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authorSébastien Picault <sebastien.picault@inra.fr>
Thu, 4 Apr 2019 19:26:49 +0000 (21:26 +0200)
committerSébastien Picault <sebastien.picault@inra.fr>
Thu, 4 Apr 2019 19:26:49 +0000 (21:26 +0200)
doc/html/_sources/pages/Install.rst.txt
doc/html/_sources/pages/Modelling_language_advanced.rst.txt
doc/html/_static/models/features/data/moves.csv
doc/html/_static/models/features/hybrid_SIR_metapop_data.py
doc/html/models.zip
doc/html/pages/Install.html
doc/html/pages/Modelling_language_advanced.html
doc/html/searchindex.js
models/features/data/moves.csv
models/features/hybrid_SIR_metapop_data.py

index d9e55f4..2bbc592 100644 (file)
@@ -69,15 +69,14 @@ This procedure assumes that you have ``git`` already
 `installed on your system <https://git-scm.com/downloads>`_.
 It is provided here for Linux or MacOS.
 
-
 #. Install (or update) required packages
 
    .. code-block:: bash
 
-      sudo pip3 install numpy scipy matplotlib sympy pandas
+      sudo pip3 install numpy scipy matplotlib pandas 'sympy<1.3' mpmath
       sudo pip3 install networkx docopt jinja2 textx
-      sudo pip3 install sortedcontainers tqdm pyyaml
-      sudo pip3 install bokeh sqlalchemy
+      sudo pip3 install sortedcontainers tqdm pyyaml colorama
+      sudo pip3 install bokeh sqlalchemy utm
 
 #. Clone the EMULSION repository
 
@@ -97,7 +96,7 @@ It is provided here for Linux or MacOS.
 
    .. code-block:: bash
 
-      echo "source $(pwd)/scripts/emulsion-completion.sh" >>$HOME/.bashrc
+      echo "source $(pwd)/src/emulsion/scripts/emulsion-completion.sh" >>$HOME/.bashrc
 
    Command-line completion (available with a bash shell, under Linux
    or MacOS) allows to use ``TAB`` key to get suggestions on what is
index 454155a..7e59b6c 100644 (file)
@@ -184,13 +184,12 @@ Produce new individuals
   - in IBM/hybrid models, a ``prototype`` must be specified for the new
     individuals
 
-    Besides, the computation of actual flows uses sampling in Poisson
-    distribution rather than binomial/multinomial sampling.
+  Besides, the computation of actual flows uses sampling in Poisson
+  distribution rather than binomial/multinomial sampling.
 
   .. seealso::
 
-     :ref:`SIR model with basic demography (births/deaths)`, :ref:`SIR
-         model with age groups`
+     :ref:`SIR model with basic demography (births/deaths)`, :ref:`SIR model with age groups`
 
 - Another way to produce new individuals is using an action: ``clone``
   (aka ``produce_offspring``) associated with a transition or
index da4ecf7..a5683a7 100644 (file)
@@ -1,3 +1,4 @@
+date,source,dest,age,qty
 2018-01-04,0,10,J,7
 2018-01-05,10,8,J,6
 2018-01-08,0,7,J,5
index de8a96e..4df9579 100644 (file)
@@ -33,9 +33,7 @@ class Metapopulation(MetapopProcessManager):
         moves = {}
         with open(Path(self.model.input_dir, DATA_FILE)) as csvfile:
             # read the CSV file
-            csvreader = csv.DictReader(csvfile,
-                                       fieldnames=['date','source','dest', 'age', 'qty'],
-                                       delimiter=',')
+            csvreader = csv.DictReader(csvfile, delimiter=',')
             for row in csvreader:
                 day = dup.parse(row['date'])
                 if day < origin:
@@ -46,10 +44,10 @@ class Metapopulation(MetapopProcessManager):
                 # group information by step and source herd
                 if step not in moves:
                     moves[step] = {}
-                    src, dest, qty = int(row['source']), int(row['dest']), int(row['qty'])
-                    if src not in moves[step]:
-                        moves[step][src] = []
-                        moves[step][src].append([dest, row['age'], qty])
+                src, dest, qty = int(row['source']), int(row['dest']), int(row['qty'])
+                if src not in moves[step]:
+                    moves[step][src] = []
+                moves[step][src].append([dest, row['age'], qty])
         self.moves = moves
 
     #----------------------------------------------------------------
index b4017fb..8b6d989 100644 (file)
Binary files a/doc/html/models.zip and b/doc/html/models.zip differ
index ad2d9ff..3035f9e 100644 (file)
@@ -93,10 +93,10 @@ setx PYTHONPATH <span class="s2">&quot;</span><span class="nv">%PYTHONPATH%</spa
 It is provided here for Linux or MacOS.</p>
 <ol class="arabic">
 <li><p class="first">Install (or update) required packages</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo pip3 install numpy scipy matplotlib sympy pandas
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo pip3 install numpy scipy matplotlib pandas <span class="s1">&#39;sympy&lt;1.3&#39;</span> mpmath
 sudo pip3 install networkx docopt jinja2 textx
-sudo pip3 install sortedcontainers tqdm pyyaml
-sudo pip3 install bokeh sqlalchemy
+sudo pip3 install sortedcontainers tqdm pyyaml colorama
+sudo pip3 install bokeh sqlalchemy utm
 </pre></div>
 </div>
 </li>
@@ -113,7 +113,7 @@ variable.</p>
 </div>
 </li>
 <li><p class="first">Install command-line completion (optional but very convenient).</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span> <span class="s2">&quot;source </span><span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span><span class="s2">/scripts/emulsion-completion.sh&quot;</span> &gt;&gt;<span class="nv">$HOME</span>/.bashrc
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span> <span class="s2">&quot;source </span><span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span><span class="s2">/src/emulsion/scripts/emulsion-completion.sh&quot;</span> &gt;&gt;<span class="nv">$HOME</span>/.bashrc
 </pre></div>
 </div>
 <p>Command-line completion (available with a bash shell, under Linux
index 5996d2a..ae9d0e1 100644 (file)
@@ -248,22 +248,16 @@ transition have to perform</li>
 <li><p class="first">Section <code class="docutils literal notranslate"><span class="pre">productions</span></code> in state machines allow to define how some
 states can produce new individuals. Production links are very
 similar to transitions in their syntax, except that:</p>
-<ul>
-<li><p class="first"><code class="docutils literal notranslate"><span class="pre">escape</span></code> conditions and <code class="docutils literal notranslate"><span class="pre">amount-all-but</span></code> quantifier are not allowed</p>
-</li>
-<li><p class="first">in IBM/hybrid models, a <code class="docutils literal notranslate"><span class="pre">prototype</span></code> must be specified for the new
-individuals</p>
+<ul class="simple">
+<li><code class="docutils literal notranslate"><span class="pre">escape</span></code> conditions and <code class="docutils literal notranslate"><span class="pre">amount-all-but</span></code> quantifier are not allowed</li>
+<li>in IBM/hybrid models, a <code class="docutils literal notranslate"><span class="pre">prototype</span></code> must be specified for the new
+individuals</li>
+</ul>
 <p>Besides, the computation of actual flows uses sampling in Poisson
 distribution rather than binomial/multinomial sampling.</p>
-</li>
-</ul>
 <div class="admonition seealso">
 <p class="first admonition-title">See also</p>
-<dl class="last docutils">
-<dt><a class="reference internal" href="Feature_examples.html#sir-model-with-basic-demography-births-deaths"><span class="std std-ref">SIR model with basic demography (births/deaths)</span></a>, :ref:<a href="#id1"><span class="problematic" id="id2">`</span></a>SIR</dt>
-<dd><p class="first last">model with age groups`</p>
-</dd>
-</dl>
+<p class="last"><a class="reference internal" href="Feature_examples.html#sir-model-with-basic-demography-births-deaths"><span class="std std-ref">SIR model with basic demography (births/deaths)</span></a>, <a class="reference internal" href="Feature_examples.html#sir-model-with-age-groups"><span class="std std-ref">SIR model with age groups</span></a></p>
 </div>
 </li>
 <li><p class="first">Another way to produce new individuals is using an action: <code class="docutils literal notranslate"><span class="pre">clone</span></code>
index ae4293d..aee57bb 100644 (file)
@@ -1 +1 @@
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pe_id:6,ultim:5,uml:5,unchang:[2,5,7],undefin:6,under:[5,11,13,14,17],undergo:3,underli:[1,2,3],ungroup:6,uniform:6,uniformli:6,union:[6,12,14],uniqu:[1,6,16],unit:[1,2,3,5,6,7,10,15,16],univ:[1,2,14],unless:[2,6,14],unnecessari:15,unord:16,until:15,unzip:11,updat:[1,2,3,6,7,10,11,13,15],update_count:[1,3],update_csv_count:6,update_output:6,update_output_inform:6,update_output_typ:6,update_time_to_exit:[2,7],upon:[6,16],upper:[1,2,6],upper_level:2,usag:[8,10,12],use:[5,6,7,8,10,11,13,14,15],used:[3,5,6,7,10,11,15,16,17,18],useful:[6,15],user:[2,3,6,7,13],uses:[1,5,10,15],using:[1,2,3,5,6,7,11,14,15],usual:15,utm:13,vaccin:5,val_if_fals:[6,7,15],val_if_tru:[6,7,15],valid:[2,3,6,7,15],valu:[1,2,3,5,6,7,10,11,15,16],value1:16,value2:16,value3:16,value4:16,value_or_funct:6,value_or_list:15,valueact:1,valueerror:6,variabl:[1,2,3,5,6,8,13,16,18],varianc:6,variou:6,varnam:15,verbal:14,veri:[6,8,10,13,15,16],verif:10,verifi:6,versa:15,version:[6,13,14,15],vertic:[10,15],veterinarian:8,viannei:12,vice:15,view:[0,3,8,9,13],view_act:5,viewag:2,viewcompart:2,visual:6,wai:[3,5,8,15,16],wait:6,walsh:12,wane:[10,11],warranti:14,web:[6,11],websit:[11,13],week:16,weight:6,weisstein:6,well:[6,15,16],were:[15,16],what:[1,2,11,13,15,16],whatev:16,when:[1,2,3,5,6,7,10,11,13,15,16,17],whenev:15,where:[1,2,3,5,6,7,10,11,13,14,16],wherev:14,whether:[6,14,15],which:[1,2,3,5,6,7,8,10,11,12,13,14,15,16,17],white:10,who:[2,3],whole:[1,6,14,16],whom:14,wide:6,width:[6,7],wiki:6,wikipedia:6,window:[6,7,8],window_s:[6,7],within:[1,3,5,6,7,10,14,15],withoth:16,without:[5,8,10,11,14,15,16],wolfram:6,word:[6,17],work:[5,6,12,13,14],worker:6,worldwid:14,would:[6,10],wow:6,write:[5,6,8,11,14,15],write_dot:[5,6],writer:6,written:[13,14],www:14,x86:13,xlabel:6,yaml:[5,6,8,10,11,13,15],year:[6,12,16],yes:[10,15,16],yet:[6,10,11],yield:6,ylab:6,you:[11,13,14,15],your:[8,10,11,14],zero:[6,15]},titles:["emulsion package","emulsion.agent package","emulsion.agent.core package","emulsion.agent.managers package","emulsion.environment package","emulsion.model package","emulsion.tools package","High-level functions for model designers","EMULSION Manual","emulsion","Feature examples","Getting started with EMULSION","Information","Installation","License","Modelling language (advanced)","Modelling language (basics)","Modelling principles","&lt;no title&gt;"],titleterms:{"function":[3,5,6,7,15],"new":15,"public":12,Going:11,abstract_ag:2,abstract_process_manag:3,acknowledg:12,action:[1,10,15,16],add:15,advanc:15,age:10,agent:[1,2,3,7],aggreg:[10,15],atom:1,attribut:15,automat:15,avail:7,basic:[7,10,16],birth:10,built:15,calendar:6,chang:[7,11,15],check:11,cite:12,code:15,compart:[1,15],compart_process_manag:3,complexifi:15,comput:7,connect:15,contact:12,content:8,contributor:12,core:2,custom:[10,15],data:10,death:10,demographi:10,design:7,diagram:[11,17],driven:10,durat:[7,10],emuls:[0,1,2,3,4,5,6,8,9,11],emulsion_ag:2,emulsion_model:5,environ:4,exampl:[6,10,11,15,16],except:[1,5],explicit:10,extern:10,featur:10,field:4,file:10,flow:17,from:17,further:11,gestat:10,get:11,git:13,graph:6,group:[2,10,15,16],group_manag:3,high:7,how:12,hybrid:15,ibm:15,ibm_process_manag:3,indic:8,individu:[10,15,17],inform:12,init_emuls:0,initial_condit:16,instal:13,introspect:7,languag:[15,16],level:[7,16],licens:14,linux:13,machin:[15,16,17],maco:13,manag:3,manual:8,master:15,meta:1,metapop_process_manag:3,metapopul:[10,15,17],misc:6,model:[5,7,10,11,15,16,17],model_info:16,model_nam:16,modul:[0,1,2,3,4,5,6],movement:10,multi_process_manag:3,nutshel:16,ons:15,our:11,output:16,packag:[0,1,2,3,4,5,6],parallel:6,paramet:[11,16],parti:13,period:10,pip:13,plot:6,popul:[10,17],principl:17,probabl:7,process:[1,16],produc:[11,15],prototyp:16,python:15,rate:7,regul:15,remov:15,requir:13,risk:10,run:11,scale:15,seir:10,select:[7,12],set:15,simul:6,sir:10,softwar:13,start:11,state:[6,7,10,15,16,17],state_machin:[5,16],statevar:16,structur:[10,16],submodul:[0,1,2,3,4,5,6],subpackag:[0,1],syntax:16,tabl:8,test:13,third:13,time:[6,15],time_info:16,todo:6,tool:6,transit:15,typic:16,usag:7,variabl:[7,10,15],view:[1,6,11],window:13,yaml:16,your:13}})
\ No newline at end of file
index da4ecf7..a5683a7 100644 (file)
@@ -1,3 +1,4 @@
+date,source,dest,age,qty
 2018-01-04,0,10,J,7
 2018-01-05,10,8,J,6
 2018-01-08,0,7,J,5
index de8a96e..4df9579 100644 (file)
@@ -33,9 +33,7 @@ class Metapopulation(MetapopProcessManager):
         moves = {}
         with open(Path(self.model.input_dir, DATA_FILE)) as csvfile:
             # read the CSV file
-            csvreader = csv.DictReader(csvfile,
-                                       fieldnames=['date','source','dest', 'age', 'qty'],
-                                       delimiter=',')
+            csvreader = csv.DictReader(csvfile, delimiter=',')
             for row in csvreader:
                 day = dup.parse(row['date'])
                 if day < origin:
@@ -46,10 +44,10 @@ class Metapopulation(MetapopProcessManager):
                 # group information by step and source herd
                 if step not in moves:
                     moves[step] = {}
-                    src, dest, qty = int(row['source']), int(row['dest']), int(row['qty'])
-                    if src not in moves[step]:
-                        moves[step][src] = []
-                        moves[step][src].append([dest, row['age'], qty])
+                src, dest, qty = int(row['source']), int(row['dest']), int(row['qty'])
+                if src not in moves[step]:
+                    moves[step][src] = []
+                moves[step][src].append([dest, row['age'], qty])
         self.moves = moves
 
     #----------------------------------------------------------------