Fix GitHub Actions - update to latest versions

Author: mfbenitezp

.DS_Store

@@ -1,4 +1,4 @@
-# GitHub Actions workflow for MkDocs deployment
+# Simplified GitHub Actions workflow for MkDocs deployment
 name: Deploy MkDocs Documentation
 
 on:
@@ -18,20 +18,21 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  build:
+  deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 
     - name: Cache pip dependencies
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
@@ -41,32 +42,17 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install mkdocs mkdocs-material mkdocstrings[python]
-        pip install mkdocs-git-revision-date-localized-plugin
-        pip install mkdocs-awesome-pages-plugin
-        # Install MagGeo package for API documentation
-        pip install maggeo>=0.2.0
-    
-    - name: Setup Pages
-      uses: actions/configure-pages@v3
-    
-    - name: Build documentation
+        pip install -r requirements.txt
+        
+    - name: Copy source code for API docs
       run: |
-        mkdocs build --clean --strict
+        cp -r maggeo/ ./
+        
+    - name: Configure Git for mkdocs-git-revision-date
+      run: |
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
     
-    - name: Upload artifact
-      uses: actions/upload-pages-artifact@v2
-      with:
-        path: ./site
-
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    needs: build
-    if: github.ref == 'refs/heads/main'
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+    - name: Build and deploy documentation
+      run: |
+        mkdocs gh-deploy --force --clean --verbose

.github/workflows/deploy.yml

@@ -0,0 +1,83 @@
+# maggeo/__init__.py
+"""
+MagGeo: Data fusion library for annotating GPS trajectories with geomagnetic satellite data from Swarm mission from ESA.
+Authors: Fernando Benitez-Paez, Urška Demšar, Jed Long, Ciaran Beggan
+
+This package materialise a data fusion method to annotate GPS trajectories with geomagnetic data from the Swarm satellite mission.
+It includes functions for data retrieval, processing, and annotation, as well as debugging utilities.
+For more information, please refer to the paper:
+
+Benitez-Paez, F., Brum-Bastos, V.d., Beggan, C.D. et al. 
+Fusion of wildlife tracking and satellite geomagnetic data for the study of animal migration. 
+Mov Ecol 9, 31 (2021). https://doi.org/10.1186/s40462-021-00268-4
+
+"""
+
+__version__ = "0.2.0"
+__author__ = "Fernando Benitez-Paez, Urška Demšar, Jed Long, Ciaran Beggan"
+__email__ = "Fernando.Benitez@st-andrews.ac.uk"
+
+# Lazy imports to avoid immediate dependency loading
+def get_main_function():
+    """Get the main annotation function with lazy import."""
+    try:
+        from .core import annotate_gps_with_geomag
+        return annotate_gps_with_geomag
+    except ImportError as e:
+        raise ImportError(f"Could not import core functionality. Please ensure all dependencies are installed: {e}")
+
+# Only expose main function, date utilities, indices, parallel functions, and swarm data manager to avoid import issues
+__all__ = ['annotate_gps_with_geomag', 'identify_unique_dates', 'get_ae_index', 'get_sme_index', 'merge_indices_with_maggeo', 
+           'SwarmDataManager', 'download_swarm_data_for_trajectory', 'load_swarm_data', 
+           'parallel_row_handler', 'parallel_st_idw_process', 'parallel_chaos_ground_values', '__version__']
+
+# Make main function, date utilities, indices, parallel functions, and swarm data manager available
+try:
+    from .core import annotate_gps_with_geomag
+    from .date_utils import identify_unique_dates
+    from .parallel_processing import parallel_row_handler
+    from .interpolation import parallel_st_idw_process
+    from .chaos import parallel_chaos_ground_values
+    from .indices import get_ae_index, get_sme_index, merge_indices_with_maggeo
+    from .swarm_data_manager import SwarmDataManager, download_swarm_data_for_trajectory, load_swarm_data
+except ImportError:
+    # Provide informative error message
+    def annotate_gps_with_geomag(*args, **kwargs):
+        raise ImportError(
+            "MagGeo core functionality is not available. "
+            "Please ensure all dependencies are installed:\n"
+            "pip install viresclient chaosmagpy pandas netCDF jupyterlab \n"
+            "or install MagGeo with conda using the provided environment.yml"
+        )
+    
+    def identify_unique_dates(*args, **kwargs):
+        raise ImportError(
+            "MagGeo core functionality is not available. "
+            "Please ensure all dependencies are installed:\n"
+            "pip install viresclient chaosmagpy pandas netCDF jupyterlab hapiclient \n"
+            "or install MagGeo with conda using the provided environment.yml"
+        )
+    
+    def get_ae_index(*args, **kwargs):
+        raise ImportError(
+            "MagGeo indices functionality is not available. "
+            "Please ensure all dependencies are installed:\n"
+            "pip install hapiclient pandas numpy \n"
+            "or install MagGeo with conda using the provided environment.yml"
+        )
+    
+    def get_sme_index(*args, **kwargs):
+        raise ImportError(
+            "MagGeo indices functionality is not available. "
+            "Please ensure all dependencies are installed:\n"
+            "pip install hapiclient pandas numpy \n"
+            "or install MagGeo with conda using the provided environment.yml"
+        )
+    
+    def merge_indices_with_maggeo(*args, **kwargs):
+        raise ImportError(
+            "MagGeo indices functionality is not available. "
+            "Please ensure all dependencies are installed:\n"
+            "pip install hapiclient pandas numpy \n"
+            "or install MagGeo with conda using the provided environment.yml"
+        )