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rename from exercise_14/starter/evaluate/wandb/run-20220803_231200-2m7twcvg/logs/debug.log rename to evaluate/wandb/run-20220803_231200-2m7twcvg/logs/debug.log diff --git a/exercise_14/starter/evaluate/wandb/run-20220803_231200-2m7twcvg/run-2m7twcvg.wandb b/evaluate/wandb/run-20220803_231200-2m7twcvg/run-2m7twcvg.wandb similarity index 100% rename from exercise_14/starter/evaluate/wandb/run-20220803_231200-2m7twcvg/run-2m7twcvg.wandb rename to evaluate/wandb/run-20220803_231200-2m7twcvg/run-2m7twcvg.wandb diff --git a/exercise_14/.DS_Store b/exercise_14/.DS_Store deleted file mode 100644 index 352ce0d..0000000 Binary files a/exercise_14/.DS_Store and /dev/null differ diff --git a/exercise_14/.Rhistory b/exercise_14/.Rhistory deleted file mode 100644 index e69de29..0000000 diff --git a/exercise_14/README.md b/exercise_14/README.md deleted file mode 100644 index eeb63b1..0000000 --- a/exercise_14/README.md +++ /dev/null @@ -1,62 +0,0 @@ -# Instructions -In this exercise we are going to bring everything together in a complete ML pipeline that -produces a trained Random Forest model. - -# Preliminary step: create a repository and commit and push the starter kit -1. Create a new GitHub repository called ``genre_classification`` in your GitHub account: - ![screenshot](create_github_repo_opt.gif "screenshot") -2. Clone the repository locally: - ```bash - git clone [repository_url] - ``` -3. Go into the repository and copy there the starter kit, - including all subdirectories: - ```bash - cd genre_classification - cp -r [path to the starter]/starter/* . - ``` -4. Add the files of the starter kit to be tracked: - ```bash - git add . - ``` -5. Commit and push: - ```bash - git commit -m "Starter kit" -a - git push - ``` - -# Steps to complete the exercise - -The starter kit contains all the steps we have previously completed, only slightly modified to -work better together. -Your task is to chain them together by completing the ``main.py`` file. Further instructions -are contained in the file. - -When you are done, commit and push to the repository. - -After running the pipeline successfully, go to W&B and tag the exported model as ``prod`` as -we did in Exercise 13. - -A few notes and instructions: -* When chaining together the steps, the output artifact of a step should be the input artifact - of the next one (when applicable). Also use the ``artifact_type`` options so that the final - visualization of the pipeline highlights the different steps. For example, you can use - ``raw_data`` for the artifact containing the downloaded data, ``preprocessed_data`` for the - artifact containing the data after the preprocessing, and so on. - -* For testing, set the ``project_name`` to ``exercise_14``. Once you are done - developing, do a production run by changing the ``project_name`` to - ``genre_classification_prod``. This way the visualization of the pipeline will not contain - all your trials and errors. Remember to tag the produced model export as ``prod`` (we are going - to use it in the next exercise) - -* When developing, you can override the parameter ``main.execute_steps`` to only execute one or - more steps of the pipeline, instead of the entire pipeline. This is useful for debugging. - For example, this only executes the ``random_forest`` step: - ```bash - mlflow run . -P hydra_options="main.execute_steps='random_forest'" - ``` - and this executes ``download`` and ``preprocess``: - ```bash - mlflow run . -P hydra_options="main.execute_steps='download,preprocess'" - ``` diff --git a/exercise_14/create_github_repo_opt.gif b/exercise_14/create_github_repo_opt.gif deleted file mode 100644 index 92f11e9..0000000 Binary files a/exercise_14/create_github_repo_opt.gif and /dev/null differ diff --git a/exercise_14/solution/check_data/conda.yml b/exercise_14/solution/check_data/conda.yml deleted file mode 100644 index 343a9c7..0000000 --- a/exercise_14/solution/check_data/conda.yml +++ /dev/null @@ -1,11 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - pandas=1.2.3 - - pip=20.3.3 - - pytest=6.2.2 - - scipy=1.6.1 - - pip: - - wandb==0.10.21 \ No newline at end of file diff --git a/exercise_14/solution/conda.yml b/exercise_14/solution/conda.yml deleted file mode 100644 index 6efdf27..0000000 --- a/exercise_14/solution/conda.