Use SPEC0 versions; drop support for python 3.8, 3.9

.flake8

@@ -12,6 +12,8 @@ ignore =
 exclude =
     hypnotoad/gui/hypnotoad_mainWindow.py,
     hypnotoad/gui/hypnotoad_preferences.py,
-    hypnotoad/gui/__init__.py
-    hypnotoad/__version__.py
-    versioneer.py
+    hypnotoad/gui/__init__.py,
+    hypnotoad/__version__.py,
+    versioneer.py,
+    build,
+    .venv

.github/workflows/pythonpackage.yml

@@ -18,23 +18,21 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: ['3.10', '3.11', '3.12']
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install .[tests]
     - name: Test with pytest
-      run: |
-        pip install pytest
-        pytest
+      run: pytest
 
 
   integrated-tests:
@@ -44,21 +42,21 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: ['3.10', '3.11', '3.12']
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         lfs: true
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install .[tests]
     - name: Integrated tests
       run: |
         pip install pytest xarray
@@ -75,13 +73,13 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         lfs: true
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -112,13 +110,13 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         lfs: true
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -153,15 +151,15 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install .
     - name: Lint with flake8
       run: |
         pip install flake8
@@ -175,11 +173,11 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pythonpublish.yml

@@ -15,21 +15,20 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install .[tests]
     - name: Test with pytest
       run: |
-        pip install pytest
         pytest
 
 
@@ -39,15 +38,15 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install .
     - name: Lint with flake8
       run: |
         pip install flake8
@@ -60,11 +59,11 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.x"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -82,9 +81,9 @@ jobs:
     needs: [pytest, flake8, black]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.gitignore

@@ -1,3 +1,128 @@
-.*.sw*
-*.nc
-__pycache__
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Other
+.DS_Store
+.idea/
+*.sw[po]

doc/conf.py

@@ -104,7 +104,7 @@ def create_options_rst(filename, title, options_factory, *, exclude=None):
             "OptionsFactory constructors in the hypnotoad source code. To change the "
             "formatting, edit the ``create_options_rst()`` function in ``conf.py``.\n\n"
         )
-        f.write(f"{title}\n{'='*len(title)}\n\n")
+        f.write(f"{title}\n{'=' * len(title)}\n\n")
         tt = options_factory.get_help_table(as_Texttable=True)
         tt.set_cols_width([62, 80, 20])
         f.write(".. table::\n   :widths: 20 75 5\n\n")

hypnotoad/core/equilibrium.py

@@ -4476,12 +4476,12 @@ def getSmoothMonotonicGridFunc(
         """
         if grad_lower is not None and (upper - lower) * grad_lower < 0:
             raise ValueError(
-                f"(upper-lower)={(upper-lower)} and grad_lower={grad_lower} have "
+                f"(upper-lower)={(upper - lower)} and grad_lower={grad_lower} have "
                 f"different signs: should both be increasing or both be decreasing."
             )
         if grad_upper is not None and (upper - lower) * grad_upper < 0:
             raise ValueError(
-                f"(upper-lower)={(upper-lower)} and grad_upper={grad_upper} have "
+                f"(upper-lower)={(upper - lower)} and grad_upper={grad_upper} have "
                 f"different signs: should both be increasing or both be decreasing."
             )
 

pyproject.toml

@@ -24,17 +24,17 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
     "boututils~=0.1.7",
     "dill~=0.3,!=0.3.5,!=0.3.5.1",
     "func_timeout~=4.3",
-    "matplotlib~=3.2",
+    "matplotlib~=3.7",
     "netCDF4~=1.5",
-    "numpy~=1.18",
+    "numpy~=1.24",
     "optionsfactory~=1.0.11",
     "PyYAML>=5.1",
-    "scipy~=1.6",
+    "scipy~=1.10",
     "Qt.py~=1.2",
 ]
 
@@ -50,6 +50,7 @@ docs = [
 ]
 tests = [
     "pytest >= 3.3.0",
+    "xarray >= 2022.9.0",
 ]
 
 [project.scripts]