Feat/improve pypi packaging

.github/dependabot.yml

@@ -0,0 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# also see
+# https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Workflow files in .github/workflows will be checked
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
+

.github/workflows/lint.yaml

@@ -0,0 +1,10 @@
+name: Linting
+on: [pull_request, push]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - uses: actions/setup-python@v5
+      - uses: pre-commit/[email protected]

.github/workflows/release.yaml

@@ -0,0 +1,41 @@
+name: Release
+
+on:
+  release:
+    types:
+      - created
+
+permissions:
+  contents: read
+
+jobs:
+  check-package:
+    name: Build & inspect our package.
+    runs-on: ubuntu-latest
+    if: ${{ github.repository }} == 'openearth/coclico-workbench'
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  release-pypi:
+    permissions:
+      id-token: write
+      contents: read
+    name: Publish released package to pypi.org
+    environment: release-pypi
+    runs-on: ubuntu-latest
+    needs: check-package
+
+    steps:
+      - name: Download packages built by build-and-inspect-python-package
+        uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+      - name: Upload package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -160,3 +160,6 @@ dist*
 
 # duckdb
 *:memory*
+
+src/coclico/_version.py
+*.vscode*

.pre-commit-config.yaml

@@ -1,23 +1,32 @@
 ci:
-  autofix_prs: false
+  autofix_prs: true
   autoupdate_schedule: weekly
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: debug-statements
+      - id: check-json
       - id: check-yaml
+      - id: check-toml
       - id: check-added-large-files
+      - id: pretty-format-json
+        exclude: '\.ipynb$'
+      - id: sort-simple-yaml
 
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.1
     hooks:
-      - id: black
-        language_version: python3.11
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout

README.md

@@ -6,14 +6,14 @@ CoCliCo workbench prototype repository with tutorials & exploratory tools for Co
 
 Notebooks can be opened in Google Colab. [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](http://colab.research.google.com/github/openearth/coclico-workbench)
 
-## Coding offline in the Workbench Environment  
+## Coding offline in the Workbench Environment
 
 Please follow the instructions to install the CoCliCo environment as outlined in the [CoCliCo Data](https://github.com/openearth/coclicodata) repository.
 After step 13, please return to the instructions here again and clone the `coclico-workbench` repo by adding ("Add" --> "clone repository" --> "URL") URL in GitHub Desktop. You can find the URL under the green "code" button at the top of this repo. Please change the local path to something like: C:\Users\***\Documents\GitHub (where you create the GitHub folder yourself). The repo will be cloned here.
 
-Next, open VS Code and select the cloned `coclico-workbench` folder as your working directory. As a test, you can open `IPCC_AR5_AR6_comparison.ipynb` in notebooks. Select your kernel (the `coclicodata` env) in the top right corner and run cells by pressing shift-enter. You should be able to progress through the notebook without any errors. 
+Next, open VS Code and select the cloned `coclico-workbench` folder as your working directory. As a test, you can open `IPCC_AR5_AR6_comparison.ipynb` in notebooks. Select your kernel (the `coclicodata` env) in the top right corner and run cells by pressing shift-enter. You should be able to progress through the notebook without any errors.
 
-Might you run into trouble with these installation guidelines, please reach out to [@EtienneKras](https://github.com/EtienneKras), [@mathvansoest](https://github.com/mathvansoest) or [@FlorisCalkoen](https://github.com/FlorisCalkoen) for help.  
+Might you run into trouble with these installation guidelines, please reach out to [@EtienneKras](https://github.com/EtienneKras), [@mathvansoest](https://github.com/mathvansoest) or [@FlorisCalkoen](https://github.com/FlorisCalkoen) for help.
 
 ## Repository structure
 
@@ -23,7 +23,7 @@ Might you run into trouble with these installation guidelines, please reach out
 
 - **tutorials**: short notebooks describing how to use the CoCliCo Data repository (STAC)
 
-- **src/coclicodata**: (OUTDATED) various scripts with basic functionalities that can be used for the tutorials & exploratory tools 
+- **src/coclicodata**: (OUTDATED) various scripts with basic functionalities that can be used for the tutorials & exploratory tools
 
 ## Contributing
 

docs/conf.py

@@ -6,9 +6,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u"coclico"
-copyright = u"2022, Floris Calkoen"
-author = u"Floris Calkoen"
+project = "coclico"
+copyright = "2022, Floris Calkoen"
+author = "Floris Calkoen"
 
 # -- General configuration ---------------------------------------------------
 

docs/example.ipynb

@@ -1,45 +1,45 @@
 {
-    "cells": [
-        {
-            "cell_type": "markdown",
-            "source": [
-                "# Example usage\n",
-                "\n",
-                "To use `coclico` in a project:"
-            ],
-            "metadata": {}
-        },
-        {
-            "cell_type": "code",
-            "execution_count": null,
-            "source": [
-                "import coclico\n",
-                "\n",
-                "print(coclico.__version__)"
-            ],
-            "outputs": [],
-            "metadata": {}
-        }
-    ],
-    "metadata": {
-        "kernelspec": {
-            "display_name": "Python 3",
-            "language": "python",
-            "name": "python3"
-        },
-        "language_info": {
-            "codemirror_mode": {
-                "name": "ipython",
-                "version": 3
-            },
-            "file_extension": ".py",
-            "mimetype": "text/x-python",
-            "name": "python",
-            "nbconvert_exporter": "python",
-            "pygments_lexer": "ipython3",
-            "version": "3.8.5"
-        }
-    },
-    "nbformat": 4,
-    "nbformat_minor": 4
-}
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example usage\n",
+    "\n",
+    "To use `coclico` in a project:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import coclico\n",
+    "\n",
+    "print(coclico.__version__)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

notebooks/IPCC_AR5_AR6_comparison.html

@@ -7841,7 +7841,7 @@ <h3 id="Geospatial-plot">Geospatial plot<a class="anchor-link" href="#Geospatial
 <span class="n">plt</span><span class="o">.</span><span class="n">gcf</span><span class="p">()</span><span class="o">.</span><span class="n">subplots_adjust</span><span class="p">(</span><span class="n">left</span><span class="o">=</span><span class="mf">0.05</span><span class="p">)</span>
 
