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Merge pull request #59 from YeChen-IDM/fix_51_57
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Change for #51, #56 and #57
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YeChen-IDM authored Jan 13, 2023
2 parents 31262a7 + 6820fb9 commit 346dc03
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Showing 66 changed files with 1,702 additions and 84 deletions.
39 changes: 21 additions & 18 deletions .github/workflows/build_test_ubuntu.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,28 +25,31 @@ jobs:
run: |
echo "upgrade pip"
python3 --version
python --version
python3 -m pip install --upgrade pip
shell: bash
- id: build
name: Build package
# - id: build
# name: Build package
# run: |
# python3 setup.py bdist_wheel
# - id: wheel
# run: python3 ./.github/scripts/get_wheel_filename.py --package-file setup.py --set-gh-actions-var wheel-file
# shell: bash
# - id: install
# name: install package
# run: |
# pip install ${{ steps.wheel.outputs.wheel-file }} --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
# # todo: remove this after emodpy-malaria has a new release
# pip install emod-malaria --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple --force-reinstall --no-cache-dir
# pip freeze
- name: installation
run: |
python3 setup.py bdist_wheel
- id: wheel
run: python3 ./.github/scripts/get_wheel_filename.py --package-file setup.py --set-gh-actions-var wheel-file
shell: bash
- id: install
name: install package
run: |
pip install ${{ steps.wheel.outputs.wheel-file }} --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
# todo: remove this after emodpy-malaria has a new release
pip install emod-malaria --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple --force-reinstall --no-cache-dir
pip install -e . -r requirements.txt
pip freeze
- name: run tests
run: python3 -m unittest discover .
working-directory: ./tests
- name: Add wheel to artifact
uses: actions/upload-artifact@v2
with:
name: idm_test.wheel
path: ${{ steps.wheel.outputs.wheel-file }}
# - name: Add wheel to artifact
# uses: actions/upload-artifact@v2
# with:
# name: idm_test.wheel
# path: ${{ steps.wheel.outputs.wheel-file }}
8 changes: 7 additions & 1 deletion create_plots/run_generate_validation_comparisons_site.py
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from simulations.manifest import simulation_output_filepath, benchmark_simulation_filepath, \
base_reference_filepath, plot_output_filepath, comps_id_folder
from simulations.helpers import load_coordinator_df
from simulations.get_version import get_era_version_from_file
from create_plots.helpers_coordinate_each_relationship import generate_age_incidence_outputs, \
generate_age_prevalence_outputs, generate_parasite_density_outputs, generate_infectiousness_outputs, \
generate_age_infection_duration_outputs
Expand All @@ -16,6 +17,11 @@
import argparse
import os

era_version = get_era_version_from_file()
simulation_output_filepath = simulation_output_filepath.parent / (simulation_output_filepath.name + "_" + era_version)
if not os.path.exists(benchmark_simulation_filepath):
benchmark_simulation_filepath = simulation_output_filepath


def run(subset="All"):
# read in data and create plots
Expand Down Expand Up @@ -76,7 +82,7 @@ def run(subset="All"):
# generate dummy file for snakemake plot rule.
if not os.path.isdir(comps_id_folder):
os.mkdir(comps_id_folder)
with open(comps_id_folder + 'plot_completed', 'w') as file:
with open(comps_id_folder / 'plot_completed', 'w') as file:
file.write('Plotting is completed.')


