From 587d59e82e2a004c6cb57b600d34c85c78c70d9d Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:06:27 -0700
Subject: [PATCH 1/8] Add basic tests using Bash scripts

---
 CMakeLists.txt           |   1 +
 test/CMakeLists.txt      |   1 +
 test/bash/CMakeLists.txt |  30 ++++++++++++
 test/bash/ssmc_tools.sh  |  95 ++++++++++++++++++++++++++++++++++++
 test/bash/test.sh        | 103 +++++++++++++++++++++++++++++++++++++++
 5 files changed, 230 insertions(+)
 create mode 100644 test/CMakeLists.txt
 create mode 100644 test/bash/CMakeLists.txt
 create mode 100644 test/bash/ssmc_tools.sh
 create mode 100644 test/bash/test.sh

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f0c953a..a215b43 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,4 +25,5 @@ target_link_libraries(${PROJECT_NAME} INTERFACE cjson)
 
 if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
   add_subdirectory(examples)
+  add_subdirectory(test)
 endif()
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
new file mode 100644
index 0000000..e8882f0
--- /dev/null
+++ b/test/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(bash)
diff --git a/test/bash/CMakeLists.txt b/test/bash/CMakeLists.txt
new file mode 100644
index 0000000..9df2e3f
--- /dev/null
+++ b/test/bash/CMakeLists.txt
@@ -0,0 +1,30 @@
+function(download_data url file_name)
+  set(DATASET_ARCHIVE ${CMAKE_BINARY_DIR}/data/${file_name})
+
+  file(DOWNLOAD
+       ${url}
+       ${DATASET_ARCHIVE})
+endfunction()
+
+download_data(https://suitesparse-collection-website.herokuapp.com/MM/DIMACS10/chesapeake.tar.gz
+              chesapeake.tar.gz)
+
+download_data(https://suitesparse-collection-website.herokuapp.com/MM/HB/1138_bus.tar.gz
+              1138_bus.tar.gz)
+
+download_data(https://suitesparse-collection-website.herokuapp.com/MM/Belcastro/mouse_gene.tar.gz
+              mouse_gene.tar.gz)
+
+download_data(https://suitesparse-collection-website.herokuapp.com/MM/Pajek/IMDB.tar.gz
+              IMDB.tar.gz)
+
+find_program(BASH_PROGRAM bash)
+
+enable_testing()
+
+if(BASH_PROGRAM)
+     add_test(NAME integration.chesapeake COMMAND ${BASH_PROGRAM} ${CMAKE_CURRENT_SOURCE_DIR}/test.sh ${CMAKE_BINARY_DIR}/data/chesapeake.tar.gz)
+     add_test(NAME integration.1138_bus COMMAND ${BASH_PROGRAM} ${CMAKE_CURRENT_SOURCE_DIR}/test.sh ${CMAKE_BINARY_DIR}/data/1138_bus.tar.gz)
+     add_test(NAME integration.mouse_gene COMMAND ${BASH_PROGRAM} ${CMAKE_CURRENT_SOURCE_DIR}/test.sh ${CMAKE_BINARY_DIR}/data/mouse_gene.tar.gz)
+     add_test(NAME integration.IMDB COMMAND ${BASH_PROGRAM} ${CMAKE_CURRENT_SOURCE_DIR}/test.sh ${CMAKE_BINARY_DIR}/data/IMDB.tar.gz)
+endif()
diff --git a/test/bash/ssmc_tools.sh b/test/bash/ssmc_tools.sh
new file mode 100644
index 0000000..5b46802
--- /dev/null
+++ b/test/bash/ssmc_tools.sh
@@ -0,0 +1,95 @@
+convert_ssmc() {
+  echo "unpacking $1"
+  fpath=$1
+
+  format=$2
+
+  if [ -z "$format" ]
+  then
+    format=COO
+  else
+    format=$2
+  fi
+
+  format_string=`echo ${format} | tr '[:upper:]' '[:lower:]'`
+
+  echo "Writing in format ${format}."
+
+  fname=`basename ${fpath}`
+  directory=`dirname ${fpath}`
+  tar -xf $fpath -C $directory
+
+  matrix_name=${fname/.tar.gz/}
+
+  main_matrix=$directory/$matrix_name/$matrix_name.mtx
+
+  dest_file=$directory/$matrix_name.${format_string}.bsp.h5
+
+  # echo "dest file ${dest_file}"
+
+  # echo "Primary matrix is \"${main_matrix}\" -> ${dest_file}/root"
+  echo "mtx2bsp ${main_matrix} ${dest_file} ${format}"
+  mtx2bsp ${main_matrix} ${dest_file} ${format}
+
+  # Set "null option" to return an empty list if no files match glob.
+  shopt -s nullglob
+
+  for secondary_matrix in ${directory}/${matrix_name}/${matrix_name}_*.mtx
+  do
+    # echo "Secondary matrix \"${secondary_matrix}\""
+    secondary_name=`basename ${secondary_matrix}`
+    secondary_name=${secondary_name/.mtx/}
+    secondary_name=${secondary_name/${matrix_name}_/}
+    echo "mtx2bsp ${secondary_matrix} ${dest_file}:${secondary_name}"
+    mtx2bsp ${secondary_matrix} ${dest_file}:${secondary_name}
+  done
+
+  rm -r ${directory}/${matrix_name}
