ci: create docker dev (#583)

* ci: Updated dependencies to run just through docker

* ci: Dockerfile now includes external test data

* test: MAde example's paths platform independent

* test: Corrected paths to be relative to the data directory

* ci: Reverted arguments in dockerfile

* test: corrected last failing example path

* test: Skipped redundant test

* test: corrected mark decorator

* ci: Modified dockerfile to include the `make` linux command

.config/Dockerfile

@@ -0,0 +1,37 @@
+# To build this docker run:
+# `docker build -t ra2ce_core_dev`
+# To run the docker for pytest:
+# `docker run -v {your_ra2ce_checkout_dir}:/usr/src/app/ -v {ra2ce_env_dir}:/usr/src/.env -t ra2ce_core_dev`
+# `poetry install`
+# `poetry run pytest -m {your_pytest_arguments}`
+
+FROM condaforge/miniforge3:latest
+
+RUN apt-get update && apt-get install libgl1 -y && apt-get install --reinstall make
+
+ARG SRC_ROOT="/usr/src"
+
+# For persisting the environment remember to mount it as well:
+# -v {your_local_tmp_dir}:/usr/src/.env
+ARG CONDA_ENV="${SRC_ROOT}/.env"
+
+# Install conda environment
+# This location needs to be mounted with your vrtool checout:
+# -v {your_ra2ce_checkout_dir}:/usr/src/app
+WORKDIR $SRC_ROOT/app
+COPY environment.yml $SRC_ROOT/.config/environment.yml
+COPY ra2ce_test_cases $SRC_ROOT/test_external_data
+
+RUN conda init bash \
+    && . ~/.bashrc \
+    && conda env create -f $SRC_ROOT/.config/environment.yml -p $CONDA_ENV
+
+# Activate conda environment
+ENV PATH $CONDA_ENV/bin:$PATH
+RUN conda activate ${CONDA_ENV} & poetry config virtualenvs.create false
+RUN echo conda init && echo "conda activate ${CONDA_ENV}" >>  ~/.bashrc
+# This ensures it's available also for `sh` instead of `bash`.
+RUN echo "conda activate ${CONDA_ENV}" > ~/.profile
+
+# Define the endpoint
+CMD [ "/bin/bash" ]

.config/environment.yml

@@ -8,4 +8,5 @@ dependencies:
   # If this does not work then exclude it from the environment and install it manually
   # with: conda install -c conda-forge poetry=1.3.2
   - conda-forge::poetry=1.3.2
-  - conda-forge::pandoc
+  - conda-forge::pandoc
+  - conda-forge::teamcity-messages

examples/example_damages_OSdamage.ipynb

@@ -47,7 +47,7 @@
                 "import numpy as np\n",
                 "import rasterio\n",
                 "\n",
-                "root_dir = Path(\".\\\\data\\\\damages_analysis_OSdamage\")\n",
+                "root_dir = Path(\"data\", \"damages_analysis_OSdamage\")\n",
                 "assert root_dir.exists(), \"root_dir not found.\""
             ]
         },

examples/example_damages_huizinga.ipynb

@@ -67,7 +67,7 @@
     "import numpy as np\n",
     "import rasterio\n",
     "\n",
-    "root_dir = Path(\".\\\\data\\\\damages_analysis_huizinga\")\n",
+    "root_dir = Path(\"data\", \"damages_analysis_huizinga\")\n",
     "assert root_dir.exists(), \"root_dir not found.\""
    ]
   },

examples/example_multi_link_losses.ipynb

@@ -25,7 +25,7 @@
     "from ra2ce.ra2ce_handler import Ra2ceHandler\n",
     "\n",
     "# Import config data\n",
-    "root_dir_multi = Path(\".\\\\data\\\\multi_link_losses\")\n",
+    "root_dir_multi = Path(\"data\", \"multi_link_losses\")\n",
     "assert root_dir_multi.exists()\n",
     "\n",
     "# Load network data.\n",

examples/example_origin_destination_analysis.ipynb

@@ -161,7 +161,7 @@
             "outputs": [],
             "source": [
                 "# specify the path to the folder holding the RA2CE folder and input data\n",
-                "root_dir = Path (\"data\", \"origin_destination_analysis_without_hazard\")"
+                "root_dir = Path(\"data\", \"origin_destination_analysis_without_hazard\")"
             ]
         },
         {
@@ -439,7 +439,7 @@
             "outputs": [],
             "source": [
                 "# specify the path to the folder holding the RA2CE folder and input data\n",
-                "root_dir = Path (\".\\\\data\\\\origin_destination_analysis_with_hazard\")"
+                "root_dir = Path(\"data\", \"origin_destination_analysis_with_hazard\")"
             ]
         },
         {

tests/test_main.py

@@ -120,7 +120,15 @@ def test_given_invalid_paths_raises_value_error(
     @pytest.mark.parametrize(
         "case_data_dir",
         [
-            pytest.param("acceptance_test_data", id="Default test data"),
+            pytest.param(
+                "acceptance_test_data",
+                id="Default test data",
+                marks=[
+                    pytest.mark.skip(
+                        reason="Test superseeded by running all jupyter notebook examples"
+                    )
+                ],
+            ),
         ]
         + _external_test_cases,
         indirect=["case_data_dir"],