Modernise, test and fix the CME codebase

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      # Only the display-free modules are installed and tested. The GUI extra
+      # needs wxPython, Mayavi and a display, and the tabs additionally import
+      # the `modules` simulation-I/O package, which is not distributed with this
+      # repository -- see README.md.
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev]"
+
+      - name: Test
+        run: python -m pytest tests/ -v
+
+      - name: Doctests
+        run: |
+          python -m pytest --doctest-modules \
+            src/cme/naming.py \
+            src/cme/cosmology.py \
+            src/cme/config.py \
+            src/cme/writers/music.py \
+            src/cme/writers/gadget.py \
+            src/cme/writers/submit.py \
+            src/cme/science/candidates.py
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install ruff
+        run: python -m pip install ruff
+
+      - name: Lint
+        run: ruff check .
+
+      # Scoped to the display-free modules and the tests. The TraitsUI tabs are
+      # not yet formatted: reflowing those nested view declarations would bury
+      # the behavioural changes in this branch under whitespace.
+      - name: Format check
+        run: |
+          ruff format --check \
+            src/cme/naming.py \
+            src/cme/cosmology.py \
+            src/cme/shell.py \
+            src/cme/config.py \
+            src/cme/writers/ \
+            src/cme/science/ \
+            tests/
+
+  syntax:
+    # The GUI modules cannot be imported without a display or the `modules`
+    # package, but they must at least parse on every supported version.
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Compile all modules
+        run: python -m compileall -q src/

.gitignore

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+# Byte-compiled / cache
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Packaging / distribution
+build/
+dist/
+*.egg-info/
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Test and lint caches
+.pytest_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+
+# Editor / OS cruft
+.DS_Store
+*.swp
+.idea/
+.vscode/
+
+# Generated simulation artifacts.
+# The Gadget tab writes its driver script into the working directory
+# (see cme/ui/gadget.py), and MUSIC leaves noise and scratch files behind.
+rungadget.sh
+wnoise_*
+temp_*
+ics.[0-9]*
+ExpansionList*
+
+# Generated configuration. These are outputs of the Initial Conditions and
+# Gadget tabs, reproducible from the GUI state, and belong with the run
+# directory rather than in version control.
+*.conf
+param.txt
+param_sub.txt
+Config.sh
+Config_sub.sh
+runscript
+runscript_sub
+
+# Run outputs
+outputs/
+OUTPUT
+ERROR
+OUTPUTsub
+ERRORsub
+*.o[0-9]*
+*.e[0-9]*

LICENSE

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+MIT License
+
+Copyright (c) 2014-2026 Brendan Griffen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.