fixed spelling, added spelling action

.github/workflows/codespell.yml

@@ -0,0 +1,18 @@
+# GitHub Action to automate the identification of common misspellings in text files
+# https://github.com/codespell-project/codespell
+# https://github.com/codespell-project/actions-codespell
+name: codespell
+on: [push, pull_request]
+permissions:
+  contents: read
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - uses: codespell-project/actions-codespell@master
+        with:
+          ignore_words_list: fom,coo,ku,inout
+          skip: .git, .github
+

clinic/index.org

@@ -185,7 +185,7 @@ understand the context.
   : world
   : hello
   : finished at 08:25:33
-- Noticable speedup but not a panacea
+- Noticeable speedup but not a panacea
 #+begin_quote
 Eventually I hope to have a version of =h5pyd= that supports =async= (or maybe
 an entirely new package), that would make it a little easier to use.
@@ -250,7 +250,7 @@ I have an application that reads groups as units and all the datasets
 use the contiguous data layout. I believe this option, if available,
 can yield a good read performance.
 #+end_quote
-- Intersting suggestions
+- Interesting suggestions
   - Elena suggested to first create all datasets with =H5D_ALLOC_TIME_LATE=
   - Mark suggested to =H5Pget_meta_block_size= to set aside sufficient
     "group space" (Maybe also =H5Pset_est_link_info=?)
@@ -674,7 +674,7 @@ int main()
 - A :: Currently, the code will skip entries >64K, because the underlying
   =H5Dcreate= will fail. (The logic and code can be much improved.) It's better
   to first run =archive_checker_64k= and see if there are any size warnings.
-  The =h5compactor= and =h5shredder= were sucessfully run on TAR archives with
+  The =h5compactor= and =h5shredder= were successfully run on TAR archives with
   tens of millions of small images (<64K).
 ** Last week's highlights
 *** Announcements
@@ -1126,7 +1126,7 @@ However, I cannot get this to work with h5py.
   #+end_quote
 - [[https://meetingorganizer.copernicus.org/EGU22/EGU22-11201.html][DIARITSup: a framework to supervise live measurements, Digital Twins modelscomputations and predictions for structures monitoring.]]
   #+begin_quote
-  DIARITSup is a chain of various softwares following the concept of ”system of
+  DIARITSup is a chain of various software following the concept of ”system of
   systems”. It interconnects hardware and software layers dedicated to in-situ
   monitoring of structures or critical components. It embeds data assimilation
   capabilities combined with specific Physical or Statistical models like
@@ -1227,7 +1227,7 @@ HDFS?
 
 ** Tips, tricks, & insights
 *** SWMR (old) and compression "issues" - take 2
-- Free-space managment is disabled in the original SWMR implementation
+- Free-space management is disabled in the original SWMR implementation
 - Can lead to file bloat when compression is enabled & overly aggressive
   flushing
 - **Question:** How does the new SWMR VFD implementation behave?
@@ -1486,7 +1486,7 @@ DATASET "/equilibrium/vacuum_toroidal_field&b0" {
 - [[https://www.youtube.com/watch?v=WlnUF3LRBj4][Awkward Array: Manipulating JSON-like Data with NumPy-like Idioms]]
   - SciPy 2020 presentation by Jim Pivarski
   - Watch this!
-- How would you repesent something like this in HDF5? (Example from Jim's video)
+- How would you represent something like this in HDF5? (Example from Jim's video)
   #+begin_src python
   import awkward as ak
   array = ak.Array([
@@ -1708,7 +1708,7 @@ Next time...
       retval = EXIT_FAILURE;
       goto fail_write;
     }
-    printf("Write successed.\n");
+    printf("Write succeeded.\n");
 
     if (H5Fflush(file, H5F_SCOPE_GLOBAL) < 0) {
       retval = EXIT_FAILURE;
@@ -1889,7 +1889,7 @@ This brings us to today's ...
 
 The expression below is a [templated] Class datatype in C++, placed in a
 non-contiguous memory location, requiring scatter-gather operators and a
-mechanism to dis-assemble reassemble the components. Becuase of the complexity
+mechanism to dis-assemble reassemble the components. Because of the complexity
 AFAIK there is no automatic support for this sort of operation.
 
