Bug/windows tests failing (#322)

* Fix test examples - Change the testing of notebook to pytest-notebook for better windows compatibility - Add comment in electromobility_example.ipynb - Fix Error in electromobility_example.ipynb through false filepath - Get module path instead of non explicit definition of filepath. - Testing the notebooks is using tempfiles there the normal paths are pointing to nothing. ´´´ from edisgo import __file__ module_path = os.path.dirname(os.path.dirname(__file__)) ´´´ * Increase timout * Change test workflow * Add colors in automated tests * Fix testing windows with python 3.9 * Added function to download vg250 data in electromobility notebook * Fix conda env files - Python version 3.8 or 3.9 * Increase timeout * Update github testing action * Minor change to electromobility notebook * Delete old import Co-authored-by: birgits <birgit.schachler@rl-institut.de> Co-authored-by: AnyaHe <anya.heider@rl-institut.de> Co-authored-by: Kilian Helfenbein <Kilian.Helfenbein@rl-institut.de> Co-authored-by: mltja <malte.jahn@rl-institut.com> Co-authored-by: Maike Held <Maike.Held@rl-institut.de>
openego · Sep 30, 2022 · 95271ab · 95271ab
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diff --git a/.github/workflows/tests-coverage.yml b/.github/workflows/tests-coverage.yml
@@ -11,17 +11,14 @@ concurrency:
 
 jobs:
   build:
-    name: "eDisGo-${{ matrix.name-suffix }} at Python ${{ matrix.python-version }} on ${{ matrix.os }}"
+    name: "${{ matrix.name-suffix }} at py${{ matrix.python-version }} on ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
         include:
-          - name-suffix: "basic"
-            os: ubuntu-latest
-            python-version: 3.8
-          - name-suffix: "dev"
+          - name-suffix: "coverage"
             os: ubuntu-latest
             python-version: 3.8
           - name-suffix: "basic"
@@ -30,6 +27,9 @@ jobs:
           - name-suffix: "basic"
             os: windows-latest
             python-version: 3.8
+          - name-suffix: "basic"
+            os: windows-latest
+            python-version: 3.9
 
     steps:
       - name: Checkout repo
@@ -40,18 +40,12 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install packages (Linux - Basic)
-        if: runner.os == 'Linux' && matrix.name-suffix == 'basic'
+      - name: Install packages (Linux)
+        if: runner.os == 'Linux'
         run: |
           pip install --upgrade pip wheel setuptools
           pip install -e "."
 
-      - name: Install packages (Linux - Dev)
-        if: runner.os == 'Linux' && matrix.name-suffix == 'dev'
-        run: |
-          pip install --upgrade pip wheel setuptools
-          pip install -e ".[dev]"
-
       - name: Install packages (Windows)
         if: runner.os == 'Windows'
         uses: conda-incubator/setup-miniconda@v2
@@ -62,16 +56,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Run tests
-        if: ${{ !(runner.os == 'Linux' && matrix.python-version == 3.8 && matrix.name-suffix == 'dev') }}
+        if: ${{ !(runner.os == 'Linux' && matrix.python-version == 3.8 && matrix.name-suffix == 'coverage') }}
         run: |
           python -m pip install pytest pytest-notebook
-          python -m pytest --runslow -vv
+          python -m pytest --runslow --disable-warnings --color=yes -v
 
       - name: Run tests, coverage and send to coveralls
-        if: runner.os == 'Linux' && matrix.python-version == 3.8 && matrix.name-suffix == 'dev'
+        if: runner.os == 'Linux' && matrix.python-version == 3.8 && matrix.name-suffix == 'coverage'
         run: |
-          pip install coveralls
-          coverage run --source=edisgo -m pytest --runslow -vv
+          pip install pytest pytest-notebook coveralls
+          coverage run --source=edisgo -m pytest --runslow --disable-warnings --color=yes -v
           coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

diff --git a/eDisGo_env.yml b/eDisGo_env.yml
@@ -3,9 +3,9 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python = 3.8
+  - python >=3.8,<3.10
   - pip
-  - pandas >= 1.2
+  - pandas >=1.2
   - conda-forge::fiona
   - conda-forge::geopy
   - conda-forge::geopandas

diff --git a/eDisGo_env_dev.yml b/eDisGo_env_dev.yml
@@ -3,9 +3,9 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python = 3.8
+  - python >=3.8,<3.10
   - pip
-  - pandas >= 1.2
+  - pandas >=1.2
   - conda-forge::fiona
   - conda-forge::geopy
   - conda-forge::geopandas