+}
+
+check_ssmc() {
+  echo "unpacking $1"
+  fpath=$1
+
+  format=$2
+
+  if [ -z "$format" ]
+  then
+    format=COO
+  else
+    format=$2
+  fi
+
+  format_string=`echo ${format} | tr '[:upper:]' '[:lower:]'`
+
+  fname=`basename ${fpath}`
+  directory=`dirname ${fpath}`
+  tar -xf $fpath -C $directory
+
+  matrix_name=${fname/.tar.gz/}
+
+  main_matrix=$directory/$matrix_name/$matrix_name.mtx
+
+  dest_file=$directory/$matrix_name.${format_string}.bsp.h5
+
+  # echo "dest file ${dest_file}"
+
+  # echo "Primary matrix is \"${main_matrix}\" -> ${dest_file}/root"
+  echo "check_equivalence ${main_matrix} ${dest_file}"
+  check_equivalence ${main_matrix} ${dest_file}
+
+  # Set "null option" to return an empty list if no files match glob.
+  shopt -s nullglob
+
+  for secondary_matrix in ${directory}/${matrix_name}/${matrix_name}_*.mtx
+  do
+    # echo "Secondary matrix \"${secondary_matrix}\""
+    secondary_name=`basename ${secondary_matrix}`
+    secondary_name=${secondary_name/.mtx/}
+    secondary_name=${secondary_name/${matrix_name}_/}
+    echo "check_equivalence ${secondary_matrix} ${dest_file}:${secondary_name}"
+    check_equivalence ${secondary_matrix} ${dest_file}:${secondary_name}
+  done
+
+  rm -r ${directory}/${matrix_name}
+}
diff --git a/test/bash/test.sh b/test/bash/test.sh
new file mode 100644
index 0000000..6a10607
--- /dev/null
+++ b/test/bash/test.sh
@@ -0,0 +1,103 @@
+#!/usr/bin/env bash
+set -e
+
+convert_ssmc() {
+  echo "unpacking $1"
+  fpath=$1
+
+  format=$2
+
+  if [ -z "$format" ]
+  then
+    format=COO
+  else
+    format=$2
+  fi
+
+  format_string=`echo ${format} | tr '[:upper:]' '[:lower:]'`
+
+  echo "Writing in format ${format}."
+
+  fname=`basename ${fpath}`
+  directory=`dirname ${fpath}`
+  tar -xf $fpath -C $directory
+
+  matrix_name=${fname/.tar.gz/}
+
+  main_matrix=$directory/$matrix_name/$matrix_name.mtx
+
+  dest_file=$directory/$matrix_name.${format_string}.bsp.h5
+
+  # echo "dest file ${dest_file}"
+
+  # echo "Primary matrix is \"${main_matrix}\" -> ${dest_file}/root"
+  echo "mtx2bsp ${main_matrix} ${dest_file} ${format}"
+  mtx2bsp ${main_matrix} ${dest_file} ${format}
+
+  # Set "null option" to return an empty list if no files match glob.
+  shopt -s nullglob
+
+  for secondary_matrix in ${directory}/${matrix_name}/${matrix_name}_*.mtx
+  do
+    # echo "Secondary matrix \"${secondary_matrix}\""
+    secondary_name=`basename ${secondary_matrix}`
+    secondary_name=${secondary_name/.mtx/}
+    secondary_name=${secondary_name/${matrix_name}_/}
+    echo "mtx2bsp ${secondary_matrix} ${dest_file}:${secondary_name}"
+    mtx2bsp ${secondary_matrix} ${dest_file}:${secondary_name}
+  done
+
+  rm -r ${directory}/${matrix_name}
+}
+
+check_ssmc() {
+  echo "unpacking $1"
+  fpath=$1
+
+  format=$2
+
+  if [ -z "$format" ]
+  then
+    format=COO
+  else
+    format=$2
+  fi
+
+  format_string=`echo ${format} | tr '[:upper:]' '[:lower:]'`
+
+  fname=`basename ${fpath}`
+  directory=`dirname ${fpath}`
+  tar -xf $fpath -C $directory
+
+  matrix_name=${fname/.tar.gz/}
+
+  main_matrix=$directory/$matrix_name/$matrix_name.mtx
+
+  dest_file=$directory/$matrix_name.${format_string}.bsp.h5
+
+  # echo "dest file ${dest_file}"
+
+  # echo "Primary matrix is \"${main_matrix}\" -> ${dest_file}/root"
+  echo "check_equivalence ${main_matrix} ${dest_file}"
+  check_equivalence ${main_matrix} ${dest_file}
+
+  # Set "null option" to return an empty list if no files match glob.
+  shopt -s nullglob
+
+  for secondary_matrix in ${directory}/${matrix_name}/${matrix_name}_*.mtx
+  do
+    # echo "Secondary matrix \"${secondary_matrix}\""
+    secondary_name=`basename ${secondary_matrix}`
+    secondary_name=${secondary_name/.mtx/}
+    secondary_name=${secondary_name/${matrix_name}_/}
+    echo "check_equivalence ${secondary_matrix} ${dest_file}:${secondary_name}"
+    check_equivalence ${secondary_matrix} ${dest_file}:${secondary_name}
+  done
+
+  rm -r ${directory}/${matrix_name}
+}
+
+export PATH=$PATH:$PWD/../../examples
+
+convert_ssmc $1 COO
+check_ssmc $1 COO