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - requests=2.24.0 - - pip=20.3.3 - - mlflow=1.14.1 - - hydra-core=1.0.6 - - pip: - - wandb==0.10.21 - - hydra-joblib-launcher==1.1.2 diff --git a/exercise_14/solution/config.yaml b/exercise_14/solution/config.yaml deleted file mode 100644 index 95ccf49..0000000 --- a/exercise_14/solution/config.yaml +++ /dev/null @@ -1,67 +0,0 @@ -main: - project_name: exercise_14 - experiment_name: dev - execute_steps: - - download - - preprocess - - check_data - - segregate - - random_forest - - evaluate - # This seed will be used to seed the random number generator - # to ensure repeatibility of the data splits and other - # pseudo-random operations - random_seed: 42 -data: - file_url: "https://github.com/udacity/nd0821-c2-build-model-workflow-exercises/blob/master/lesson-2-data-exploration-and-preparation/exercises/exercise_4/starter/genres_mod.parquet?raw=true" - reference_dataset: "exercise_14/preprocessed_data.csv:latest" - # Threshold for Kolomorov-Smirnov test - ks_alpha: 0.05 - test_size: 0.3 - val_size: 0.3 - # Stratify according to the target when splitting the data - # in train/test or in train/val - stratify: genre -random_forest_pipeline: - random_forest: - n_estimators: 100 - criterion: 'gini' - max_depth: 13 - min_samples_split: 2 - min_samples_leaf: 1 - min_weight_fraction_leaf: 0.0 - max_features: 'auto' - max_leaf_nodes: null - min_impurity_decrease: 0.0 - min_impurity_split: null - bootstrap: true - oob_score: false - n_jobs: null - # This is a different random seed than main.random_seed, - # because this is used only within the RandomForest - random_state: 42 - verbose: 0 - warm_start: false - class_weight: "balanced" - ccp_alpha: 0.0 - max_samples: null - tfidf: - max_features: 10 - features: - numerical: - - "danceability" - - "energy" - - "loudness" - - "speechiness" - - "acousticness" - - "instrumentalness" - - "liveness" - - "valence" - - "tempo" - - "duration_ms" - categorical: - - "time_signature" - - "key" - nlp: - - "text_feature" - export_artifact: "model_export" diff --git a/exercise_14/solution/download/conda.yml b/exercise_14/solution/download/conda.yml deleted file mode 100644 index 42cd9c8..0000000 --- a/exercise_14/solution/download/conda.yml +++ /dev/null @@ -1,9 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - requests=2.24.0 - - pip=20.3.3 - - pip: - - wandb==0.10.21 \ No newline at end of file diff --git a/exercise_14/solution/evaluate/conda.yml b/exercise_14/solution/evaluate/conda.yml deleted file mode 100644 index 7bdbc70..0000000 --- a/exercise_14/solution/evaluate/conda.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - pandas=1.2.3 - - pip=20.3.3 - - scikit-learn=0.24.1 - - matplotlib==3.2.2 - - plotly==4.4.1 - - pillow=8.1.2 - - mlflow=1.14.1 - - pip: - - wandb==0.10.21 diff --git a/exercise_14/solution/main.py b/exercise_14/solution/main.py deleted file mode 100644 index 18bfaa7..0000000 --- a/exercise_14/solution/main.py +++ /dev/null @@ -1,110 +0,0 @@ -import mlflow -import os -import hydra -from omegaconf import DictConfig, OmegaConf - - -# This automatically reads in the configuration -@hydra.main(config_name='config') -def go(config: DictConfig): - - # Setup the wandb experiment. All runs will be grouped under this name - os.environ["WANDB_PROJECT"] = config["main"]["project_name"] - os.environ["WANDB_RUN_GROUP"] = config["main"]["experiment_name"] - - # You can get the path at the root of the MLflow project with this: - root_path = hydra.utils.get_original_cwd() - - # Check which steps we need to execute - if isinstance(config["main"]["execute_steps"], str): - # This was passed on the command line as a comma-separated list of steps - steps_to_execute = config["main"]["execute_steps"].split(",") - else: - - steps_to_execute = list(config["main"]["execute_steps"]) - - # Download step - if "download" in steps_to_execute: - - _ = mlflow.run( - os.path.join(root_path, "download"), - "main", - parameters={ - "file_url": config["data"]["file_url"], - "artifact_name": "raw_data.parquet", - "artifact_type": "raw_data", - "artifact_description": "Data as downloaded" - }, - ) - - if "preprocess" in steps_to_execute: - _ = mlflow.run( - os.path.join(root_path, "preprocess"), - "main", - parameters={ - "input_artifact": "raw_data.parquet:latest", - "artifact_name": "preprocessed_data.csv", - "artifact_type": "preprocessed_data", - "artifact_description": "Data with preprocessing applied" - }, - ) - - if "check_data" in steps_to_execute: - _ = mlflow.run( - os.path.join(root_path, "check_data"), - "main", - parameters={ - "reference_artifact": config["data"]["reference_dataset"], - "sample_artifact": "preprocessed_data.csv:latest", - "ks_alpha": config["data"]["ks_alpha"] - }, - ) - - if "segregate" in steps_to_execute: - - _ = mlflow.run( - os.path.join(root_path, "segregate"), - "main", - parameters={ - "input_artifact": "preprocessed_data.csv:latest", - "artifact_root": "data", - "artifact_type": "segregated_data", - "test_size": config["data"]["test_size"], - "stratify": config["data"]["stratify"] - }, - ) - - if "random_forest" in steps_to_execute: - # Serialize decision tree configuration - model_config = os.path.abspath("random_forest_config.yml") - - with open(model_config, "w+") as fp: - fp.write(OmegaConf.to_yaml(config["random_forest_pipeline"])) - - _ = mlflow.run( - os.path.join(root_path, "random_forest"), - "main", - parameters={ - "train_data": "data_train.csv:latest", - "model_config": model_config, - "export_artifact": config["random_forest_pipeline"]["export_artifact"], - "random_seed": config["main"]["random_seed"], - "val_size": config["data"]["test_size"], - "stratify": config["data"]["stratify"] - }, - ) - - if "evaluate" in steps_to_execute: - - _ = mlflow.run( - os.path.join(root_path, "evaluate"), - "main", - parameters={ - "model_export": f"{config['random_forest_pipeline']['export_artifact']}:latest", - "test_data": "data_test.csv:latest" - }, - ) - - -if __name__ == "__main__": - go() diff --git a/exercise_14/solution/preprocess/conda.yml b/exercise_14/solution/preprocess/conda.yml deleted file mode 100644 index 038b0c2..0000000 --- a/exercise_14/solution/preprocess/conda.