Merge pull request #318 from cgre-aachen/dev_gemgis2

Updating tests and enhance coverage

.github/workflows/testing.yml

@@ -1,41 +1,49 @@
-name: GemGIS CI
-
-on:
-  push:
-    branches: [ main, dev_aj, dev_alex ]
-
-  pull_request:
-    branches: [ main ]
-
-    # Allows you to run this workflow manually from the Actions tab
-    workflow_dispatch:
-
+name: Pytest
+on: [push]
 jobs:
-  # A workflow run is made up of one or more jobs that can run sequentially or in parallel
-  testing:
-    name: Testing
-    runs-on: "ubuntu-latest"
-    defaults:
-      run:
-        shell: bash -l {0}
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: '3.10'
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: gemgis_testing
-          environment-file: environment.yml
-          python-version: 3.9
-          channels: conda-forge
-      - name: List dependencies
-        run: |
-          conda list pygeos
-          conda list geopandas
-          conda list rasterio
-          conda list pyvista
-          conda list gemgis
-      - name: Install dependencies
-        run: |
-          pip install -r requirements_optional.txt
-      - name: Run tests with pytest
-        run: |
-          pytest
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.10'
+    - name: Install Dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install owslib geopy gempy==2.3.1 xmltodict pypdf mplstereonet scikit-image scipy rioxarray tqdm
+    - name: Debug
+      run: |
+        ls -R  # List all files and directories recursively
+        pwd    # Print the current working directory
+    - name: Generate coverage report
+      working-directory: ./tests
+      run: |
+        pip install pytest
+        pip install pytest-cov
+        pytest --cov=./ --cov-report=xml
+    - name: Debug
+      run: |
+        ls -R  # List all files and directories recursively
+        pwd    # Print the current working directory
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        directory: ./
+        #coverage/reports/
+        env_vars: OS,PYTHON
+        fail_ci_if_error: true
+        files: coverage.xml
+        #,./coverage2.xml,!./cache
+        flags: unittests
+        name: codecov-umbrella
+        verbose: true

README.md

@@ -12,6 +12,9 @@
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.03709/status.svg)](https://doi.org/10.21105/joss.03709)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6511767.svg)](https://doi.org/10.5281/zenodo.6511767)
 [![DOI](https://img.shields.io/badge/DOI-https%3A%2F%2Fdoi.org%2F10.5194%2Fegusphere--egu21--4613-blue)](https://doi.org/10.5194/egusphere-egu21-4613)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/GemGIS)
+
 
 <p align="center"><img src="https://raw.githubusercontent.com/cgre-aachen/gemgis/main/docs/getting_started/images/task1.png" width="200"><img src="https://raw.githubusercontent.com/cgre-aachen/gemgis/main/docs/getting_started/images/model1.png" width="300"></p>
 

docs/getting_started/tutorial/63_displaying_well_log_along_well_path.ipynb

@@ -43,7 +43,7 @@
    "id": "9a8518ee",
    "metadata": {},
    "source": [
-    "# Defining well and well log values\n",
+    "## Defining well and well log values\n",
     "\n",
     "First, we define an arbitrary well path using three points as NumPy Array. The measured depths (`dist`) and and some random values are defined as 1D NumPy arrays. "
    ]
@@ -258,7 +258,7 @@
    "id": "ae3c83df",
    "metadata": {},
    "source": [
-    "# Interpolate/Resample between points\n",
+    "## Interpolate/Resample between points\n",
     "\n",
     "The second step is to resample linearly between each provided well path point. A spacing of 5 cm between each point is chosen by default. "
    ]
@@ -426,7 +426,7 @@
    "id": "4608fa6c",
    "metadata": {},
    "source": [
-    "# Create Polyline from well path coordinates\n",
+    "## Create Polyline from well path coordinates\n",
     "\n",
     "Then, we create a polyline of the original well path for visualization purposes. "
    ]
@@ -479,7 +479,7 @@
    "id": "fec8f8a7",
    "metadata": {},
    "source": [
-    "# Creating Spline from resampled well path coordinates\n",
+    "## Creating Spline from resampled well path coordinates\n",
     "\n",
     "Now, we are creating spline of the resampled points. This automatically calculates the `arc_length` which will be utilized in the next step. "
    ]
@@ -539,7 +539,7 @@
    "id": "2efa0148",
    "metadata": {},
    "source": [
-    "# Getting the Points along the resampled Spline\n",
+    "## Getting the Points along the resampled Spline\n",
     "\n",
     "The main step is to assign a resampled value to a measured value using `get_points_along_spline`. "
    ]
@@ -680,7 +680,7 @@
    "id": "22425c69",
    "metadata": {},
    "source": [
-    "# Creating Polyline from Points, assigning values and creating Tube\n",
+    "## Creating Polyline from Points, assigning values and creating Tube\n",
     "\n",
     "Once we have extracted the points, we again create a PolyLine from it. We then assign the measured well log values as data array to the newly created PolyLine and create a tube from it using the `values` to define the radius of the tube. The `radius_factor` is a scaling factor that needs to changed according to the length of the well. "
    ]
@@ -743,7 +743,7 @@
    "id": "45f3f992",
    "metadata": {},
    "source": [
-    "# Combined Function"
+    "## Combined Function"
    ]
   },
   {
@@ -802,7 +802,7 @@
    "id": "51451276",
    "metadata": {},
    "source": [
-    "# Plotting the result"
+    "## Plotting the result"
    ]
   },
   {
@@ -867,7 +867,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,