modify makefiles to make reorg work, change README

README.md

@@ -46,7 +46,6 @@ This library provides some basic building blocks. The recommended strategy is to
 
 ### Cdf auxiliary functions
 
-To help with the above core strategy, this library provides convenience functions, which take a cdf, and return a sample from the distribution produced by that cdf. This might make it easier to program models, at the cost of a 20x to 60x slowdown in the parts of the code that use it.
 
 ### Nested functions and compilation with tcc.
 
@@ -60,29 +59,6 @@ GCC has an extension which allows a program to define a function inside another
 
 My recommendation would be to use tcc while drawing a small number of samples for fast iteration, and then using gcc for the final version with lots of samples, and possibly with nested functions for ease of reading by others.
 
-### Error propagation vs exiting on error
-
-The process of taking a cdf and returning a sample might fail, e.g., it's a Newton method which might fail to converge because of cdf artifacts. The cdf itself might also fail, e.g., if a distribution only accepts a range of parameters, but is fed parameters outside that range.
-
-This library provides two approaches:
-
-1. Print the line and function in which the error occured, then exit on error
-2. In situations where there might be an error, return a struct containing either the correct value or an error message:
-
-```C
-struct box {
-    int empty;
-    double content;
-    char* error_msg;
-};
-```
-
-The first approach produces terser programs but might not scale. The second approach seems like it could lead to more robust programmes, but is more verbose.
-
-Behaviour on error can be toggled by the `EXIT_ON_ERROR` variable. This library also provides a convenient macro, `PROCESS_ERROR`, to make error handling in either case much terser—see the usage in example 4 in the examples/ folder.
-
-Overall, I'd describe the error handling capabilities of this library as pretty rudimentary. For example, this program might fail in surprising ways if you ask for a lognormal with negative standard deviation, because I haven't added error checking for that case yet.
-
 ### Guarantees and licensing
 
 - I offer no guarantees about stability, correctness, performance, etc. I might, for instance, abandon the version in C and rewrite it in Zig, Nim or Rust.
@@ -272,6 +248,49 @@ make tidy
 
 It emits one warning about something I already took care of, so by default I've suppressed it. I think this is good news in terms of making me more confident that this simple library is correct :).
 
+### Division between core functions and extraneous expansions
+
+This library differentiates between core functions, which are pretty tightly scoped, and expansions and convenience functions, which are more meandering. Expansions are in `extra.c` and `extra.h`. To use them, take care to link them:
+
+```
+// In your C source file
+#include "extra.h"
+```
+
+```
+# When compiling:
+gcc -std=c99 -Wall -O3 example.c squiggle.c extra.c -lm -o ./example
+
+```
+
+#### Extra: Cdf auxiliary functions
+
+I provide some Take a cdf, and return a sample from the distribution produced by that cdf. This might make it easier to program models, at the cost of a 20x to 60x slowdown in the parts of the code that use it. 
+
+#### Extra: Error propagation vs exiting on error
+
+The process of taking a cdf and returning a sample might fail, e.g., it's a Newton method which might fail to converge because of cdf artifacts. The cdf itself might also fail, e.g., if a distribution only accepts a range of parameters, but is fed parameters outside that range.
+
+This library provides two approaches:
+
+1. Print the line and function in which the error occured, then exit on error
+2. In situations where there might be an error, return a struct containing either the correct value or an error message:
+
+```C
+struct box {
+    int empty;
+    double content;
+    char* error_msg;
+};
+```
+
+The first approach produces terser programs but might not scale. The second approach seems like it could lead to more robust programmes, but is more verbose.
+
+Behaviour on error can be toggled by the `EXIT_ON_ERROR` variable. This library also provides a convenient macro, `PROCESS_ERROR`, to make error handling in either case much terser—see the usage in example 4 in the examples/ folder.
+
+Overall, I'd describe the error handling capabilities of this library as pretty rudimentary. For example, this program might fail in surprising ways if you ask for a lognormal with negative standard deviation, because I haven't added error checking for that case yet.
+
+
 ## Related projects
 
 - [Squiggle](https://www.squiggle-language.com/)

examples/04_sample_from_cdf_simple/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/04_sample_from_cdf_simple/makefile