From 6b79b3e5b78435510a9f2d6cc72251266eecf9a8 Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:10:17 -0700
Subject: [PATCH 2/8] Add basic GitHub Actions CI

---
 .github/workflows/ci.yml | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 .github/workflows/ci.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..f6aecee
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,38 @@
+name: "CI"
+
+on:
+  push:
+    branches:
+      - main
+
+  pull_request:
+
+jobs:
+  checks:
+    runs-on: 'ubuntu-latest'
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+        cache: 'pip'
+    - run: pip install -r requirements.txt
+    - name: Checks
+      uses: pre-commit/action@v3.0.0
+
+  gcc:
+    runs-on: 'ubuntu-latest'
+    strategy:
+      matrix:
+        cxx: [gcc, clang]
+    name: ${{ matrix.cxx }}
+    env:
+      CXX: ${{ matrix.cxx }}
+    steps:
+    - uses: actions/checkout@v4
+    - name: CMake
+      run: cmake -B build
+    - name: Build
+      run: make -C build -j `nproc`
+    - name: Test
+      run: ctest build/test/bash

From a4452b1cfbf32a90e3a1085549e1045b48eab042 Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:13:56 -0700
Subject: [PATCH 3/8] Update CI to install HDF5

---
 .github/workflows/ci.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f6aecee..2d32e68 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,10 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: CMake
-      run: cmake -B build
+      run: |
+        sudo apt-get update
+        sudo apt-get install libhdf5-dev
+        cmake -B build
     - name: Build
       run: make -C build -j `nproc`
     - name: Test

From e1a0160a8afed453a179cb3e57e9a9f1c5c0127b Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:15:17 -0700
Subject: [PATCH 4/8] Troubleshoot failing to run tests

---
 .github/workflows/ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2d32e68..4f770dc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,4 +38,6 @@ jobs:
     - name: Build
       run: make -C build -j `nproc`
     - name: Test
-      run: ctest build/test/bash
+      run: |
+        pwd
+        ctest ./build/test/bash

From 76d247e403ac56ac5c7ae4d2477bad70643450c6 Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:18:07 -0700
Subject: [PATCH 5/8] Fix to select correct test dir

---
 .github/workflows/ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4f770dc..b6af5ef 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,6 +38,4 @@ jobs:
     - name: Build
       run: make -C build -j `nproc`
     - name: Test
-      run: |
-        pwd
-        ctest ./build/test/bash
+      run: ctest --test-dir ./build/test/bash

From c44399aff4dfda97e64fe8f99c1a7a9129603af6 Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:20:18 -0700
Subject: [PATCH 6/8] Testing if CI fails with a breaking change.

---
 examples/mtx2bsp.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/examples/mtx2bsp.c b/examples/mtx2bsp.c
index 6b18639..48945ce 100644
--- a/examples/mtx2bsp.c
+++ b/examples/mtx2bsp.c
@@ -114,6 +114,8 @@ int main(int argc, char** argv) {
 
   bsp_print_matrix_info(matrix);
 
+  bsp_array_write(matrix.values, 0, -12);
+
   printf(" === Writing to %s... ===\n", output_fname);
   bsp_write_matrix(output_fname, matrix, group_name, user_json);
   printf(" === Done writing. ===\n");

From 9e06aaa8e8e41b5d6948eaaf03ea0d6a604456b7 Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:22:26 -0700
Subject: [PATCH 7/8] Undoing breaking change - CI should now pass.

