Merge pull request #115 from AllenCellModeling/feature/update-libczi-…

…2024-03

update libczi and actions

.github/workflows/build-docs.yml

@@ -9,11 +9,11 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install Dependencies

.github/workflows/cpp-build-main.yml

@@ -35,7 +35,7 @@ jobs:
             cc: "clang", cxx: "clang++"
           }
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: build and test

.github/workflows/cpp-build-pr.yml

@@ -29,7 +29,7 @@ jobs:
             cc: "clang", cxx: "clang++"
           }
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: build and test

.github/workflows/py-build-main.yml

@@ -20,11 +20,11 @@ jobs:
         python-version: [3.7, 3.8, 3.9, "3.10", 3.11]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -35,17 +35,17 @@ jobs:
         run: |
           pytest --cov-report xml --cov=aicspylibczi aicspylibczi/tests
       - name: Upload codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
 
   lint:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -61,7 +61,7 @@ jobs:
     needs: [python-test, lint]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: true
 
@@ -96,7 +96,7 @@ jobs:
             cibw-arch: win_amd64
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: true
 
@@ -124,7 +124,7 @@ jobs:
     if: "contains(github.event.head_commit.message, 'Bump version')"
 
     steps:
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
 
     - uses: actions/download-artifact@v2
       with:

.github/workflows/py-build-pr.yml

@@ -10,11 +10,11 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: setup python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install aicspylibczi
@@ -32,17 +32,17 @@ jobs:
           pip install dist/aicspylibczi-$MY_VERSION.tar.gz
         shell: bash
       - name: Upload codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
 
   lint:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies

_aicspylibczi/Reader.cpp

@@ -20,7 +20,7 @@ Reader::Reader(std::shared_ptr<libCZI::IStream> istream_)
   : m_czireader(new CCZIReader)
   , m_specifyScene(true)
 {
-  m_czireader->Open(std::move(istream_));
+  m_czireader->Open(std::move(istream_), nullptr);
   m_statistics = m_czireader->GetStatistics();
   m_pixelType = libCZI::PixelType::Invalid; // get the pixeltype of the first readable subblock
 
@@ -34,7 +34,7 @@ Reader::Reader(const wchar_t* file_name_)
 {
   std::shared_ptr<libCZI::IStream> sp;
   sp = std::shared_ptr<libCZI::IStream>(new StreamImplLockingRead(file_name_));
-  m_czireader->Open(sp);
+  m_czireader->Open(sp, nullptr);
   m_statistics = m_czireader->GetStatistics();
   // create a reference for finding one or more subblock indices from a CDimCoordinate
   checkSceneShapes();

c_tests/test_Reader.cpp

@@ -99,7 +99,7 @@ class CziCreatorIStream
   CziCreatorIStream()
     : m_czi()
   {
-    auto fp = std::shared_ptr<libCZI::IStream>(new CSimpleStreamImplCppStreams(L"resources/s_1_t_1_c_1_z_1.czi"));
+    auto fp = std::shared_ptr<libCZI::IInputOutputStream>(libCZI::CreateInputOutputStreamForFile(L"resources/s_1_t_1_c_1_z_1.czi"));
     m_czi = std::make_unique<pylibczi::Reader>(fp);
   }
   pylibczi::Reader* get() { return m_czi.get(); }