Merge pull request #38 from eXascaleInfolab/naterq_soutenance

1. refactoring and testing

.github/workflows/pytest_contamination.yml

@@ -1,4 +1,4 @@
-name: Pytest - ImputeGAP - Contamination - MCAR - 12
+name: Pytest - ImputeGAP - Contamination - 12
 
 on:
   push:

.github/workflows/pytest_imputation.yml

@@ -1,4 +1,3 @@
-
 name: Pytest - ImputeGAP - IMPUTATION - 12
 
 on:
@@ -8,30 +7,23 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
-
     steps:
     - uses: actions/checkout@v3
       with:
         lfs: true
-
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.12'
-
     - name: Install dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install libmlpack-dev
-        sudo apt-get install libopenblas-dev
-        sudo apt-get install python3-dev build-essential
+        sudo apt-get install -y libmlpack-dev libopenblas-dev python3-dev build-essential
         pip install -r requirements.txt
-        pip install mypy
-        pip install pytest
-
+        pip install mypy pytest
     - name: Run pytest
       run: |
         python -m pytest ./tests/test_imputation_cdrec.py
         python -m pytest ./tests/test_imputation_iim.py
         python -m pytest ./tests/test_imputation_mrnn.py
-        python -m pytest ./tests/test_imputation_stmvl.py
+        python -m pytest ./tests/test_imputation_stmvl.py

README.md

@@ -8,7 +8,7 @@ ImputeGAP is a comprehensive framework designed for time series imputation algor
 ![Python](https://img.shields.io/badge/Python-v3.12-blue) 
 ![Release](https://img.shields.io/badge/Release-v0.2.2-brightgreen) 
 ![License](https://img.shields.io/badge/License-GPLv3-blue?style=flat&logo=gnu)
-![Coverage](https://img.shields.io/badge/Coverage-91%25-brightgreen)
+![Coverage](https://img.shields.io/badge/Coverage-93%25-brightgreen)
 ![PyPI](https://img.shields.io/pypi/v/imputegap?label=PyPI&color=blue)
 ![Language](https://img.shields.io/badge/Language-English-blue)
 ![Platform](https://img.shields.io/badge/platform-Windows%20%7C%20Linux%20%7C%20MacOS-informational)

