Various enhancements (#13)

- fix LCOT calculation (multiply OPEX with distance) - add AC-DC loss to AEP calculation - add distance to shore calculations - fix redefined-outer-name in notebooks - use subprocess.run instead of os.system - update plots - update leaflet map zoom - generate PNG images for paper - fix some docstings - update docs/requirements.txt - add GitHub workflow for building Sphinx Docs to host on GitHub Pages - add amsmath, dollarmath to docs config - update installation instructions - update nbconvert command (use ClearOutputPreprocessor) and regenerate scripts - update .pylintrc - disable pointless-statement, line-too-long - update .gitignore - update matplotlibrc - update pyproject.toml - update .vscode/tasks.json
wind-to-hydrogen-toolkit · Aug 29, 2024 · fc0a7f4 · fc0a7f4
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diff --git a/.github/workflows/sphinx.yml b/.github/workflows/sphinx.yml
@@ -0,0 +1,47 @@
+# https://www.sphinx-doc.org/en/master/tutorial/deploying.html
+name: 'Sphinx: Render docs'
+
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - 'docs/**'
+      - 'h2ss/**'
+      - 'tests/**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    # permissions:
+    #   contents: write
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@v4
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+        cache-dependency-path: docs/requirements.txt
+    - name: Install setup dependencies
+      run: python -m pip install --upgrade pip setuptools wheel
+    - name: Install docs dependencies
+      run: python -m pip install -r docs/requirements.txt
+    - name: Make HTML
+      run: cd docs && make html
+    # - name: Build HTML
+    #   uses: ammaraskar/sphinx-action@master
+    #   with:
+    #     pre-build-command: 'python -m pip install --upgrade pip setuptools wheel'
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-docs
+        path: docs/_build/html/
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/_build/html
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,7 @@
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -27,8 +31,8 @@ share/python-wheels/
 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.
+#  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
 
@@ -92,18 +96,18 @@ ipython_config.py
 #   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
+#Pipfile.lock
 
 # poetry
 #   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-# poetry.lock
+#poetry.lock
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-# pdm.lock
+#pdm.lock
 #   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
 #   in version control.
 #   https://pdm.fming.dev/#use-with-ide
@@ -153,11 +157,23 @@ dmypy.json
 cython_debug/
 
 # PyCharm
-#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#   and can be added to the global gitignore or merged into this file. For a more nuclear
-#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
-# .idea/
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
 
 data/*
 temp/

diff --git a/.pylintrc b/.pylintrc
@@ -1,3 +1,4 @@
 [MASTER]
 init-hook="import sys; sys.path.append('.')"
 ignore-paths=data/
+disable=pointless-statement, line-too-long
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
@@ -6,7 +6,7 @@
         {
             "label": "convert-notebooks",
             "type": "shell",
-            "command": "source .venv/bin/activate && ./convert-notebooks.sh",
+            "command": "source .venv/bin/activate && jupyter nbconvert --to script --ClearOutputPreprocessor.enabled=True docs/notebooks/*.ipynb && rm -rf scripts/* && mv docs/notebooks/*.py scripts",
             "problemMatcher": [],
             "group": {
                 "kind": "build"
@@ -60,7 +60,7 @@
             }
         },
         {
-            "label": "pylint-scripts",
+            "label": "pylint-functions",
             "type": "shell",
             "command": "source .venv/bin/activate && pylint h2ss/*.py tests/*.py",
             "problemMatcher": [],

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,30 @@
 # Changelog
 
+## [2024.08.0](https://github.com/wind-to-hydrogen-toolkit/hydrogen-salt-storage/tree/2024.08.0)
+
+[Various enhancements](https://github.com/wind-to-hydrogen-toolkit/hydrogen-salt-storage/pull/13) by @nmstreethran.
+[**Full Changelog**](https://github.com/wind-to-hydrogen-toolkit/hydrogen-salt-storage/compare/2024.05.0...2024.08.0).
+
+- fix LCOT calculation (multiply OPEX with distance)
+- add AC-DC loss to AEP calculation
+- add distance to shore calculations
+- fix redefined-outer-name in notebooks
+- use subprocess.run instead of os.system
+- update plots
+- update leaflet map zoom
+- generate PNG images for paper
+- fix some docstings
+- update docs/requirements.txt
+- add GitHub workflow for building Sphinx Docs to host on GitHub Pages
+- add amsmath, dollarmath to docs config
+- update installation instructions
+- update nbconvert command (use ClearOutputPreprocessor) and regenerate scripts
+- update .pylintrc - disable pointless-statement, line-too-long
+- update .gitignore
+- update matplotlibrc
+- update pyproject.toml
+- update .vscode/tasks.json
+
 ## [2024.05.0](https://github.com/wind-to-hydrogen-toolkit/hydrogen-salt-storage/tree/2024.05.0)
 