 <span class="c1"># populate AR5 plot</span>
-<span class="n">ax1</span><span class="o">.</span><span class="n">set_facecolor</span><span class="p">((</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">))</span> 
+<span class="n">ax1</span><span class="o">.</span><span class="n">set_facecolor</span><span class="p">((</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">))</span>
 <span class="n">im5</span> <span class="o">=</span> <span class="n">ar5_item</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span>
     <span class="n">ax</span><span class="o">=</span><span class="n">ax1</span><span class="p">,</span>
     <span class="n">add_colorbar</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
@@ -7998,11 +7998,11 @@ <h3 id="Temporal-plot">Temporal plot<a class="anchor-link" href="#Temporal-plot"
 <span class="c1"># 2014 data (related to AR5, in m)</span>
 <span class="n">WGHL_2030l</span> <span class="o">=</span> <span class="mf">0.1</span>
 <span class="n">WGHL_2030h</span> <span class="o">=</span> <span class="mf">0.25</span>
-<span class="n">GLGH_2050l</span> <span class="o">=</span> <span class="mf">0.15</span> 
+<span class="n">GLGH_2050l</span> <span class="o">=</span> <span class="mf">0.15</span>
 <span class="n">GLGH_2050h</span> <span class="o">=</span> <span class="mf">0.3</span>
 <span class="n">GLGH_2085l</span> <span class="o">=</span> <span class="mf">0.25</span>
 <span class="n">GLGH_2085h</span> <span class="o">=</span> <span class="mf">0.6</span>
-<span class="n">WLWH_2050l</span> <span class="o">=</span> <span class="mf">0.2</span> 
+<span class="n">WLWH_2050l</span> <span class="o">=</span> <span class="mf">0.2</span>
 <span class="n">WLWH_2050h</span> <span class="o">=</span> <span class="mf">0.4</span>
 <span class="n">WLWH_2085l</span> <span class="o">=</span> <span class="mf">0.45</span>
 <span class="n">WLWH_2085h</span> <span class="o">=</span> <span class="mf">0.8</span>
@@ -8026,7 +8026,7 @@ <h3 id="Temporal-plot">Temporal plot<a class="anchor-link" href="#Temporal-plot"
 <span class="c1"># pre-processing function</span>
 <span class="k">def</span> <span class="nf">preprocess</span><span class="p">(</span><span class="n">ds</span><span class="p">):</span>
     <span class="n">point_geom</span> <span class="o">=</span> <span class="n">shapely</span><span class="o">.</span><span class="n">Point</span><span class="p">(</span><span class="n">point_location</span><span class="p">)</span>
-    
+
     <span class="n">ds</span> <span class="o">=</span> <span class="p">(</span>
         <span class="n">ds</span><span class="o">.</span><span class="n">rio</span><span class="o">.</span><span class="n">clip</span><span class="p">([</span><span class="n">point_geom</span><span class="p">])</span>
         <span class="o">.</span><span class="n">sel</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">point_location</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">y</span><span class="o">=</span><span class="n">point_location</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">method</span><span class="o">=</span><span class="s2">"nearest"</span><span class="p">)</span>
@@ -8137,7 +8137,7 @@ <h3 id="Temporal-plot">Temporal plot<a class="anchor-link" href="#Temporal-plot"
     <span class="n">ax1</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="mf">2030.2</span><span class="p">,</span> <span class="n">ymin</span><span class="o">=</span><span class="n">WGHL_2030l</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="n">WGHL_2030h</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="s2">"AR5-RCP-8.5"</span><span class="p">],</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">":"</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.8</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">"KNMI'14 - RCP8.5 (W) low-high"</span><span class="p">)</span>
     <span class="n">ax1</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="mf">2050.2</span><span class="p">,</span> <span class="n">ymin</span><span class="o">=</span><span class="n">WLWH_2050l</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="n">WLWH_2050h</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="s2">"AR5-RCP-8.5"</span><span class="p">],</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">":"</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.8</span><span class="p">)</span>
     <span class="n">ax1</span><span class="o">.</span><span class="n">vlines</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="mf">2085.2</span><span class="p">,</span> <span class="n">ymin</span><span class="o">=</span><span class="n">WLWH_2085l</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="n">WLWH_2085h</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="s2">"AR5-RCP-8.5"</span><span class="p">],</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">":"</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.8</span><span class="p">)</span>
-    
+
 <span class="n">ax1</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">"upper left"</span><span class="p">)</span>
 
 <span class="c1"># AR6</span>
@@ -8256,7 +8256,7 @@ <h3 id="Export-notebook">Export notebook<a class="anchor-link" href="#Export-not
 <div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
 <div class="cm-editor cm-s-jupyter">
-<div class="highlight hl-ipython3"><pre><span></span> 
+<div class="highlight hl-ipython3"><pre><span></span>
 </pre></div>
 </div>
 </div>