Add time varying parameters

.github/workflows/test-reusable.yml

@@ -52,10 +52,22 @@ jobs:
         python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       shell: bash -el {0}
 
-    - name: Test with pytest
+    - name: Test unit with pytest
       if: ${{ !inputs.use_min_dep_versions }}
       run: |
-        python -m pytest --cov=mobility --cov-config=.coveragerc --cov-report=xml:coverage.xml --log-cli-level=INFO --clear_inputs
+        python -m pytest tests/back/unit --cov=mobility --cov-config=.coveragerc --cov-append --log-cli-level=INFO --clear_inputs
+      shell: bash -el {0}
+
+    - name: Test integration with pytest
+      if: ${{ !inputs.use_min_dep_versions }}
+      run: |
+        python -m pytest tests/back/integration --cov=mobility --cov-config=.coveragerc --cov-append --log-cli-level=INFO --clear_inputs
+      shell: bash -el {0}
+
+    - name: Build coverage report
+      if: ${{ !inputs.use_min_dep_versions }}
+      run: |
+        python -m coverage xml -o coverage.xml
       shell: bash -el {0}
 
     - name: Test with pytest without coverage

.gitignore

@@ -101,6 +101,14 @@ ipython_config.py
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
 #poetry.lock
 
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
@@ -151,6 +159,15 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+# Poetry local configuration file
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
 # History files
 .Rhistory
 .Rapp.history
@@ -198,29 +215,16 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 
-# Input data files
-mobility/data/surveys/emp-2019/*
-!mobility/data/surveys/emp-2019/.gitkeep 
-
-mobility/data/surveys/entd-2008/*
-!mobility/data/surveys/entd-2008/.gitkeep 
-
-mobility/data/insee/work/*
-mobility/data/insee/facilities/*
-mobility/data/insee/esane/*
-mobility/data/insee/work_home_flows/*
-
-mobility/data/ign/admin-express/*
-mobility/data/insee/territories/UU2020_au_01-01-2023.xlsx
-.Rproj.user
-
+# R package: bookdown caching files
+/*_files/
 
 **/.env
 
 .DS_Store
 
 certs/
-nngeo-master
-front/gtfsrouter-main
 
-.vscode/
+.vscode/
+
+# Local scratch file created while refreshing ignore rules
+.gitignore-new

docs/source/modes.rst

@@ -141,5 +141,5 @@ Functions
 You must describe the transport modes that you want to model. Most usual modes are available, and you can use a combination of any mode with public transport.
 Available modes : walk, bicycle, car, carpool, public transport (+any mode before or after using public transport).
 
- .. automodule:: mobility.transport_modes
+ .. automodule:: mobility.transport.modes
     :members:

docs/source/radiation_model.rst

@@ -2,13 +2,9 @@
 Radiation model
 ================
 
-With the implementation of the radiation model developed in
-`Liu et Yan 2020 <https://www.nature.com/articles/s41598-020-61613-y>`_,
-you can reproduce spatially the mobility flows linked to a purpose
-(such as home-work trips).
+The legacy radiation model module was removed from the package during the
+refactor and is no longer part of the documented public API.
 
- .. automodule:: mobility.radiation_model
-    :members:
-
-This radiation model could be used for any contiguous subset of French departments.
-You can find an example of this model in <https://github.com/mobility-team/mobility/tree/main/examples/Millau>.
+Older examples may still reference it historically, but this page is kept only
+to avoid broken documentation links while the replacement workflow is being
+documented.

docs/source/set_params.rst

@@ -4,5 +4,5 @@ Set parameters
 
 Use set_params to define the folders you want to work, to initiate the R libraries or to debug your code.
 
- .. automodule:: mobility.set_params
+ .. automodule:: mobility.config
     :members:

docs/source/transport_zones.rst

@@ -4,16 +4,16 @@ Transport zones
 
 Use TransportZones to define the area that will be covered by your model.
 
- .. automodule:: mobility.transport_zones
+ .. automodule:: mobility.spatial.transport_zones
     :members:
 
 The TransportZones will call the StudyArea class to manage data in the area.
 
- .. automodule:: mobility.study_area
+ .. automodule:: mobility.spatial.study_area
     :members:
 
 
 StudyArea will itself call the LocalAdminUnits class to grab data from the local admin units.
 
