sim-tools 1.0.2__tar.gz → 1.0.4__tar.gz

{sim_tools-1.0.2 → sim_tools-1.0.4}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: sim-tools
-Version: 1.0.2
+Version: 1.0.4
 Summary: Simulation Tools for Education and Practice
-Project-URL: Homepage, https://github.com/TomMonks/sim-tools
-Project-URL: Bug Tracker, https://github.com/TomMonks/sim-tools/issues
-Project-URL: Documentation, https://tommonks.github.io/sim-tools
+Project-URL: Homepage, https://github.com/sim-tools/sim-tools
+Project-URL: Bug Tracker, https://github.com/sim-tools/sim-tools/issues
+Project-URL: Documentation, https://sim-tools.github.io/sim-tools
 Author-email: Thomas Monks <t.m.w.monks@exeter.ac.uk>, Amy Heather <A.Heather2@exeter.ac.uk>, Alison Harper <A.L.Harper@exeter.ac.uk>
 License-Expression: MIT
 License-File: LICENSE
@@ -36,7 +36,7 @@ Description-Content-Type: text/markdown
 [![PyPI version fury.io](https://badge.fury.io/py/sim-tools.svg)](https://pypi.python.org/pypi/sim-tools/)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/sim-tools/badges/version.svg)](https://anaconda.org/conda-forge/sim-tools)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/sim-tools/badges/platforms.svg)](https://anaconda.org/conda-forge/sim-tools)
-[![Read the Docs](https://readthedocs.org/projects/pip/badge/?version=latest)](https://tommonks.github.io/sim-tools)
+[![Read the Docs](https://readthedocs.org/projects/pip/badge/?version=latest)](https://sim-tools.github.io/sim-tools)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/release/python-360+/)
 
@@ -89,12 +89,12 @@ mamba install sim-tools
 
 ### Binder
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TomMonks/sim-tools/HEAD)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sim-tools/sim-tools/HEAD)
 
 
 ## Learn how to use `sim-tools`
 
-* Online documentation: https://tommonks.github.io/sim-tools
+* Online documentation: https://sim-tools.github.io/sim-tools
 * Introduction to DES in python: https://health-data-science-or.github.io/simpy-streamlit-tutorial/
 
 ## Citation
@@ -116,7 +116,7 @@ If you use sim-tools for research, a practical report, education or any reason p
 
 # Online Tutorials
 
-* Optimisation Via Simulation [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/TomMonks/sim-tools/blob/master/docs/02_ovs/03_sw21_tutorial.ipynb)
+* Optimisation Via Simulation [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/sim-tools/sim-tools/blob/master/docs/02_ovs/03_sw21_tutorial.ipynb)
 
 
 ## Contributing to sim-tools
@@ -151,4 +151,4 @@ To lint the repository, run:
 bash lint.sh
 ```
 
-NumPy style docstrings are used.
+NumPy style docstrings are used.

{sim_tools-1.0.2 → sim_tools-1.0.4}/README.md

@@ -11,7 +11,7 @@
 [![PyPI version fury.io](https://badge.fury.io/py/sim-tools.svg)](https://pypi.python.org/pypi/sim-tools/)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/sim-tools/badges/version.svg)](https://anaconda.org/conda-forge/sim-tools)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/sim-tools/badges/platforms.svg)](https://anaconda.org/conda-forge/sim-tools)
-[![Read the Docs](https://readthedocs.org/projects/pip/badge/?version=latest)](https://tommonks.github.io/sim-tools)
+[![Read the Docs](https://readthedocs.org/projects/pip/badge/?version=latest)](https://sim-tools.github.io/sim-tools)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/release/python-360+/)
 
@@ -64,12 +64,12 @@ mamba install sim-tools
 
 ### Binder
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TomMonks/sim-tools/HEAD)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sim-tools/sim-tools/HEAD)
 
 
 ## Learn how to use `sim-tools`
 
-* Online documentation: https://tommonks.github.io/sim-tools
+* Online documentation: https://sim-tools.github.io/sim-tools
 * Introduction to DES in python: https://health-data-science-or.github.io/simpy-streamlit-tutorial/
 
 ## Citation
@@ -91,7 +91,7 @@ If you use sim-tools for research, a practical report, education or any reason p
 
 # Online Tutorials
 
-* Optimisation Via Simulation [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/TomMonks/sim-tools/blob/master/docs/02_ovs/03_sw21_tutorial.ipynb)
+* Optimisation Via Simulation [![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/sim-tools/sim-tools/blob/master/docs/02_ovs/03_sw21_tutorial.ipynb)
 
 
 ## Contributing to sim-tools
@@ -126,4 +126,4 @@ To lint the repository, run:
 bash lint.sh
 ```
 
-NumPy style docstrings are used.
+NumPy style docstrings are used.