@@ -9,7 +9,7 @@ CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
+SRC=example.c ../../squiggle.c ../../extra.c
 OUTPUT=./example
 
 ## Dependencies

examples/05_sample_from_cdf_beta/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/05_sample_from_cdf_beta/makefile

@@ -9,7 +9,7 @@
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
+SRC=example.c ../../squiggle.c ../../extra.c
 OUTPUT=./example
 
 ## Dependencies

examples/07_ci_beta/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>

examples/07_ci_beta/makefile

@@ -9,7 +9,7 @@ CC=gcc
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
+SRC=example.c ../../squiggle.c ../../extra.c
 OUTPUT=example
 
 ## Dependencies

examples/08_nuclear_war/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/08_nuclear_war/makefile

@@ -9,7 +9,7 @@ CC=gcc
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
+SRC=example.c ../../squiggle.c ../../extra.c
 OUTPUT=example
 
 ## Dependencies

examples/09_burn_10kg_fat/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/09_burn_10kg_fat/makefile

@@ -5,22 +5,25 @@
 #   make run
 
 # Compiler
-CC=gcc
+CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
-OUTPUT=example
+SRC=example.c ../../squiggle.c ../../extra.c
+OUTPUT=./example
 
 ## Dependencies
 MATH=-lm
+DEPENDENCIES=$(MATH)
+# OPENMP=-fopenmp
 
 ## Flags
 DEBUG= #'-g'
-STANDARD=-std=c99
+STANDARD=-std=c99 ## gnu99 allows for nested functions.
+EXTENSIONS= #-fnested-functions
 WARNINGS=-Wall
-OPTIMIZED=-O3  #-Ofast
-# OPENMP=-fopenmp
+OPTIMIZED=-O3#-Ofast
+CFLAGS=$(DEBUG) $(STANDARD) $(EXTENSIONS) $(WARNINGS) $(OPTIMIZED)
 
 ## Formatter
 STYLE_BLUEPRINT=webkit
@@ -28,13 +31,14 @@ FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
 
 ## make build
 build: $(SRC)
-	$(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(MATH) -o $(OUTPUT)
+	# gcc -std=gnu99 example.c -lm -o example
+	$(CC) $(CFLAGS) $(SRC) $(DEPENDENCIES) -o $(OUTPUT)
 
 format: $(SRC)
 	$(FORMATTER) $(SRC)
 
 run: $(SRC) $(OUTPUT)
-	OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+	./$(OUTPUT) && echo
 
 time-linux: 
 	@echo "Requires /bin/time, found on GNU/Linux systems" && echo

examples/10_nuclear_recovery/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/10_nuclear_recovery/makefile

@@ -5,22 +5,25 @@
 #   make run
 
 # Compiler
-CC=gcc
+CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
-OUTPUT=example
+SRC=example.c ../../squiggle.c ../../extra.c
+OUTPUT=./example
 
 ## Dependencies
 MATH=-lm
+DEPENDENCIES=$(MATH)
+# OPENMP=-fopenmp
 
 ## Flags
 DEBUG= #'-g'
-STANDARD=-std=c99
+STANDARD=-std=c99 ## gnu99 allows for nested functions.
+EXTENSIONS= #-fnested-functions
 WARNINGS=-Wall
-OPTIMIZED=-O3  #-Ofast
-# OPENMP=-fopenmp
+OPTIMIZED=-O3#-Ofast
+CFLAGS=$(DEBUG) $(STANDARD) $(EXTENSIONS) $(WARNINGS) $(OPTIMIZED)
 
 ## Formatter
 STYLE_BLUEPRINT=webkit
@@ -28,13 +31,14 @@ FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
 
 ## make build
 build: $(SRC)
-	$(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(MATH) -o $(OUTPUT)
+	# gcc -std=gnu99 example.c -lm -o example
+	$(CC) $(CFLAGS) $(SRC) $(DEPENDENCIES) -o $(OUTPUT)
 
 format: $(SRC)
 	$(FORMATTER) $(SRC)
 
 run: $(SRC) $(OUTPUT)
-	OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+	./$(OUTPUT) && echo
 
 time-linux: 
 	@echo "Requires /bin/time, found on GNU/Linux systems" && echo

examples/11_algebra/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/11_algebra/makefile