diff --git a/examples/edisgo_simple_example.ipynb b/examples/edisgo_simple_example.ipynb
@@ -892,7 +892,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.8.13"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/examples/electromobility_example.ipynb b/examples/electromobility_example.ipynb
@@ -55,7 +55,8 @@
     "\n",
     "from edisgo.edisgo import EDisGo\n",
     "from edisgo.tools.logger import setup_logger\n",
-    "from edisgo.tools.plots import plot_dash, plot_plotly"
+    "from edisgo.tools.plots import plot_dash, plot_plotly\n",
+    "\n"
    ]
   },
   {
@@ -65,6 +66,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# interactive matplotlib\n",
     "%matplotlib notebook"
    ]
   },
@@ -215,9 +217,18 @@
    "source": [
     "### Download 'Verwaltungsgebiete' data\n",
     "\n",
-    "The following code shows you how to download the original municipality geodata. To make the example faster we will however skip the download and use a reduced version of the dataset containing only the municipalities that intersect with the grid district used in this example. The reduced dataset is loaded in the next cell.\n",
-    "\n",
+    "The following code shows you how to download the original municipality geodata. To make the example faster we will however skip the download and use a reduced version of the dataset containing only the municipalities that intersect with the grid district used in this example. The reduced dataset is loaded in the next cell."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ccb74f72",
+   "metadata": {},
+   "source": [
     "```python\n",
+    "vg250_path = os.path.join(\n",
+    "        os.path.expanduser(\"~\"), \".edisgo\", \"vg250\"\n",
+    "    )\n",
     "target = Path(vg250_path, \"vg250_01-01.geo84.shape.ebenen/vg250_ebenen_0101/VG250_GEM.shp\")\n",
     "\n",
     "if not target.is_file():\n",
@@ -245,7 +256,37 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vg250 = gpd.read_file(os.path.join(\"data\", \"vg250.shp\"))"
+    "def download_vg250_data():\n",
+    "\n",
+    "    # create directory to save vg250 data into\n",
+    "    vg250_path = os.path.join(\n",
+    "        os.path.expanduser(\"~\"), \".edisgo\", \"vg250\"\n",
+    "    )\n",
+    "    os.makedirs(vg250_path, exist_ok=True)\n",
+    "    \n",
+    "    # download files\n",
+    "    filenames = [\n",
+    "        \"vg250.cpg\",\n",
+    "        \"vg250.dbf\",\n",
+    "        \"vg250.prj\",\n",
+    "        \"vg250.shp\",\n",
+    "        \"vg250.shx\",\n",
+    "    ]\n",
+    "\n",
+    "    for file in filenames:\n",
+    "        req = requests.get(\n",
+    "            \"https://raw.githubusercontent.com/openego/eDisGo/dev/examples/data/{}\".format(\n",
+    "                file\n",
+    "            )\n",
+    "        )\n",
+    "        filename = os.path.join(vg250_path, f\"{file}\")\n",
+    "        with open(filename, \"wb\") as fout:\n",
+    "            fout.write(req.content)\n",
+    "\n",
+    "    return vg250_path\n",
+    "\n",
+    "vg250_path = download_vg250_data()\n",
+    "vg250 = gpd.read_file(os.path.join(vg250_path, \"vg250.shp\"))"
    ]
   },
   {

diff --git a/examples/plot_example.ipynb b/examples/plot_example.ipynb
@@ -396,7 +396,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.8.13"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/tests/test_examples.py b/tests/test_examples.py
@@ -1,9 +1,6 @@
 import logging
 import os
-import subprocess
-import tempfile
 
-import nbformat
 import pytest
 import pytest_notebook
 
@@ -15,64 +12,47 @@ def setup_class(self):
             os.path.dirname(os.path.dirname(__file__)), "examples"
         )
 
-    def _notebook_run(self, path):
-        """
-        Execute a notebook via nbconvert and collect output.
-        Returns (parsed nb object, execution errors)
-        """
-        dirname, __ = os.path.split(path)
-        os.chdir(dirname)
-        with tempfile.NamedTemporaryFile(suffix=".ipynb") as fout:
-            args = [
-                "jupyter",
-                "nbconvert",
-                path,
-                "--output",
-                fout.name,
-                "--to",
-                "notebook",
-                "--execute",
-                "--ExecutePreprocessor.timeout=150",
-            ]
-            subprocess.check_call(args)
-
-            fout.seek(0)
-            nb = nbformat.read(fout, nbformat.current_nbformat)
-
-        errors = [
-            output
-            for cell in nb.cells
-            if "outputs" in cell
-            for output in cell["outputs"]
-            if output.output_type == "error"
-        ]
-
-        return nb, errors
-
     @pytest.mark.slow
     def test_plot_example_ipynb(self):
         path = os.path.join(self.examples_dir_path, "plot_example.ipynb")
         notebook = pytest_notebook.notebook.load_notebook(path=path)
         result = pytest_notebook.execution.execute_notebook(
-            notebook, with_coverage=False, timeout=20
+            notebook,
+            with_coverage=False,
+            timeout=600,
         )
+        if result.exec_error is not None:
+            print(result.exec_error)
         assert result.exec_error is None
 
     @pytest.mark.slow
     def test_electromobility_example_ipynb(self):
-        nb, errors = self._notebook_run(
-            os.path.join(self.examples_dir_path, "electromobility_example.ipynb")
+        path = os.path.join(self.examples_dir_path, "electromobility_example.ipynb")
+        notebook = pytest_notebook.notebook.load_notebook(path=path)
+        result = pytest_notebook.execution.execute_notebook(
+            notebook,
+            with_coverage=False,
+            timeout=600,
         )
-        assert errors == []
+        if result.exec_error is not None:
+            print(result.exec_error)
+        assert result.exec_error is None
 
     @pytest.mark.slow
     def test_edisgo_simple_example_ipynb(self):
-        nb, errors = self._notebook_run(
-            os.path.join(self.examples_dir_path, "edisgo_simple_example.ipynb")
+        path = os.path.join(self.examples_dir_path, "edisgo_simple_example.ipynb")
+        notebook = pytest_notebook.notebook.load_notebook(path=path)
+        result = pytest_notebook.execution.execute_notebook(
+            notebook,
+            with_coverage=False,
+            timeout=600,
         )
-        assert errors == []
+        if result.exec_error is not None:
+            print(result.exec_error)
+        assert result.exec_error is None
 
     @classmethod
     def teardown_class(cls):
         logger = logging.getLogger("edisgo")
+        logger.handlers.clear()
         logger.propagate = True