Merge pull request #437 from EnergySystemsModellingLab/develop

PR for v1.2.0rc1 release

Author: alexdewar

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.0
+current_version = 1.2.0rc1
 commit = True
 tag = True
 

.codespell_ignore.txt

@@ -0,0 +1,3 @@
+datas
+raison
+fom

.editorconfig

@@ -1,12 +1,21 @@
-# EditorConfig is awesome: http://EditorConfig.org
-
-# top-most EditorConfig file
 root = true
 
-[*.py]
-indent_style = space
-indent_size = 4
-tab_width = 4
+[*]
 charset = utf-8
-max_line_length=88
 insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+max_line_length = 88
+
+[*.md]
+indent_size = 2
+
+[*.yaml]
+indent_size = 2
+
+[*.yml]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

.flake8

@@ -8,24 +8,26 @@ assignees: ''
 ---
 
 ## Describe the bug
-A clear and concise description of what the bug is, including error messages.
 
+A clear and concise description of what the bug is, including error messages.
 
 ## To Reproduce
-Steps to reproduce the behavior. Attache any input file that might be required.
 
+Steps to reproduce the behavior. Attach any input file that might be required.
 
 ## Expected behavior
+
 A clear and concise description of what you expected to happen.
 
 ## Screenshots
+
 If applicable, add screenshots to help explain your problem.
 
 ## Context
 
 Please, complete the following to better understand the system you are using to run MUSE.
 
-- Operative system (eg. Windows 10):
+- Operating system (eg. Windows 10):
 - MUSE version (eg. 1.0.1):
 - Installation method (eg. pipx, pip, development mode):
 - Python version (you can get this running `python --version`):

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,14 +7,18 @@ assignees: ''
 
 ---
 
-## Is your feature request related to a problem? Please describe.
+## Is your feature request related to a problem? Please describe
+
 A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
 
 ## Describe the solution you'd like
+
 A clear and concise description of what you want to happen.
 
 ## Describe alternatives you've considered
+
 A clear and concise description of any alternative solutions or features you've considered.
 
 ## Additional context
+
 Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -11,17 +11,15 @@ assignees: ''
 
 (Please, describe in detail what you want to achieve and what parts of the documentation you have checked to do so)
 
-
 ## What you have tried
 
 (If you have already taken some steps, please, describe here what you have tried. Provide any input files you are trying to use).
 
-
 ## Context
 
 Please, complete the following to better understand the system you are using to run MUSE.
 
-- Operative system (eg. Windows 10):
+- Operating system (eg. Windows 10):
 - MUSE version (eg. 1.0.1):
 - Installation method (eg. pipx, pip, development mode):
 - Python version (you can get this running `python --version`):

.github/ISSUE_TEMPLATE/usage-support.md

@@ -9,7 +9,7 @@ Fixes # (issue)
 ## Type of change
 
 Please add a line in the relevant section of
-[CHANGELOG.md](https://github.com/SGIModel/StarMuse/blob/development/CHANGELOG.md) to
+[CHANGELOG.md](https://github.com/EnergySystemsModellingLab/MUSE_OS/blob/development/CHANGELOG.md) to
 document the change (include PR #) - note reverse order of PR #s.
 
 - [ ] New feature (non-breaking change which adds functionality)

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,4 +14,4 @@ jobs:
         uses: ruzickap/action-my-broken-link-checker@v2
         with:
           url: https://muse-os.readthedocs.io/en/latest/
-          cmd_params: '--timeout=20 --buffer-size=8192 --max-connections=3 --color=always --skip-tls-verification --header="User-Agent:curl/7.54.0"'  # muffet parameters
+          cmd_params: '--timeout=20 --buffer-size=8192 --max-connections=3 --color=always --skip-tls-verification --header="User-Agent:curl/7.54.0"' # muffet parameters

.github/workflows/broken-link-check.yml

@@ -1,183 +1,76 @@
-name: QA, tests and publishing
+name: Tests
 
 on:
-    pull_request:
-        types: [opened, synchronize, reopened]
-    push:
-      branches: [main, develop]
-      tags:
-        - '*'
-jobs:
-  # Checks the style using the pre-commit hooks
-  qa:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: pre-commit/action@v3.0.0
+  pull_request:
+    types: [opened, synchronize, reopened]
+  push:
+    branches: [main, develop]
+  workflow_call:
 
