From c9293a7a751cd26001d4a2c0adda389872b320a2 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Sun, 11 Jul 2021 21:57:33 -0400 Subject: [PATCH 01/11] Update train.py --- train.py | 118 ++++++++++++++++++++++++++++++++++++++++++------------- 1 file changed, 90 insertions(+), 28 deletions(-) diff --git a/train.py b/train.py index e37f0eb5..2a90f4fd 100644 --- a/train.py +++ b/train.py @@ -11,43 +11,105 @@ import matplotlib.pyplot as plt from sklearn.impute import SimpleImputer -df = pd.read_csv("data_processed.csv") +### -#### Get features ready to model! -y = df.pop("cons_general").to_numpy() -y[y< 4] = 0 -y[y>= 4] = 1 +df = pd.read_csv('BostonData.csv',header=0) -X = df.to_numpy() -X = preprocessing.scale(X) # Is standard -# Impute NaNs -imp = SimpleImputer(missing_values=np.nan, strategy='mean') -imp.fit(X) -X = imp.transform(X) -# Linear model -clf = LogisticRegression() -yhat = cross_val_predict(clf, X, y, cv=5) -acc = np.mean(yhat==y) -tn, fp, fn, tp = confusion_matrix(y, yhat).ravel() -specificity = tn / (tn+fp) -sensitivity = tp / (tp + fn) -# Now print to file -with open("metrics.json", 'w') as outfile: - json.dump({ "accuracy": acc, "specificity": specificity, "sensitivity":sensitivity}, outfile) +# In[4]: + + +df_correl = df.corr() + -# Let's visualize within several slices of the dataset -score = yhat == y -score_int = [int(s) for s in score] -df['pred_accuracy'] = score_int +# In[5]: + + +####import seaborn as sns +####import matplotlib.pyplot as plt +#plt.figure(figsize=(12,10)) +#sns.heatmap(df_correl,annot=True) -# Bar plot by region sns.set_color_codes("dark") -ax = sns.barplot(x="region", y="pred_accuracy", data=df, palette = "Greens_d") -ax.set(xlabel="Region", ylabel = "Model accuracy") +ax = sns.heatmap(df_correl,annot=True) plt.savefig("by_region.png",dpi=80) + + + +from sklearn.preprocessing import StandardScaler + + +# In[9]: + + +# standardize everything except CHAS and MEDV +features_stdz = list(set(df.columns) - {"CHAS","MEDV"}) + + +# In[10]: + + +std_trans = StandardScaler() +df_trans = pd.DataFrame(std_trans.fit_transform(df[features_stdz]),columns=features_stdz) + + +# In[11]: + + +df0 = df_trans.merge(df[["CHAS","MEDV"]],right_index=True,left_index=True) + + +# In[12]: + + +df0 + + +# In[13]: + + +from sklearn.model_selection import train_test_split + + +# In[14]: + + +X = df0.iloc[:,0:13] +y = df0["MEDV"] + + +# In[15]: + + +X_train,X_test,y_train,y_test = train_test_split(X,y,test_size=0.2) + + +# In[16]: + + +from sklearn.linear_model import LinearRegression +reg = LinearRegression() +model = reg.fit(X_train,y_train) + + +# In[17]: + + +print("y-intercept",model.coef_[0]) + +with open("metrics.json", 'w') as outfile: + json.dump({ "y0": model.coef_[0], outfile) +# In[18]: + +## UNCOMMENT FOR MLFLOW REPORTING +#mlflow.set_experiment(experiment_name="experiment1") +#mlflow.set_tracking_uri("http://localhost:5000") +#with mlflow.start_run(): +# mlflow.log_param("alpha1",model.coef_[0]) +# mlflow.log_param("beta1",model.coef_[1]) + From 6c377a7266757ecee73280629f65fefcf410fd04 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Sun, 11 Jul 2021 22:01:01 -0400 Subject: [PATCH 02/11] Update dvc.yaml --- dvc.yaml | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/dvc.yaml b/dvc.yaml index 84e2efc3..f76b8f3a 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -1,24 +1,11 @@ stages: - get_data: - cmd: python get_data.py - deps: - - get_data.py - outs: - - data_raw.csv - process: - cmd: python process_data.py - deps: - - process_data.py - - data_raw.csv - outs: - - data_processed.csv + train: cmd: python train.py deps: - train.py - - data_processed.csv outs: - by_region.png metrics: - metrics.json: - cache: false \ No newline at end of file + cache: false From 4183331a5d6bd7255c419fa42ab819e094789a3d Mon Sep 17 00:00:00 2001 From: hhurchand Date: Sun, 11 Jul 2021 22:01:45 -0400 Subject: [PATCH 03/11] Add files via upload --- BostonData.csv | 507 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 507 insertions(+) create mode 100644 BostonData.csv diff --git a/BostonData.csv b/BostonData.csv new file mode 100644 index 00000000..069b2150 --- /dev/null +++ b/BostonData.csv @@ -0,0 +1,507 @@ +,CRIM,ZN,INDUS,CHAS,NOX,RM,AGE,DIS,RAD,TAX,PTRATIO,B,LSTAT,MEDV +0,0.00632,18.0,2.31,0,0.5379999999999999,6.575,65.2,4.09,1,296,15.3,396.9,4.98,24.0 +1,0.02731,0.0,7.07,0,0.469,6.421,78.9,4.9671,2,242,17.8,396.9,9.14,21.6 +2,0.02729,0.0,7.07,0,0.469,7.185,61.1,4.9671,2,242,17.8,392.83,4.03,34.7 +3,0.032369999999999996,0.0,2.18,0,0.45799999999999996,6.997999999999999,45.8,6.0622,3,222,18.7,394.63,2.94,33.4 +4,0.06905,0.0,2.18,0,0.45799999999999996,7.147,54.2,6.0622,3,222,18.7,396.9,5.33,36.2 +5,0.02985,0.0,2.18,0,0.45799999999999996,6.43,58.7,6.0622,3,222,18.7,394.12,5.21,28.7 +6,0.08829,12.5,7.87,0,0.524,6.0120000000000005,66.6,5.5605,5,311,15.2,395.6,12.43,22.9 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+504,0.10959,0.0,11.93,0,0.573,6.794,89.3,2.3889,1,273,21.0,393.45,6.48,22.0 +505,0.04741,0.0,11.93,0,0.573,6.03,80.8,2.505,1,273,21.0,396.9,7.88,11.9 From 677d69ca1097affe8da2cd2ca0d7658fb620742f Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 01:25:41 -0400 Subject: [PATCH 04/11] Update train.py New metrics added --- train.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/train.py b/train.py index 2a90f4fd..d7dff2e3 100644 --- a/train.py +++ b/train.py @@ -95,7 +95,13 @@ from sklearn.linear_model import LinearRegression reg = LinearRegression() model = reg.fit(X_train,y_train) +y_pred = model.predict(X_test) +from sklearn.metrics import mean_squared_error, r2_score +import math +mse = mean_squared_error(y_test, y_pred, squared=False) +rmse = math.sqrt(mse) +r2 = r2_score(y_test, y_pred) # In[17]: @@ -103,7 +109,7 @@ print("y-intercept",model.coef_[0]) with open("metrics.json", 'w') as outfile: - json.dump({ "y0": model.coef_[0], outfile) + json.dump({ "MSE": mse, "RMSE":rmse,"R2":r2 }, outfile) # In[18]: ## UNCOMMENT FOR MLFLOW REPORTING From ccaa4a9f38ccca1321786a9a9d0a6deeb5c6fe42 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 01:31:38 -0400 Subject: [PATCH 05/11] Update train.py --- train.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/train.py b/train.py index d7dff2e3..5a2e1c97 100644 --- a/train.py +++ b/train.py @@ -110,6 +110,8 @@ with open("metrics.json", 'w') as outfile: json.dump({ "MSE": mse, "RMSE":rmse,"R2":r2 }, outfile) + +pickle.dump(model,open('model.pkl','wb')) # In[18]: ## UNCOMMENT FOR MLFLOW REPORTING From 5409f066b3e4b6715f5227b88f0a9c49d1c077ec Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 01:34:05 -0400 Subject: [PATCH 06/11] Update train.py Added pickle file --- train.