build/lib/imputegap/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

build/lib/imputegap/assets/shap/chlorine_cdrec_results.txt

@@ -1,22 +1,22 @@
-Feature : 6     cdrec      with a score of 58.98      Geometry           Proportion of high incremental changes in the series              MD_hrv_classic_pnn40
-Feature : 5     cdrec      with a score of 9.1        Correlation        Time reversibility                                                CO_trev_1_num
-Feature : 2     cdrec      with a score of 6.02       Correlation        First 1/e crossing of the ACF                                     CO_f1ecac
-Feature : 1     cdrec      with a score of 4.52       Geometry           10-bin histogram mode                                             DN_HistogramMode_10
-Feature : 10    cdrec      with a score of 4.42       Geometry           Goodness of exponential fit to embedding distance distribution    CO_Embed2_Dist_tau_d_expfit_meandiff
-Feature : 15    cdrec      with a score of 4.1        Transformation     Power in the lowest 20% of frequencies                            SP_Summaries_welch_rect_area_5_1
-Feature : 21    cdrec      with a score of 3.56       Trend              Error of 3-point rolling mean forecast                            FC_LocalSimple_mean3_stderr
-Feature : 12    cdrec      with a score of 3.44       Correlation        Change in autocorrelation timescale after incremental differencing FC_LocalSimple_mean1_tauresrat
-Feature : 0     cdrec      with a score of 2.64       Geometry           5-bin histogram mode                                              DN_HistogramMode_5
-Feature : 17    cdrec      with a score of 1.41       Trend              Entropy of successive pairs in symbolized series                  SB_MotifThree_quantile_hh
-Feature : 4     cdrec      with a score of 0.86       Correlation        Histogram-based automutual information (lag 2, 5 bins)            CO_HistogramAMI_even_2_5
-Feature : 8     cdrec      with a score of 0.48       Geometry           Transition matrix column variance                                 SB_TransitionMatrix_3ac_sumdiagcov
-Feature : 13    cdrec      with a score of 0.46       Geometry           Positive outlier timing                                           DN_OutlierInclude_p_001_mdrmd
-Feature : 14    cdrec      with a score of 0.01       Geometry           Negative outlier timing                                           DN_OutlierInclude_n_001_mdrmd
-Feature : 3     cdrec      with a score of 0.0        Correlation        First minimum of the ACF                                          CO_FirstMin_ac
+Feature : 1     cdrec      with a score of 90.54      Geometry           10-bin histogram mode                                             DN_HistogramMode_10
+Feature : 12    cdrec      with a score of 3.99       Correlation        Change in autocorrelation timescale after incremental differencing FC_LocalSimple_mean1_tauresrat
+Feature : 5     cdrec      with a score of 3.83       Correlation        Time reversibility                                                CO_trev_1_num
+Feature : 18    cdrec      with a score of 0.57       Geometry           Rescaled range fluctuation analysis (low-scale scaling)           SC_FluctAnal_2_rsrangefit_50_1_logi_prop_r1
+Feature : 13    cdrec      with a score of 0.37       Geometry           Positive outlier timing                                           DN_OutlierInclude_p_001_mdrmd
+Feature : 3     cdrec      with a score of 0.33       Correlation        First minimum of the ACF                                          CO_FirstMin_ac
+Feature : 14    cdrec      with a score of 0.29       Geometry           Negative outlier timing                                           DN_OutlierInclude_n_001_mdrmd
+Feature : 6     cdrec      with a score of 0.09       Geometry           Proportion of high incremental changes in the series              MD_hrv_classic_pnn40
+Feature : 0     cdrec      with a score of 0.0        Geometry           5-bin histogram mode                                              DN_HistogramMode_5
+Feature : 2     cdrec      with a score of 0.0        Correlation        First 1/e crossing of the ACF                                     CO_f1ecac
+Feature : 4     cdrec      with a score of 0.0        Correlation        Histogram-based automutual information (lag 2, 5 bins)            CO_HistogramAMI_even_2_5
 Feature : 7     cdrec      with a score of 0.0        Geometry           Longest stretch of above-mean values                              SB_BinaryStats_mean_longstretch1
+Feature : 8     cdrec      with a score of 0.0        Geometry           Transition matrix column variance                                 SB_TransitionMatrix_3ac_sumdiagcov
 Feature : 9     cdrec      with a score of 0.0        Trend              Wangs periodicity metric                                          PD_PeriodicityWang_th0_01
+Feature : 10    cdrec      with a score of 0.0        Geometry           Goodness of exponential fit to embedding distance distribution    CO_Embed2_Dist_tau_d_expfit_meandiff
 Feature : 11    cdrec      with a score of 0.0        Correlation        First minimum of the AMI function                                 IN_AutoMutualInfoStats_40_gaussian_fmmi
+Feature : 15    cdrec      with a score of 0.0        Transformation     Power in the lowest 20% of frequencies                            SP_Summaries_welch_rect_area_5_1
 Feature : 16    cdrec      with a score of 0.0        Geometry           Longest stretch of decreasing values                              SB_BinaryStats_diff_longstretch0
-Feature : 18    cdrec      with a score of 0.0        Geometry           Rescaled range fluctuation analysis (low-scale scaling)           SC_FluctAnal_2_rsrangefit_50_1_logi_prop_r1
+Feature : 17    cdrec      with a score of 0.0        Trend              Entropy of successive pairs in symbolized series                  SB_MotifThree_quantile_hh
 Feature : 19    cdrec      with a score of 0.0        Geometry           Detrended fluctuation analysis (low-scale scaling)                SC_FluctAnal_2_dfa_50_1_2_logi_prop_r1
 Feature : 20    cdrec      with a score of 0.0        Transformation     Centroid frequency                                                SP_Summaries_welch_rect_centroid
+Feature : 21    cdrec      with a score of 0.0        Trend              Error of 3-point rolling mean forecast                            FC_LocalSimple_mean3_stderr

build/lib/imputegap/assets/shap/fmri-objectviewing_cdrec_results.txt

@@ -0,0 +1,22 @@
+Feature : 1     cdrec      with a score of 33.18      Geometry           10-bin histogram mode                                             DN_HistogramMode_10
+Feature : 0     cdrec      with a score of 31.45      Geometry           5-bin histogram mode                                              DN_HistogramMode_5
+Feature : 6     cdrec      with a score of 8.37       Geometry           Proportion of high incremental changes in the series              MD_hrv_classic_pnn40
+Feature : 5     cdrec      with a score of 7.89       Correlation        Time reversibility                                                CO_trev_1_num
+Feature : 2     cdrec      with a score of 4.04       Correlation        First 1/e crossing of the ACF                                     CO_f1ecac
+Feature : 21    cdrec      with a score of 3.72       Trend              Error of 3-point rolling mean forecast                            FC_LocalSimple_mean3_stderr
+Feature : 13    cdrec      with a score of 2.65       Geometry           Positive outlier timing                                           DN_OutlierInclude_p_001_mdrmd
+Feature : 17    cdrec      with a score of 2.16       Trend              Entropy of successive pairs in symbolized series                  SB_MotifThree_quantile_hh
+Feature : 15    cdrec      with a score of 2.02       Transformation     Power in the lowest 20% of frequencies                            SP_Summaries_welch_rect_area_5_1
+Feature : 4     cdrec      with a score of 1.76       Correlation        Histogram-based automutual information (lag 2, 5 bins)            CO_HistogramAMI_even_2_5
+Feature : 10    cdrec      with a score of 1.32       Geometry           Goodness of exponential fit to embedding distance distribution    CO_Embed2_Dist_tau_d_expfit_meandiff
+Feature : 12    cdrec      with a score of 0.76       Correlation        Change in autocorrelation timescale after incremental differencing FC_LocalSimple_mean1_tauresrat
+Feature : 14    cdrec      with a score of 0.36       Geometry           Negative outlier timing                                           DN_OutlierInclude_n_001_mdrmd
+Feature : 8     cdrec      with a score of 0.33       Geometry           Transition matrix column variance                                 SB_TransitionMatrix_3ac_sumdiagcov
+Feature : 3     cdrec      with a score of 0.0        Correlation        First minimum of the ACF                                          CO_FirstMin_ac
+Feature : 7     cdrec      with a score of 0.0        Geometry           Longest stretch of above-mean values                              SB_BinaryStats_mean_longstretch1
+Feature : 9     cdrec      with a score of 0.0        Trend              Wangs periodicity metric                                          PD_PeriodicityWang_th0_01
+Feature : 11    cdrec      with a score of 0.0        Correlation        First minimum of the AMI function                                 IN_AutoMutualInfoStats_40_gaussian_fmmi
+Feature : 16    cdrec      with a score of 0.0        Geometry           Longest stretch of decreasing values                              SB_BinaryStats_diff_longstretch0
+Feature : 18    cdrec      with a score of 0.0        Geometry           Rescaled range fluctuation analysis (low-scale scaling)           SC_FluctAnal_2_rsrangefit_50_1_logi_prop_r1
+Feature : 19    cdrec      with a score of 0.0        Geometry           Detrended fluctuation analysis (low-scale scaling)                SC_FluctAnal_2_dfa_50_1_2_logi_prop_r1
+Feature : 20    cdrec      with a score of 0.0        Transformation     Centroid frequency                                                SP_Summaries_welch_rect_centroid