- .. automodule:: mobility.parsers.local_admin_units
+ .. automodule:: mobility.spatial.local_admin_units
     :members:

docs/source/trips.rst

@@ -3,59 +3,42 @@ Trips
 ================
 
 ----------------
-PopulationTrips
+GroupDayTrips
 ----------------
 
-Trips for a given population can be generated using the class ``population_trips``.
+Group-level day plans for a given population can be generated using
+the class ``GroupDayTrips``.
 
- .. automodule:: mobility.choice_models.population_trips
+ .. automodule:: mobility.trips.group_day_trips
     :members:
 
-Use ``PopulationTripsParameters`` to change the parameters.
+Use ``Parameters`` to change the model configuration.
 
- .. automodule:: mobility.choice_models.population_trips_parameters
+ .. automodule:: mobility.trips.group_day_trips.core.parameters
     :members:
 
-``population_trips`` uses different other classes :
-# ``StateInitializer``: initialises the data
-# ``DestinationSequenceSampler`` samples destinations sequences
-# ``TopKModeSequenceSearch`` finds the k best modal chains for each destination sequence
-# ``StateUpdater`` updates population state distributions over motive/destination/mode sequence
-
- .. automodule:: mobility.choice_models.state_initializer
-    :members:
-
- .. automodule:: mobility.choice_models.destination_sequence_sampler
-    :members:
-
- .. automodule:: mobility.choice_models.top_k_mode_sequence_search
-    :members:
-
- .. automodule:: mobility.choice_models.state_updater
-    :members:
-
-
 ----------------
 Helpers
 ----------------
-``TopKModeSequenceSearch`` uses the function ``add_index`` to ensure a stable integer index exists for a categorical or string column.
-
+``GroupDayTrips`` produces results through ``RunResults`` and stores
+transition events that can be analyzed with the evaluation helpers.
 
- .. automodule:: mobility.choice_models.add_index
+ .. automodule:: mobility.trips.group_day_trips.core.results
     :members:
 
 
 ----------------
-Trips
+IndividualYearTrips
 ----------------
 
-Besides population_trips, trips can be sampled using the class ``Trips``. Use the .get() method to access a dataframe with those trips.
+Individual trips can be sampled using the class ``IndividualYearTrips``.
+Use ``.get()`` to access the generated dataframe.
 
- .. automodule:: mobility.trips
+ .. automodule:: mobility.trips.individual_year_trips
     :members:
 
 The trip generation uses the ``safe_sample`` module to ensure we do not use non-representative data
 (from a group below the minimal sample size).
 
- .. automodule:: mobility.safe_sample
+ .. automodule:: mobility.trips.individual_year_trips.safe_sample
     :members:

examples/old_examples/Hauts-Doubs/radiation-JU-NE-25-39.py

@@ -1,5 +1,5 @@
-from mobility.radiation_departments import run_model_for_territory
-from mobility.radiation_FR_CH import get_franco_swiss_data_for_model
+from mobility.runtime.r_integrationadiation_departments import run_model_for_territory
+from mobility.runtime.r_integrationadiation_FR_CH import get_franco_swiss_data_for_model
 
 terr = ["25", "39", "NE", "VD"]
 # terr  =["25","39"]

examples/old_examples/Millau/Millau_example.py

@@ -18,7 +18,7 @@
       (communes_surfaces_csv)
 """
 
-from mobility.radiation_departments import *
+from mobility.runtime.r_integrationadiation_departments import *
 import time
 
 

examples/old_examples/Millau/pa.py

@@ -1,4 +1,4 @@
-from mobility.radiation_departments import *
+from mobility.runtime.r_integrationadiation_departments import *
 
 dep =["64"]
 

examples/old_examples/mobility_survey/mobility_survey.py

@@ -2,7 +2,7 @@
 import dotenv
 import mobility
 
-from mobility.parsers import MobilitySurvey
+from mobility.surveys import MobilitySurvey
 
 dotenv.load_dotenv()
 
@@ -12,4 +12,4 @@
 )
 
 ms_2019 = MobilitySurvey(source="EMP-2019")
-ms_2008 = MobilitySurvey(source="ENTD-2008")
+ms_2008 = MobilitySurvey(source="ENTD-2008")