Replace H5E_ATOM major error category with H5E_ID (#121)

* Renames H5I_ATOM to H5I_ID, among other related changes

* Java has been updated.
* Fortran is failing on my VM, even though I don't touch that.

* Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes

* Fixes typos in comments

7 files changed, 28 insertions, 28 deletions

diff --git a/java/src/Makefile.am b/java/src/Makefile.am
index 0df48bd..4f691a1 100644
--- a/java/src/Makefile.am
+++ b/java/src/Makefile.am
@@ -70,7 +70,7 @@ hdf5_java_JAVA =  \
     ${pkgpath}/callbacks/H5P_prp_set_func_cb.java \
  	${pkgpath}/callbacks/H5P_iterate_cb.java \
 	${pkgpath}/callbacks/H5P_iterate_t.java \
-	${pkgpath}/exceptions/HDF5AtomException.java  \
+	${pkgpath}/exceptions/HDF5IdException.java  \
 	${pkgpath}/exceptions/HDF5AttributeException.java  \
 	${pkgpath}/exceptions/HDF5BtreeException.java  \
 	${pkgpath}/exceptions/HDF5DataFiltersException.java  \
diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt
index f3d9b8d..5651031 100644
--- a/java/src/hdf/hdf5lib/CMakeLists.txt
+++ b/java/src/hdf/hdf5lib/CMakeLists.txt
@@ -42,7 +42,7 @@ set (HDF5_JAVA_HDF_HDF5_CALLBACKS_SOURCES
 
 set (HDF5_JAVA_HDF_HDF5_EXCEPTIONS_SOURCES
     exceptions/HDF5Exception.java
-    exceptions/HDF5AtomException.java
+    exceptions/HDF5IdException.java
     exceptions/HDF5AttributeException.java
     exceptions/HDF5BtreeException.java
     exceptions/HDF5DataFiltersException.java
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 7ecfe95..520836c 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -109,15 +109,15 @@ public class HDF5Constants {
     public static final long H5E_ALREADYINIT = H5E_ALREADYINIT();
     /** Major error codes - Invalid arguments to routine */
     public static final long H5E_ARGS = H5E_ARGS();
-    /** Major error codes - Object atom */
-    public static final long H5E_ATOM = H5E_ATOM();
+    /** Major error codes - Object ID */
+    public static final long H5E_ID = H5E_ID();
     /** Major error codes - Attribute */
     public static final long H5E_ATTR = H5E_ATTR();
-    /** Minor error codes - Object atom related errors - Unable to find atom information (already closed?) */
-    public static final long H5E_BADATOM = H5E_BADATOM();
+    /** Minor error codes - Object ID related errors - Unable to find ID information (already closed?) */
+    public static final long H5E_BADID = H5E_BADID();
     /** Minor error codes - File accessibility errors - Bad file ID accessed */
     public static final long H5E_BADFILE = H5E_BADFILE();
-    /** Minor error codes - Object atom related errors - Unable to find ID group information */
+    /** Minor error codes - Object ID related errors - Unable to find ID group information */
     public static final long H5E_BADGROUP = H5E_BADGROUP();
     /** Minor error codes - Object header related errors - Iteration failed */
     public static final long H5E_BADITER = H5E_BADITER();
@@ -169,7 +169,7 @@ public class HDF5Constants {
     public static final long H5E_CANTCOUNT = H5E_CANTCOUNT();
     /** Minor error codes - File accessibility errors - Unable to create file */
     public static final long H5E_CANTCREATE = H5E_CANTCREATE();
-    /** Minor error codes - Object atom related errors - Unable to decrement reference count */
+    /** Minor error codes - Object ID related errors - Unable to decrement reference count */
     public static final long H5E_CANTDEC = H5E_CANTDEC();
     /** Minor error codes - B-tree related errors - Unable to decode value */
     public static final long H5E_CANTDECODE = H5E_CANTDECODE();
@@ -201,7 +201,7 @@ public class HDF5Constants {
     public static final long H5E_CANTGET = H5E_CANTGET();
     /** Minor error codes - Resource errors - Unable to compute size */
     public static final long H5E_CANTGETSIZE = H5E_CANTGETSIZE();
-    /** Minor error codes - Object atom related errors - Unable to increment reference count */
+    /** Minor error codes - Object ID related errors - Unable to increment reference count */
     public static final long H5E_CANTINC = H5E_CANTINC();
     /** Minor error codes - Function entry/exit interface - Unable to initialize object */
     public static final long H5E_CANTINIT = H5E_CANTINIT();
@@ -251,7 +251,7 @@ public class HDF5Constants {
     public static final long H5E_CANTRECV = H5E_CANTRECV();
     /** Minor error codes - B-tree related errors - Unable to redistribute records */
     public static final long H5E_CANTREDISTRIBUTE = H5E_CANTREDISTRIBUTE();
-    /** Minor error codes - Object atom related errors - Unable to register new atom */
+    /** Minor error codes - Object ID related errors - Unable to register new ID */
     public static final long H5E_CANTREGISTER = H5E_CANTREGISTER();
     /** Minor error codes - Function entry/exit interface - Unable to release object */
     public static final long H5E_CANTRELEASE = H5E_CANTRELEASE();
@@ -367,7 +367,7 @@ public class HDF5Constants {
     public static final long H5E_NOENCODER = H5E_NOENCODER();
     /** I/O pipeline errors - Requested filter is not available */
     public static final long H5E_NOFILTER = H5E_NOFILTER();
-    /** Minor error codes - Object atom related errors - Out of IDs for group */
+    /** Minor error codes - Object ID related errors - Out of IDs for group */
     public static final long H5E_NOIDS = H5E_NOIDS();
     /** Major error codes - No error */
     public static final long H5E_NONE_MAJOR = H5E_NONE_MAJOR();
@@ -1157,11 +1157,11 @@ public class HDF5Constants {
 
     private static native final long H5E_ARGS();
 