---
 examples/mtx2bsp.c | 2 --
 1 file changed, 2 deletions(-)

diff --git a/examples/mtx2bsp.c b/examples/mtx2bsp.c
index 48945ce..6b18639 100644
--- a/examples/mtx2bsp.c
+++ b/examples/mtx2bsp.c
@@ -114,8 +114,6 @@ int main(int argc, char** argv) {
 
   bsp_print_matrix_info(matrix);
 
-  bsp_array_write(matrix.values, 0, -12);
-
   printf(" === Writing to %s... ===\n", output_fname);
   bsp_write_matrix(output_fname, matrix, group_name, user_json);
   printf(" === Done writing. ===\n");

From 77e77c264aead54ffb2531a1b7310a3d09fc7804 Mon Sep 17 00:00:00 2001
From: Benjamin Brock <benjamin.brock@intel.com>
Date: Mon, 20 May 2024 14:23:25 -0700
Subject: [PATCH 8/8] Removing unused file `ssmc_tools.sh`

---
 test/bash/ssmc_tools.sh | 95 -----------------------------------------
 1 file changed, 95 deletions(-)
 delete mode 100644 test/bash/ssmc_tools.sh

diff --git a/test/bash/ssmc_tools.sh b/test/bash/ssmc_tools.sh
deleted file mode 100644
index 5b46802..0000000
--- a/test/bash/ssmc_tools.sh
+++ /dev/null
@@ -1,95 +0,0 @@
-convert_ssmc() {
-  echo "unpacking $1"
-  fpath=$1
-
-  format=$2
-
-  if [ -z "$format" ]
-  then
-    format=COO
-  else
-    format=$2
-  fi
-
-  format_string=`echo ${format} | tr '[:upper:]' '[:lower:]'`
-
-  echo "Writing in format ${format}."
-
-  fname=`basename ${fpath}`
-  directory=`dirname ${fpath}`
-  tar -xf $fpath -C $directory
-
-  matrix_name=${fname/.tar.gz/}
-
-  main_matrix=$directory/$matrix_name/$matrix_name.mtx
-
-  dest_file=$directory/$matrix_name.${format_string}.bsp.h5
-
-  # echo "dest file ${dest_file}"
-
-  # echo "Primary matrix is \"${main_matrix}\" -> ${dest_file}/root"
-  echo "mtx2bsp ${main_matrix} ${dest_file} ${format}"
-  mtx2bsp ${main_matrix} ${dest_file} ${format}
-
-  # Set "null option" to return an empty list if no files match glob.
-  shopt -s nullglob
-
-  for secondary_matrix in ${directory}/${matrix_name}/${matrix_name}_*.mtx
-  do
-    # echo "Secondary matrix \"${secondary_matrix}\""
-    secondary_name=`basename ${secondary_matrix}`
-    secondary_name=${secondary_name/.mtx/}
-    secondary_name=${secondary_name/${matrix_name}_/}
-    echo "mtx2bsp ${secondary_matrix} ${dest_file}:${secondary_name}"
-    mtx2bsp ${secondary_matrix} ${dest_file}:${secondary_name}
-  done
-
-  rm -r ${directory}/${matrix_name}
-}
-
-check_ssmc() {
-  echo "unpacking $1"
-  fpath=$1
-
-  format=$2
-
-  if [ -z "$format" ]
-  then
-    format=COO
-  else
-    format=$2
-  fi
-
-  format_string=`echo ${format} | tr '[:upper:]' '[:lower:]'`
-
-  fname=`basename ${fpath}`
-  directory=`dirname ${fpath}`
-  tar -xf $fpath -C $directory
-
-  matrix_name=${fname/.tar.gz/}
-
-  main_matrix=$directory/$matrix_name/$matrix_name.mtx
-
-  dest_file=$directory/$matrix_name.${format_string}.bsp.h5
-
-  # echo "dest file ${dest_file}"
-
-  # echo "Primary matrix is \"${main_matrix}\" -> ${dest_file}/root"
-  echo "check_equivalence ${main_matrix} ${dest_file}"
-  check_equivalence ${main_matrix} ${dest_file}
-
-  # Set "null option" to return an empty list if no files match glob.
-  shopt -s nullglob
-
-  for secondary_matrix in ${directory}/${matrix_name}/${matrix_name}_*.mtx
-  do
-    # echo "Secondary matrix \"${secondary_matrix}\""
-    secondary_name=`basename ${secondary_matrix}`
-    secondary_name=${secondary_name/.mtx/}
-    secondary_name=${secondary_name/${matrix_name}_/}
-    echo "check_equivalence ${secondary_matrix} ${dest_file}:${secondary_name}"
-    check_equivalence ${secondary_matrix} ${dest_file}:${secondary_name}
-  done
-
-  rm -r ${directory}/${matrix_name}
-}