diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index 0a9844b0..421f3563 100644 --- a/.github/workflows/build-docs.yml +++ b/.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 diff --git a/.github/workflows/cpp-build-main.yml b/.github/workflows/cpp-build-main.yml index c001b23e..fcba02eb 100644 --- a/.github/workflows/cpp-build-main.yml +++ b/.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 diff --git a/.github/workflows/cpp-build-pr.yml b/.github/workflows/cpp-build-pr.yml index 7a57c691..2c39f4b3 100644 --- a/.github/workflows/cpp-build-pr.yml +++ b/.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 diff --git a/.github/workflows/py-build-main.yml b/.github/workflows/py-build-main.yml index b89eee0a..9f371bec 100644 --- a/.github/workflows/py-build-main.yml +++ b/.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: diff --git a/.github/workflows/py-build-pr.yml b/.github/workflows/py-build-pr.yml index edb405d2..06ae0888 100644 --- a/.github/workflows/py-build-pr.yml +++ b/.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 diff --git a/_aicspylibczi/Reader.cpp b/_aicspylibczi/Reader.cpp index 94718a2d..73aae63c 100644 --- a/_aicspylibczi/Reader.cpp +++ b/_aicspylibczi/Reader.cpp @@ -20,7 +20,7 @@ Reader::Reader(std::shared_ptr 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 sp; sp = std::shared_ptr(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(); diff --git a/c_tests/test_Reader.cpp b/c_tests/test_Reader.cpp index faa648d0..9d61bb55 100644 --- a/c_tests/test_Reader.cpp +++ b/c_tests/test_Reader.cpp @@ -99,7 +99,7 @@ class CziCreatorIStream CziCreatorIStream() : m_czi() { - auto fp = std::shared_ptr(new CSimpleStreamImplCppStreams(L"resources/s_1_t_1_c_1_z_1.czi")); + auto fp = std::shared_ptr(libCZI::CreateInputOutputStreamForFile(L"resources/s_1_t_1_c_1_z_1.czi")); m_czi = std::make_unique(fp); } pylibczi::Reader* get() { return m_czi.get(); } diff --git a/libCZI b/libCZI index 9460669c..b0898cbf 160000 --- a/libCZI +++ b/libCZI @@ -1 +1 @@ -Subproject commit 9460669ce533ffb79be0cf41cd3f9d39efd04d31 +Subproject commit b0898cbf1f90eb2b61791baefce1c6df9ea8fa3d