CD for pypi: environment added

.flake8

@@ -14,7 +14,7 @@ exclude =
     dist,
     .conda,
     tests/autogenerated_*,
-    docs/source/_autogenerated
+    docs/source/api
     .venv,
     venv
 

.github/workflows/docs.yml

@@ -9,7 +9,7 @@ permissions:
   contents: write
 
 jobs:
-  build-and-deploy:
+  build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -41,8 +41,24 @@ jobs:
           rm ./source/*.rst
           make html
           touch ./build/html/.nojekyll
-      - name: Deploy to GitHub Pages
+          mkdir -p ./build/html/_autogenerated
-        uses: JamesIves/github-pages-deploy-action@v4
+          cp ./build/html/api/* ./build/html/_autogenerated/
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          branch: gh-pages
+          path: docs/build/html
-          folder: docs/build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/publish.yml

@@ -10,6 +10,10 @@ jobs:
     name: Build and publish
     runs-on: ubuntu-latest
 
+    environment:
+      name: pypi
+      url: https://pypi.org/project/${{ github.event.repository.name }}/
+
     steps:
       - uses: actions/checkout@v3
 

.gitignore

@@ -9,7 +9,7 @@ __pycache__
 .pytest_cache
 tests/autogenerated_*.py
 docs/build/
-docs/source/_autogenerated/
+docs/source/api/
 venv/
 .venv/
 thermo_data/combined_data.yaml

docs/source/generate_class_list.py

@@ -27,7 +27,7 @@ def write_classes(f: TextIOWrapper, patterns: list[str], module_name: str, title
     write_dochtree(f, title, classes)
 
     for cls in classes:
-        with open(f'docs/source/_autogenerated/{cls}.md', 'w') as f2:
+        with open(f'docs/source/api/{cls}.md', 'w') as f2:
             f2.write(f'# {module_name}.{cls}\n')
             f2.write('```{eval-rst}\n')
             f2.write(f'.. autoclass:: {module_name}.{cls}\n')
@@ -43,7 +43,7 @@ def write_functions(f: TextIOWrapper, patterns: list[str], module_name: str, tit
     module = importlib.import_module(module_name)
 
     functions = [
-        name for name, obj in inspect.getmembers(module, inspect.isfunction)
+        name for name, _ in inspect.getmembers(module, inspect.isfunction)
         if (any(fnmatch.fnmatch(name, pat) for pat in patterns if pat not in exclude))
     ]
 
@@ -54,7 +54,7 @@ def write_functions(f: TextIOWrapper, patterns: list[str], module_name: str, tit
 
     for func in functions:
         if not func.startswith('_'):
-            with open(f'docs/source/_autogenerated/{func}.md', 'w') as f2:
+            with open(f'docs/source/api/{func}.md', 'w') as f2:
                 f2.write(f'# {module_name}.{func}\n')
                 f2.write('```{eval-rst}\n')
                 f2.write(f'.. autofunction:: {module_name}.{func}\n')
@@ -74,9 +74,9 @@ def write_dochtree(f: TextIOWrapper, title: str, items: list[str]):
 
 if __name__ == "__main__":
     # Ensure the output directory exists
-    os.makedirs('docs/source/_autogenerated', exist_ok=True)
+    os.makedirs('docs/source/api', exist_ok=True)
 
-    with open('docs/source/_autogenerated/index.md', 'w') as f:
+    with open('docs/source/api/index.md', 'w') as f:
         f.write('# Classes and functions\n\n')
 
         write_classes(f, ['*'], 'gaspype', title='Classes')

docs/source/index.md

@@ -1,8 +1,9 @@
 ```{toctree}
 :maxdepth: 1
 :hidden:
-_autogenerated/index
+api/index
-_autogenerated/examples
+api/examples
+repo
 ```
 
 ```{include} ../../README.md

docs/source/render_examples.py

@@ -51,7 +51,7 @@ def render_examples(filter: str, example_file: str):
         f.write('## Download Jupyter Notebooks\n\n')
         for path, name in zip(files, names):
             if name.lower() != 'readme':
-                run_rendering(path, 'docs/source/_autogenerated')
+                run_rendering(path, 'docs/source/api')
                 notebook = name + '.ipynb'
                 f.write(f'- [{notebook}]({notebook})\n\n')
 
@@ -63,4 +63,4 @@ def render_examples(filter: str, example_file: str):
 
 
 if __name__ == "__main__":
-    render_examples('examples/*.md', 'docs/source/_autogenerated/examples.md')
+    render_examples('examples/*.md', 'docs/source/api/examples.md')

docs/source/repo.md

@@ -0,0 +1,3 @@
+# Code repository
+
+Code repository is on GitHub: [github.com/DLR-Institute-of-Future-Fuels/gaspype](https://github.com/DLR-Institute-of-Future-Fuels/gaspype).

examples/README.md

@@ -11,11 +11,11 @@ The conversion is done like the following automated by the
 [docs/source/render_examples.py](../docs/source/render_examples.py) script:
 ``` bash
 # Converting markdown with code sections to Jupyter Notebook and run it:
-notedown examples/soec_methane.md --to notebook --output docs/source/_autogenerated/soec_methane.ipynb --run
+notedown examples/soec_methane.md --to notebook --output docs/source/api/soec_methane.ipynb --run
 