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/train.py b/train.py index 5a2e1c97..b5d131f2 100644 --- a/train.py +++ b/train.py @@ -106,8 +106,6 @@ # In[17]: -print("y-intercept",model.coef_[0]) - with open("metrics.json", 'w') as outfile: json.dump({ "MSE": mse, "RMSE":rmse,"R2":r2 }, outfile) From 858fd0304eba1df01126dd6edea40878edabe44e Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 01:38:25 -0400 Subject: [PATCH 07/11] Create train.py Added missing pickle library --- train.py | 1 + 1 file changed, 1 insertion(+) diff --git a/train.py b/train.py index b5d131f2..564b872d 100644 --- a/train.py +++ b/train.py @@ -10,6 +10,7 @@ import seaborn as sns import matplotlib.pyplot as plt from sklearn.impute import SimpleImputer +import pickle ### From 19610d82bd297bde4412c81e06b99b5149450cb4 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 11:09:45 -0400 Subject: [PATCH 08/11] Create train.py --- train.py | 86 ++++++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 78 insertions(+), 8 deletions(-) diff --git a/train.py b/train.py index 564b872d..6ab2e67e 100644 --- a/train.py +++ b/train.py @@ -1,25 +1,50 @@ import pandas as pd import numpy as np -from sklearn.linear_model import LogisticRegression from sklearn import preprocessing from sklearn.model_selection import cross_val_predict -from sklearn.metrics import confusion_matrix -from sklearn.metrics import roc_curve + from sklearn.model_selection import train_test_split import json import seaborn as sns import matplotlib.pyplot as plt from sklearn.impute import SimpleImputer + +#!/usr/bin/env python +# coding: utf-8 + +# In[1]: + +import os +import lightgbm as lgb +import neptune + +from neptunecontrib.monitoring.lightgbm import neptune_monitor + +import numpy as np +import pandas as pd + import pickle + +import logging +logging.basicConfig(level=logging.WARN) +logger = logging.getLogger(__name__) + -### +# In[2]: +neptune.init(api_token=os.getenv('NEPTUNE_API_TOKEN'), + project_qualified_name=os.getenv('NEPTUNE_PROJECT_NAME')) df = pd.read_csv('BostonData.csv',header=0) +#df.to_csv(r'C:\Users\hhurc\BostonData\BostonData.csv') +# ## EDA +# In[3]: +df.head(5) + # In[4]: @@ -36,12 +61,22 @@ #sns.heatmap(df_correl,annot=True) -sns.set_color_codes("dark") -ax = sns.heatmap(df_correl,annot=True) -plt.savefig("by_region.png",dpi=80) +# In[6]: + +#df.info() +# In[7]: + + +#sns.pairplot(df) + + +# In[8]: + + +#standardize predictors from sklearn.preprocessing import StandardScaler @@ -87,7 +122,15 @@ # In[15]: -X_train,X_test,y_train,y_test = train_test_split(X,y,test_size=0.2) +X_train,X_test,y_train,y_test = train_test_split(X,y,test_size=0.5) + + +neptune.init(api_token=os.getenv('NEPTUNE_API_TOKEN'), + project_qualified_name=os.getenv('NEPTUNE_PROJECT_NAME')) + +neptune.create_experiment('BostonData-NEPTUNE') + + # In[16]: @@ -96,6 +139,8 @@ from sklearn.linear_model import LinearRegression reg = LinearRegression() model = reg.fit(X_train,y_train) +pickle.dump(model,open('model.pkl','wb')) + y_pred = model.predict(X_test) from sklearn.metrics import mean_squared_error, r2_score @@ -104,9 +149,34 @@ rmse = math.sqrt(mse) r2 = r2_score(y_test, y_pred) +neptune.log_metric('mse',mse) +neptune.log_metric('rmse', rmse) +neptune.log_metric('r2', r2) # In[17]: +print("y-intercept",model.coef_[0]) + + +# In[18]: + +## UNCOMMENT FOR MLFLOW REPORTING +#mlflow.set_experiment(experiment_name="experiment1") +#mlflow.set_tracking_uri("http://localhost:5000") +#with mlflow.start_run(): +# mlflow.log_param("alpha1",model.coef_[0]) +# mlflow.log_param("beta1",model.coef_[1]) + + +# In[ ]: + +if os.getenv('CI') == "true": + neptune.append_tag('ci-pipeline', os.getenv('NEPTUNE_EXPERIMENT_TAG_ID')) + + + + + with open("metrics.json", 'w') as outfile: json.dump({ "MSE": mse, "RMSE":rmse,"R2":r2 }, outfile) From 