Merge branch 'master' into jinxin/annotate_arrival_time

.github/workflows/conda-build.yml

@@ -0,0 +1,100 @@
+name: Conda build
+
+on:
+  schedule:
+    - cron: '21 21 * * 5'
+  push:
+    branches: [ master ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  release:
+    types: [published]
+
+jobs:
+  conda-build-arm64:
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'schedule' || github.event_name == 'release' }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Setup for Multi-platform image
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and publish conda package arm64
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: scripts/Dockerfile_conda_build
+          platforms: linux/arm64
+          build-args: |
+            PYTHON_VERSION=${{ matrix.python-version }}
+            ANACONDA_API_TOKEN=${{ secrets.CONDA_TOKEN }}
+
+  conda-build-amd64:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Setup for Multi-platform image
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and publish conda package amd64
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: scripts/Dockerfile_conda_build
+          platforms: linux/amd64
+          build-args: |
+            PYTHON_VERSION=${{ matrix.python-version }}
+            ANACONDA_API_TOKEN=${{ secrets.CONDA_TOKEN }}
+
+  conda-build-osx:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: ["macos-14", "macos-13"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+          channels: conda-forge,defaults
+          activate-environment: anaconda-client-env
+      - shell: bash -el {0}
+        run: |
+          export PYTHON_VERSION=${{ matrix.python-version }}
+          conda install -y conda-build anaconda-client
+          conda config --set anaconda_upload no
+          export ANACONDA_API_TOKEN=${{ secrets.CONDA_TOKEN }}
+          PACKAGE_PATH=$(conda build . --python ${{ matrix.python-version }} --output)
+          conda build . --python ${{ matrix.python-version }}
+          if [ "${{ matrix.python-version }}" == "3.11" ]; then
+            anaconda -t $ANACONDA_API_TOKEN upload $PACKAGE_PATH --label main --label py3.11 --force
+          else
+            anaconda -t $ANACONDA_API_TOKEN upload $PACKAGE_PATH --label py${{ matrix.python-version }} --force
+          fi
+

.github/workflows/docker-publish.yml

@@ -14,6 +14,8 @@ on:
     tags: [ 'v*.*.*' ]
   pull_request:
     branches: [ master ]
+  release:
+    types: [published]
 
 env:
   # Use docker.io for Docker Hub if empty
@@ -32,7 +34,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       # Setup for Multi-platform image
       - name: Set up QEMU
@@ -86,7 +90,7 @@ jobs:
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image (amd64 only)
         uses: docker/build-push-action@v4
-        if: ${{ github.event_name != 'schedule' }}
+        if: ${{ github.event_name != 'schedule' || github.event_name != 'release' }}
         with:
           context: .
           platforms: linux/amd64
@@ -98,7 +102,7 @@ jobs:
 
       - name: Build and push Docker image (amd64 and arm64)
         uses: docker/build-push-action@v4
-        if: ${{ github.event_name == 'schedule' }}
+        if: ${{ github.event_name == 'schedule' || github.event_name == 'release' }}
         with:
           context: .
           platforms: linux/amd64,linux/arm64
@@ -125,7 +129,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       # Setup for Multi-platform image
       - name: Set up QEMU
@@ -173,7 +179,7 @@ jobs:
       # Build and push dev image
       - name: Build and push dev image (amd64 only)
         uses: docker/build-push-action@v4
-        if: ${{ github.event_name != 'schedule' }}
+        if: ${{ github.event_name != 'schedule' || github.event_name != 'release' }}
         with:
           context: .
           file: Dockerfile_dev
@@ -188,7 +194,7 @@ jobs:
 
       - name: Build and push dev image (amd64 amd arm64)
         uses: docker/build-push-action@v4
-        if: ${{ github.event_name == 'schedule' }}
+        if: ${{ github.event_name == 'schedule' || github.event_name == 'release' }}
         with:
           context: .
           file: Dockerfile_dev
@@ -218,7 +224,9 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       # Setup for Multi-platform image
       - name: Set up QEMU

