Fix DEBUG_HDF5 and some minor leaks, add fromH5 for ref objects

.github/workflows/ci.yml

@@ -7,6 +7,8 @@ on:
       - 'docs/**'
       - 'nimhdf5.nimble'
       - '.github/workflows/ci.yml'
+    branches:
+      - 'master'
   pull_request:
     paths:
       - 'tests/**'

src/nimhdf5/attributes.nim

@@ -6,7 +6,7 @@
 
 import typeinfo
 import tables
 import strutils, sequtils
 
 import hdf5_wrapper, h5util, H5nimtypes, datatypes, dataspaces, util
 
@@ -398,6 +398,7 @@
   result = newSeq[string](npoints)
   for i, s in buf:
     result[i] = $s
+    discard H5free_memory(s[0].address)
 
 proc readStringAttribute(attr: H5Attr): string =
   ## proc to read a string attribute from a H5 file, for an existing
@@ -413,6 +414,7 @@
     var buf: cstring
     readAttribute(attr, nativeType, buf.addr)
     result = $buf
+    discard H5free_memory(buf.addr)
   else:
     let nativeType = getNativeType(attr.dtype_c)
     let string_len = H5Aget_storage_size(attr.attr_id.id)

src/nimhdf5/dataspaces.nim

@@ -43,7 +43,7 @@ func simple_dataspace*[T: (seq | int)](shape: T, maxshape: seq[int] = @[]): Data
   ## TODO: rewrite this
   var m_maxshape: seq[hsize_t] = parseMaxShape(maxshape)
   withDebug:
-    echo "Creating memory dataspace of shape ", shape
+    debugecho "Creating memory dataspace of shape ", shape
   when T is seq:
     # convert ints to hsize_t (== culonglong) and create mutable copy (need
     # an address to hand it to C function as pointer)

src/nimhdf5/datatypes.nim

@@ -320,8 +320,8 @@
 
 proc close*(h5id: H5Id | H5IdObj, msg = "")
 proc `=copy`*(target: var H5IdObj, source: H5IdObj) {.error: "H5Id identifiers cannot be copied.".}
 proc `=destroy`*(h5id: var H5IdObj) = # {.error: "`=destroy` of a raw `H5Id` is not a valid operation.".}
   h5id.close()
   `=destroy`(h5id.kind)
   `=destroy`(h5id.id)
 
@@ -519,7 +519,9 @@
 proc getMemberName*(typ: DatatypeID, idx: int): string =
   ## Get the name of the member of the H5T_COMPOUND type at index `idx`
   ## The argument *must* correspond to a compound datatype. We do not check.
-  result = $H5Tget_member_name(typ.id, idx.cuint)
+  var name = H5Tget_member_name(typ.id, idx.cuint)
+  result = $name
+  discard H5free_memory(name[0].addr)
 
 proc getSize*(typ: DatatypeID): int =
   result = H5Tget_size(typ.id).int
@@ -626,9 +628,9 @@
 proc close*(dset: H5DataSet) = dset[].close()
 
 when (NimMajor, NimMinor, NimPatch) >= (1, 6, 0):
   proc `=destroy`*(attr: var H5AttrObj) {.raises: [HDF5LibraryError].} =
     ## Closes the given attribute.
     attr.close()
     for name, field in fieldPairs(attr):
       when typeof(field).distinctBase() isnot H5Id:
         `=destroy`(field)
@@ -636,21 +638,21 @@
         if cast[pointer](field) != nil:
           `=destroy`(field)
 
   proc `=destroy`*(attrs: var H5AttributesObj) =
     ## Closes all attributes that are stored in this `H5Attributes` table.
     if attrs.attr_tab != nil:
       `=destroy`(attrs.attr_tab)
     for name, field in fieldPairs(attrs):
       when typeof(field).distinctBase() isnot H5Id:
         if name.normalize != "attrtab":
           `=destroy`(field)
       else:
         if cast[pointer](field) != nil:
           `=destroy`(field)
 
   proc `=destroy`*(dset: var H5DataSetObj) {.raises: [HDF5LibraryError].} =
     ## Closes the dataset and resets all references to nil.
     dset.close() # closes its dataspace etc. as well
     dset.opened = false
     if dset.attrs != nil:
       `=destroy`(dset.attrs)
@@ -663,7 +665,7 @@
           `=destroy`(field)
 