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - pandas=1.2.3 - - pip=20.3.3 - - pyarrow=2.0 - - pip: - - wandb==0.10.21 \ No newline at end of file diff --git a/exercise_14/solution/random_forest/conda.yml b/exercise_14/solution/random_forest/conda.yml deleted file mode 100644 index c9b150a..0000000 --- a/exercise_14/solution/random_forest/conda.yml +++ /dev/null @@ -1,15 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - pandas=1.2.3 - - pip=20.3.3 - - scikit-learn=0.24.1 - - matplotlib=3.2.2 - - plotly=4.4.1 - - pillow=8.1.2 - - mlflow=1.14.1 - - pip: - - wandb==0.10.21 - - omegaconf==2.0.6 \ No newline at end of file diff --git a/exercise_14/solution/segregate/conda.yml b/exercise_14/solution/segregate/conda.yml deleted file mode 100644 index f4ddc20..0000000 --- a/exercise_14/solution/segregate/conda.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: download_data -channels: - - conda-forge - - defaults -dependencies: - - pandas=1.2.3 - - pip=20.3.3 - - scikit-learn=0.24.1 - - pip: - - wandb==0.10.21 \ No newline at end of file diff --git a/exercise_14/starter/MLproject b/exercise_14/starter/MLproject deleted file mode 100644 index 08ed647..0000000 --- a/exercise_14/starter/MLproject +++ /dev/null @@ -1,12 +0,0 @@ -name: download_data -conda_env: conda.yml - -entry_points: - main: - parameters: - hydra_options: - description: Hydra parameters to override - type: str - default: '' - command: >- - python main.py $(echo {hydra_options}) diff --git a/exercise_14/starter/check_data/MLproject b/exercise_14/starter/check_data/MLproject deleted file mode 100644 index fbb28da..0000000 --- a/exercise_14/starter/check_data/MLproject +++ /dev/null @@ -1,21 +0,0 @@ -name: exercise_9 -conda_env: conda.yml - -entry_points: - main: - parameters: - reference_artifact: - description: Fully-qualitied name for the artifact to be used as reference dataset - type: str - sample_artifact: - description: Fully-qualitied name for the artifact to be used as new data sample - type: str - ks_alpha: - description: Threshold for the (pre-trial) p-value for the KS test - type: float - # NOTE: the -s flag is necessary, otherwise pytest will capture all the output and it - # will not be uploaded to W&B. Hence, the log in W&B will be empty. - command: >- - pytest -s -vv . --reference_artifact {reference_artifact} \ - --sample_artifact {sample_artifact} \ - --ks_alpha {ks_alpha} diff --git a/exercise_14/starter/check_data/conftest.py b/exercise_14/starter/check_data/conftest.py deleted file mode 100644 index 6b30ca4..0000000 --- a/exercise_14/starter/check_data/conftest.py +++ /dev/null @@ -1,44 +0,0 @@ -import pytest -import pandas as pd -import wandb - - -run = wandb.init(job_type="data_tests") - - -def pytest_addoption(parser): - parser.addoption("--reference_artifact", action="store") - parser.addoption("--sample_artifact", action="store") - parser.addoption("--ks_alpha", action="store") - - -@pytest.fixture(scope="session") -def data(request): - - reference_artifact = request.config.option.reference_artifact - - if reference_artifact is None: - pytest.fail("--reference_artifact missing on command line") - - sample_artifact = request.config.option.sample_artifact - - if sample_artifact is None: - pytest.fail("--sample_artifact missing on command line") - - local_path = run.use_artifact(reference_artifact).file() - sample1 = pd.read_csv(local_path) - - local_path = run.use_artifact(sample_artifact).file() - sample2 = pd.read_csv(local_path) - - return sample1, sample2 - - -@pytest.fixture(scope='session') -def ks_alpha(request): - ks_alpha = request.config.option.ks_alpha - - if ks_alpha is None: - pytest.fail("--ks_threshold missing on command line") - - return float(ks_alpha) diff --git a/exercise_14/starter/check_data/test_data.py b/exercise_14/starter/check_data/test_data.py deleted file mode 100644 index dd3cefe..0000000 --- a/exercise_14/starter/check_data/test_data.py +++ /dev/null @@ -1,120 +0,0 @@ -import scipy.stats -import pandas as pd - - -def test_column_presence_and_type(data): - - # Disregard the reference dataset - _, data = data - - required_columns = { - "time_signature": pd.api.types.is_integer_dtype, - "key": pd.api.types.is_integer_dtype, - "danceability": pd.api.types.is_float_dtype, - "energy": pd.api.types.is_float_dtype, - "loudness": pd.api.types.is_float_dtype, - "speechiness": pd.api.types.is_float_dtype, - "acousticness": pd.api.types.is_float_dtype, - "instrumentalness": pd.api.types.is_float_dtype, - "liveness": pd.api.types.is_float_dtype, - "valence": pd.api.types.is_float_dtype, - "tempo": pd.api.types.is_float_dtype, - "duration_ms": pd.api.types.is_integer_dtype, # This is