-    private static native final long H5E_ATOM();
+    private static native final long H5E_ID();
 
     private static native final long H5E_ATTR();
 
-    private static native final long H5E_BADATOM();
+    private static native final long H5E_BADID();
 
     private static native final long H5E_BADFILE();
 
diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java b/java/src/hdf/hdf5lib/exceptions/HDF5IdException.java
index 850044c..37f0956 100644
--- a/java/src/hdf/hdf5lib/exceptions/HDF5AtomException.java
+++ b/java/src/hdf/hdf5lib/exceptions/HDF5IdException.java
@@ -16,26 +16,26 @@ package hdf.hdf5lib.exceptions;
 /**
  * The class HDF5LibraryException returns errors raised by the HDF5 library.
  * <p>
- * This sub-class represents HDF-5 major error code <b>H5E_ATOM</b>
+ * This sub-class represents HDF-5 major error code <b>H5E_ID</b>
  */
 
-public class HDF5AtomException extends HDF5LibraryException {
+public class HDF5IdException extends HDF5LibraryException {
     /**
-     * Constructs an <code>HDF5AtomException</code> with no specified detail
+     * Constructs an <code>HDF5IdException</code> with no specified detail
      * message.
      */
-    public HDF5AtomException() {
+    public HDF5IdException() {
         super();
     }
 
     /**
-     * Constructs an <code>HDF5AtomException</code> with the specified detail
+     * Constructs an <code>HDF5IdException</code> with the specified detail
      * message.
      *
      * @param s
      *            the detail message.
      */
-    public HDF5AtomException(String s) {
+    public HDF5IdException(String s) {
         super(s);
     }
 
diff --git a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java
index 54acbdd..9bd43e8 100644
--- a/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java
+++ b/java/src/hdf/hdf5lib/exceptions/HDF5LibraryException.java
@@ -201,14 +201,14 @@ public class HDF5LibraryException extends HDF5Exception {
         else if (err_code == HDF5Constants.H5E_CANTRELEASE) {
             return "Can't release object";
         }
-        else if (err_code == HDF5Constants.H5E_BADATOM) {
-            return "Can't find atom information";
+        else if (err_code == HDF5Constants.H5E_BADID) {
+            return "Can't find ID information";
         }
         else if (err_code == HDF5Constants.H5E_BADGROUP) {
             return "Can't find group information";
         }
         else if (err_code == HDF5Constants.H5E_CANTREGISTER) {
-            return "Can't register new atom";
+            return "Can't register new ID";
         }
         else if (err_code == HDF5Constants.H5E_CANTINC) {
             return "Can't increment reference count";
diff --git a/java/src/jni/exceptionImp.c b/java/src/jni/exceptionImp.c
index c5e7d85..6bb956e 100644
--- a/java/src/jni/exceptionImp.c
+++ b/java/src/jni/exceptionImp.c
@@ -442,8 +442,8 @@ defineHDF5LibraryException(hid_t maj_num)
         return "hdf/hdf5lib/exceptions/HDF5LowLevelIOException";
     else if (H5E_FUNC == err_num)
         return "hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException";
-    else if (H5E_ATOM == err_num)
-        return "hdf/hdf5lib/exceptions/HDF5AtomException";
+    else if (H5E_ID == err_num)
+        return "hdf/hdf5lib/exceptions/HDF5IdException";
     else if (H5E_CACHE == err_num)
         return "hdf/hdf5lib/exceptions/HDF5MetaDataCacheException";
     else if (H5E_BTREE == err_num)
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 94d5b19..ceb75fb 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -330,9 +330,9 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1ARGS(JNIEnv *env, jclass cls)
     return H5E_ARGS;
 }
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5E_1ATOM(JNIEnv *env, jclass cls)
+Java_hdf_hdf5lib_HDF5Constants_H5E_1ID(JNIEnv *env, jclass cls)
 {
-    return H5E_ATOM;
+    return H5E_ID;
 }
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1ATTR(JNIEnv *env, jclass cls)
@@ -340,9 +340,9 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1ATTR(JNIEnv *env, jclass cls)
     return H5E_ATTR;
 }
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5E_1BADATOM(JNIEnv *env, jclass cls)
+Java_hdf_hdf5lib_HDF5Constants_H5E_1BADID(JNIEnv *env, jclass cls)
 {
-    return H5E_BADATOM;
+    return H5E_BADID;
 }
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1BADFILE(JNIEnv *env, jclass cls)