Clean docstrings and refs

docs/activity_plans.md

@@ -1,7 +1,7 @@
 # Activity Plans
 
 PAM supports arbitrarily complex chains of activities connected by 'legs' (these are equivalent to 'trips').
-The main rules are (i) that plans must consist of sequences of alternate `pam.activity.Activity` and `pam.activity.Leg` objects and (ii) that a plan must start and end with an `Activity`:
+The main rules are (i) that plans must consist of sequences of alternate [][pam.activity.Activity] and [][pam.activity.Leg] objects and (ii) that a plan must start and end with an `Activity`:
 
 ``` python
 from pam.core import Person
@@ -130,9 +130,9 @@ This need not be a `home` activity, for example in the case of night workers.
 We have encountered many variations of sequences for plans, including wrapping and wrapping.
 Although they are generally edge cases, they exists and generally represent real people.
 We are therefore endeavoring to support all these cases in our plan modifiers.
-This is resulting some difficult to follow logic (eg `pam.activity.Plan.fill_plan()`).
+This is resulting some difficult to follow logic (e.g., [][pam.activity.Plan.fill_plan]).
 
 ## Plan cropping
-The `pam.cropping` module allows to spatially subset populations, by simplifying plan components that take place outside the "core" area.
+The [`pam.operations.cropping`](reference/pam/operations/cropping.md) module allows to spatially subset populations, by simplifying plan components that take place outside the "core" area.
 Any activities or legs that do not affect that core area are removed from the agents' plans, and agents with fully-external plans are removed from the population.
-Examples of using the module can be found in the `18_plan_cropping.ipynb` notebook.
+Examples of using the module can be found in the [][plan-cropping] notebook.

docs/modelling_policy_impact.md

@@ -1,7 +1,7 @@
 # Modelling the impact of policies on populations
 
-PAM uses **policies** to model change to a population. 
-For example, based on social distancing requirements we might want to reflect that people are expected to make less shared shopping trips or tours. 
+PAM uses **policies** to model change to a population.
+For example, based on social distancing requirements we might want to reflect that people are expected to make less shared shopping trips or tours.
 We can do this using the following policy, if you want to define the policy from first principles:
 
 ``` python
@@ -27,23 +27,23 @@ This policy removes all but one the household's shared shopping tours:
 In general, a policy is defined in the following way:
 
 1. You first select the level at which is should be applied:
-    - `HouseholdPolicy`
-    - `PersonPolicy`
-    - `ActivityPolicy`
+    - [HouseholdPolicy][pam.policy.policies.HouseholdPolicy]
+    - [PersonPolicy][pam.policy.policies.PersonPolicy]
+    - [ActivityPolicy][pam.policy.policies.ActivityPolicy]
 2. You then select the modifier, which performs the actions to a person's activities
-    - `RemoveActivity`
-    - `ReduceSharedActivity`
-    - `MoveActivityTourToHomeLocation`
-3. Finally, you give a likelihood value with which the policy should be applied with. 
+    - [RemoveActivity][pam.policy.modifiers.RemoveActivity]
+    - [ReduceSharedActivity][pam.policy.modifiers.ReduceSharedActivity]
+    - [MoveActivityTourToHomeLocation][pam.policy.modifiers.MoveActivityTourToHomeLocation]
+3. Finally, you give a likelihood value with which the policy should be applied with.
     You have a few choices here:
-    - a number greater than 0 and less or equal to 1. 
+    - a number greater than 0 and less or equal to 1.
     This will be understood to be at the level at which the policy is applied.
     E.g. `#!python PersonPolicy(RemoveActivity(['work']), 0.5)` will give each person a fifty-fifty chance of having their work activities removed.
 
     - you can explicitly define at which level a number greater than 0 and less or equal to 1 will be applied.
     E.g. `#!python HouseholdPolicy(RemoveActivity(['work']), PersonProbability(0.5))` will apply a probability of 0.5 per person in a household, and apply the policy to all persons within a household if selected.
 