integer, not float as one might expect - "text_feature": pd.api.types.is_string_dtype, - "genre": pd.api.types.is_string_dtype - } - - # Check column presence - assert set(data.columns.values).issuperset(set(required_columns.keys())) - - for col_name, format_verification_funct in required_columns.items(): - - assert format_verification_funct(data[col_name]), f"Column {col_name} failed test {format_verification_funct}" - - -def test_class_names(data): - - # Disregard the reference dataset - _, data = data - - # Check that only the known classes are present - known_classes = [ - "Dark Trap", - "Underground Rap", - "Trap Metal", - "Emo", - "Rap", - "RnB", - "Pop", - "Hiphop", - "techhouse", - "techno", - "trance", - "psytrance", - "trap", - "dnb", - "hardstyle", - ] - - assert data["genre"].isin(known_classes).all() - - -def test_column_ranges(data): - - # Disregard the reference dataset - _, data = data - - ranges = { - "time_signature": (1, 5), - "key": (0, 11), - "danceability": (0, 1), - "energy": (0, 1), - "loudness": (-35, 5), - "speechiness": (0, 1), - "acousticness": (0, 1), - "instrumentalness": (0, 1), - "liveness": (0, 1), - "valence": (0, 1), - "tempo": (50, 250), - "duration_ms": (20000, 1000000), - } - - for col_name, (minimum, maximum) in ranges.items(): - - assert data[col_name].dropna().between(minimum, maximum).all(), ( - f"Column {col_name} failed the test. Should be between {minimum} and {maximum}, " - f"instead min={data[col_name].min()} and max={data[col_name].max()}" - ) - - -def test_kolmogorov_smirnov(data, ks_alpha): - - sample1, sample2 = data - - columns = [ - "danceability", - "energy", - "loudness", - "speechiness", - "acousticness", - "instrumentalness", - "liveness", - "valence", - "tempo", - "duration_ms" - ] - - # Bonferroni correction for multiple hypothesis testing - # (see my blog post on this topic to see where this comes from: - # https://towardsdatascience.com/precision-and-recall-trade-off-and-multiple-hypothesis-testing-family-wise-error-rate-vs-false-71a85057ca2b) - alpha_prime = 1 - (1 - ks_alpha)**(1 / len(columns)) - - for col in columns: - - ts, p_value = scipy.stats.ks_2samp(sample1[col], sample2[col]) - - # NOTE: as always, the p-value should be interpreted as the probability of - # obtaining a test statistic (TS) equal or more extreme that the one we got - # by chance, when the null hypothesis is true. If this probability is not - # large enough, this dataset should be looked at carefully, hence we fail - assert p_value > alpha_prime diff --git a/exercise_14/starter/download/MLproject b/exercise_14/starter/download/MLproject deleted file mode 100644 index a0aec05..0000000 --- a/exercise_14/starter/download/MLproject +++ /dev/null @@ -1,25 +0,0 @@ -name: download_data -conda_env: conda.yml - -entry_points: - main: - parameters: - file_url: - description: URL of the file to download - type: uri - artifact_name: - description: Name for the W&B artifact that will be created - type: str - artifact_type: - description: Type of the artifact to create - type: str - default: raw_data - artifact_description: - description: Description for the artifact - type: str - - command: >- - python download_data.py --file_url {file_url} \ - --artifact_name {artifact_name} \ - --artifact_type {artifact_type} \ - --artifact_description {artifact_description} diff --git a/exercise_14/starter/download/download_data.py b/exercise_14/starter/download/download_data.py deleted file mode 100644 index 93a1e1c..0000000 --- a/exercise_14/starter/download/download_data.py +++ /dev/null @@ -1,78 +0,0 @@ -#!/usr/bin/env python -import argparse -import logging -import pathlib -import wandb -import requests -import tempfile - - -logging.basicConfig(level=logging.INFO, format="%(asctime)-15s %(message)s") -logger = logging.getLogger() - - -def go(args): - - # Derive the base name of the file from the URL - basename = pathlib.Path(args.file_url).name.split("?")[0].split("#")[0] - - # Download file, streaming so we can download files larger than - # the available memory. We use a named temporary file that gets - # destroyed at the end of the context, so we don't leave anything - # behind and the file gets removed even in case of errors - logger.info(f"Downloading {args.file_url} ...") - with tempfile.NamedTemporaryFile(mode='wb+') as fp: - - logger.info("Creating run") - with wandb.init(job_type="download_data") as run: - # Download the file streaming and write to open temp file - with requests.get(args.file_url, stream=True) as r: - for chunk in r.iter_content(chunk_size=8192): - fp.write(chunk) - - # Make sure the file has been written to disk before uploading - # to W&B - fp.flush() - - logger.info("Creating artifact") - artifact = wandb.Artifact( - name=args.artifact_name, - type=args.artifact_type, - description=args.artifact_description, - metadata={'original_url': args.file_url} - ) - artifact.add_file(fp.name, name=basename) - - logger.info("Logging artifact") - run.log_artifact(artifact) - - artifact.wait() - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Download