{sim_tools-1.0.2 → sim_tools-1.0.4}/pyproject.toml

@@ -33,9 +33,9 @@ dependencies = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/TomMonks/sim-tools"
-"Bug Tracker" = "https://github.com/TomMonks/sim-tools/issues"
-Documentation = "https://tommonks.github.io/sim-tools"
+Homepage = "https://github.com/sim-tools/sim-tools"
+"Bug Tracker" = "https://github.com/sim-tools/sim-tools/issues"
+Documentation = "https://sim-tools.github.io/sim-tools"
 
 [tool.hatch.version]
 path = "sim_tools/__init__.py"

{sim_tools-1.0.2 → sim_tools-1.0.4}/sim_tools/__init__.py

@@ -1,5 +1,5 @@
 """sim-tools"""
 
-__version__ = "1.0.2"
+__version__ = "1.0.4"
 
 from . import datasets, distributions, time_dependent, ovs, output_analysis

{sim_tools-1.0.2 → sim_tools-1.0.4}/sim_tools/time_dependent.py

@@ -8,7 +8,7 @@ import numpy as np
 from numpy.random import SeedSequence
 import pandas as pd
 import matplotlib.pyplot as plt
-
+import itertools
 
 # pylint: disable=too-few-public-methods
 class NSPPThinning:
@@ -33,7 +33,7 @@ class NSPPThinning:
         """
         Non Stationary Poisson Process via Thinning.
 
-        Time dependency is andled for a single table
+        Time dependency is handled for a single table
         consisting of equally spaced intervals.
 
         Parameters
@@ -54,12 +54,37 @@ class NSPPThinning:
             Random seed for the uniform distribution used
             for acceptance/rejection sampling.
         """
+
+        # -- Defensive parameter check added by TM as part of fix v1.0.4 --
+    
+        # data must be a dataframe
+        if not isinstance(data, pd.DataFrame):
+            raise TypeError(f"Data should be a DataFrame, but got {type(data).__name__}")
+        
+        # Check required columns t and mean_iat are provided. 
+        required_cols = ["t", "mean_iat"]
+        missing_cols = [col for col in required_cols if col not in data.columns]
+        if missing_cols:
+            raise ValueError(f"Missing required columns: {missing_cols}")
+        
+        # empty dataframe or only a single row.
+        if data.empty:
+            raise ValueError(f"Dataframe does not contain any rows. Add at least 2.")
+        elif len(data) == 1:
+            msg = "Dataframe contains a single time point. Add more of use Exponential class."
+            raise ValueError(msg)
+
+        # -- end of defensive code --
+
         self.data = data
         self.arr_rng = np.random.default_rng(random_seed1)
         self.thinning_rng = np.random.default_rng(random_seed2)
 
-        # Find the minimum mean IAT (corresponds to the maximum arrival rate)
-        self.min_iat = data["mean_iat"].min()
+        # drop to numpy for lookup speed
+        self.mean_iats = data["mean_iat"].to_numpy(dtype=float)
+
+        # Get the minimum mean IAT (corresponds to the maximum arrival rate)
+        self.min_iat = self.mean_iats.min()
 
         if self.min_iat <= 0:
             raise ValueError("Mean inter-arrival times must be positive")
@@ -75,6 +100,10 @@ class NSPPThinning:
                 "With only one data point, interval_width must be provided"
             )
 
+        # Pre-compute the acceptance probabilities. Added by TM v1.0.4
+        self.accept_prob = self.min_iat / self.mean_iats
+        self.n_periods = self.mean_iats.size
+
         self.rejects_last_sample = None
 
     def __repr__(self):
@@ -90,6 +119,7 @@ class NSPPThinning:
             f"{self.__class__.__name__}(data={data_str}, " +
             f"interval={self.interval})"
         )
+    
 
     def sample(self, simulation_time: float) -> float:
         """
@@ -99,36 +129,30 @@ class NSPPThinning:
         Parameters
         ----------
         simulation_time: float
-            The current simulation time. This is used to look up
-            the mean IAT for the time period.
+            The current simulation time. 
 
         Returns
         -------
         float
             The inter-arrival time
         """
-
-        # this gives us the index of dataframe to use
-        t = int(simulation_time // self.interval) % len(self.data)
-        mean_iat_t = self.data["mean_iat"].iloc[t]
-
-        # set to a large number so that at least 1 sample taken!
-        u = np.inf
-
-        # included for audit and tracking purposes.
-        self.rejects_last_sample = 0
-
+        
         interarrival_time = 0.0
-
-        # We accept the sample if u < (min_iat / mean_iat_t)
-        # This is equivalent to the original u < (lambda_t / lambda_max)
-        # since lambda = 1/mean_iat
-        while u >= (self.min_iat / mean_iat_t):
-            self.rejects_last_sample += 1
+        
+        for self.rejects_last_sample in itertools.count(start=0):
+            # sample the next inter-arrival time and calculate clock time
             interarrival_time += self.arr_rng.exponential(self.min_iat)
-            u = self.thinning_rng.uniform(0.0, 1.0)
+            arrival_sim_clock_time = simulation_time + interarrival_time
+
+            # get the t index of the candidate arrival
+            # fix v1.0.4 to use 'candidate_arrival_time' Fix by Sammi Rosser
+            t_idx = int(arrival_sim_clock_time // self.interval) % self.n_periods
 
-        return interarrival_time
+            # accept or reject? TM modified v1.0.4 to use pre-computed probabilities
+            u = self.thinning_rng.uniform()
+            if u <= self.accept_prob[t_idx]:
+                # accepted so return inter-arrival time
+                return interarrival_time
 
 
 def nspp_simulation(