99b66f7a91b286f634199cff87adacaface6dc00 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 11:25:47 -0400 Subject: [PATCH 09/11] Update train.yaml --- .github/workflows/train.yaml | 69 +++++++++++++++++++++++++++++++++++- 1 file changed, 68 insertions(+), 1 deletion(-) diff --git a/.github/workflows/train.yaml b/.github/workflows/train.yaml index bc1f8001..9cc40044 100644 --- a/.github/workflows/train.yaml +++ b/.github/workflows/train.yaml @@ -1,5 +1,72 @@ name: farmers + on: [push] + +jobs: + compare-experiments: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.7] + env: + NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_API_TOKEN }} + NEPTUNE_PROJECT_NAME: ${{ secrets.NEPTUNE_PROJECT_NAME }} + + steps: + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + + - name: Checkout pull request branch + uses: actions/checkout@v2 + with: + ref: newNeptune + + - name: Setup pull request branch environment and run experiment + id: experiment_pr + run: | + echo "Hello2" + pip install -r requirements.txt + export NEPTUNE_EXPERIMENT_TAG_ID=$(uuidgen) + python train.py + echo ::set-output name=experiment_tag_id::$NEPTUNE_EXPERIMENT_TAG_ID + + - name: Checkout main branch + uses: actions/checkout@v2 + with: + ref: master + + - name: Setup main branch environment and run experiment + id: experiment_main + run: | + pip install -r requirements.txt + export NEPTUNE_EXPERIMENT_TAG_ID=$(uuidgen) + python train.py + echo ::set-output name=experiment_tag_id::$NEPTUNE_EXPERIMENT_TAG_ID + + - name: Get Neptune experiments + env: + MAIN_BRANCH_EXPERIMENT_TAG_ID: ${{ steps.experiment_main.outputs.experiment_tag_id }} + PR_BRANCH_EXPERIMENT_TAG_ID: ${{ steps.experiment_pr.outputs.experiment_tag_id }} + id: compare + run: | + pip install -r requirements.txt + python -m neptunecontrib.create_experiment_comparison_comment \ + --api_token $NEPTUNE_API_TOKEN \ + --project_name $NEPTUNE_PROJECT_NAME \ + --tag_names $MAIN_BRANCH_EXPERIMENT_TAG_ID $PR_BRANCH_EXPERIMENT_TAG_ID \ + --filepath comment_body.md + result=$(cat comment_body.md) + echo ::set-output name=result::$result + + - name: Create a comment + uses: peter-evans/commit-comment@v1 + with: + body: | + ${{ steps.compare.outputs.result }} + + jobs: run: runs-on: [ubuntu-latest] @@ -19,4 +86,4 @@ jobs: # Add figure to the report echo "## Validating results by region" cml-publish by_region.png --md >> report.md - cml-send-comment report.md \ No newline at end of file + cml-send-comment report.md From 878636201743b9bce8a3232fae66b22624347704 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 11:30:26 -0400 Subject: [PATCH 10/11] Update train.py --- train.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/train.py b/train.py index 6ab2e67e..057dad69 100644 --- a/train.py +++ b/train.py @@ -189,4 +189,5 @@ #with mlflow.start_run(): # mlflow.log_param("alpha1",model.coef_[0]) # mlflow.log_param("beta1",model.coef_[1]) - +if os.getenv('CI') == "true": + neptune.append_tag('ci-pipeline', os.getenv('NEPTUNE_EXPERIMENT_TAG_ID')) From c65a27008242d243145f9372c3b078699fcc5531 Mon Sep 17 00:00:00 2001 From: hhurchand Date: Mon, 12 Jul 2021 11:32:02 -0400 Subject: [PATCH 11/11] Update requirements.txt --- requirements.txt | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 51f3da2a..6bcdfa00 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,10 @@ wget -sklearn pandas seaborn matplotlib +lightgbm==2.3.1 +neptune-client>=0.9.8 +neptune-contrib==0.24.8 +numpy==1.19.0 +scikit-learn==0.23.1 +scikit-plot==0.3.7