a file and upload it as an artifact to W&B", fromfile_prefix_chars="@" - ) - - parser.add_argument( - "--file_url", type=str, help="URL to the input file", required=True - ) - - parser.add_argument( - "--artifact_name", type=str, help="Name for the artifact", required=True - ) - - parser.add_argument( - "--artifact_type", type=str, help="Type for the artifact", required=True - ) - - parser.add_argument( - "--artifact_description", - type=str, - help="Description for the artifact", - required=True, - ) - - args = parser.parse_args() - - go(args) diff --git a/exercise_14/starter/evaluate/MLproject b/exercise_14/starter/evaluate/MLproject deleted file mode 100644 index 07f99a8..0000000 --- a/exercise_14/starter/evaluate/MLproject +++ /dev/null @@ -1,15 +0,0 @@ -name: download_data -conda_env: conda.yml - -entry_points: - main: - parameters: - model_export: - description: Fully-qualified artifact name for the exported model to evaluate - type: str - test_data: - description: Fully-qualified artifact name for the test data - type: str - command: >- - python run.py --model_export {model_export} \ - --test_data {test_data} diff --git a/exercise_14/starter/evaluate/run.py b/exercise_14/starter/evaluate/run.py deleted file mode 100644 index d6e1780..0000000 --- a/exercise_14/starter/evaluate/run.py +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env python -import argparse -import itertools -import logging -import pandas as pd -import wandb -import mlflow.sklearn -import matplotlib.pyplot as plt -from sklearn.metrics import roc_auc_score, plot_confusion_matrix - -logging.basicConfig(level=logging.INFO, format="%(asctime)-15s %(message)s") -logger = logging.getLogger() - - -def go(args): - - run = wandb.init(job_type="test") - - logger.info("Downloading and reading test artifact") - test_data_path = run.use_artifact(args.test_data).file() - df = pd.read_csv(test_data_path, low_memory=False) - - # Extract the target from the features - logger.info("Extracting target from dataframe") - X_test = df.copy() - y_test = X_test.pop("genre") - - logger.info("Downloading and reading the exported model") - model_export_path = run.use_artifact(args.model_export).download() - - pipe = mlflow.sklearn.load_model(model_export_path) - - used_columns = list(itertools.chain.from_iterable([x[2] for x in pipe['preprocessor'].transformers])) - pred_proba = pipe.predict_proba(X_test[used_columns]) - - logger.info("Scoring") - score = roc_auc_score(y_test, pred_proba, average="macro", multi_class="ovo") - - run.summary["AUC"] = score - - logger.info("Computing confusion matrix") - fig_cm, sub_cm = plt.subplots(figsize=(10, 10)) - plot_confusion_matrix( - pipe, - X_test[used_columns], - y_test, - ax=sub_cm, - normalize="true", - values_format=".1f", - xticks_rotation=90, - ) - fig_cm.tight_layout() - - run.log( - { - "confusion_matrix": wandb.Image(fig_cm) - } - ) - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Test the provided model on the test artifact", - fromfile_prefix_chars="@", - ) - - parser.add_argument( - "--model_export", - type=str, - help="Fully-qualified artifact name for the exported model to evaluate", - required=True, - ) - - parser.add_argument( - "--test_data", - type=str, - help="Fully-qualified artifact name for the test data", - required=True, - ) - - args = parser.parse_args() - - go(args) diff --git a/exercise_14/starter/preprocess/MLproject b/exercise_14/starter/preprocess/MLproject deleted file mode 100644 index 521ed87..0000000 --- a/exercise_14/starter/preprocess/MLproject +++ /dev/null @@ -1,25 +0,0 @@ -name: download_data -conda_env: conda.yml - -entry_points: - main: - parameters: - input_artifact: - description: Fully qualified name for the artifact - type: str - artifact_name: - description: Name for the W&B artifact that will be created - type: str - artifact_type: - description: Type of the artifact to create - type: str - default: raw_data - artifact_description: - description: Description for the artifact - type: str - - command: >- - python run.py --input_artifact {input_artifact} \ - --artifact_name {artifact_name} \ - --artifact_type {artifact_type} \ - --artifact_description {artifact_description} diff --git a/exercise_14/starter/preprocess/run.py b/exercise_14/starter/preprocess/run.py deleted file mode 100644 index 54ad734..0000000 --- a/exercise_14/starter/preprocess/run.py +++ /dev/null @@ -1,80 +0,0 @@ -#!