 [Various enhancements](https://github.com/wind-to-hydrogen-toolkit/hydrogen-salt-storage/pull/12) by @nmstreethran.

diff --git a/CITATION.cff b/CITATION.cff
@@ -35,4 +35,4 @@ keywords:
   - hydrogen economy in Ireland
   - geological storage
 license: Apache-2.0
-version: 2024.05.0
+version: 2024.08.0
diff --git a/README.md b/README.md
@@ -24,7 +24,7 @@ Create a virtual environment and install all requirements:
 ```sh
 python -m venv .venv
 source .venv/bin/activate
-python -m pip install --upgrade pip
+python -m pip install --upgrade pip setuptools wheel
 python -m pip install -r requirements.txt
 ```
 
@@ -39,7 +39,7 @@ python -m pytest --cov
 ```sh
 python -m venv .venv
 source .venv/bin/activate
-python -m pip install --upgrade pip
+python -m pip install --upgrade pip setuptools wheel
 python -m pip install https://github.com/wind-to-hydrogen-toolkit/hydrogen-salt-storage/archive/refs/heads/main.zip
 ```
 

diff --git a/convert-notebooks.sh b/convert-notebooks.sh
diff --git a/docs/conf.py b/docs/conf.py
@@ -33,6 +33,12 @@
 
 viewcode_line_numbers = True
 
+# https://myst-parser.readthedocs.io/en/latest/syntax/optional.html
+myst_enable_extensions = [
+    "amsmath",
+    "dollarmath",
+]
+
 # templates_path = ["_templates"]
 
 exclude_patterns = [
@@ -69,10 +75,6 @@
         }
     ],
     "navbar_align": "right",
-    "secondary_sidebar_items": {
-        "datasets": [],
-        "map": [],
-    },
 }
 
 html_sidebars = {

diff --git a/docs/index.rst b/docs/index.rst
@@ -46,7 +46,7 @@ Create a virtual environment and install all requirements:
 
    python -m venv .venv
    source .venv/bin/activate
-   python -m pip install --upgrade pip
+   python -m pip install --upgrade pip setuptools wheel
    python -m pip install -r requirements.txt
 
 Run tests:

diff --git a/docs/map.ipynb b/docs/map.ipynb
diff --git a/docs/notebooks/bathymetry.ipynb b/docs/notebooks/bathymetry.ipynb
@@ -42,9 +42,7 @@
    "outputs": [],
    "source": [
     "plt.rcParams[\"xtick.major.size\"] = 0\n",
-    "plt.rcParams[\"ytick.major.size\"] = 0\n",
-    "plt.rcParams[\"xtick.minor.size\"] = 0\n",
-    "plt.rcParams[\"ytick.minor.size\"] = 0"
+    "plt.rcParams[\"ytick.major.size\"] = 0"
    ]
   },
   {
@@ -2851,7 +2849,7 @@
    "outputs": [],
    "source": [
     "bath = rd.bathymetry_layer(\n",
-    "    dat_extent=extent,\n",
+    "    dat_extent=extent.buffer(3000),\n",
     "    bathymetry_path=os.path.join(\"data\", \"bathymetry\"),\n",
     ")"
    ]
@@ -2876,7 +2874,7 @@
    ],
    "source": [
     "plt.figure(figsize=(10, 7))\n",
-    "ax = plt.axes(projection=ccrs.epsg(rd.CRS))\n",
+    "ax2 = plt.axes(projection=ccrs.epsg(rd.CRS))\n",
     "bath[\"elevation\"].plot.contourf(cmap=\"mako\", levels=10, robust=True)\n",
     "CS = bath[\"elevation\"].plot.contour(\n",
     "    # colors=\"darkslategrey\",\n",
@@ -2888,9 +2886,9 @@
     "    robust=True,\n",
     ")\n",
     "plt.clabel(CS, inline=True)\n",
-    "cx.add_basemap(ax, source=cx.providers.CartoDB.VoyagerNoLabels, crs=rd.CRS)\n",
-    "cx.add_basemap(ax, source=cx.providers.CartoDB.VoyagerOnlyLabels, crs=rd.CRS)\n",
-    "ax.gridlines(\n",
+    "cx.add_basemap(ax2, source=cx.providers.CartoDB.VoyagerNoLabels, crs=rd.CRS)\n",
+    "cx.add_basemap(ax2, source=cx.providers.CartoDB.VoyagerOnlyLabels, crs=rd.CRS)\n",
+    "ax2.gridlines(\n",
     "    draw_labels={\"bottom\": \"x\", \"left\": \"y\"},\n",
     "    alpha=0.25,\n",
     "    color=\"darkslategrey\",\n",

