Merge doxygen2 into develop (#553)

* Fixed warnings and started H5Epublic.h.

* Include H5FD* headers to correctly resolve references.

* Doxygen2 (#330)

* H5Eauto_is_v2.

* Added a few more calls.

* Added a few more H5E calls.

* First cut of H5E v2.

* Added the deprecated v1 calls.

* Updated spacing.

* Once more.

* Taking some inspiration from Eigen3.

* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)

* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.

* doxygen work. fixs format by using clang-format.

* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.

* added documentation for H5P APIs (#350)

* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios

* format corrections

* fixed grammer

* fixed herr_t

* Better name.

* A fresh look.

* add doxygen to H5Ppublic.h

* use attention instead of warning

* Add doxygen comments in H5Ppublic.h (#375)

* Add doxygen comments in H5Ppublic.h

* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops

* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt

* Fix clang-format errors

* Fix filenames in doxygen/examples

* add doxygen to H5Ppublic.h (#378)

* add doxygen to H5Ppublic.h

* use attention instead of warning

Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>

* Revert "add doxygen to H5Ppublic.h (#378)"

This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2.

* Updated Doxygen variables.

* I forgot to copy two images.

* Enable desktop search by default.

* Add my assigned Doxygen documentation.

* Remove whitespace at EOL.  Appease clang-format.

* Addressed Chris' comments.

* Added an alias for asynchronous functions.

* One space is enough for all of us.

* Slightly restructured RM page.

* address some issues

* reformatting

* Style external links.

* reformatting

* reformatting

* Added "Metadata Caching in HDF5" as a technical note example.

* Revise this soon!

* Added specification examples.

* Fixed references.

* Added H5AC cache image stuff and file format study.

* Added older FMT versions. Where did 1.0 go?

* Updated C/C++ note and replaced ambiguous labels.

* Reformat source with clang v10.0.1.

* Added the VFL technical note.

* Added what I believe might be called version 1.0 of the format.

* Added the remaining specs.

* Added H5Z callback documentation and fixed a few mistakes.

* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.

* clang-format happy?

* Ok?

* Bonus track: Deprecated H5D functions.

* Carry over the more detailed group description.

* Added documentation for the missing and deprecated H5R calls.

* Life is easier and less repetitive w/ snippets. Use them!

* Eliminate the snippet block ID artifacts in the HTML rendering.

* Fixed snippet HTML artifacts and added a few missing calls.

* Under 20 H5Ps to go!

* Almost complete!

* "This is a form of pedantry up with which I will not put." (Churchill)

* Let's not waste as much space on bulleted lists!

* First complete (?) draft of the Doxygen-based RM.

* Completeness check and minor fixes along the way.

* Pedantry.

* Adding missing H5FD calls checkpoint.

* Pedantry.

* More pedantry.

* Added H5Pset_fapl_log.

* First draft of H5ES.

* Fixed warnings.

* Prep. for map module.

* First cut of the map module.

* Pedantry.

* Possible H5F introduction.

* Fix the indentation.

* Pedantry.

* Ditto.

* Thanks to the reviewers for their comments.

* Added missing images.

* Line numbers are a distraction here.

* More examples, references, and clean-up. Don't repeat yourself!

* Clang pedantry.

* Ditto.

* More reviewer comments...

* Templatized references and cleaned up \todos.

* Committing clang-format changes

* Fixed MANIFEST.

* Addressed Quincey's comments. (OCPLs)

* Fixed a few more \todo items.

* Fixed more \todo items.

* Added attribute life cycle.

* Forgot the examples file.

* Committing clang-format changes

* Pedantry.

* Live and learn!

* Added a sample H5D life cycle.

* Committing clang-format changes

* Pedantry.

Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

1 files changed, 187 insertions, 0 deletions

diff --git a/doxygen/examples/H5F_examples.c b/doxygen/examples/H5F_examples.c
new file mode 100644
index 0000000..a7ce6fb
--- /dev/null
+++ b/doxygen/examples/H5F_examples.c
@@ -0,0 +1,187 @@
+/* -*- c-file-style: "stroustrup" -*- */
+
+#include "hdf5.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+
+int
+main(void)
+{
+    int ret_val = EXIT_SUCCESS;
+
+    //! <!-- [life_cycle] -->
+    {
+        __label__ fail_fapl, fail_fcpl, fail_file;
+        hid_t fcpl, fapl, file;
+
+        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fcpl;
+        }
+        else {
+            // adjust the file creation properties
+        }
+
+        if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fapl;
+        }
+        else {
+            // adjust the file access properties
+        }
+
+        unsigned mode   = H5F_ACC_EXCL;
+        char     name[] = "f1.h5";
+
+        if ((file = H5Fcreate(name, mode, fcpl, fapl)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_file;
+        }
+
+        // do something useful with FILE
+
+        H5Fclose(file);
+fail_file:
+        H5Pclose(fapl);
+fail_fapl:
+        H5Pclose(fcpl);
+fail_fcpl:;
+    }
+    //! <!-- [life_cycle] -->
+
+    //! <!-- [life_cycle_w_open] -->
+    {
+        __label__ fail_fapl, fail_file;
+        hid_t fapl, file;
+
+        if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_fapl;
+        }
+        else {
+            // adjust the file access properties
+        }
+
+        unsigned mode   = H5F_ACC_RDWR;
+        char     name[] = "f1.h5";
+
+        if ((file = H5Fopen(name, mode, fapl)) == H5I_INVALID_HID) {
+            ret_val = EXIT_FAILURE;
+            goto fail_file;
+        }
+
+        // do something useful with FILE
+
+        H5Fclose(file);
+fail_file:
+        H5Pclose(fapl);
+fail_fapl:;
+    }
+    //! <!-- [life_cycle_w_open] -->
+
+    //! <!-- [minimal] -->
+    {
+        unsigned mode   = H5F_ACC_TRUNC;
+        char     name[] = "f11.h5";
+
+        hid_t file = H5Fcreate(name, mode, H5P_DEFAULT, H5P_DEFAULT);
+        if (file != H5I_INVALID_HID)
+            H5Fclose(file);
+        else
+            ret_val = EXIT_FAILURE;
+    }
+    //! <!-- [minimal] -->
+
+    //! <!-- [open] -->
+    {
+        unsigned mode   = H5F_ACC_RDONLY;
+        char     name[] = "f11.h5";
+
+        hid_t file = H5Fopen(name, mode, H5P_DEFAULT);
+        if (file != H5I_INVALID_HID)
+            H5Fclose(file);
+        else
+            ret_val = EXIT_FAILURE;
+    }
+    //! <!-- [open] -->
+
+    //! <!-- [flush] -->
+    {
+        unsigned mode   = H5F_ACC_RDWR;
+        char     name[] = "f11.h5";
+
+        hid_t file = H5Fopen(name, mode, H5P_DEFAULT);
+        if (file != H5I_INVALID_HID) {
+            int step;
+            for (step = 0; step < 1000; ++step) {
+
+                // do important work & flush every 20 steps
+
+                if (step % 20 == 0) {
+                    if (H5Fflush(file, H5F_SCOPE_LOCAL) < 0) {
+                        perror("H5Fflush failed.");
+                        ret_val = EXIT_FAILURE;
+                        break;
+                    }
+                }
+            }
+
+            if (H5Fclose(file) < 0)
+                perror("H5Fclose failed.");
+        }
+        else
+            ret_val = EXIT_FAILURE;
+    }
+    //! <!-- [flush] -->
+
+    //! <!-- [libver_bounds] -->
+    {
+        unsigned mode   = H5F_ACC_RDWR;
+        char     name[] = "f11.h5";
+
+        hid_t file = H5Fopen(name, mode, H5P_DEFAULT);
+        if (file != H5I_INVALID_HID) {
+            if (H5Fset_libver_bounds(file, H5F_LIBVER_EARLIEST, H5F_LIBVER_V18) >= 0) {
+
+                // object creation will not exceed HDF5 version 1.8.x
+            }
+            else
+                perror("H5Fset_libver_bounds failed.");
+
+            if (H5Fclose(file) < 0)
+                perror("H5Fclose failed.");
+        }
+        else
+            ret_val = EXIT_FAILURE;
+    }
+    //! <!-- [libver_bounds] -->
+
+    //! <!-- [mount] -->
+    {
+        hid_t file = H5Fopen("f11.h5", H5F_ACC_RDWR, H5P_DEFAULT);
+        if (file != H5I_INVALID_HID) {
+            hid_t group, child;
+            if ((group = H5Gcreate1(file, "mount_point", H5P_DEFAULT)) != H5I_INVALID_HID) {
+                if ((child = H5Fopen("f1.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) != H5I_INVALID_HID) {
+                    if (H5Fmount(group, ".", child, H5P_DEFAULT) >= 0) {
+
+                        // do something useful w/ the mounted file
+                    }
+                    else {
+                        ret_val = EXIT_FAILURE;
+                        perror("H5Fmount failed.");
+                    }
+                    H5Fclose(child);
+                }
+                H5Gclose(group);
+            }
+            H5Fclose(file);
+        }
+        else
+            ret_val = EXIT_FAILURE;
+    }
+    //! <!-- [mount] -->
+
+    return ret_val;
+}