build/lib/imputegap/assets/shap/fmri-objectviewing_iim_results.txt

@@ -0,0 +1,22 @@
+Feature : 0     iim        with a score of 34.56      Geometry           5-bin histogram mode                                              DN_HistogramMode_5
+Feature : 1     iim        with a score of 25.08      Geometry           10-bin histogram mode                                             DN_HistogramMode_10
+Feature : 4     iim        with a score of 14.99      Correlation        Histogram-based automutual information (lag 2, 5 bins)            CO_HistogramAMI_even_2_5
+Feature : 15    iim        with a score of 7.09       Transformation     Power in the lowest 20% of frequencies                            SP_Summaries_welch_rect_area_5_1
+Feature : 21    iim        with a score of 6.78       Trend              Error of 3-point rolling mean forecast                            FC_LocalSimple_mean3_stderr
+Feature : 5     iim        with a score of 6.36       Correlation        Time reversibility                                                CO_trev_1_num
+Feature : 6     iim        with a score of 1.45       Geometry           Proportion of high incremental changes in the series              MD_hrv_classic_pnn40
+Feature : 14    iim        with a score of 0.94       Geometry           Negative outlier timing                                           DN_OutlierInclude_n_001_mdrmd
+Feature : 10    iim        with a score of 0.9        Geometry           Goodness of exponential fit to embedding distance distribution    CO_Embed2_Dist_tau_d_expfit_meandiff
+Feature : 17    iim        with a score of 0.73       Trend              Entropy of successive pairs in symbolized series                  SB_MotifThree_quantile_hh
+Feature : 2     iim        with a score of 0.66       Correlation        First 1/e crossing of the ACF                                     CO_f1ecac
+Feature : 8     iim        with a score of 0.23       Geometry           Transition matrix column variance                                 SB_TransitionMatrix_3ac_sumdiagcov
+Feature : 12    iim        with a score of 0.2        Correlation        Change in autocorrelation timescale after incremental differencing FC_LocalSimple_mean1_tauresrat
+Feature : 13    iim        with a score of 0.03       Geometry           Positive outlier timing                                           DN_OutlierInclude_p_001_mdrmd
+Feature : 3     iim        with a score of 0.0        Correlation        First minimum of the ACF                                          CO_FirstMin_ac
+Feature : 7     iim        with a score of 0.0        Geometry           Longest stretch of above-mean values                              SB_BinaryStats_mean_longstretch1
+Feature : 9     iim        with a score of 0.0        Trend              Wangs periodicity metric                                          PD_PeriodicityWang_th0_01
+Feature : 11    iim        with a score of 0.0        Correlation        First minimum of the AMI function                                 IN_AutoMutualInfoStats_40_gaussian_fmmi
+Feature : 16    iim        with a score of 0.0        Geometry           Longest stretch of decreasing values                              SB_BinaryStats_diff_longstretch0
+Feature : 18    iim        with a score of 0.0        Geometry           Rescaled range fluctuation analysis (low-scale scaling)           SC_FluctAnal_2_rsrangefit_50_1_logi_prop_r1
+Feature : 19    iim        with a score of 0.0        Geometry           Detrended fluctuation analysis (low-scale scaling)                SC_FluctAnal_2_dfa_50_1_2_logi_prop_r1
+Feature : 20    iim        with a score of 0.0        Transformation     Centroid frequency                                                SP_Summaries_welch_rect_centroid