Revise uses of apop_rng_get_thread

apop_asst.m4.c

@@ -378,10 +378,10 @@ of <tt>gsl_rng</tt>s is extended to length \c thread, and each element extended
 This function can be used anywhere a \ref gsl_rng would be used.
 
 \param thread_in The number of the RNG to retrieve, starting at zero (which is
-how OpenMP numbers its threads). If blank, I'll look up the current thread (via \c
+how OpenMP numbers its threads). If -1, I'll look up the current thread (via \c
 omp_get_thread_num) for you.
 
-See \ref threading for additional notes.
+See \ref threading for additional notes. In most cases, you want to use <tt>apop_rng_get_thread(-1)</tt>.
 
 \return The appropriate RNG, initialized if necessary.
 \hideinitializer

apop_conversions.m4.c

@@ -336,7 +336,7 @@ gsl_matrix *apop_matrix_copy(const gsl_matrix *in){
 
 /** \page text_format Input text file formatting
 
-This section describes the assumptions made by \ref apop_text_to_db and \ref apop_text_to_data.
+This reference section describes the assumptions made by \ref apop_text_to_db and \ref apop_text_to_data.
 
 Each row of the file will be converted to one record in the database or one row in the
 matrix. Values on one row are separated by delimiters. Fixed-width input is also OK;
@@ -350,25 +350,20 @@ will delimit separate entries.  To change the default, use an argument to
 The input text file must be UTF-8 or traditional ASCII encoding. Delimiters must be ASCII characters. 
 If your data is in another encoding, try the POSIX-standard \c iconv program to filter the data to UTF-8.
 
-\li The character after a backslash is read as a normal character, even if it is a delimiter, \c #, or \c ".
-
-\li If a field contains several such special characters, surround it by \c "s. The surrounding marks are stripped and the text read verbatim.
-
-\li Text does not need to be delimited by quotes (unless there are special characters). If a text field is quote-delimited, I'll strip them.
-E.g., "Males, 30-40", is an OK column name, as is "Males named \\"Joe\\"".
-
-\li Everything after a # is taken to be comments and ignored. 
-
-\li Blank lines (empty or consisting only of white space) are also ignored.
-
-\li If you are reading into the <tt>gsl_matrix</tt> element of an \ref apop_data set,
+  \li The character after a backslash is read as a normal character, even if it is a delimiter, \c #, or \c ".
+  \li If a field contains several such special characters, surround it by \c "s. The
+surrounding marks are stripped and the text read verbatim.
+  \li Text does not need to be delimited by quotes (unless there are special characters). If a text field is quote-delimited, I'll strip them.
+E.g., "Males, 30-40", is an OK column name, as is "Males named \"Joe\\"".
+  \li Everything after an unprotected # is taken to be comments and ignored. 
+  \li Blank lines (empty or consisting only of white space) are also ignored.
+  \li If you are reading into the <tt>gsl_matrix</tt> element of an \ref apop_data set,
 all text fields are taken as zeros. You will be warned of such substitutions unless
-you set \code apop_opts.verbose==0\endcode beforehand. For mixed text/numeric data,
+you set <tt>apop_opts.verbose==0</tt> beforehand. For mixed text/numeric data,
 try using \ref apop_text_to_db and then \ref apop_query_to_mixed_data.
-
-\li There are often two delimiters in a row, e.g., "23, 32,, 12". When it's two commas
+  \li There are often two delimiters in a row, e.g., "23, 32,, 12". When it's two commas
 like this, the user typically means that there is a missing value and the system should
-insert an NAN; when it is two tabs in a row, this is typically just a formatting
+insert a NAN; when it is two tabs in a row, this is typically just a formatting
 glitch. Thus, if there are multiple delimiters in a row, I check whether the second
 (and subsequent) is a space or a tab; if it is, then it is ignored, and if it is any
 other delimiter (including the end of the line) then a NaN is inserted.
@@ -393,22 +388,18 @@ apop_opts.nan_string = NULL;
 \endcode
 
 SQLite stores these NaN-type values internally as \c NULL; that means that functions like
-\ref apop_query_to_data will convert both your \c nan_string string and \c NULL to an \c NaN value.
+\ref apop_query_to_data will convert both your \c nan_string string and \c NULL to \c NaN.
 
-\li The system uses the standards for C's \c atof() function for
+  \li The system uses the standards for C's \c atof() function for
 floating-point numbers: INFINITY, -INFINITY, and NaN work as expected.
-
-\li If there are row names and column names, then the input will not be perfectly square:
+  \li If there are row names and column names, then the input will not be perfectly square:
 there should be no first entry in the sequence of column names like <tt>row names</tt>. That is,
 for a 100x100 data set with row and column names, there are 100 names in the top row,
 and 101 entries in each subsequent row (name plus 100 data points).
-
-\li White space before or after a field is ignored. So <tt>1, 2,3, 4 , 5, " six ",7 </tt>
+  \li White space before or after a field is ignored. So <tt>1, 2,3, 4 , 5, " six ",7 </tt>
 is eqivalent to <tt>1,2,3,4,5," six ",7</tt>.
-
-\li NUL characters are treated as white space, so if your fields have NULs as padding, you should have no problem. NULs inside of a string will probably break.
-
-\li Fixed-width formats are supported (for plain ASCII encoding only), but you have to provide a list of field ending positions. For example, given
+  \li NUL characters (<tt>'\0'</tt>) are treated as white space, so if your fields have NULs as padding, you should have no problem. NULs inside of a string terminates the string as it always does in C.
+  \li Fixed-width formats are supported (for plain ASCII encoding only), but you have to provide a list of field ending positions. For example, given
 \code
 NUMLEOL
 123AABB