.github/workflows/python-package.yml

@@ -57,8 +57,10 @@ jobs:
         pytest --cov=mspasspy python/tests/
         make test -C build/temp.*/
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
+        fail_ci_if_error: false 
+        token: ${{ secrets.CODECOV_TOKEN }} # required
         env_vars: OS,PYTHON
         verbose: true
     - name: Build Documentation
@@ -78,3 +80,4 @@ jobs:
         BRANCH: gh-pages 
         FOLDER: docs/build/html 
         CLEAN: false
+

Dockerfile

@@ -190,8 +190,9 @@ ADD setup.py /mspass/setup.py
 ADD pyproject.toml /mspass/pyproject.toml
 ADD requirements.txt /mspass/requirements.txt
 ADD python /mspass/python
+ADD .git /mspass/.git
 RUN pip3 install /mspass -v \
-	&& rm -rf /mspass/build && docker-clean
+	&& rm -rf /mspass/build /mspass/.git && docker-clean
 
 # Install jedi
 RUN pip3 --no-cache-dir install jedi==0.17.2 && docker-clean

Dockerfile_dev

@@ -190,8 +190,9 @@ ADD setup.py /mspass/setup.py
 ADD python /mspass/python
 ADD pyproject.toml /mspass/pyproject.toml
 ADD requirements.txt /mspass/requirements.txt
+ADD .git /mspass/.git
 RUN pip3 install -C--global-option=build -C--global-option=--debug /mspass -v \
-	&& rm -rf /mspass/build && docker-clean
+	&& rm -rf /mspass/build /mspass/.git && docker-clean
 
 # Add docs and dependencies to build docs
 ADD docs /mspass/docs

Dockerfile_mpi

@@ -186,8 +186,9 @@ ADD setup.py /mspass/setup.py
 ADD python /mspass/python
 ADD pyproject.toml /mspass/pyproject.toml
 ADD requirements.txt /mspass/requirements.txt
+ADD .git /mspass/.git
 RUN pip3 install /mspass -v \
-	&& rm -rf /mspass/build && docker-clean
+	&& rm -rf /mspass/build /mspass/.git && docker-clean
 
 # Install jedi
 RUN pip3 --no-cache-dir install jedi==0.17.2 && docker-clean

cxx/CMakeLists.txt

@@ -41,7 +41,6 @@ endif ()
 message (STATUS "YAML_CPP_LIBRARIES   = ${YAML_CPP_LIBRARIES}")
 message (STATUS "YAML_CPP_INCLUDE_DIR = ${YAML_CPP_INCLUDE_DIR}")
 
-
 find_package (Boost 1.64.0 COMPONENTS serialization)
 if (NOT Boost_FOUND)
   message (STATUS "Building Boost")
@@ -111,9 +110,31 @@ fetch_mseed (
 message (STATUS "MSEED_LIBRARIES   = ${MSEED_LIBRARIES}")
 message (STATUS "MSEED_INCLUDE_DIR = ${MSEED_INCLUDE_DIR}")
 
-find_package (PythonInterp 3)
 