-    - you can also pass a function that operates on a `core.Household`, `core.Person` or `core.Activity` object and returns a number between 0 and 1.
+    - you can also pass a function that operates on a [Household][pam.core.Household], [Person][pam.core.Person] or [Activity][pam.activity.Activity] object and returns a number between 0 and 1.
     E.g. if our function is:
     ``` python
     def sampler(person):

docs/read_data.md

@@ -24,8 +24,8 @@ population.print()
 
 ## Read methods
 
-The first step in any application is to load your data into the core pam format (pam.core.Population). We
-are trying to support common tabular formats ('travel diaries') using `pam.read.load_travel_diary`. A
+The first step in any application is to load your data into the core pam format ([][pam.core.Population]). We
+are trying to support common tabular formats ('travel diaries') using [][pam.read.load_travel_diary]. A
 travel diary can be composed of three tables:
 
 - `trips` (required) -  a trip diary for all people in the population, with rows representing trips
@@ -99,7 +99,7 @@ The `trips` input **may** also include the following fields:
 
 **'trip purpose' vs 'tour purpose':**
 
-We've encountered a few different ways that trip purpose can be encoded. The preferred way being to encode a trip purpose as being the activity of the destination, so that a trip home would be encoded as `purp = home`. However we've also seen the more complex 'tour purpose' encoding, in which case a return trip from work to home is encoded as `purp = work`. Good news is that the `pam.read.load_travel_diary` will deal ok with either. But it's worth checking.
+We've encountered a few different ways that trip purpose can be encoded. The preferred way being to encode a trip purpose as being the activity of the destination, so that a trip home would be encoded as `purp = home`. However we've also seen the more complex 'tour purpose' encoding, in which case a return trip from work to home is encoded as `purp = work`. Good news is that the [][pam.read.load_travel_diary] will deal ok with either. But it's worth checking.
 
 **Using persons_attributes and /or households_attributes**
 
@@ -125,7 +125,7 @@ If you are using persons_attributes (`persons_attributes`) this table must conta
 
 **A note about 'freq':**
 
-Frequencies (aka 'weights') for trips, persons or households can optionally be added to the respective input tables using columns called `freq`. We generally assume a frequency to represent expected occurrences in a full population. For example if we use a person frequency (`person.freq`) the the sum of all these frequencies (`population.size`), will equal the expected population size.
+Frequencies (aka 'weights') for trips, persons or households can optionally be added to the respective input tables using columns called `freq`. We generally assume a frequency to represent expected occurrences in a full population. For example if we use a person frequency ([][pam.core.Person.freq]) the the sum of all these frequencies ([][pam.core.Population.size]), will equal the expected population size.
 
 Because it is quite common to provide a person or household `freq` in the trips table, there are two special options (`trip_freq_as_person_freq = True` and `trip_freq_as_hh_freq = True`) that can be used to pass the `freq` field from the trips table to either the people or households table instead.
 
@@ -141,8 +141,11 @@ for pid, person in household:
 
 ### Read/Write/Other formats
 
-PAM can read/write to tabular formats and MATSim xml (`pam.read.read_matsim` and `pam.write.write_matsim`). PAM can also write to segmented OD matrices using `pam.write.write_od_matrices`.
+PAM can read/write to tabular formats and MATSim xml ([][pam.read.read_matsim] and [][pam.write.write_matsim]).
+PAM can also write to segmented OD matrices using [][pam.write.write_od_matrices].
 
-Benchmark or summary data and cross-tabulations can be extracted with the `pam.write.write_benchmarks` method, passing as arguments the data field(s) to summarise, the dimension(s) to group by, and the aggregation function(s). For example `pam.write_benchmarks(population, dimensions = ['duration_category'], data_fields= ['freq'], aggfunc = [sum]` returns the frequency breakdown of trips' duration. The `write` module also provides a number of wrappers for frequently-used benchmarks under the `write_*****_benchmark` name.
+Benchmark or summary data and cross-tabulations can be extracted with the [benchmarking CLI method](api/cli.md#pam-report-benchmarks).
+For more fine-grain control, pandas dataframes for specific data field(s), dimension(s) and aggregation function(s) can be generated with [][pam.report.benchmarks.create_benchmark].
+For example `pam.report.benchmarks.create_benchmark(population.trips_df(), dimensions = ['duration_category'], data_fields= ['freq'], aggfunc = [sum]` returns the frequency breakdown of trips' duration.
 
