       os: macOS-13

diff --git a/.github/workflows/test-windows.yml b/.github/workflows/test-windows.yml
@@ -1,4 +1,4 @@
-name: windows // CPython 3.9 — 3.12
+name: '🏢-🐍3.9--3.12'
 
 on:
   push:
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         version: ["3.9", "3.10", "3.11", "3.12"]
-    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@951ebbd277e18b0a5b88a4e67535e262bc59f979
+    uses: sandialabs/sansmic/.github/workflows/pytest-workflow.yml@7952e59342a8c8d1c8ad833121049bac58277167
     with:
       version: ${{ matrix.version }}
       os: windows-latest

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,19 +1,54 @@
 # CHANGELOG
 
 
-## v1.0.2 (2024-10-17)
+## v1.0.3 (2024-10-23)
 
 ### Refactoring
 
-* refactor: logging capabilities and configuration (#58)
+* refactor(cpp): abstract out a BaseModel class for API clarity (#71)
 
-* refactor: convert to click from argparse
+* refactor: change the way logging is done, make output directories more explicit (not enforced yet)
+
+* refactor: modify logging output formats
+
+* refactor: move certain elements out of Model into a BaseModel
+
+* ci: Check output of a continuous release process
+
+* ci: modify semantic-release pr requests to choose between release and chore
+
+* refactor(version): move location of version number to avoid circular imports
+
+* refactor(test): fix test to match refactor of license and copyright text names
+
+* ci(test): Test using re-usable workflow for testing
+
+* ci(test): update test workflows to use same reusable workflow underneath
+
+* ci(test): create separate tests for each of the OSes
+
+* ci(testsuite): change titles of os-specific workflows for brevity ([`926fa56`](https://github.com/sandialabs/sansmic/commit/926fa56840545cc103ffd9671f4557b1e0a19d98))
+
+### Unknown
+
+* Merge branch 'main' into staging
+
+Signed-off-by: David Hart <[email protected]> ([`9416c06`](https://github.com/sandialabs/sansmic/commit/9416c0659d0e12cc463abc669ef8f6a1db07acbc))
 
-* refactor: change the way logging is done, make output directories more explicit (not enforced yet) ([`4feff68`](https://github.com/sandialabs/sansmic/commit/4feff688fdf1773331dd9864f3fe13a6bf17395c))
+
+## v1.0.2 (2024-10-17)
 
 
 ## v1.0.1 (2024-10-12)
 
+### Bug Fixes
+
+* fix: change workflows for proper execution ([`c4ea2f4`](https://github.com/sandialabs/sansmic/commit/c4ea2f4464cbcbdf8d16a94e392fca404348e48e))
+
+* fix: semantic release workflow syntax errors ([`9f7d215`](https://github.com/sandialabs/sansmic/commit/9f7d215439feb7348068bcae8748452b3737b2d5))
+
+* fix: test semantic release and conventional commits ([`54423b1`](https://github.com/sandialabs/sansmic/commit/54423b194057e493def5456b290a3c4ec2f62098))
+
 ### Documentation
 
 * docs: build script failed to check out ([`a39a03f`](https://github.com/sandialabs/sansmic/commit/a39a03faa171c1fa36b955c68db1ebfc17ad7813))
@@ -60,14 +95,6 @@ Update the README on github.
 
 Signed-off-by: David Hart <[email protected]> ([`11a5215`](https://github.com/sandialabs/sansmic/commit/11a521545d994ea8777ed654fd7c1f40e287e683))
 
-### Fixes
-
-* fix: change workflows for proper execution ([`c4ea2f4`](https://github.com/sandialabs/sansmic/commit/c4ea2f4464cbcbdf8d16a94e392fca404348e48e))
-
-* fix: semantic release workflow syntax errors ([`9f7d215`](https://github.com/sandialabs/sansmic/commit/9f7d215439feb7348068bcae8748452b3737b2d5))
-
-* fix: test semantic release and conventional commits ([`54423b1`](https://github.com/sandialabs/sansmic/commit/54423b194057e493def5456b290a3c4ec2f62098))
-
 ### Refactoring
 
 * refactor: Convert command-line interface to click instead of argparse (#54)

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,5 +1,5 @@
 Sphinx==8.1.3
-pydata-sphinx-theme==0.15.4
+pydata-sphinx-theme==0.16.0
 sphinx_design==0.6.1
 sphinxcontrib-bibtex==2.6.3
 breathe==4.35.0

diff --git a/pyproject.toml b/pyproject.toml
@@ -3,7 +3,7 @@ name = "sansmic"
 description = "Sandia solution mining modeling software"
 readme = "README.md"
 requires-python = ">=3.9"
-version = "1.0.2"
+version = "1.0.3"
 authors = [
     { name = "National Technology & Engineering Solutions of Sandia, LLC (NTESS)" },
     { name = "SANSMIC Authors (see AUTHORS.md)" },

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -6,7 +6,7 @@ pytest-cov==5.0.0
 black==24.10.0
 nbmake==1.5.4
 matplotlib==3.9.2
-python-semantic-release==9.11.0
+python-semantic-release==9.12.0
 h5py==3.12.1
 openpyxl==3.1.5
 tabulate==0.9.0

diff --git a/requirements.txt b/requirements.txt
@@ -1,5 +1,5 @@
 numpy==2.1.2
 pandas==2.2.3
 pybind11==2.13.6
-setuptools==75.1.0
+setuptools==75.2.0
 click==8.1.7
diff --git a/setup.py b/setup.py
@@ -7,7 +7,7 @@
 from setuptools import find_packages, setup
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 
-__version__ = "1.0.2"
+__version__ = "1.0.3"
 
 here = path.abspath(path.dirname(__file__))
 

diff --git a/src/python/sansmic/_version.py b/src/python/sansmic/_version.py
@@ -6,7 +6,7 @@
 #
 # SPDX-License-Identifier: BSD-3-Clause.
 
-__version__ = "1.0.2"
+__version__ = "1.0.3"
 
 copyright = f"""Copyright (c) 2024 National Technology and Engineering Solutions of Sandia,
 LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S.