 
   proc `=destroy`*(grp: var H5GroupObj) {.raises: [HDF5LibraryError].} =
     ## Closes the group and resets all references to nil.
     if grp.file_ref != nil:
       `=destroy`(grp.file_ref) # only destroy the `ref` to the file!
@@ -674,7 +676,7 @@
     if grp.groups != nil:
       `=destroy`(grp.groups)
     if grp.attrs != nil:
       `=destroy`(grp.attrs)
     for name, field in fieldPairs(grp):
       when typeof(field).distinctBase() isnot H5Id:
         if name notin ["attrs", "groups", "datasets", "file_ref"]:
@@ -725,11 +727,11 @@
   if err >= 0:
     # successful
     withDebug:
-      debugEcho "getNumAttrs(): ", h5attr
+      debugEcho "getNumAttrs(): ", $(h5attr[])
     result = int(h5info.num_attrs)
   else:
     withDebug:
-      debugEcho "getNumAttrs(): ", h5attr
+      debugEcho "getNumAttrs(): ", $(h5attr[])
     raise newException(HDF5LibraryError, "Call to HDF5 library failed in `getNumAttr` when reading $#" % $h5attr.parent_name)
 
 proc initH5Attributes*(p_id: sink ParentID, p_name: string = "", p_type: string = ""): H5Attributes =

src/nimhdf5/files.nim

@@ -131,7 +131,7 @@ proc activateSWMR*(h5f: H5File) =
     h5f.accessFlags.incl akWriteSWMR
   elif akWriteSWMR in h5f.accessFlags:
     withDebug:
-      echo "File was already in SWMR mode: ", h5f
+      echo "File was already in SWMR mode: ", $(h5f[])
     discard # already activated
   else:
     raise newException(IOError, "Cannot activate SWMR mode for an input file that misses " &

src/nimhdf5/serialize.nim

@@ -180,7 +180,7 @@ proc fromH5*[T: char | string | cstring | bool](h5f: H5File, res: var T, name =
       res = parseBool(obj.attrs[name, string])
     elif T is char:
       let s = obj.attrs[name, string]
-      doASsert s.len == 0, "Trying to read a char from a string with more than one element."
+      doAssert s.len == 1, "Trying to read a char from a string with more than one element."
       res = s[0]
     elif T is string:
       res = obj.attrs[name, string]
@@ -292,14 +292,19 @@ proc fromH5*[T: object](h5f: H5File, res: var T, name = "", path = "/", exclude:
   for field, val in fieldPairs(res):
     if field notin exclude:
       h5f.fromH5(val, field, grp)
+proc fromH5*[T: ref object](h5f: H5File, res: var T, name = "", path = "/", exclude: seq[string] = @[]) =
+  bind `/`
+  let grp = path / name
+  res = T()
+  fromH5(h5f, res[], name, path, exclude)
 
-proc deserializeH5*[T: object](h5f: H5File, name = "", path = "/", exclude: seq[string] = @[]): T =
+proc deserializeH5*[T](h5f: H5File, name = "", path = "/", exclude: seq[string] = @[]): T =
   ## Cannot name it same as `fromH5` because that causes the compiler to get confused. I don't understand,
   ## but with `LikelihoodContext` it ends up calling the `var set[LikelihoodContext]` overload, which does
   ## not make any sense.
   h5f.fromH5(result, name, path, exclude)
 
-proc deserializeH5*[T: object](fname: string, name = "", path = "/", exclude: seq[string] = @[]): T =
+proc deserializeH5*[T](fname: string, name = "", path = "/", exclude: seq[string] = @[]): T =
   ## Cannot name it same as `fromH5` because that causes the compiler to get confused. I don't understand,
   ## but with `LikelihoodContext` it ends up calling the `var set[LikelihoodContext]` overload, which does
   ## not make any sense.

src/nimhdf5/util.nim

@@ -18,8 +18,9 @@ template withDebug*(actions: untyped) =
   ## to this template are only performed, if the
   ## -d:DEBUG_HDF5
   ## compiler flag is set.
-  when defined(DEBUG_HDF5):
-    actions
+  block:
+    when defined(DEBUG_HDF5):
+      actions
 
 proc formatName*(name: string): string =
   # this procedure formats a given group / dataset name by prepending