1 10 Fix java data export functions (#450)

* HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source
HDFGroup · Mar 10, 2021 · dd5b8a8 · dd5b8a8
1 parent 2524ad1
commit dd5b8a8
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diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
@@ -1,5 +1,6 @@
 name: clang-format Check
-on: [workflow_dispatch, push, pull_request]
+on:
+  pull_request:
 jobs:
   formatting-check:
     name: Formatting Check

diff --git a/.github/workflows/clang-format-fix.yml b/.github/workflows/clang-format-fix.yml
@@ -0,0 +1,25 @@
+name: clang-format Check
+on: 
+  workflow_dispatch:
+  push:
+jobs:
+  formatting-check:
+    name: Formatting Check
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'skip-ci')"
+    steps:
+    - uses: actions/checkout@v2
+    - name: Run clang-format style check for C programs.
+      uses: DoozyX/clang-format-lint-action@v0.11
+      with:
+        source: '.'
+        extensions: 'c,h,cpp,hpp'
+        clangFormatVersion: 10
+        inplace: True
+        style: file
+        exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'
+    - uses: EndBug/add-and-commit@v7
+      with:
+          author_name: github-actions
+          author_email: 41898282+github-actions[bot]@users.noreply.github.com
+          message: 'Committing clang-format changes'
diff --git a/MANIFEST b/MANIFEST
@@ -35,6 +35,7 @@
 
 ./.clang-format
 ./.github/CODEOWNERS  _DO_NOT_DISTRIBUTE_
+./.github/workflows/clang-format-fix.yml  _DO_NOT_DISTRIBUTE_
 ./.github/workflows/clang-format-check.yml  _DO_NOT_DISTRIBUTE_
 ./.github/workflows/main.yml  _DO_NOT_DISTRIBUTE_
 ./.github/workflows/pr-check.yml  _DO_NOT_DISTRIBUTE_

diff --git a/java/examples/datasets/H5Ex_D_Alloc.java b/java/examples/datasets/H5Ex_D_Alloc.java
@@ -64,11 +64,11 @@ public static H5D_space_status get(int code) {
     }
 
     private static void allocation() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id1 = -1;
-        long dataset_id2 = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id1 = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id2 = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
         int space_status = 0;

diff --git a/java/examples/datasets/H5Ex_D_Checksum.java b/java/examples/datasets/H5Ex_D_Checksum.java
@@ -92,10 +92,10 @@ private static boolean checkFletcher32Filter() {
     }
 
     private static void writeChecksum() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -192,9 +192,9 @@ private static void writeChecksum() {
     }
 
     private static void readChecksum() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Chunk.java b/java/examples/datasets/H5Ex_D_Chunk.java
@@ -65,10 +65,10 @@ public static H5D_layout get(int code) {
     }
 
     private static void writeChunk() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -200,10 +200,10 @@ private static void writeChunk() {
     }
 
     private static void readChunk() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Compact.java b/java/examples/datasets/H5Ex_D_Compact.java
@@ -59,10 +59,10 @@ public static H5D_layout get(int code) {
     }
 
     private static void writeCompact() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -162,10 +162,10 @@ private static void writeCompact() {
     }
 
     private static void readCompact() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open file and dataset using the default properties.

diff --git a/java/examples/datasets/H5Ex_D_External.java b/java/examples/datasets/H5Ex_D_External.java
@@ -33,10 +33,10 @@ public class H5Ex_D_External {
     private static final int NAME_BUF_SIZE = 32;
 
     private static void writeExternal() {
-        long file_id = -1;
-        long dcpl_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -137,9 +137,9 @@ private static void writeExternal() {
     }
 
     private static void readExternal() {
-        long file_id = -1;
-        long dcpl_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
         String[] Xname = new String[1];
 

diff --git a/java/examples/datasets/H5Ex_D_FillValue.java b/java/examples/datasets/H5Ex_D_FillValue.java
@@ -39,10 +39,10 @@ public class H5Ex_D_FillValue {
     private static final int FILLVAL = 99;
 
     private static void fillValue() {
-        long file_id = -1;
-        long dcpl_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] extdims = { EDIM_X, EDIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };

diff --git a/java/examples/datasets/H5Ex_D_Gzip.java b/java/examples/datasets/H5Ex_D_Gzip.java
@@ -94,10 +94,10 @@ private static boolean checkGzipFilter() {
     }
 
     private static void writeGzip() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -195,9 +195,9 @@ private static void writeGzip() {
     }
 
     private static void readGzip() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Hyperslab.java b/java/examples/datasets/H5Ex_D_Hyperslab.java
@@ -33,9 +33,9 @@ public class H5Ex_D_Hyperslab {
     private static final int RANK = 2;
 
     private static void writeHyperslab() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -141,10 +141,10 @@ private static void writeHyperslab() {
     }
 
     private static void readHyperslab() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Nbit.java b/java/examples/datasets/H5Ex_D_Nbit.java
@@ -95,11 +95,11 @@ private static boolean checkNbitFilter() {
     }
 
     private static void writeData() throws Exception {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dtype_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dtype_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -156,9 +156,9 @@ private static void writeData() throws Exception {
     }
 
     private static void readData() throws Exception {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_ReadWrite.java b/java/examples/datasets/H5Ex_D_ReadWrite.java
@@ -31,9 +31,9 @@ public class H5Ex_D_ReadWrite {
     private static final int RANK = 2;
 
     private static void WriteDataset() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -108,8 +108,8 @@ private static void WriteDataset() {
     }
 
     private static void ReadDataset() {
-        long file_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open file using the default properties.

diff --git a/java/examples/datasets/H5Ex_D_Shuffle.java b/java/examples/datasets/H5Ex_D_Shuffle.java
@@ -121,10 +121,10 @@ private static boolean checkShuffleFilter() {
     }
 
     private static void writeShuffle() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -228,9 +228,9 @@ private static void writeShuffle() {
     }
 
     private static void readShuffle() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Sofloat.java b/java/examples/datasets/H5Ex_D_Sofloat.java
@@ -95,10 +95,10 @@ private static boolean checkScaleoffsetFilter() {
     }
 
     private static void writeData() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         double[][] dset_data = new double[DIM_X][DIM_Y];
@@ -212,9 +212,9 @@ private static void writeData() {
     }
 
     private static void readData() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         double[][] dset_data = new double[DIM_X][DIM_Y];
 
         // Open file using the default properties.

diff --git a/java/examples/datasets/H5Ex_D_Soint.java b/java/examples/datasets/H5Ex_D_Soint.java
@@ -95,10 +95,10 @@ private static boolean checkScaleoffsetFilter() {
     }
 
     private static void writeData() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -194,9 +194,9 @@ private static void writeData() {
     }
 
     private static void readData() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open file using the default properties.