 # Converting the Jupyter Notebook to Markdown and a folder with image
-# files placed in docs/source/_autogenerated/:
+# files placed in docs/source/api/:
-jupyter nbconvert --to markdown docs/source/_autogenerated/soec_methane.ipynb --output soec_methane.md
+jupyter nbconvert --to markdown docs/source/api/soec_methane.ipynb --output soec_methane.md
 ```
 
 A new example Markdown file can be created from a Jupyter Notebook running

examples/soec_syngas.md

@@ -1,7 +1,7 @@
 # SOEC Co-Electrolysis
 
-This example shows a 1D isothermal SOEC (Solid oxide electrolyzer cell) model.
+This example shows a 1D isothermal SOEC (Solid oxide electrolyzer cell) model for
-Converting CO2 and H2 into syngas.
+converting carbon dioxide and steam into syngas.
 
 The operating parameters chosen here are not necessarily realistic. For example,
 a utilization of 0.95 causes issues with the formation of solid carbon.
@@ -66,13 +66,12 @@ ax.plot(conversion, np.stack([o2_fuel_side, o2_air_side], axis=1), '-')
 ax.legend(['o2_fuel_side', 'o2_air_side'])
 ```
 
-
 The high oxygen partial pressure at the inlet is in reality lower.
 The assumption that gas inter-diffusion in the flow direction is slower
 than the gas velocity does not hold at this very high gradient. However
 often the oxygen partial pressure is still to high to prevent oxidation of the
 cell/electrode. This can be effectively prevented by recycling small amounts of
-the output gas.
+the hydrogen riche output gas.
 
 Calculation of the local nernst potential between fuel and air side:
 ```python

examples/sofc_methane.md

@@ -116,3 +116,26 @@ ax.set_ylabel("Current density / A/cm²")
 ax.plot(z_position, node_current, '-')
 ```
 
+Based on the cell current and voltage the energy balance can be calculated.
+In the following the electric cell output power (often referred to as "DC power")
+and lower heating value (LHV) are calculated. The numbers here are per cell area for
+being cell and stack size independent. The quotient of both is often referred to as
+LHV based DC efficiency.
+
+```python
+dc_power = cell_voltage * terminal_current  # W/cm²
+print(f"DC power: {dc_power:.2f} W/cm²")
+
+lhv = gp.fluid({'CH4': 1, 'H2O': -2, 'CO2': -1}).get_H(25 + 273.15)  # J/mol (LHV of methane)
+
+# LHV based chemical input power:
+lhv_power = lhv * terminal_current / (2 * z_O2 * F)  # W/cm² (two O2 per CH4 for full oxidation)
+efficiency = dc_power / lhv_power
+print(f"LHV based DC efficiency: {efficiency*100:.1f} %")
+
+# Or by shortening the therms:
+lhv_voltage = lhv / (2 * z_O2 * F)  # V
+print(f"LHV voltage: {lhv_voltage:.2f} V")
+efficiency = cell_voltage / lhv_voltage  # LHV based DC efficiency
+print(f"LHV based DC efficiency: {efficiency*100:.1f} %")
+```

tests/md_to_code.py

@@ -96,6 +96,7 @@ def segments_to_test(segments: Iterable[markdown_segment], script_language: str
                 ret_block_flag = lines[-1] if (not re.match(r'^[^(]*=', lines[-1]) and
                                                not lines[-1].startswith('import ') and
                                                not lines[-1].startswith('from ') and
+                                               not lines[-1].startswith('print(') and
                                                not lines[-1].startswith(' ')) else None
                 # print('Last line: ', ret_block_flag, '-----------', lines[-1])