Merge branch 'main' into feat/qualitative

README.md

@@ -49,8 +49,14 @@ Set environment variable `MOCK_TA1` to `False` and adding the correct endpoints
 To add additional scenarios, create a new directory in `tests/scenarios`. The directory must contain a `config.yaml` where each tests you wish to be run
 will be specified in `enabled`. 
 
+The `.env` will be used to specify the `MOCK_TA1` setting as well as the appropriate endpoints and can be passed into the test suite with:
+```
+poetry shell && export $(cat .env | xargs) && pytest -s
+```
+
 Run `poetry run poe report`, to generate `tests/output/report.json` which contains the status of each scenario and operation.
 
+
 ## License
 
 [Apache License 2.0](LICENSE)

tests/resources.yaml

@@ -2,21 +2,16 @@
 pdf_extraction:
  - text.json
  - paper.pdf
- - extractions.json
 pdf_to_text:
- - text.json
  - paper.pdf
 code_to_amr:
  - code.py
- - amr.json
 equations_to_amr:
  - equations.txt
- - amr.json
 profile_dataset:
  - text.json
  - paper.pdf
  - data.csv
- - data_card.json
 profile_model:
  - text.json
  - paper.pdf

tests/scenarios/sidarthe/code.py

@@ -0,0 +1,76 @@
+from scipy.integrate import odeint
+import numpy as np
+import pandas as pd
+import plotly.express as px
+import matplotlib.pyplot as plt
+
+def SIDARTHE_model(y, t, alpha, beta, gamma, delta, epsilon, mu, zeta, lamb, eta, rho, theta, kappa, nu, xi, sigma, tau):
+ S, I, D, A, R, T, H, E = y
+ dSdt = -S*(alpha(t)*I + beta(t)*D + gamma(t)*A + delta(t)*R)
+ dIdt = S*(alpha(t)*I + gamma(t)*D + beta(t)*A + delta(t)*R) - (zeta(t) + lamb(t))*I
+ dDdt = epsilon(t)/3*I - (eta(t))*D
+ dAdt = zeta(t)*I - (theta(t) + mu(t) + kappa(t))*A
+ dRdt = eta(t)*D + theta(t)*A - (nu(t) + xi(t))*R
+ dTdt = mu(t)*A + nu(t)*R - sigma(t)*T + tau(t)*T
+ dHdt = lamb(t)*I + sigma(t)*D + xi(t)*R + kappa(t)*T
+ dEdt = -tau(t)*T
+
+ return dSdt, dIdt, dDdt, dAdt, dRdt, dTdt, dHdt, dEdt
+
+# Example Simulation and Plot
+
+def alpha(t): return np.piecewise(t, [t>=0], [0.75])
+def beta(t): return np.piecewise(t, [t>=0], [0.1])
+def delta(t): return np.piecewise(t, [t>=0], [0.05])
+def gamma(t): return np.piecewise(t, [t>=0], [0.2])
+
+def epsilon(t): return np.piecewise(t, [t>=0], [0.1])
+def theta(t): return np.piecewise(t, [t>=0], [0.1])
+
+def zeta(t): return np.piecewise(t, [t>=0], [0.05])
+def eta(t): return np.piecewise(t, [t>=0], [0.05])
+
+def mu(t): return np.piecewise(t, [t>=0], [0.05])
+def nu(t): return np.piecewise(t, [t>=0], [0.05])
+def lamb(t): return np.piecewise(t, [t>=0], [0.05])
+def rho(t): return np.piecewise(t, [t>=0], [0.05])
+
+def kappa(t): return np.piecewise(t, [t>=0], [0.01])
+def xi(t): return np.piecewise(t, [t>=0], [0.01])
+def sigma(t): return np.piecewise(t, [t>=0], [0.01])
+
+def tau(t): return np.piecewise(t, [t>=0], [0.05])
+
+N0 = 1e6
+I0, D0, A0, R0, T0, H0, E0 = 50/N0, 50/N0, 5/N0, 1/N0, 0, 0, 0
+S0 = 1-I0-D0-A0-R0-T0-H0-E0
+y0 = S0, I0, D0, A0, R0, T0, H0, E0 # Initial conditions vector
+
+dt = 2
+tstart = 0
+tend = 40
+tvect = np.arange(tstart, tend, dt) 
+
+sim = odeint(SIDARTHE_model, y0, tvect, args=(alpha, beta, gamma, delta, epsilon, mu, zeta, lamb, eta, rho, theta, kappa, nu, xi, sigma, tau))
+S, I, D, A, R, T, H, E = sim.T
+
+f, ax = plt.subplots(1,1,figsize=(10,4))
+ax.plot(tvect, S, 'b', alpha=0.7, linewidth=2, label='Susceptible')
+ax.plot(tvect, I, 'r', alpha=0.7, linewidth=2, label='Infected (Asymptomatic, Infected, Undetected)')
+ax.plot(tvect, D, 'r.', alpha=0.7, linewidth=2, label='Diagnosed (Asymptomatic, Infected, Detected)')
+ax.plot(tvect, A, 'r:', alpha=0.7, linewidth=2, label='Ailing (Symptomatic, Infected, Undetected)')
+ax.plot(tvect, R, 'r--', alpha=0.7, linewidth=2, label='Recognized (Symptomatic, Infected, Detected)')
+ax.plot(tvect, T, 'r-.', alpha=0.7, linewidth=2, label='Threatened (Acutely Symptomatic)')
+ax.plot(tvect, H, 'g', alpha=0.7, linewidth=2, label='Healed')
+ax.plot(tvect, E, 'k', alpha=0.7, linewidth=2, label='Extinct (Dead)')
+
+ax.set_xlabel('Time (days)')
+ax.set_ylabel('Fraction of population')
+
+ax.yaxis.set_tick_params(length=0)
+ax.xaxis.set_tick_params(length=0)
+ax.grid(b=True, which='major', c='w', lw=2, ls='-')
+legend = ax.legend()
+legend.get_frame().set_alpha(0.5)
+
+plt.show();

tests/scenarios/sidarthe/config.yaml

@@ -0,0 +1,7 @@
+---
+name: "SIDARTHE"
+description: "Scenario to process SIDARTHE paper and code"
+enabled:
+ - pdf_extraction
+ - pdf_to_text
+ - code_to_amr