Merge remote-tracking branch 'upstream/develop'

.github/workflows/github-actions-ci.yml

@@ -0,0 +1,29 @@
+name: GitHub Actions Demo
+on: [push, pull_request]
+jobs:
+  Github-Actions-CI:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - run: |
+          echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Add conda to system path
+        run: |
+          # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install dependencies
+        run: |
+          conda env create --file environment.yml
+      - name: test GDL's 3 major modes
+        run: |
+          source /usr/share/miniconda/etc/profile.d/conda.sh
+          conda activate geo_deep_env
+          unzip ./data/massachusetts_buildings.zip -d ./data
+          python GDL.py mode=sampling
+          python GDL.py mode=train
+          python GDL.py mode=inference

Dockerfile

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+FROM continuumio/miniconda3
+
+WORKDIR /app
+
+# Create the environment:
+COPY environment.yml .
+RUN conda env create -f environment.yml
+
+# Make RUN commands use the new environment:
+SHELL ["conda", "run", "-n", "geo_deep_env", "/bin/bash", "-c"]
+
+# Make sure the environment is activated:
+RUN echo "Make sure flask is installed:"
+RUN python -c "import flask"
+
+# The code to run when container is started:
+#COPY run.py .
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "geo_deep_env", "python"]

GDL.py

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+import os
+import time
+import hydra
+import logging
+from omegaconf import DictConfig, OmegaConf, open_dict
+from utils.utils import load_obj, print_config, get_git_hash, getpath
+
+
+@hydra.main(config_path="config", config_name="gdl_config_template")
+def run_gdl(cfg: DictConfig) -> None:
+    """
+    Function general for Geo Deep-Learning using Hydra library to rules all the
+    parameters and functions using during the task wanted to execute.
+
+    Process
+    -------
+    1. Read and convert the `gdl_config.yaml` to a dictionary.
+    2. Verify if the code and other information need to be save.
+    3. If the debug option is activate, the entire config yaml will be printed
+       and save in a log. In addition of that, if the mode is `train`, a
+       validation run will precede the training to assure the well functioning
+       of the code.
+    4. Verify is the chosen mode is available.
+    5. Verify is the chosen task is available and run the code link to that
+       task.
+
+    -------
+    :param cfg: (DictConfig) Parameters and functions in the main yaml config
+                file.
+    """
+    cfg = OmegaConf.create(cfg)
+
+    # debug config
+    if cfg.debug:
+        pass
+        # cfg.training.num_sanity_val_steps = 1  # only work with pytorch lightning
+        # logging.info(OmegaConf.to_yaml(cfg, resolve=True))
+
+    # check if the mode is chosen
+    if type(cfg.mode) is DictConfig:
+        msg = "You need to choose between those modes: {}"
+        raise logging.critical(msg.format(list(cfg.mode.keys())))
+
+    # save all overwritten parameters
+    logging.info('\nOverwritten parameters in the config: \n' + cfg.general.config_override_dirname)
+
+    # Start -----------------------------------
+    msg = "Let's start {} for {} !!!".format(cfg.mode, cfg.task.task_name)
+    logging.info(
+        "\n" + "-" * len(msg) + "\n" + msg +
+        "\n" + "-" * len(msg)
+    )
+    # -----------------------------------------
+
+    # Start the timer
+    start_time = time.time()
+    # Read the task and execute it
+    task = load_obj(cfg.task.path_task_function)
+    task(cfg)
+
+    # Add git hash from current commit to parameters.
+    with open_dict(cfg):
+        cfg.general.git_hash = get_git_hash()
+
+    # Pretty print config using Rich library
+    if cfg.get("print_config"):
+        print_config(cfg, resolve=True)
+
+    # End --------------------------------
+    msg = "End of {} !!!".format(cfg.mode)
+    logging.info(
+        "\n" + "-" * len(msg) + "\n" + msg + "\n" +
+        "Elapsed time: {:.2f}s".format(time.time() - start_time) +
+        "\n" + "-" * len(msg) + "\n"
+    )
+    # ------------------------------------
+
+
+if __name__ == '__main__':
+    run_gdl()