apop_db_sqlite.c

@@ -135,7 +135,8 @@ static void powFn(sqlite3_context *context, int argc, sqlite3_value **argv){
 
 static void rngFn(sqlite3_context *context, int argc, sqlite3_value **argv){
     Staticdef(gsl_rng *, rng, apop_rng_alloc(apop_opts.rng_seed++));
-    sqlite3_result_double(context, gsl_rng_uniform(rng));
+    //sqlite3_result_double(context, gsl_rng_uniform(rng));
+    sqlite3_result_double(context, gsl_rng_uniform(apop_rng_get_thread(-1)));
 }
 
 #define sqfn(name) static void name##Fn(sqlite3_context *context, int argc, sqlite3_value **argv){ \

apop_mcmc.m4.c

@@ -281,7 +281,7 @@ APOP_VAR_HEAD apop_model *apop_model_metropolis(apop_data *d, gsl_rng *rng, apop
     apop_data *apop_varad_var(d, NULL);
     apop_model *apop_varad_var(m, NULL);
     Apop_stopif(!m, return NULL, 0, "NULL model input.");
-    gsl_rng *apop_varad_var(rng, apop_rng_get_thread());
+    gsl_rng *apop_varad_var(rng, apop_rng_get_thread(-1));
 APOP_VAR_END_HEAD
     apop_model *outp;
     OMP_critical(metropolis)

apop_model.c

@@ -400,7 +400,7 @@ int apop_model_metropolis_draw(double *out, gsl_rng* rng, apop_model *params);//
 \return Zero on success; nozero on failure. <tt>out[0]</tt> is probably \c NAN on failure.
 */
 int apop_draw(double *out, gsl_rng *r, apop_model *m){
-    if (!r) r = apop_rng_get_thread();
+    if (!r) r = apop_rng_get_thread(-1);
     if (m->draw)
         return m->draw(out, r, m); 
     else if (m->dsize == 1)

apop_stats.m4.c

@@ -702,7 +702,7 @@ APOP_VAR_HEAD long double apop_kl_divergence(apop_model *from, apop_model *to, i
     Apop_stopif(!from, return NAN, 0, "The first model is NULL; returning NaN.");
     Apop_stopif(!to, return NAN, 0, "The second model is NULL.");
     double apop_varad_var(draw_ct, 1e5);
-    gsl_rng * apop_varad_var(rng, apop_rng_get_thread());
+    gsl_rng * apop_varad_var(rng, apop_rng_get_thread(-1));
 APOP_VAR_ENDHEAD
     double div = 0;
     Apop_notify(3, "p(from)\tp(to)\tfrom*log(from/to)\n");
@@ -728,7 +728,7 @@ APOP_VAR_ENDHEAD
         apop_data *draw_list = apop_data_alloc(draw_ct, 2);
         OMP_for_reduce(+:div,    int i=0; i < draw_ct; i++){
             double draw[from->dsize];
-            apop_draw(draw, apop_rng_get_thread(), from);
+            apop_draw(draw, apop_rng_get_thread(-1), from);
             gsl_matrix_view dm = gsl_matrix_view_array(draw, 1, from->dsize);
             double pi = apop_p(&(apop_data){.matrix=&(dm.matrix)}, from);
             double qi = apop_p(&(apop_data){.matrix=&(dm.matrix)}, to);

apop_update.m4.c

@@ -184,7 +184,7 @@ APOP_VAR_HEAD apop_model * apop_update(apop_data *data, apop_model *prior, apop_
     apop_data *apop_varad_var(data, NULL);
     apop_model *apop_varad_var(prior, NULL);
     apop_model *apop_varad_var(likelihood, NULL);
-    gsl_rng *apop_varad_var(rng, apop_rng_get_thread());
+    gsl_rng *apop_varad_var(rng, apop_rng_get_thread(-1));
 APOP_VAR_END_HEAD
     static int setup=0; if (!(setup++)){
         apop_update_vtable_add(betabinom, apop_beta, apop_binomial);

docs/adjust

@@ -12,8 +12,7 @@ sed -i 's/pdflatex/xelatex/' latex/Makefile
 sed -i "/familydefault.*sfdefault/ d" latex/refman.tex
 
 #No footer
-sed -i "/fancyhead/ d" latex/refman.tex
-sed -i "/fancyfoot/ d" latex/refman.tex
+sed -i -e "/fancyhead/ d" -e "/fancyfoot/ d" -e "Generated by Doxygen/ d" latex/refman.tex
 
 #Fix enumerations -> model documentation
 sed -i -f edit_group.sed latex/group__models.tex