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12 changes: 6 additions & 6 deletions report/_plots_Python/comparison_metric_table_incidence_age.csv
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
chonyi_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.439261308486312,0.14796578722119708
dielmo_1990,1.4081812654541295,1.2458223958828656,1.4662896933383196,0.9136326384809177,2.788786163966403,0.3311051298078479
dongubougou_1999,0.20347658923882472,0.20058805816706715,1.0841408131583619,0.8655226920015985,0.5908511281184664,0.05591566317290126
chonyi_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.43926130848631,0.14796578722119694
dielmo_1990,1.4081812654541295,1.2458223958828658,1.4662896933383196,0.9136326384809175,2.7887861639664027,0.33110512980784806
dongubougou_1999,0.20347658923882464,0.20058805816706704,1.0841408131583619,0.8655226920015985,0.5908511281184662,0.055915663172901246
ebolakounou_1997,3.5298250987213704,1.3500864647430642,1.591015084482229,0.36079816878572557,5.540963413406026,0.09385532642413291
koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.583784813025154,4.061363882148547,0.2988974553053057
ndiop_1993,0.46935752353216675,0.5183624018079345,1.3707184658549694,0.8617239579850393,1.4238643917237108,0.06385891135139789
ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632832
koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.5837848130251536,4.061363882148547,0.29889745530530576
ndiop_1993,0.46935752353216664,0.5183624018079344,1.3707184658549694,0.8617239579850393,1.4238643917237106,0.06385891135139789
ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632835
sotuba_1999,0.3696682793427051,0.5674355266406905,0.07836804114542992,0.018623563537865394,1.0594253967100906,0.040875299422955785
all_sites,1.6610911744982817,0.9404107512855068,,,,
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
chonyi_1999_month7,0.6825254910261515,0.3393820994465812,0.15663097557129418,0.4301695105868461,12.214132279434569,0.042317923534964316
dielmo_1990_monthmultiple,0.5711687112890077,0.3965314003825952,0.6219099246260962,0.9274859257167193,0.8630959749052138,0.02034695680585351
dielmo_1990_monthmultiple,0.5711687112890077,0.3965314003825952,0.6219099246260963,0.9274859257167195,0.8630959749052143,0.020346956805853512
dongubougou_1999_monthmultiple,0.2921917392007317,0.17073999016392666,0.13038640523567407,0.09423861595745166,0.6506923472111071,0.02470917658914631
ebolakounou_1997_monthmultiple,0.6858638609195971,0.3886452217302862,-0.10398602600941884,0.09180777382837431,0.8668243442164759,0.010454242841899759
koundou_1997_monthmultiple,0.5614177043381496,0.3462386846857258,0.43728547052724426,0.7472381451807503,1.3249240850644364,0.005923631221470194
matsari_1970_month10,0.39820928816459034,0.18674109376023418,0.7863094941336288,0.9256435924626562,1.3770296193627964,0.012248340369871116
matsari_1970_month2,0.6299855911450253,0.3950905744647875,0.7864003185032957,0.9932297717710127,,0.0024505860481569366
matsari_1970_month7,0.4404135744799402,0.23401638055083646,0.676475606141136,0.8707864429680627,0.9187147875941255,0.0083184951107307
matsari_1970_month7,0.4404135744799402,0.23401638055083646,0.676475606141136,0.8707864429680627,0.9187147875941257,0.008318495110730701
ndiop_1993_monthmultiple,0.4657205735231557,0.14894292742359438,0.5214373120598216,0.795715073267172,0.6319126797626777,0.008540974359763517
ngerenya_1999_month7,0.8510846198405031,0.2561096994580539,-0.002692043148475209,0.00011484196242583909,0.9246367805158168,0.03231061623631442
ngerenya_1999_month7,0.8510846198405031,0.2561096994580539,-0.002692043148475208,0.00011484196242583901,0.9246367805158167,0.03231061623631442
rafin_marke_1970_month10,0.33576501065627096,0.14162445663845127,0.889262048689702,0.7164946161179646,0.5855068867610722,0.01670433705872292
rafin_marke_1970_month2,0.6895323478189561,0.39644790640199684,0.3791186726125504,0.9147342032022373,0.49487086565326166,0.007303359628916402
rafin_marke_1970_month7,0.36662216745724924,0.1732038206493545,0.5313418689033182,0.8040591037631534,60.7957816844913,0.010211641021033455
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2 changes: 1 addition & 1 deletion report/_plots_Python/loglikelihood_prevalence_age.csv
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
site_month,loglikelihood_new_sim,loglikelihood_benchmark_sim
dielmo_1990_monthmultiple,-3466.6023937629197,-3466.6023937629197
dielmo_1990_monthmultiple,-3466.6023937629193,-3466.6023937629193
dongubougou_1999_monthmultiple,-84.26103051901676,-84.26103051901676
ebolakounou_1997_monthmultiple,-1363.029630690697,-1363.029630690697
koundou_1997_monthmultiple,-1245.5403763380814,-1245.5403763380814
Expand Down
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10 changes: 10 additions & 0 deletions report/_plots_v1.2.0/comparison_metric_table_incidence_age.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
chonyi_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.43926130848631,0.14796578722119694
dielmo_1990,1.4081812654541295,1.2458223958828658,1.4662896933383196,0.9136326384809175,2.7887861639664027,0.33110512980784806
dongubougou_1999,0.20347658923882464,0.20058805816706704,1.0841408131583619,0.8655226920015985,0.5908511281184662,0.055915663172901246
ebolakounou_1997,3.5298250987213704,1.3500864647430642,1.591015084482229,0.36079816878572557,5.540963413406026,0.09385532642413291
koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.5837848130251536,4.061363882148547,0.29889745530530576
ndiop_1993,0.46935752353216664,0.5183624018079344,1.3707184658549694,0.8617239579850393,1.4238643917237106,0.06385891135139789
ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632835
sotuba_1999,0.3696682793427051,0.5674355266406905,0.07836804114542992,0.018623563537865394,1.0594253967100906,0.040875299422955785
all_sites,1.6610911744982817,0.9404107512855068,,,,
19 changes: 19 additions & 0 deletions report/_plots_v1.2.0/comparison_metric_table_prevalence_age.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
chonyi_1999_month7,0.6825254910261515,0.3393820994465812,0.15663097557129418,0.4301695105868461,12.214132279434569,0.042317923534964316