 #+begin_src C++
@@ -2091,7 +2091,7 @@ the process writing to the file was killed.
 - Face-to-face at [[https://www.iter.org/][ITER]] in Saint Paul-lez-Durance, France
 - Reserve your spot before telling your friends! =;-)=
 
-**** ASCR Workshop January 2022 on the Managment and Storage of Scientific Data
+**** ASCR Workshop January 2022 on the Management and Storage of Scientific Data
 - [[https://www.osti.gov/biblio/1843500-position-papers-ascr-workshop-management-storage-scientific-data][Position Papers]]
 - [[https://www.osti.gov/biblio/1845705][Technical Report]]
 
@@ -2572,7 +2572,7 @@ All solutions come with different trade-offs!
 
 ** Tips, tricks, & insights
 *** How do HDF5-UDF work?
-Currently, they are repesented as chunked datasets with a single chunk. That's
+Currently, they are represented as chunked datasets with a single chunk. That's
 why they work fine with existing tools. The UDF itself is executed as part of the
 HDF5 filter pipeline. Its code is stored in the dataset blob data plus metadata
 and managed by the UDF handler.
@@ -2950,9 +2950,9 @@ if I set it to a big value (1024).
 
 I wasn’t able to find how parallelism is exactly implemented. From the above
 behaviour it looks like the file is being locked which then blocks my whole
-programm, especially if the stride is big (more time for the other ranks to run
-into a lock and be idle inbetween). Is that really the case? I write data
-continously, so theoretically there is no need for a lock. Is is possible to
+program, especially if the stride is big (more time for the other ranks to run
+into a lock and be idle in between). Is that really the case? I write data
+continuously, so theoretically there is no need for a lock. Is is possible to
 tell the driver “don’t lock the file”?
 #+end_quote
 - What's a 'stride'? (not a hyperslab stride...)
@@ -3649,7 +3649,7 @@ fail_file:
 
 #+END_SRC
 
-- The ouput file produce looks like this:
+- The output file produce looks like this:
 
 #+BEGIN_EXAMPLE
 
@@ -3791,7 +3791,7 @@ export HDF5_USE_FILE_LOCKING="FALSE"
 - "Partial I/O gets in the way" - sorting fields by name or offset
   - Happens on each write call => overhead
 - Can this be avoided? User might provide a patch...
-**** [[https://forum.hdfgroup.org/t/read-write-specific-coordiantes-in-multi-dimensional-dataset/9137][Read/write specific coordiantes in multi-dimensional dataset?]]
+**** [[https://forum.hdfgroup.org/t/read-write-specific-coordinates-in-multi-dimensional-dataset/9137][Read/write specific coordinates in multi-dimensional dataset?]]
 - Thomas is looking for use cases from =h5py= users
   #+BEGIN_SRC python
 

documentation/hdf5-docs/Migrating+from+HDF5+1.12+to+HDF5+1.14.md

@@ -35,4 +35,4 @@ The way optional operations are handled in the virtual object layer (VOL) change
 The virtual file layer has changed in HDF5 1.14.0. Existing virtual file drivers (VFDs) will have to be updated to work with this version of the library.
 
 ## Virtual Object Layer (VOL) Changes
-The virtual object layer has changed significantly in HDF5 1.14.0 and the 1.12 VOL API is now considered deprecated and unsupported. Existing virtual object layer connectors shoul be updated to work with this version of the library.
+The virtual object layer has changed significantly in HDF5 1.14.0 and the 1.12 VOL API is now considered deprecated and unsupported. Existing virtual object layer connectors should be updated to work with this version of the library.

documentation/hdf5-docs/hdf5_topics/DebugH5App.md

@@ -62,7 +62,7 @@ Code to accumulate statistics is included at compile time by using the --enable-
 | hl | No  | Local heaps |
 | i  | Yes | Interface abstraction |
 | mf | No  | File memory management |
-| mm | Yes | Library memory managment |
+| mm | Yes | Library memory management |
 | o  | No  | Object headers and messages |
 | p  | Yes | Property lists |
 | s  | Yes | Data spaces |

documentation/hdf5-docs/release_specifics/Migrating_from_HDF5_1.12_to_HDF5_1.14.md

@@ -35,4 +35,4 @@ The way optional operations are handled in the virtual object layer (VOL) change
 The virtual file layer has changed in HDF5 1.14.0. Existing virtual file drivers (VFDs) will have to be updated to work with this version of the library.
 