-  # Only then, normal testing proceeds
+jobs:
   unit-tests:
-    needs: qa
     runs-on: ${{ matrix.os }}
 
-
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9"]
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip==22.1.2
-        pip install -U setuptools==62.6.0 wheel xlrd==1.2.0
-        pip install -e .[all]
-
-    # The unit tests, with coverage under linux
-    - name: Unit tests (linux)
-      if: (runner.os == 'Linux')
-      run: |
-        pip install pytest-cov
-        pytest -m "not regression and not notebook" --junitxml=junit/pytest.xml \
-            --cov=muse \
-            --cov-branch \
-            --cov-report=xml
-
-    - name: Upload coverage to Codecov
-      if: success() && (runner.os == 'Linux' && matrix.python-version == 3.9)
-      uses: codecov/codecov-action@v3
-
-    - name: Unit tests (not linux)
-      if: (runner.os != 'Linux')
-      run: pytest -m "not regression and not notebook"
-
-  regression-tests:
-    needs: qa
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9"]
+        # Test with the earliest and the latest python versions supported
+        python-version: ["3.9", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: pip
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip==22.1.2
-          pip install -U setuptools==62.6.0 wheel xlrd==1.2.0
-          pip install -e .[all]
-
-      # The regression tests (with non coverage)
-      - name: Regression tests
-        run: pytest tests/test_fullsim_regression.py
-
-  # If all tests pass, we try to build a wheel
-  build-wheel:
-    # needs: [regression-tests, unit-tests]
-    name: Build source distribution
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
+        run: pip install -e .[all]
 
-      - name: Build sdist
+      # The unit tests, with coverage under linux
+      - name: Unit tests (linux)
+        if: (runner.os == 'Linux')
         run: |
-          python -m pip install --upgrade build
-          python -m build
-
-      - uses: actions/upload-artifact@v3
+          pip install pytest-cov
+          pytest -m "not regression and not notebook" --junitxml=junit/pytest.xml \
+              --cov=muse \
+              --cov-branch \
+              --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        if: success() && (runner.os == 'Linux' && matrix.python-version == 3.9)
+        uses: codecov/codecov-action@v4
         with:
-          path: dist/MUSE*
-
-  # And if we are pushing a tag, then we try to publish it
-  publish-TestPyPI:
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-    needs: build-wheel
-    name: Publish MUSE to TestPyPI
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
 
-    steps:
-
-      - name: Download sdist artifact
-        uses: actions/download-artifact@v3
-        with:
-          name: artifact
-          path: dist
-
-      - name: Display structure of downloaded files
-        run: ls -R dist
-
-      - name: Publish package distributions to TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository-url: https://test.pypi.org/legacy/
-          skip-existing: true
-
-  publish-PyPI:
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-    needs: publish-TestPyPI
-    name: Publish MUSE to PyPI
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-
-    steps:
+      - name: Unit tests (not linux)
+        if: (runner.os != 'Linux')
+        run: pytest -m "not regression and not notebook"
 
-      - name: Download sdist artifact
-        uses: actions/download-artifact@v3
-        with:
-          name: artifact
-          path: dist
-
-      - name: Display structure of downloaded files
-        run: ls -R dist
-
-      - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-
-  build-standalone:
-    needs: publish-PyPI
-    name: Build standalone executables
+  regression-tests:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: [ windows-latest ]
-        python-version: [ "3.9" ]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        # Test with the earliest and the latest python versions supported
+        python-version: ["3.9", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        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 pyinstaller
-          python -m pip install -e .[dev,gui]
-
-      - name: Build directory-based standalone
-        run: pyinstaller muse_dir.spec --distpath standalone
+        run: pip install -e .[all]
 
-      - uses: actions/upload-artifact@v3
-        with:
-          path: standalone/MUSE*
-          name: MUSE
+      # The regression tests (with non coverage)
+      - name: Regression tests
+        run: pytest tests/test_fullsim_regression.py