@@ -5,22 +5,25 @@
 #   make run
 
 # Compiler
-CC=gcc
+CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
-OUTPUT=example
+SRC=example.c ../../squiggle.c ../../extra.c
+OUTPUT=./example
 
 ## Dependencies
 MATH=-lm
+DEPENDENCIES=$(MATH)
+# OPENMP=-fopenmp
 
 ## Flags
 DEBUG= #'-g'
-STANDARD=-std=c99
+STANDARD=-std=c99 ## gnu99 allows for nested functions.
+EXTENSIONS= #-fnested-functions
 WARNINGS=-Wall
-OPTIMIZED=-O3  #-Ofast
-# OPENMP=-fopenmp
+OPTIMIZED=-O3#-Ofast
+CFLAGS=$(DEBUG) $(STANDARD) $(EXTENSIONS) $(WARNINGS) $(OPTIMIZED)
 
 ## Formatter
 STYLE_BLUEPRINT=webkit
@@ -28,13 +31,14 @@ FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
 
 ## make build
 build: $(SRC)
-	$(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(MATH) -o $(OUTPUT)
+	# gcc -std=gnu99 example.c -lm -o example
+	$(CC) $(CFLAGS) $(SRC) $(DEPENDENCIES) -o $(OUTPUT)
 
 format: $(SRC)
 	$(FORMATTER) $(SRC)
 
 run: $(SRC) $(OUTPUT)
-	OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+	./$(OUTPUT) && echo
 
 time-linux: 
 	@echo "Requires /bin/time, found on GNU/Linux systems" && echo

examples/12_algebra_and_conversion/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/12_algebra_and_conversion/makefile

@@ -5,22 +5,25 @@
 #   make run
 
 # Compiler
-CC=gcc
+CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
-OUTPUT=example
+SRC=example.c ../../squiggle.c ../../extra.c
+OUTPUT=./example
 
 ## Dependencies
 MATH=-lm
+DEPENDENCIES=$(MATH)
+# OPENMP=-fopenmp
 
 ## Flags
 DEBUG= #'-g'
-STANDARD=-std=c99
+STANDARD=-std=c99 ## gnu99 allows for nested functions.
+EXTENSIONS= #-fnested-functions
 WARNINGS=-Wall
-OPTIMIZED=-O3  #-Ofast
-# OPENMP=-fopenmp
+OPTIMIZED=-O3#-Ofast
+CFLAGS=$(DEBUG) $(STANDARD) $(EXTENSIONS) $(WARNINGS) $(OPTIMIZED)
 
 ## Formatter
 STYLE_BLUEPRINT=webkit
@@ -28,13 +31,14 @@ FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
 
 ## make build
 build: $(SRC)
-	$(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(MATH) -o $(OUTPUT)
+	# gcc -std=gnu99 example.c -lm -o example
+	$(CC) $(CFLAGS) $(SRC) $(DEPENDENCIES) -o $(OUTPUT)
 
 format: $(SRC)
 	$(FORMATTER) $(SRC)
 
 run: $(SRC) $(OUTPUT)
-	OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+	./$(OUTPUT) && echo
 
 time-linux: 
 	@echo "Requires /bin/time, found on GNU/Linux systems" && echo

examples/13_ergonomic_algebra/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <math.h>
 #include <stdint.h>
 #include <stdio.h>

examples/13_ergonomic_algebra/makefile

@@ -5,22 +5,25 @@
 #   make run
 
 # Compiler
-CC=gcc
+CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
-OUTPUT=example
+SRC=example.c ../../squiggle.c ../../extra.c
+OUTPUT=./example
 
