Rename hmr to hmmer_reader and update Makefile

- Renamed hmr.c and hmr.h to hmmer_reader.c and hmmer_reader.h
- Updated include statements to reflect new filenames
- Modified Makefile to use new filenames and added PREFIX variable
- Changed optimization flag in CFLAGS from -O2 to -O3

hmmer-reader/Makefile

@@ -1,10 +1,10 @@
-CC = gcc
-CFLAGS = -std=c11 -Wall -Wextra -pedantic -O2 -MMD -MP
+CC     ?= gcc
+CFLAGS ?= -std=c11 -Wall -Wextra -pedantic -O3 -MMD -MP
+PREFIX ?= /usr/local
 SRC = $(filter-out $(wildcard test_*.c),$(wildcard *.c))
 OBJ = $(SRC:.c=.o)
-HDR = hmr.h
+HDR = hmmer_reader.h
 LIB = libhmmer_reader.a
-PREFIX ?= /usr/local
 
 all: $(LIB)
 

hmmer-reader/error.c

@@ -1,5 +1,5 @@
 #include "error.h"
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include <assert.h>
 #include <errno.h>
 #include <string.h>

hmmer-reader/fsm.c

@@ -1,6 +1,6 @@
 #include "fsm.h"
 #include "error.h"
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include "position.h"
 #include "posix.h"
 #include "to.h"

hmmer-reader/fsm.h

@@ -1,7 +1,7 @@
 #ifndef FSM_H
 #define FSM_H
 
-#include "hmr.h"
+#include "hmmer_reader.h"
 
 struct hmr_position;
 struct hmr_profile;

hmmer-reader/hmr.c → hmmer-reader/hmmer_reader.c

@@ -1,4 +1,4 @@
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include "fsm.h"
 #include "profile.h"
 #include "token.h"

hmmer-reader/hmr.h → hmmer-reader/hmmer_reader.h

@@ -1,5 +1,5 @@
-#ifndef HMR_H
-#define HMR_H
+#ifndef HMMER_READER_H
+#define HMMER_READER_H
 
 #include <stdbool.h>
 #include <stddef.h>

hmmer-reader/node.h

@@ -1,7 +1,7 @@
 #ifndef NODE_H
 #define NODE_H
 
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include <math.h>
 
 static void hmr_node_init(struct hmr_node *node)

hmmer-reader/position.h

@@ -1,7 +1,7 @@
 #ifndef POSITION_H
 #define POSITION_H
 
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include <stddef.h>
 
 static void hmr_position_init(struct hmr_position *pos)

hmmer-reader/profile.c

@@ -1,7 +1,7 @@
 #include "profile.h"
 #include "error.h"
 #include "fsm.h"
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include "node.h"
 #include "position.h"
 #include "token.h"

hmmer-reader/profile.h

@@ -1,7 +1,7 @@
 #ifndef PROFILE_H
 #define PROFILE_H
 
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include <stdio.h>
 
 struct hmr_position;

hmmer-reader/test_hmr.c

@@ -1,5 +1,5 @@
 #include "aye.h"
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include <math.h>
 #include <string.h>
 

hmmer-reader/token.c

@@ -1,6 +1,6 @@
 #include "token.h"
 #include "error.h"
-#include "hmr.h"
+#include "hmmer_reader.h"
 #include "posix.h"
 #include <string.h>