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authorSébastien Picault <sebastien.picault@inra.fr>
Mon, 1 Jul 2019 18:58:59 +0000 (20:58 +0200)
committerSébastien Picault <sebastien.picault@inra.fr>
Mon, 1 Jul 2019 18:58:59 +0000 (20:58 +0200)
commit50d826763abe4c9d5ebeba501a462c3b859ede85
tree9ae7b76adf224e3643d78ff91744726681f61ecf
parent54bf733c4c731f2990ea51fcd64953b18c378a1b
Released version 1.0.7 of EMULSION under license Apache-2.0

* New in 1.0.7
** EMULSION DSL
- added built-in action =record_change= to add the number of agents
  performing an action to a state variable from the population level
  (useful e.g. for counting the cumulative incidence).  Syntax:
  #+BEGIN_EXAMPLE
  states:
    - I:
      ...
      on_enter:
        - record_change: cumulative_incidence
  #+END_EXAMPLE
- modified keyword =random= in prototype definition to allow choosing
  states proportionnally to a list of weights, e.g. to have generic
  individuals initialized in a SIR model with a given prevalence
  (assuming all non-infectious individuals are susceptible):
  #+BEGIN_EXAMPLE
  health_state: random(1-prevalence, prevalence, 0)
  #+END_EXAMPLE
- modified initial conditions for hybird/IBM models, now accepting a
  multinomial sampling between several prototypes. Syntax:
  #+BEGIN_EXAMPLE
  level:
    - prototype: [list of prototypes]
      amount: total_nb_of_individuals
      proba: [list of probabilities]
  #+END_EXAMPLE
- added two keywords in state definition, and two in prototype
  definition, respectively =next= and =previous= for states,
  =next_state= and =previous_state= for prototypes. They allow to
  define a predecessor/successor relationship between nodes (by
  default, the definition order between non-autoremove nodes is used),
  and to use it for changing a statevar related to a state machine
- added built-in variables =duration_of_EVENT= where =EVENT= is any
  event declared in the calendar section. The duration is expressed in
  time units
- added built-in action =log_vars= to store information about
  agents. This action is followed by a list of variables or
  expressions. Results are stored in a file =log.txt= in the output
  dir
** EMULSION generic engine
- added built-in action =RecordChange= to implement DSL
  =record_change=
- modified model parsing to handle the new =random(...)= syntax
- modified model and =MultiProcessManager= to handle initial
  conditions with multinomial sampling of prototypes
- modified prototype parsing to allow across-reference to statevars in
  the values of variables used in a prototype definition. For
  instance, a prototype is used to define the =health_state= of the
  future calf, via a variable =health_state_calf= ; then at birth the
  prototype of the newborn uses =health_state: health_state_calf=
- modified prototype parsing to include =next_state= and
  =previous_state=
- modified state machine parsing to include node properties =next= and
  =previous=, with the corresponding modifications in state machines
- modified parsing of calendar section to define variables
  =duration_of_EVENT=
- added an action class =LogVarsAction= to implement built-in action
  =log_vars=
** EMULSION documentation
- improved the documentation of functions availale for models
- documented new DSL features
- added examples regarding new features

** Bugfixes
- fixed calculation error on periodic calendars for intervals with begin > end
130 files changed:
README.md
doc/html/.buildinfo
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doc/html/_sources/emulsion_for_modellers.rst.txt
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doc/html/_sources/pages/Feature_examples.rst.txt
doc/html/_sources/pages/Getting_started.rst.txt
doc/html/_sources/pages/Install.rst.txt
doc/html/_sources/pages/Modelling_language_advanced.rst.txt
doc/html/_sources/pages/Modelling_language_basics.rst.txt
doc/html/_static/basic.css
doc/html/_static/doctools.js
doc/html/_static/documentation_options.js
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doc/html/_static/models/features/IBM_SIR_JA_demo_random.yaml [new file with mode: 0644]
doc/html/_static/models/features/IBM_SIR_cumul_inc.yaml [new file with mode: 0644]
doc/html/_static/models/features/IBM_gest.yaml
doc/html/_static/models/features/compart_SIR_cumul_inc.yaml [new file with mode: 0644]
doc/html/_static/models/features/hybrid_SIR_JA_demo_random.yaml [new file with mode: 0644]
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models/features/IBM_SIR_JA_demo_random.yaml [new file with mode: 0644]
models/features/IBM_SIR_cumul_inc.yaml [new file with mode: 0644]
models/features/IBM_gest.yaml
models/features/compart_SIR_cumul_inc.yaml [new file with mode: 0644]
models/features/hybrid_SIR_JA_demo_random.yaml [new file with mode: 0644]
models/features/hybrid_SIR_cumul_inc.yaml [new file with mode: 0644]
models/features/hybrid_gest.yaml
src/emulsion/__init__.py
src/emulsion/__main__.py
src/emulsion/agent/action.py
src/emulsion/agent/core/abstract_agent.py
src/emulsion/agent/core/emulsion_agent.py
src/emulsion/agent/managers/abstract_process_manager.py
src/emulsion/agent/managers/compart_process_manager.py
src/emulsion/agent/managers/multi_process_manager.py
src/emulsion/model/emulsion_model.py
src/emulsion/model/state_machines.py
src/emulsion/resources/emulsion.tx
src/emulsion/templates/specific_code.py
src/emulsion/tools/calendar.py
src/emulsion/tools/functions.py
src/emulsion/tools/misc.py
src/emulsion/tools/simulation.py
src/emulsion/tools/state.py