 ## Dependencies
 MATH=-lm
+DEPENDENCIES=$(MATH)
+# OPENMP=-fopenmp
 
 ## Flags
 DEBUG= #'-g'
-STANDARD=-std=c99
+STANDARD=-std=c99 ## gnu99 allows for nested functions.
+EXTENSIONS= #-fnested-functions
 WARNINGS=-Wall
-OPTIMIZED=-O3  #-Ofast
-# OPENMP=-fopenmp
+OPTIMIZED=-O3#-Ofast
+CFLAGS=$(DEBUG) $(STANDARD) $(EXTENSIONS) $(WARNINGS) $(OPTIMIZED)
 
 ## Formatter
 STYLE_BLUEPRINT=webkit
@@ -28,13 +31,14 @@ FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
 
 ## make build
 build: $(SRC)
-	$(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(MATH) -o $(OUTPUT)
+	# gcc -std=gnu99 example.c -lm -o example
+	$(CC) $(CFLAGS) $(SRC) $(DEPENDENCIES) -o $(OUTPUT)
 
 format: $(SRC)
 	$(FORMATTER) $(SRC)
 
 run: $(SRC) $(OUTPUT)
-	OMP_NUM_THREADS=1 ./$(OUTPUT) && echo
+	./$(OUTPUT) && echo
 
 time-linux: 
 	@echo "Requires /bin/time, found on GNU/Linux systems" && echo

examples/14_twitter_thread_example/example.c

@@ -1,4 +1,5 @@
 #include "../../squiggle.h"
+#include "../../extra.h"
 #include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>

examples/14_twitter_thread_example/makefile

@@ -5,22 +5,25 @@
 #   make run
 
 # Compiler
-CC=gcc
+CC=gcc # required for nested functions
 # CC=tcc # <= faster compilation
 
 # Main file
-SRC=example.c ../../squiggle.c
-OUTPUT=example
+SRC=example.c ../../squiggle.c ../../extra.c
+OUTPUT=./example
 
 ## Dependencies
 MATH=-lm
+DEPENDENCIES=$(MATH)
+# OPENMP=-fopenmp
 
 ## Flags
 DEBUG= #'-g'
-STANDARD=-std=c99
+STANDARD=-std=c99 ## gnu99 allows for nested functions.
+EXTENSIONS= #-fnested-functions
 WARNINGS=-Wall
-OPTIMIZED=-O3  #-Ofast
-# OPENMP=-fopenmp
+OPTIMIZED=-O3#-Ofast
+CFLAGS=$(DEBUG) $(STANDARD) $(EXTENSIONS) $(WARNINGS) $(OPTIMIZED)
 
 ## Formatter
 STYLE_BLUEPRINT=webkit
@@ -28,7 +31,8 @@ FORMATTER=clang-format -i -style=$(STYLE_BLUEPRINT)
 
 ## make build
 build: $(SRC)
-	$(CC) $(OPTIMIZED) $(DEBUG) $(SRC) $(MATH) -o $(OUTPUT)
+	# gcc -std=gnu99 example.c -lm -o example
+	$(CC) $(CFLAGS) $(SRC) $(DEPENDENCIES) -o $(OUTPUT)
 
 format: $(SRC)
 	$(FORMATTER) $(SRC)
@@ -40,7 +44,7 @@ time-linux:
 	@echo "Requires /bin/time, found on GNU/Linux systems" && echo
 	
 	@echo "Running 100x and taking avg time $(OUTPUT)"
-	@t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do ./$(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 1 thread: |" | sed 's|$$|ms|' && echo
+	@t=$$(/usr/bin/time -f "%e" -p bash -c 'for i in {1..100}; do $(OUTPUT); done' 2>&1 >/dev/null | grep real | awk '{print $$2}' ); echo "scale=2; 1000 * $$t / 100" | bc | sed "s|^|Time using 1 thread: |" | sed 's|$$|ms|' && echo
 
 ## Profiling
 

extra.c

@@ -6,15 +6,58 @@
 #include <stdlib.h>
 #include <sys/types.h>
 #include <time.h>
+#include "squiggle.h"
+
+// math constants
+#define PI 3.14159265358979323846 // M_PI in gcc gnu99
+#define NORMAL90CONFIDENCE 1.6448536269514727
 