/usr/bin/env python -import argparse -import logging -import os - -import pandas as pd -import wandb - - -logging.basicConfig(level=logging.INFO, format="%(asctime)-15s %(message)s") -logger = logging.getLogger() - - -def go(args): - - run = wandb.init(job_type="process_data") - - logger.info("Downloading artifact") - artifact = run.use_artifact(args.input_artifact) - artifact_path = artifact.file() - - df = pd.read_parquet(artifact_path) - - # Drop the duplicates - logger.info("Dropping duplicates") - df = df.drop_duplicates().reset_index(drop=True) - - # A minimal feature engineering step: a new feature - logger.info("Feature engineering") - df['title'].fillna(value='', inplace=True) - df['song_name'].fillna(value='', inplace=True) - df['text_feature'] = df['title'] + ' ' + df['song_name'] - - filename = "processed_data.csv" - df.to_csv(filename) - - artifact = wandb.Artifact( - name=args.artifact_name, - type=args.artifact_type, - description=args.artifact_description, - ) - artifact.add_file(filename) - - logger.info("Logging artifact") - run.log_artifact(artifact) - - os.remove(filename) - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Preprocess a dataset", - fromfile_prefix_chars="@", - ) - - parser.add_argument( - "--input_artifact", - type=str, - help="Fully-qualified name for the input artifact", - required=True, - ) - - parser.add_argument( - "--artifact_name", type=str, help="Name for the artifact", required=True - ) - - parser.add_argument( - "--artifact_type", type=str, help="Type for the artifact", required=True - ) - - parser.add_argument( - "--artifact_description", - type=str, - help="Description for the artifact", - required=True, - ) - - args = parser.parse_args() - - go(args) diff --git a/exercise_14/starter/random_forest/MLproject b/exercise_14/starter/random_forest/MLproject deleted file mode 100644 index 09b52a1..0000000 --- a/exercise_14/starter/random_forest/MLproject +++ /dev/null @@ -1,35 +0,0 @@ -name: decision_tree -conda_env: conda.yml - -entry_points: - main: - parameters: - train_data: - description: Fully-qualified name for the training data artifact - type: str - model_config: - description: JSON blurb containing the configuration for the decision tree - type: str - export_artifact: - description: Name for the artifact to use for the model export. Use "null" if you do not want to export. - type: str - default: null - random_seed: - description: Seed for the random number generator. - type: str - default: 42 - val_size: - description: Size for the validation set as a fraction of the training set - type: number - default: 0.3 - stratify: - description: "Name of a column to be used for stratified sampling. Default: 'null', i.e., no stratification" - type: str - default: null - command: >- - python run.py --train_data {train_data} \ - --model_config {model_config} \ - --export_artifact {export_artifact} \ - --random_seed {random_seed} \ - --val_size {val_size} \ - --stratify {stratify} diff --git a/exercise_14/starter/random_forest/run.py b/exercise_14/starter/random_forest/run.py deleted file mode 100644 index 06cade8..0000000 --- a/exercise_14/starter/random_forest/run.py +++ /dev/null @@ -1,263 +0,0 @@ -#!/usr/bin/env python -import argparse -import itertools -import logging -import os - -import yaml -import tempfile -import mlflow -import pandas as pd -import numpy as np -from mlflow.models import infer_signature -from sklearn.compose import ColumnTransformer -from sklearn.ensemble import RandomForestClassifier -from sklearn.feature_extraction.text import TfidfVectorizer -from sklearn.metrics import roc_auc_score, plot_confusion_matrix -from sklearn.model_selection import train_test_split -from sklearn.preprocessing import OrdinalEncoder, StandardScaler, FunctionTransformer -import matplotlib.pyplot as plt -import wandb -from sklearn.pipeline import Pipeline, make_pipeline -from sklearn.impute import SimpleImputer - -logging.basicConfig(level=logging.INFO, format="%(asctime)-15s %(message)s") -logger = logging.getLogger() - - -def go(args): - - run = wandb.init(job_type="train") - - logger.info("Downloading and reading train artifact") - train_data_path = run.use_artifact(args.train_data).file() - df = pd.read_csv(train_data_path, low_memory=False) - - # Extract the target from the features - logger.info("Extracting target from dataframe") - X = df.copy() - y = X.pop("genre") - - logger.info("Splitting train/val") - X_train, X_val, y_train, y_val = train_test_split( - X, - y, - test_size=args.val_size, - stratify=df[args.stratify] if args.stratify != "null" else None, - random_state=args.random_seed, - ) - - logger.info("Setting up pipeline") - - pipe, used_columns = get_training_inference_pipeline(args) - - logger.info("Fitting") - pipe.fit(X_train[used_columns], y_train) - - # Evaluate - pred = pipe.predict(X_val[used_columns]) - pred_proba = pipe.predict_proba(X_val[used_columns]) - - logger.info("Scoring") - score = roc_auc_score(y_val, pred_proba, average="macro", multi_class="ovo") - - run.summary["AUC"] = score - - # Export if required - if args.export_artifact != "null": - - export_model(run, pipe, used_columns, X_val, pred, args.export_artifact) - - # Some useful plots - fig_feat_imp = plot_feature_importance(pipe) - - fig_cm, sub_cm = plt.subplots(figsize=(10, 10)) - plot_confusion_matrix( - pipe, - X_val[used_columns], - y_val, - ax=sub_cm, - normalize="true", - values_format=".1f", - xticks_rotation=90, - ) - fig_cm.tight_layout() - - run.log( - { - "feature_importance": wandb.Image(fig_feat_imp), - "confusion_matrix": wandb.Image(fig_cm), - } - ) - - -def export_model(run, pipe, used_columns, X_val, val_pred, export_artifact): - - # Infer the signature of the model - - # Get