 Please get in touch if you would like additional support or feel free to add your own.

mkdocs.yml

@@ -66,6 +66,7 @@ plugins:
             signature_crossrefs: true
             show_root_toc_entry: false
             show_signature_annotations: false
+            inherited_members: true
           import:
             - https://docs.python.org/3/objects.inv
             - https://shapely.readthedocs.io/en/stable/objects.inv

pam/planner/choice_location.py

@@ -261,20 +261,18 @@ def __init__(self, population: Population, od: OD, zones: pd.DataFrame) -> None:
 
 
 class DiscretionaryTrips:
-    """
-    Solve discretionary trip location choice of a PAM plan
-    """
-
     def __init__(self, plan: Plan, od: OD) -> None:
+        """Solve discretionary trip location choice of a PAM plan.
+
+        Args:
+            plan (Plan): PAM plan.
+            od (OD): An object holding origin-destination matrices.
+        """
         self._plan = plan
         self._od = od
 
     def update_plan(self):
-        """Update the locations (in-place) of each non-mandatory activity location in the plan.
-
-        Returns:
-            None
-        """
+        """Update the locations (in-place) of each non-mandatory activity location in the plan."""
         trip_chains = get_trip_chains_either_anchor(self._plan)
         for trip_chain in trip_chains:
             # if only one achor, convert to round-trip
@@ -289,22 +287,20 @@ def update_plan(self):
 
 class DiscretionaryTrip(ABC):
     def __init__(self, trip_chain: list[Union[Activity, Leg]], od: OD) -> None:
-        """
-        Location choice for discretionary trips
-            in a trip chain
+        """Location choice for discretionary trips in a trip chain.
 
         Cases:
-            a) O->discretionary->O (DiscretionaryTripRound)
-            b) O->discretionary->D (DiscretionaryTripOD)
-            c) O->discretionary->discretionary->O
-            d) O->discretionary->discretionary->D
+            1. O->discretionary->O (DiscretionaryTripRound)
+            2. O->discretionary->D (DiscretionaryTripOD)
+            3. O->discretionary->discretionary->O
+            4. O->discretionary->discretionary->D
 
-        Chains with multiple discretionary trips are solved
-            recursively, updating the first location each time,
-            and then keeping it fixed as we solve downstream.
+        Chains with multiple discretionary trips are solved recursively,
+            updating the first location each time, and then keeping it fixed as we solve downstream.
 
         Args:
-            list[Union[Activity, Leg]]: A trip chain between two long-term activities.
+            trip_chain (list[Union[Activity, Leg]]): A trip chain between two long-term activities.
+            od (OD): An object holding origin-destination matrices.
         """
         self._trip_chain = trip_chain
         self._od = od
@@ -326,22 +322,17 @@ def __init__(self, trip_chain: list[Union[Activity, Leg]], od: OD) -> None:
             raise TypeError("Each even element in the trip chain should be an activity")
 
     @abstractmethod
-    def choose_destination(self):
-        """Selects a destination for the discretionary activity
+    def choose_destination(self) -> str:
+        """Selects a destination for the discretionary activity.
 
         Returns:
             str: Selected destination zone name.
         """
 
     def update_plan(self):
         """
-        Update the PAM activity locations of the first activity activity
-            in the trip chain,
-            and continue downstream until the entire chain is solved.
-
-        Returns:
-            None
-
+        Update the PAM activity locations of the first activity in the trip chain,
+        and continue downstream until the entire chain is solved.
         """
         if len(self.act_names) > 2:
             # update locations
@@ -362,20 +353,23 @@ def update_plan(self):
                 DiscretionaryTripOD(trip_chain=self._trip_chain[2:], od=self._od).update_plan()
 
     @property
-    def od(self):
+    def od(self) -> OD:
         return self._od
 
 
 class DiscretionaryTripRound(DiscretionaryTrip):
     """
-    Location choice for a single discretionary trip,
-        where we have the same anchor at the start and end of the chain.
+    Location choice for a single discretionary trip, where we have the same anchor at the start and end of the chain.
 