dielmo_1990_monthmultiple,0.5711687112890077,0.3965314003825952,0.6219099246260963,0.9274859257167195,0.8630959749052143,0.020346956805853512
dongubougou_1999_monthmultiple,0.2921917392007317,0.17073999016392666,0.13038640523567407,0.09423861595745166,0.6506923472111071,0.02470917658914631
ebolakounou_1997_monthmultiple,0.6858638609195971,0.3886452217302862,-0.10398602600941884,0.09180777382837431,0.8668243442164759,0.010454242841899759
koundou_1997_monthmultiple,0.5614177043381496,0.3462386846857258,0.43728547052724426,0.7472381451807503,1.3249240850644364,0.005923631221470194
matsari_1970_month10,0.39820928816459034,0.18674109376023418,0.7863094941336288,0.9256435924626562,1.3770296193627964,0.012248340369871116
matsari_1970_month2,0.6299855911450253,0.3950905744647875,0.7864003185032957,0.9932297717710127,,0.0024505860481569366
matsari_1970_month7,0.4404135744799402,0.23401638055083646,0.676475606141136,0.8707864429680627,0.9187147875941257,0.008318495110730701
ndiop_1993_monthmultiple,0.4657205735231557,0.14894292742359438,0.5214373120598216,0.795715073267172,0.6319126797626777,0.008540974359763517
ngerenya_1999_month7,0.8510846198405031,0.2561096994580539,-0.002692043148475208,0.00011484196242583901,0.9246367805158167,0.03231061623631442
rafin_marke_1970_month10,0.33576501065627096,0.14162445663845127,0.889262048689702,0.7164946161179646,0.5855068867610722,0.01670433705872292
rafin_marke_1970_month2,0.6895323478189561,0.39644790640199684,0.3791186726125504,0.9147342032022373,0.49487086565326166,0.007303359628916402
rafin_marke_1970_month7,0.36662216745724924,0.1732038206493545,0.5313418689033182,0.8040591037631534,60.7957816844913,0.010211641021033455
sotuba_1999_monthmultiple,2.484336072291313,0.18349964579147138,0.1513331198191235,0.01728434589322891,3.9181738234540444,0.008653389560842968
sugungum_1970_month10,0.46487882168073275,0.21334317162823746,0.892301300941384,0.9153345760653759,1.881581244676297,0.008059387929131905
sugungum_1970_month2,0.6236851050207368,0.3273411507035959,0.5575133570794679,0.8693862147591017,1.8861647797218364,0.009580442352786923
sugungum_1970_month7,0.2850904482414568,0.12479898222550063,0.7565180071793607,0.7648414997099265,1.7616882910570792,0.012480177680226892
all_sites,0.7060172162703156,0.26559137003721556,,,,
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16 changes: 16 additions & 0 deletions report/_plots_v1.2.0/loglikelihood_prevalence_age.csv
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@@ -0,0 +1,16 @@
site_month,loglikelihood_new_sim,loglikelihood_benchmark_sim
dielmo_1990_monthmultiple,-3466.6023937629193,-3466.6023937629193
dongubougou_1999_monthmultiple,-84.26103051901676,-84.26103051901676
ebolakounou_1997_monthmultiple,-1363.029630690697,-1363.029630690697
koundou_1997_monthmultiple,-1245.5403763380814,-1245.5403763380814
matsari_1970_month10,-50.662599543326195,-50.662599543326195
matsari_1970_month2,-263.25804760282097,-263.25804760282097
matsari_1970_month7,-67.33292846410185,-67.33292846410185
ndiop_1993_monthmultiple,,
rafin_marke_1970_month10,-29.387106539215623,-29.387106539215623
rafin_marke_1970_month2,-145.89519905060365,-145.89519905060365
rafin_marke_1970_month7,-63.78842174861791,-63.78842174861791
sotuba_1999_monthmultiple,-272.37015246943747,-272.37015246943747
sugungum_1970_month10,-152.7494668500975,-152.7494668500975
sugungum_1970_month2,-335.01903047385656,-335.01903047385656
sugungum_1970_month7,-31.504463570505617,-31.504463570505617
16 changes: 16 additions & 0 deletions report/_plots_v1.2.0/loglikelihoods_par_dens.csv
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@@ -0,0 +1,16 @@
site_month,loglike_asex,benchmark_loglike_asex,loglike_gamet,benchmark_loglike_gamet
matsari_1970_month2,-388.5658647314641,-388.5658647314641,-1126.5067540609252,-1126.5067540609252
matsari_1970_month7,-622.6123330019673,-622.6123330019673,-647.0310739624263,-647.0310739624263
matsari_1970_month10,-925.2131658352293,-925.2131658352293,-1214.3526893895782,-1214.3526893895782
rafin_marke_1970_month2,-151.38873119340678,-151.38873119340678,-239.0289626836029,-239.0289626836029
rafin_marke_1970_month7,-646.3403432364206,-646.3403432364206,-661.756709133003,-661.756709133003
rafin_marke_1970_month10,-554.7327641446915,-554.7327641446915,-876.7543574963095,-876.7543574963095
sugungum_1970_month2,-547.6560613702462,-547.6560613702462,-1327.1606844138018,-1327.1606844138018
sugungum_1970_month7,-1105.657401526858,-1105.657401526858,-982.89151714405,-982.89151714405
sugungum_1970_month10,-1513.5441864504005,-1513.5441864504005,-2254.2505145215273,-2254.2505145215273
laye_2007_month7,-63.207838404281006,-63.207838404281006,-74.69789236018474,-74.69789236018474
laye_2007_month9,-85.93548761815548,-85.93548761815548,-inf,-inf
laye_2007_month1,-37.23525174199905,-37.23525174199905,-25.42118634676641,-25.42118634676641
dapelogo_2007_month7,-70.52422100003385,-70.52422100003385,-inf,-inf
dapelogo_2007_month9,-55.79528949321428,-55.79528949321428,-43.3042021524024,-43.3042021524024
dapelogo_2007_month1,-51.00728916075721,-51.00728916075721,-inf,-inf
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6 changes: 6 additions & 0 deletions report/_plots_v1.2.0/summary_table_sim_benchmark.csv
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@@ -0,0 +1,6 @@
validation_relationship,abs_diff_new,abs_diff_bench,num_sites_better,num_sites_similar,num_sites_worse
age_incidence,0.9404107512855068,0.9404107512855068,0,8,0
age_prevalence,0.2655913700372155,0.2655913700372155,0,17,0
asexual_par_dens,0.188549310757321,0.188549310757321,0,15,0
gamet_par_dens,0.2416610186586396,0.2416610186586396,0,15,0
infectiousness,0.14141331785076117,0.14141331785076117,0,6,0
17 changes: 14 additions & 3 deletions report/create_pdf_report.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@
plot_folder = manifest.plot_output_filepath
title = 'Malaria Model Validation Results'
pdf_name = plot_folder.parent / f'Malaria_model_validation_output_{date}({time}).pdf'
table_not_found_icon = plot_folder.parent / 'FileNotFoundIcon_table_v2.png'
file_not_found_icon = plot_folder.parent / 'FileNotFoundIcon.png'


class PDF(FPDF):
Expand Down Expand Up @@ -94,13 +96,18 @@ def _create_content(self):

# remove table or image that are not generated
if table_name and not os.path.isfile(table_name):
table_name = None
print(f"Warning: {table_name} is not found. Skip this table in the report.")
table_name = None
if not image_list:
image_list = list()
image_list.append(table_not_found_icon)

if image_list:
for image_path in image_list[:]:
if not os.path.isfile(image_path):
image_list.remove(image_path)
print(f"Warning: {image_path} is not found. Skip this image in the report.")
image_list.append(file_not_found_icon)

self.pdf.start_section(f'{self.section_number}.{j + 1} ' + subsection_name, level=self.level + 1)
new_section(
Expand Down Expand Up @@ -162,7 +169,7 @@ def main(subset):
# generate dummy file for snakemake plot rule.
if not os.path.isdir(manifest.comps_id_folder):
os.mkdir(manifest.comps_id_folder)
with open(manifest.comps_id_folder + 'report_completed', 'w') as file:
with open(manifest.comps_id_folder / 'report_completed', 'w') as file:
file.write(f'Report file {pdf_name} is generated.')


Expand Down Expand Up @@ -411,7 +418,11 @@ def new_section(pdf: FPDF, text: str, image_list: list = None, table_name: str =
if image_list:
pdf.ln(10)
for image_name in image_list:
pdf.image(image_name, w=185)
if image_name in [file_not_found_icon, table_not_found_icon]:
pdf.image(image_name, w=125)
else:
pdf.image(image_name, w=185)

if table_name:
pdf.ln(10)
df = pd.read_csv(table_name)
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ fpdf2~=2.6
seaborn~=0.12
scikit-learn~=1.1
scipy~=1.9
snakemake~=7.18
snakemake~=7.19
plotnine~=0.10
datar~=0.9
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def load_arguments_from_file(filepath, arguments_list):

setuptools.setup(
name="malaria_model_validation",
version="1.1.0",
version="1.2.0",
author=[author[0] for author in authors],
author_email=[author[1] for author in authors],
description="malaria-model_validation package",
Expand Down
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