the columns that we are really using from the pipeline - signature = infer_signature(X_val[used_columns], val_pred) - - with tempfile.TemporaryDirectory() as temp_dir: - - export_path = os.path.join(temp_dir, "model_export") - - mlflow.sklearn.save_model( - pipe, - export_path, - serialization_format=mlflow.sklearn.SERIALIZATION_FORMAT_CLOUDPICKLE, - signature=signature, - input_example=X_val.iloc[:2], - ) - - artifact = wandb.Artifact( - export_artifact, - type="model_export", - description="Random Forest pipeline export", - ) - artifact.add_dir(export_path) - - run.log_artifact(artifact) - - # Make sure the artifact is uploaded before the temp dir - # gets deleted - artifact.wait() - - -def plot_feature_importance(pipe): - - # We collect the feature importance for all non-nlp features first - feat_names = np.array( - pipe["preprocessor"].transformers[0][-1] - + pipe["preprocessor"].transformers[1][-1] - ) - feat_imp = pipe["classifier"].feature_importances_[: len(feat_names)] - # For the NLP feature we sum across all the TF-IDF dimensions into a global - # NLP importance - nlp_importance = sum(pipe["classifier"].feature_importances_[len(feat_names) :]) - feat_imp = np.append(feat_imp, nlp_importance) - feat_names = np.append(feat_names, "title + song_name") - fig_feat_imp, sub_feat_imp = plt.subplots(figsize=(10, 10)) - idx = np.argsort(feat_imp)[::-1] - sub_feat_imp.bar(range(feat_imp.shape[0]), feat_imp[idx], color="r", align="center") - _ = sub_feat_imp.set_xticks(range(feat_imp.shape[0])) - _ = sub_feat_imp.set_xticklabels(feat_names[idx], rotation=90) - fig_feat_imp.tight_layout() - return fig_feat_imp - - -def get_training_inference_pipeline(args): - - # Get the configuration for the pipeline - with open(args.model_config) as fp: - model_config = yaml.safe_load(fp) - # Add it to the W&B configuration so the values for the hyperparams - # are tracked - wandb.config.update(model_config) - - # We need 3 separate preprocessing "tracks": - # - one for categorical features - # - one for numerical features - # - one for textual ("nlp") features - # Categorical preprocessing pipeline - categorical_features = sorted(model_config["features"]["categorical"]) - categorical_transformer = make_pipeline( - SimpleImputer(strategy="constant", fill_value=0), OrdinalEncoder() - ) - # Numerical preprocessing pipeline - numeric_features = sorted(model_config["features"]["numerical"]) - numeric_transformer = make_pipeline( - SimpleImputer(strategy="median"), StandardScaler() - ) - # Textual ("nlp") preprocessing pipeline - nlp_features = sorted(model_config["features"]["nlp"]) - # This trick is needed because SimpleImputer wants a 2d input, but - # TfidfVectorizer wants a 1d input. So we reshape in between the two steps - reshape_to_1d = FunctionTransformer(np.reshape, kw_args={"newshape": -1}) - nlp_transformer = make_pipeline( - SimpleImputer(strategy="constant", fill_value=""), - reshape_to_1d, - TfidfVectorizer( - binary=True, max_features=model_config["tfidf"]["max_features"] - ), - ) - # Put the 3 tracks together into one pipeline using the ColumnTransformer - # This also drops the columns that we are not explicitly transforming - preprocessor = ColumnTransformer( - transformers=[ - ("num", numeric_transformer, numeric_features), - ("cat", categorical_transformer, categorical_features), - ("nlp1", nlp_transformer, nlp_features), - ], - remainder="drop", # This drops the columns that we do not transform - ) - - # Get a list of the columns we used - used_columns = list(itertools.chain.from_iterable([x[2] for x in preprocessor.transformers])) - - # Append classifier to preprocessing pipeline. - # Now we have a full prediction pipeline. - pipe = Pipeline( - steps=[ - ("preprocessor", preprocessor), - ("classifier", RandomForestClassifier(**model_config["random_forest"])), - ] - ) - return pipe, used_columns - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Train a Random Forest", - fromfile_prefix_chars="@", - ) - - parser.add_argument( - "--train_data", - type=str, - help="Fully-qualified name for the training data artifact", - required=True, - ) - - parser.add_argument( - "--model_config", - type=str, - help="Path to a YAML file containing the configuration for the random forest", - required=True, - ) - - parser.add_argument( - "--export_artifact", - type=str, - help="Name of the artifact for the exported model. Use 'null' for no export.", - required=False, - default="null", - ) - - parser.add_argument( - "--random_seed", - type=int, - help="Seed for the random number generator.", - required=False, - default=42 - ) - - parser.add_argument( - "--val_size", - type=float, - help="Size for the validation set as a fraction of the training set", - required=False, - default=0.3 - ) - - parser.add_argument( - "--stratify", - type=str, - help="Name of a column to be used for stratified sampling. Default: 'null', i.e., no stratification", - required=False, - default="null", - ) - - args = parser.parse_args() - - go(args) diff --git a/exercise_14/starter/segregate/MLproject b/exercise_14/starter/segregate/MLproject