diff --git a/docs/notebooks/frequent_shipping_routes.ipynb b/docs/notebooks/frequent_shipping_routes.ipynb
@@ -55,9 +55,7 @@
    "outputs": [],
    "source": [
     "plt.rcParams[\"xtick.major.size\"] = 0\n",
-    "plt.rcParams[\"ytick.major.size\"] = 0\n",
-    "plt.rcParams[\"xtick.minor.size\"] = 0\n",
-    "plt.rcParams[\"ytick.minor.size\"] = 0"
+    "plt.rcParams[\"ytick.major.size\"] = 0"
    ]
   },
   {

diff --git a/docs/notebooks/ireland_boundary.ipynb b/docs/notebooks/ireland_boundary.ipynb
@@ -33,9 +33,7 @@
    "outputs": [],
    "source": [
     "plt.rcParams[\"xtick.major.size\"] = 0\n",
-    "plt.rcParams[\"ytick.major.size\"] = 0\n",
-    "plt.rcParams[\"xtick.minor.size\"] = 0\n",
-    "plt.rcParams[\"ytick.minor.size\"] = 0"
+    "plt.rcParams[\"ytick.major.size\"] = 0"
    ]
   },
   {

diff --git a/docs/notebooks/kish_basin_caverns.ipynb b/docs/notebooks/kish_basin_caverns.ipynb
@@ -41,9 +41,7 @@
    "outputs": [],
    "source": [
     "plt.rcParams[\"xtick.major.size\"] = 0\n",
-    "plt.rcParams[\"ytick.major.size\"] = 0\n",
-    "plt.rcParams[\"xtick.minor.size\"] = 0\n",
-    "plt.rcParams[\"ytick.minor.size\"] = 0"
+    "plt.rcParams[\"ytick.major.size\"] = 0"
    ]
   },
   {

diff --git a/docs/notebooks/kish_basin_caverns_capacity.ipynb b/docs/notebooks/kish_basin_caverns_capacity.ipynb
@@ -1538,7 +1538,7 @@
     "        alpha=0.25,\n",
     "        color=\"darkslategrey\",\n",
     "        xlabel_style={\"fontsize\": fontsize},\n",
-    "        ylabel_style={\"fontsize\": fontsize, \"rotation\": 90},\n",
+    "        ylabel_style={\"fontsize\": fontsize, \"rotation\": 89.9},\n",
     "        xformatter=LongitudeFormatter(auto_hide=False, dms=True),\n",
     "        yformatter=LatitudeFormatter(auto_hide=False, dms=True),\n",
     "    )\n",
@@ -1562,8 +1562,8 @@
     "\n",
     "    plt.tight_layout()\n",
     "    # plt.savefig(\n",
-    "    #     os.path.join(\"graphics\", \"fig_caverns_capacity.jpg\"),\n",
-    "    #     format=\"jpg\",\n",
+    "    #     os.path.join(\"graphics\", \"Figure_8.png\"),\n",
+    "    #     format=\"png\",\n",
     "    #     dpi=600,\n",
     "    # )\n",
     "    plt.show()"
@@ -1610,7 +1610,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0rc1"
+   "version": "3.11.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/kish_basin_caverns_height.ipynb b/docs/notebooks/kish_basin_caverns_height.ipynb
@@ -1815,7 +1815,7 @@
     "        alpha=0.25,\n",
     "        color=\"darkslategrey\",\n",
     "        xlabel_style={\"fontsize\": fontsize},\n",
-    "        ylabel_style={\"fontsize\": fontsize, \"rotation\": 90},\n",
+    "        ylabel_style={\"fontsize\": fontsize, \"rotation\": 89.9},\n",
     "        xformatter=LongitudeFormatter(auto_hide=False, dms=True),\n",
     "        yformatter=LatitudeFormatter(auto_hide=False, dms=True),\n",
     "    )\n",
@@ -1838,8 +1838,8 @@
     "\n",
     "    plt.tight_layout()\n",
     "    # plt.savefig(\n",
-    "    #     os.path.join(\"graphics\", \"fig_caverns_capacity_height.jpg\"),\n",
-    "    #     format=\"jpg\",\n",
+    "    #     os.path.join(\"graphics\", \"Figure_7.png\"),\n",
+    "    #     format=\"png\",\n",
     "    #     dpi=600,\n",
     "    # )\n",
     "    plt.show()"
@@ -1884,7 +1884,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0rc1"
+   "version": "3.11.0"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/kish_basin_dat_files.ipynb b/docs/notebooks/kish_basin_dat_files.ipynb
@@ -38,9 +38,7 @@
    "outputs": [],
    "source": [
     "plt.rcParams[\"xtick.major.size\"] = 0\n",
-    "plt.rcParams[\"ytick.major.size\"] = 0\n",
-    "plt.rcParams[\"xtick.minor.size\"] = 0\n",
-    "plt.rcParams[\"ytick.minor.size\"] = 0"
+    "plt.rcParams[\"ytick.major.size\"] = 0"
    ]
   },
   {