-    The class infers the location of the first discretionary
-        activity in the trip chain.
+    The class infers the location of the first discretionary activity in the trip chain.
     """
 
     def choose_destination(self) -> str:
+        """Selects a destination for the discretionary activity.
+
+        Returns:
+            str: Selected destination zone name.
+        """
         assert isinstance(self._trip_chain[1], Leg)
         destination_p = self._od["od_probs", self.anchor_zone_start, :, self.trmode]
         destination_p = destination_p / destination_p.sum()
@@ -386,19 +380,18 @@ def choose_destination(self) -> str:
 
 
 class DiscretionaryTripOD(DiscretionaryTrip):
-    """
-    Location choice for a single discretionary trip,
-        where we have different anchors at the start and end of the chain.
+    """Location choice for a single discretionary trip, where we have different anchors at the start and end of the chain.
 
     The class infers the location of the first trip in the trip chain.
 
-    Methodology
-    We combine three conditions:
-      1) Distribution of leg compared to total trip
-      2) Diversion factor (compared to direct trips)
-      3) Zone attraction
-    Final probabilities are defined as (1) * (2) * (3)
-      (and then normalised to sum up to 1)
+    Methodology:
+        We combine three conditions:
+
+        1. Distribution of leg compared to total trip
+        2. Diversion factor (compared to direct trips)
+        3. Zone attraction
+
+        Final probabilities are defined as (1) * (2) * (3) (and then normalised to sum up to 1).
 
     """
 
@@ -446,8 +439,7 @@ def leg_ratio_p(self) -> np.array:
     @property
     def diversion_factors(self) -> np.array:
         """
-        Calculate the diversion factor for each potential destination
-            (as compared to a direct trip between anchors).
+        Calculate the diversion factor for each potential destination (as compared to a direct trip between anchors).
 
         Returns:
             np.array: An array of the time diversion factors for each candidate intermediate destination.
@@ -463,10 +455,9 @@ def diversion_factors(self) -> np.array:
         return diversion_factors
 
     @property
-    def diversion_p(self):
+    def diversion_p(self) -> np.array:
         """Diversion factor probabilities
 
-
         Returns:
             np.array: An array of the time diversion factor probabilities for each candidate intermediate destination.
 
@@ -475,20 +466,16 @@ def diversion_p(self):
 
     @property
     def attraction_p(self):
-        """Attraction probabilities
-
-        Returns:
-            None
-        """
+        """Attraction probabilities."""
         probs = self._od["od_probs", self.anchor_zone_start, :, self.trmode]
         probs = probs / probs.sum()
         return probs
 
     @property
     def destination_p(self) -> np.array:
         """Get the destination probabilities.
-        Combines the leg ratio, diversion, and attraction factors probabilities
-            by calculating their product.
+
+        Combines the leg ratio, diversion, and attraction factors probabilities by calculating their product.
 
         Returns:
             np.array: Final destination probabilities.
@@ -498,6 +485,11 @@ def destination_p(self) -> np.array:
         return p
 
     def choose_destination(self) -> str:
+        """Selects a destination for the discretionary activity.
+
+        Returns:
+            str: Selected destination zone name.
+        """
         zone = sample_weighted(self.destination_p)
         area = self._od.labels.destination_zones[zone]
 

pam/planner/od.py

@@ -3,7 +3,6 @@
 from typing import NamedTuple, Union
 
 import numpy as np
-import pandas as pd
 
 
 class Labels(NamedTuple):
@@ -107,10 +106,10 @@ def from_matrices(cls, matrices: list[ODMatrix]) -> OD:
     @staticmethod
     def prepare_labels(matrices: list[ODMatrix]) -> Labels:
         labels = Labels(
-            vars=list(pd.unique([mat.var for mat in matrices])),
+            vars=list(dict.fromkeys(mat.var for mat in matrices)),
             origin_zones=matrices[0].origin_zones,
             destination_zones=matrices[0].destination_zones,
-            mode=list(pd.unique([mat.mode for mat in matrices])),
+            mode=list(dict.fromkeys(mat.mode for mat in matrices)),
         )
         return labels
 

pam/scoring.py

@@ -93,7 +93,7 @@ def score_person(
 
         Args:
           person (Person):
-          subpopulation (str, optional): person attribute name for subpopulation. Defaults to "subpopulation".
+          key (str, optional): person attribute name for subpopulation. Defaults to "subpopulation".
           plan_costs (float, optional): Optionally add monetary costs such as tolls. Defaults to None.
 
         Returns: