Merge pull request #461 from stan-dev/release/v2.1.0

Release/v2.1.0

.gitignore

@@ -35,13 +35,22 @@ stan.kdev4
 src/test/gm/model_specs/compiled/*
 !src/test/gm/model_specs/compiled/*.stan
 !src/test/gm/model_specs/compiled/.gitignore
+src/test/gm/model_specs/no_main/*.cpp
+src/test/gm/model_specs/printer
+src/test/gm/model_specs/printer.exe
+src/test/gm/model_specs/printer.cpp
+src/test/io/test_model/example.cpp
 src/test/mcmc/models/improper
 src/test/mcmc/models/improper.exe
 src/test/mcmc/models/improper.cpp
+src/test/mcmc/hmc/hamiltonians/models/funnel.cpp
+src/test/mcmc/hmc/integrators/models/gauss.cpp
+src/test/mcmc/hmc/integrators/models/command.cpp
 src/test/gm/arguments/test_model
 src/test/gm/arguments/test_model.exe
 src/test/gm/arguments/test_model.cpp
 
+
 src/test/mcmc/models/*
 !src/test/mcmc/models/*.stan
 
@@ -58,4 +67,4 @@ src/test/agrad/distributions/multivariate/discrete/*_generated_test.cpp
 #auto generated by RStan make
 rstan/rstan/R/git_head.R
 rstan/rstan/inst/include/stanlib
-rstan/rstan/inst/include/stansrc
+rstan/rstan/inst/include/stansrc

.travis.yml

@@ -2,7 +2,10 @@ language: cpp
 compiler:
   - clang
   - gcc
-script: make test-unit CC=$CXX
+env:
+  - RUN_TARGET=build TEST_TARGET=test-unit
+  - RUN_TARGET=docs
+script: make CC="$CXX" ${RUN_TARGET} ${TEST_TARGET}
 branches:
   only:
     - develop
@@ -13,3 +16,9 @@ notifications:
   email:
     on_success: change
     on_failure: always
+matrix:
+  exclude: # only make docs once:
+    - compiler: clang
+      env: RUN_TARGET=docs
+      script: make CC="$CXX" "${RUN_TARGET}" "${TEST_TARGET}"
+

doc/api/html/_eigen___num_traits_8hpp.html

@@ -96,7 +96,7 @@
 <div class="contents">
 <div class="textblock"><code>#include &lt;limits&gt;</code><br/>
 <code>#include &lt;<a class="el" href="_eigen_8hpp_source.html">stan/math/matrix/Eigen.hpp</a>&gt;</code><br/>
-<code>#include &lt;<a class="el" href="rev_2var_8hpp_source.html">stan/agrad/rev/var.hpp</a>&gt;</code><br/>
+<code>#include &lt;<a class="el" href="var_8hpp_source.html">stan/agrad/rev/var.hpp</a>&gt;</code><br/>
 </div>
 <p><a href="_eigen___num_traits_8hpp_source.html">Go to the source code of this file.</a></p>
 <table class="memberdecls">

doc/api/html/_eigen___num_traits_8hpp_source.html

@@ -96,7 +96,7 @@
 <div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="preprocessor"></span></div>
 <div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#include &lt;limits&gt;</span></div>
 <div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="_eigen_8hpp.html">stan/math/matrix/Eigen.hpp</a>&gt;</span></div>
-<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="rev_2var_8hpp.html">stan/agrad/rev/var.hpp</a>&gt;</span></div>
+<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="var_8hpp.html">stan/agrad/rev/var.hpp</a>&gt;</span></div>
 <div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;</div>
 <div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="keyword">namespace </span>stan {</div>
 <div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;  <span class="keyword">namespace </span>agrad {</div>

doc/api/html/adapt__dense__e__nuts_8hpp_source.html

@@ -111,10 +111,10 @@
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+<div class="line"><a name="l00021"></a><span class="lineno"><a class="code" href="classstan_1_1mcmc_1_1adapt__dense__e__nuts.html#a7f2a7a4f48cbc0f7667f01e9045e069a">   21</a></span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1adapt__dense__e__nuts.html#a7f2a7a4f48cbc0f7667f01e9045e069a">adapt_dense_e_nuts</a>(M &amp;m, BaseRNG&amp; rng,</div>
 <div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;                           std::ostream* o = &amp;std::cout, std::ostream* <a class="code" href="namespacestan_1_1math.html#a3b650a0131d41167ef4837ecc7d02be5" title="Return the base of the natural logarithm.">e</a> = 0):</div>
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-<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html">stepsize_covar_adapter</a>(m.num_params_r(), max_adapt)</div>
+<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html">stepsize_covar_adapter</a>(m.num_params_r())</div>
 <div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;      {};</div>
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@@ -127,7 +127,7 @@
 <div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;          </div>
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-<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;          <span class="keywordtype">bool</span> update = this-&gt;<a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html#a81e2e0c870bf71ae803ed7bc29e7c10d">_covar_adaptation</a>.<a class="code" href="classstan_1_1mcmc_1_1covar__adaptation.html#a617dcf2c153fcb4c0a75ae3bcbb05097">learn_covariance</a>(this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#abaa8c5f40b664481b188c8342f3917db">_z</a>.<a class="code" href="classstan_1_1mcmc_1_1dense__e__point.html#abf64e065e1579f7aeb211d764dc62eb1">mInv</a>, this-&gt;_z.q);</div>
+<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;          <span class="keywordtype">bool</span> update = this-&gt;<a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html#a81e2e0c870bf71ae803ed7bc29e7c10d">_covar_adaptation</a>.<a class="code" href="classstan_1_1mcmc_1_1covar__adaptation.html#a6c50cab9f1bebe465e8c28db2a9581f4">learn_covariance</a>(this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#abaa8c5f40b664481b188c8342f3917db">_z</a>.<a class="code" href="classstan_1_1mcmc_1_1dense__e__point.html#abf64e065e1579f7aeb211d764dc62eb1">mInv</a>, this-&gt;_z.q);</div>
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 <div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;          <span class="keywordflow">if</span>(update) {</div>
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doc/api/html/adapt__dense__e__static__hmc_8hpp_source.html

@@ -112,10 +112,10 @@
 <div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;      </div>
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+<div class="line"><a name="l00022"></a><span class="lineno"><a class="code" href="classstan_1_1mcmc_1_1adapt__dense__e__static__hmc.html#a7d57f187b6877982cf329800e47b5370">   22</a></span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1adapt__dense__e__static__hmc.html#a7d57f187b6877982cf329800e47b5370">adapt_dense_e_static_hmc</a>(M &amp;m, BaseRNG&amp; rng,</div>
 <div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;                                 std::ostream* o = &amp;std::cout, std::ostream* <a class="code" href="namespacestan_1_1math.html#a3b650a0131d41167ef4837ecc7d02be5" title="Return the base of the natural logarithm.">e</a> = 0):</div>
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-<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html">stepsize_covar_adapter</a>(m.num_params_r(), max_adapt)</div>
+<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html">stepsize_covar_adapter</a>(m.num_params_r())</div>
 <div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;      {};</div>
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@@ -129,7 +129,7 @@
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 <div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;          this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__static__hmc.html#a99f17a731044a9880298f5e254b94a69">_update_L</a>();</div>
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-<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;          <span class="keywordtype">bool</span> update = this-&gt;<a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html#a81e2e0c870bf71ae803ed7bc29e7c10d">_covar_adaptation</a>.<a class="code" href="classstan_1_1mcmc_1_1covar__adaptation.html#a617dcf2c153fcb4c0a75ae3bcbb05097">learn_covariance</a>(this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#abaa8c5f40b664481b188c8342f3917db">_z</a>.<a class="code" href="classstan_1_1mcmc_1_1dense__e__point.html#abf64e065e1579f7aeb211d764dc62eb1">mInv</a>, this-&gt;_z.q);</div>
+<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;          <span class="keywordtype">bool</span> update = this-&gt;<a class="code" href="classstan_1_1mcmc_1_1stepsize__covar__adapter.html#a81e2e0c870bf71ae803ed7bc29e7c10d">_covar_adaptation</a>.<a class="code" href="classstan_1_1mcmc_1_1covar__adaptation.html#a6c50cab9f1bebe465e8c28db2a9581f4">learn_covariance</a>(this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#abaa8c5f40b664481b188c8342f3917db">_z</a>.<a class="code" href="classstan_1_1mcmc_1_1dense__e__point.html#abf64e065e1579f7aeb211d764dc62eb1">mInv</a>, this-&gt;_z.q);</div>
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 <div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;          <span class="keywordflow">if</span>(update) {</div>
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doc/api/html/adapt__diag__e__nuts_8hpp_source.html

@@ -111,10 +111,10 @@
 <div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;      </div>
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+<div class="line"><a name="l00021"></a><span class="lineno"><a class="code" href="classstan_1_1mcmc_1_1adapt__diag__e__nuts.html#a8e2eb81bdeed65fb1cdf8512643c5247">   21</a></span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1adapt__diag__e__nuts.html#a8e2eb81bdeed65fb1cdf8512643c5247">adapt_diag_e_nuts</a>(M &amp;m, BaseRNG&amp; rng,</div>
 <div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;                          std::ostream* o = &amp;std::cout, std::ostream* <a class="code" href="namespacestan_1_1math.html#a3b650a0131d41167ef4837ecc7d02be5" title="Return the base of the natural logarithm.">e</a> = 0):</div>
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-<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1stepsize__var__adapter.html">stepsize_var_adapter</a>(m.num_params_r(), max_adapt)</div>
+<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;        <a class="code" href="classstan_1_1mcmc_1_1stepsize__var__adapter.html">stepsize_var_adapter</a>(m.num_params_r())</div>
 <div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;      {};</div>
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@@ -127,7 +127,7 @@
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-<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;          <span class="keywordtype">bool</span> update = this-&gt;<a class="code" href="classstan_1_1mcmc_1_1stepsize__var__adapter.html#a4b0e0a10b281ecbc17a22731cabd5032">_var_adaptation</a>.<a class="code" href="classstan_1_1mcmc_1_1var__adaptation.html#af8ca0bc31467c2615a89ebf6369992f4">learn_variance</a>(this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#abaa8c5f40b664481b188c8342f3917db">_z</a>.<a class="code" href="classstan_1_1mcmc_1_1diag__e__point.html#aaeb41431de534f7237ea8a180b2b3d1a">mInv</a>, this-&gt;_z.q);</div>
+<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;          <span class="keywordtype">bool</span> update = this-&gt;<a class="code" href="classstan_1_1mcmc_1_1stepsize__var__adapter.html#a4b0e0a10b281ecbc17a22731cabd5032">_var_adaptation</a>.<a class="code" href="classstan_1_1mcmc_1_1var__adaptation.html#a52f68d10bf0c8628b395bf18a00ba34e">learn_variance</a>(this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#abaa8c5f40b664481b188c8342f3917db">_z</a>.<a class="code" href="classstan_1_1mcmc_1_1diag__e__point.html#aaeb41431de534f7237ea8a180b2b3d1a">mInv</a>, this-&gt;_z.q);</div>
 <div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;          </div>
 <div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;          <span class="keywordflow">if</span>(update) {</div>
 <div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;            this-&gt;<a class="code" href="classstan_1_1mcmc_1_1base__hmc.html#a6ec1af08b215fda50b23dade2aa615a8">init_stepsize</a>();</div>