 ## Virtual Object Layer (VOL) Changes
-The virtual object layer has changed significantly in HDF5 1.14.0 and the 1.12 VOL API is now considered deprecated and unsupported. Existing virtual object layer connectors shoul be updated to work with this version of the library.
+The virtual object layer has changed significantly in HDF5 1.14.0 and the 1.12 VOL API is now considered deprecated and unsupported. Existing virtual object layer connectors should be updated to work with this version of the library.

documentation/hdf5-docs/release_specifics/sw_changes_1.10.md

@@ -18,7 +18,7 @@ Note that bug fixes and performance enhancements in the C library are automatica
 
 The following information is included below.
 
-* <a href="#compatiblity">Compatiblity and Performance Issues</a>
+* <a href="#compatibility">Compatibility and Performance Issues</a>
 * <a href="#9versus8">Release 1.10.9 versus 1.10.8]</a>
 * <a href="#8versus7">Release 1.10.8 versus 1.10.7</a>
 * <a href="#7versus6">Release 1.10.7 versus 1.10.6</a>
@@ -32,7 +32,7 @@ The following information is included below.
 
 See [API Compatibility Reports for 1.10]() for information regarding compatibility with previous releases.
 
-<h2 id="compatiblity">Compatiblity and Performance Issues</h2>
+<h2 id="compatibility">Compatibility and Performance Issues</h2>
 
 Not all HDF5-1.10 releases are compatible. Users should NOT be using 1.10 releases prior to HDF5-1.10.3. See the compatibility matrix below for details on compatibility between 1.10 releases:
 
@@ -529,7 +529,7 @@ hid\_t
 
 Changed from a 32-bit to a 64-bit value.
 
-hid\_t is the type is used for all HDF5 identifiers. This change, which is necessary to accomodate the capacities of modern computing systems, therefore affects all HDF5 applications. If an application has been using HDF5's hid\_t the type, recompilation will normally be sufficient to take advantage of HDF5 Release 1.10.0. If an application uses an integer type instead of HDF5's hid\_t type, those identifiers must be changed to a 64-bit type when the application is ported to the 1.10.x series.
+hid\_t is the type is used for all HDF5 identifiers. This change, which is necessary to accommodate the capacities of modern computing systems, therefore affects all HDF5 applications. If an application has been using HDF5's hid\_t the type, recompilation will normally be sufficient to take advantage of HDF5 Release 1.10.0. If an application uses an integer type instead of HDF5's hid\_t type, those identifiers must be changed to a 64-bit type when the application is ported to the 1.10.x series.
 
 New Features and Feature Sets
 Several new features are introduced in HDF5 Release 1.10.0.
@@ -998,7 +998,7 @@ The original function is renamed to H5Fget\_info1 and deprecated.
 
 A new version of the function, H5Fget\_info2, is introduced.
 
-The compatiblity macro H5Fget\_info is introduced.
+The compatibility macro H5Fget\_info is introduced.
 
 H5F\_info\_t
 
@@ -1008,15 +1008,15 @@ The original struct is renamed to H5F\_info1\_t and deprecated.
 
 A new version of the struct, H5F\_info2\_t, is introduced.
 
-The compatiblity macro H5F\_info\_t is introduced.
+The compatibility macro H5F\_info\_t is introduced.
 
 H5Rdereference
 
 The original function is renamed to H5Rdereference1 and deprecated.
 
 A new version of the function, H5Rdereference2, is introduced.
 
-The compatiblity macro H5Rdereference is introduced.
+The compatibility macro H5Rdereference is introduced.
 
 ### Autotools Configuration and Large File Support
 Autotools configuration has been extensively reworked and autotool's handling of large file support has been overhauled in this release.

documentation/hdf5-docs/release_specifics/sw_changes_1.12.md

@@ -94,7 +94,7 @@ For a description of the major new features that were introduced, please see [Ne
 
 ### In the C/Fortran Interface (main library)
 
-Folllowing are the new or changed APIs introduced in HDF5-1.12.0. Those introduced with a new feature list the specific new feature that they were added for.
+Following are the new or changed APIs introduced in HDF5-1.12.0. Those introduced with a new feature list the specific new feature that they were added for.
 
 | Function              | Fortran      | Description                                  |
 | ----------------------|------------- | -------------------------------------------- |