v1.0.0-rc.145 (#55)

This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144.

* **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future.
* XDS plugin: Improve performance of VDS reading.
* jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD.
* jfjoch_writer: Clean-up of HDF5 routines to better handle issues.

Reviewed-on: #55

writer/HDF5DataFile.cpp

@@ -75,12 +75,25 @@ std::optional<HDF5DataFileStatistics> HDF5DataFile::Close() {
         data_set
                 ->Attr("image_nr_low", (int32_t) (image_low + 1))
                 .Attr("image_nr_high", (int32_t) (image_low + 1 + max_image_number));
+        data_set->Close();
         data_set.reset();
     }
-    data_file.reset();
 
-    if (manage_file && (!std::filesystem::exists(filename.c_str()) || overwrite))
-        std::rename(tmp_filename.c_str(), filename.c_str());
+    if (manage_file ) {
+        data_file->Close();
+        data_file.reset();
+
+        if (std::filesystem::exists(filename) && !overwrite)
+            throw JFJochException(JFJochExceptionCategory::FileWriteError, "File already exists");
+        std::error_code ec;
+        std::filesystem::rename(tmp_filename, filename, ec);
+        if (ec)
+            throw JFJochException(JFJochExceptionCategory::FileWriteError,
+                                  "Cannot rename temporary HDF5 file " + tmp_filename +
+                                  " to " + filename + ": " + ec.message());
+    } else {
+        data_file.reset();
+    }
 
     closed = true;
 
@@ -89,13 +102,20 @@ std::optional<HDF5DataFileStatistics> HDF5DataFile::Close() {
     ret.total_images = nimages;
     ret.filename = filename;
     ret.file_number = file_number + 1;
+
     return ret;
 }
 
 HDF5DataFile::~HDF5DataFile() {
     if (data_file) {
         try {
-            Close();
+            data_set.reset();
+            data_set_image_number.reset();
+            data_file.reset();
+            if (manage_file) {
+                std::error_code ec;
+                std::filesystem::remove(tmp_filename, ec);
+            }
         } catch (const std::exception &e) {
             std::cerr << "HDF5DataFile::~HDF5DataFile: " << e.what() << std::endl;
         } catch (...) {