update slow5lib and workflows

.github/workflows/c-cpp.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [ '*' ]
 
+env:
+  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
+
 jobs:
   ubuntu_14:
     name: ubuntu_14
@@ -98,9 +101,38 @@ jobs:
       run: make CC=icc -j8
     - name: test
       run: make test
-  os_x_11:
-    name: OSX 11
-    runs-on: macos-11
+  ubuntu_24:
+    name: Ubuntu 24
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v2
+    - name: install packages
+      run: sudo apt-get update && sudo apt-get install zlib1g-dev
+    - name: build
+      run: make -j8
+    - name: test
+      run: make test
+  os_x_12:
+    name: OSX 12
+    runs-on: macos-12
+    steps:
+    - uses: actions/checkout@v2
+    - name: build
+      run: make -j8
+    - name: test
+      run: make test
+  os_x_13:
+    name: OSX 13
+    runs-on: macos-13
+    steps:
+    - uses: actions/checkout@v2
+    - name: build
+      run: make -j8
+    - name: test
+      run: make test
+  os_x_14:
+    name: OSX 14
+    runs-on: macos-14
     steps:
     - uses: actions/checkout@v2
     - name: build

.github/workflows/release-simulation.yml

@@ -7,6 +7,9 @@ on:
   pull_request:
     branches: [ dev ]
 
+env:
+  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
+
 jobs:
   ubuntu_14:
     name: ubuntu_14

.github/workflows/release.yml

@@ -6,6 +6,9 @@ on:
     tags:
       - "v*"
 
+env:
+  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
+
 jobs:
   ubuntu_14:
     name: ubuntu_14

slow5lib/Makefile

@@ -55,10 +55,10 @@ $(SHAREDLIB): $(OBJ) $(SVBLIB)
 $(SVBLIB):
 	make -C $(SVB) no_simd=$(no_simd) libstreamvbyte.a
 
-$(BUILD_DIR)/slow5.o: src/slow5.c src/slow5_extra.h src/slow5_idx.h src/slow5_misc.h src/klib/ksort.h $(SLOW5_H)
+$(BUILD_DIR)/slow5.o: src/slow5.c src/slow5_extra.h src/slow5_idx.h src/slow5_misc.h src/klib/ksort.h src/slow5_byte.h $(SLOW5_H)
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -fpic -o $@
 
-$(BUILD_DIR)/slow5_idx.o: src/slow5_idx.c src/slow5_idx.h src/slow5_extra.h src/slow5_misc.h $(SLOW5_H)
+$(BUILD_DIR)/slow5_idx.o: src/slow5_idx.c src/slow5_idx.h src/slow5_extra.h src/slow5_misc.h src/slow5_byte.h $(SLOW5_H)
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -fpic -o $@
 
 $(BUILD_DIR)/slow5_misc.o: src/slow5_misc.c src/slow5_misc.h include/slow5/slow5_error.h

slow5lib/include/slow5/slow5.h

@@ -624,6 +624,10 @@ void slow5_set_log_level(enum slow5_log_level_opt log_level);
 //sets a global variable, so not thread safe
 void slow5_set_exit_condition(enum slow5_exit_condition_opt exit_condition);
 
+//experimental
+/* no error messages printed and not exit when a requested read ID is not found in index*/
+// being tested, do not use until added to documentation
+void slow5_set_skip_rid();
 
 //get the list of hdr data keys in sorted order (only the returned pointer must be freed, not the ones inside - subjet to change)
 //len is the numberof elements

slow5lib/include/slow5/slow5_defs.h

@@ -44,7 +44,7 @@ The API documentation is available at https://hasindu2008.github.io/slow5tools/
 */
 
 // library version
-#define SLOW5_LIB_VERSION "1.2.0-beta"
+#define SLOW5_LIB_VERSION "1.2.0"
 
 // maximum file version supported by this library - independent of slow5 library version above
 // if updating change all 4 below

slow5lib/include/slow5/slow5_mt.h

@@ -12,8 +12,6 @@ extern "C" {
  ***  Easy Multi-thread API *************************************************************************
  **************************************************************************************************/
 
-/**************** This API is still in beta stage, there could be bugs *************************/
-
 /*
 This is a easy multi-thread API that can fetch a batch of slow5 records using multiple threads in parallel.
 This API uses a fork-join thread model. It is not meant to be used by a programmer who has the expertise to write multi-threaded code and use the slow5 low-level API directly.