 // Some error niceties; these won't be used until later
 #define MAX_ERROR_LENGTH 500
 #define EXIT_ON_ERROR 0
 #define PROCESS_ERROR(error_msg) process_error(error_msg, EXIT_ON_ERROR, __FILE__, __LINE__)
 
-// # More cool stuff
-// This is no longer necessary to do basic estimation,
-// but is still cool
+// Get confidence intervals, given a sampler
+// Not in core yet because I'm not sure how much I like the interface,
+// to do: add n to function parameters and document
+
+typedef struct ci_t {
+    float low;
+    float high;
+} ci;
+int compare_doubles(const void* p, const void* q)
+{
+    // https://wikiless.esmailelbob.xyz/wiki/Qsort?lang=en
+    double x = *(const double*)p;
+    double y = *(const double*)q;
+
+    /* Avoid return x - y, which can cause undefined behaviour
+       because of signed integer overflow. */
+    if (x < y)
+        return -1; // Return -1 if you want ascending, 1 if you want descending order.
+    else if (x > y)
+        return 1; // Return 1 if you want ascending, -1 if you want descending order.
+
+    return 0;
+}
+ci get_90_confidence_interval(double (*sampler)(uint64_t*), uint64_t* seed)
+{
+    int n = 100 * 1000;
+    double* samples_array = malloc(n * sizeof(double));
+    for (int i = 0; i < n; i++) {
+        samples_array[i] = sampler(seed);
+    }
+    qsort(samples_array, n, sizeof(double), compare_doubles);
+
+    ci result = {
+        .low = samples_array[5000],
+        .high = samples_array[94999],
+    };
+    free(samples_array);
+
+    return result;
+}
+
 
 // ## Sample from an arbitrary cdf
 struct box {
@@ -210,45 +253,6 @@ double sampler_danger(struct box cdf(double), uint64_t* seed)
 }
 */
 
-// Get confidence intervals, given a sampler
-
-typedef struct ci_t {
-    float low;
-    float high;
-} ci;
-int compare_doubles(const void* p, const void* q)
-{
-    // https://wikiless.esmailelbob.xyz/wiki/Qsort?lang=en
-    double x = *(const double*)p;
-    double y = *(const double*)q;
-
-    /* Avoid return x - y, which can cause undefined behaviour
-       because of signed integer overflow. */
-    if (x < y)
-        return -1; // Return -1 if you want ascending, 1 if you want descending order.
-    else if (x > y)
-        return 1; // Return 1 if you want ascending, -1 if you want descending order.
-
-    return 0;
-}
-ci get_90_confidence_interval(double (*sampler)(uint64_t*), uint64_t* seed)
-{
-    int n = 100 * 1000;
-    double* samples_array = malloc(n * sizeof(double));
-    for (int i = 0; i < n; i++) {
-        samples_array[i] = sampler(seed);
-    }
-    qsort(samples_array, n, sizeof(double), compare_doubles);
-
-    ci result = {
-        .low = samples_array[5000],
-        .high = samples_array[94999],
-    };
-    free(samples_array);
-
-    return result;
-}
-
 // # Small algebra manipulations
 
 // here I discover named structs,

extra.h

@@ -43,10 +43,7 @@ typedef struct lognormal_params_t {
 } lognormal_params;
 lognormal_params algebra_product_lognormals(lognormal_params a, lognormal_params b);
 
-
 lognormal_params convert_ci_to_lognormal_params(ci x);
-
-
-ci convert_lognormal_params_to_ci(lognormal_params y);
+ci               convert_lognormal_params_to_ci(lognormal_params y);
 
 #endif

squiggle.c

@@ -7,13 +7,14 @@
 #include <sys/types.h>
 #include <time.h>
 
-#define PI 3.14159265358979323846 // M_PI in gcc gnu99
-#define NORMAL90CONFIDENCE 1.6448536269514727
-
 // # Key functionality
 // Define the minimum number of functions needed to do simple estimation
 // Starts here, ends until the end of the mixture function
 
+// math constants
+#define PI 3.14159265358979323846 // M_PI in gcc gnu99
+#define NORMAL90CONFIDENCE 1.6448536269514727
+
 // Pseudo Random number generator
 uint64_t xorshift32(uint32_t* seed)
 {