deleted file mode 100644 index cd86a73..0000000 --- a/exercise_14/starter/segregate/MLproject +++ /dev/null @@ -1,35 +0,0 @@ -name: split_data -conda_env: conda.yml - -entry_points: - main: - parameters: - input_artifact: - description: Fully qualified name for the artifact - type: str - artifact_root: - description: Name for the W&B artifact that will be created - type: str - artifact_type: - description: Type of the artifact to create - type: str - default: raw_data - test_size: - description: Description for the artifact - type: float - random_state: - description: Integer to use to seed the random number generator - type: str - default: 42 - stratify: - description: If provided, it is considered a column name to be used for stratified splitting - type: str - default: "null" - - command: >- - python run.py --input_artifact {input_artifact} \ - --artifact_root {artifact_root} \ - --artifact_type {artifact_type} \ - --test_size {test_size} \ - --random_state {random_state} \ - --stratify {stratify} diff --git a/exercise_14/starter/segregate/run.py b/exercise_14/starter/segregate/run.py deleted file mode 100644 index f5af1f6..0000000 --- a/exercise_14/starter/segregate/run.py +++ /dev/null @@ -1,122 +0,0 @@ -#!/usr/bin/env python -import argparse -import logging -import os -import tempfile - -import pandas as pd -import wandb -from sklearn.model_selection import train_test_split - - -logging.basicConfig(level=logging.INFO, format="%(asctime)-15s %(message)s") -logger = logging.getLogger() - - -def go(args): - - run = wandb.init(job_type="split_data") - - logger.info("Downloading and reading artifact") - artifact = run.use_artifact(args.input_artifact) - artifact_path = artifact.file() - - df = pd.read_csv(artifact_path, low_memory=False) - - # Split first in model_dev/test, then we further divide model_dev in train and validation - logger.info("Splitting data into train, val and test") - splits = {} - - splits["train"], splits["test"] = train_test_split( - df, - test_size=args.test_size, - random_state=args.random_state, - stratify=df[args.stratify] if args.stratify != 'null' else None, - ) - - # Save the artifacts. We use a temporary directory so we do not leave - # any trace behind - with tempfile.TemporaryDirectory() as tmp_dir: - - for split, df in splits.items(): - - # Make the artifact name from the provided root plus the name of the split - artifact_name = f"{args.artifact_root}_{split}.csv" - - # Get the path on disk within the temp directory - temp_path = os.path.join(tmp_dir, artifact_name) - - logger.info(f"Uploading the {split} dataset to {artifact_name}") - - # Save then upload to W&B - df.to_csv(temp_path) - - artifact = wandb.Artifact( - name=artifact_name, - type=args.artifact_type, - description=f"{split} split of dataset {args.input_artifact}", - ) - artifact.add_file(temp_path) - - logger.info("Logging artifact") - run.log_artifact(artifact) - - # This waits for the artifact to be uploaded to W&B. If you - # do not add this, the temp directory might be removed before - # W&B had a chance to upload the datasets, and the upload - # might fail - artifact.wait() - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - description="Split a dataset into train and test", - fromfile_prefix_chars="@", - ) - - parser.add_argument( - "--input_artifact", - type=str, - help="Fully-qualified name for the input artifact", - required=True, - ) - - parser.add_argument( - "--artifact_root", - type=str, - help="Root for the names of the produced artifacts. The script will produce 2 artifacts: " - "{root}_train.csv and {root}_test.csv", - required=True, - ) - - parser.add_argument( - "--artifact_type", type=str, help="Type for the produced artifacts", required=True - ) - - parser.add_argument( - "--test_size", - help="Fraction of dataset or number of items to include in the test split", - type=float, - required=True - ) - - parser.add_argument( - "--random_state", - help="An integer number to use to init the random number generator. It ensures repeatibility in the" - "splitting", - type=int, - required=False, - default=42 - ) - - parser.add_argument( - "--stratify", - help="If set, it is the name of a column to use for stratified splitting", - type=str, - required=False, - default='null' # unfortunately mlflow does not support well optional parameters - ) - - args = parser.parse_args() - - go(args) diff --git a/exercise_14/starter/main.py b/main.py similarity index 100% rename from exercise_14/starter/main.py rename to main.py diff --git a/exercise_14/starter/mlruns/0/0a728757eeef474e8f562d34e37abb94/meta.yaml b/mlruns/0/0a728757eeef474e8f562d34e37abb94/meta.yaml similarity index 100% rename from exercise_14/starter/mlruns/0/0a728757eeef474e8f562d34e37abb94/meta.yaml rename to mlruns/0/0a728757eeef474e8f562d34e37abb94/meta.yaml diff --git a/exercise_14/starter/mlruns/0/0a728757eeef474e8f562d34e37abb94/params/hydra_options b/mlruns/0/0a728757eeef474e8f562d34e37abb94/params/hydra_options similarity index 100% rename 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