-if (PYTHONINTERP_FOUND)
+find_program(MY_PYTHON_EXECUTABLE NAMES python3 python)
+
+if(NOT MY_PYTHON_EXECUTABLE)
+    message(WARNING "Python interpreter not found.")
+    find_package(Python COMPONENTS Interpreter Development)
+else()
+
+    # Get the version of the Python interpreter
+    execute_process(
+        COMMAND ${MY_PYTHON_EXECUTABLE} --version
+        OUTPUT_VARIABLE PYTHON_VERSION_OUTPUT
+        ERROR_VARIABLE PYTHON_VERSION_OUTPUT
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        ERROR_STRIP_TRAILING_WHITESPACE
+    )
+
+    string(REGEX MATCH "Python ([0-9]+\\.[0-9]+)" _ ${PYTHON_VERSION_OUTPUT})
+    set(MY_PYTHON_VERSION ${CMAKE_MATCH_1})
+
+    message(STATUS "Found Python version: ${MY_PYTHON_VERSION}")
+    find_package(Python ${MY_PYTHON_VERSION} EXACT COMPONENTS Interpreter Development)
+endif()
+
+if (Python_FOUND)
   find_package (pybind11)
   if (NOT pybind11_FOUND)
     message (STATUS "Building Pybind11")
@@ -123,9 +144,9 @@ if (PYTHONINTERP_FOUND)
       ${PROJECT_BINARY_DIR}/pybind11
       )
   endif ()
-  message (STATUS "PYTHON_LIBRARIES = ${PYTHON_LIBRARIES}")
-  message (STATUS "PYTHON_EXECUTABLE = ${PYTHON_EXECUTABLE}")
-  message (STATUS "PYTHON_INCLUDE_DIRS = ${PYTHON_INCLUDE_DIRS}")
+  message (STATUS "Python_LIBRARIES = ${Python_LIBRARIES}")
+  message (STATUS "Python_EXECUTABLE = ${Python_EXECUTABLE}")
+  message (STATUS "Python_INCLUDE_DIRS = ${Python_INCLUDE_DIRS}")
   message (STATUS "pybind11_LIBRARIES = ${pybind11_LIBRARIES}")
   message (STATUS "pybind11_INCLUDE_DIR= ${pybind11_INCLUDE_DIR}")
   add_subdirectory (python)

cxx/cmake/openblas-download.cmake

@@ -8,12 +8,12 @@ ExternalProject_Add(
   openblas
   SOURCE_DIR "@OPENBLAS_DOWNLOAD_ROOT@/openblas-src"
   GIT_REPOSITORY
-    https://github.com/xianyi/OpenBLAS.git 
+    https://github.com/OpenMathLib/OpenBLAS.git 
   GIT_TAG
-    v0.3.7
+    v0.3.27
   UPDATE_COMMAND ""
   CONFIGURE_COMMAND ""
-  BUILD_COMMAND make libs -j 8 PREFIX=${PROJECT_BINARY_DIR} NO_SHARED=1 USE_THREAD=0 USE_OPENMP=0
+  BUILD_COMMAND make libs -j 8 PREFIX=${PROJECT_BINARY_DIR} NO_SHARED=1 USE_THREAD=0 USE_OPENMP=0 DYNAMIC_ARCH=1 DYNAMIC_OLDER=1 TARGET=GENERIC
   BUILD_IN_SOURCE 1
   INSTALL_COMMAND make install PREFIX=${PROJECT_BINARY_DIR} NO_SHARED=1
   TEST_COMMAND ""

cxx/python/algorithms/CMakeLists.txt

@@ -2,24 +2,27 @@ include_directories(
   ${Boost_INCLUDE_DIRS}
   ${GSL_INCLUDE_DIRS}
   ${pylib11_INCLUDE_DIRS}
-  ${PYTHON_INCLUDE_DIRS}
+  ${Python_INCLUDE_DIRS}
   ${PROJECT_SOURCE_DIR}/include
   ${PROJECT_SOURCE_DIR}
   ${PROJECT_BINARY_DIR}/include)
 
 #add_library(mspasspython STATIC ${sources_python})
-#target_link_libraries(mspasspython PRIVATE mspass ${PYTHON_LIBRARIES})
+#target_link_libraries(mspasspython PRIVATE mspass ${Python_LIBRARIES})
 
-pybind11_add_module(pybasic basic_py.cc)
-target_link_libraries(pybasic PRIVATE mspass ${Boost_LIBRARIES})
+#pybind11_add_module(pybasic basic_py.cc)
+Python_add_library(pybasic basic_py.cc)
+target_link_libraries(pybasic PRIVATE mspass ${Boost_LIBRARIES} pybind11::headers)
 set_target_properties(pybasic PROPERTIES OUTPUT_NAME "basic")
 
-pybind11_add_module(pyamplitudes amplitudes_py.cc)
-target_link_libraries(pyamplitudes PRIVATE mspass ${Boost_LIBRARIES})
+#pybind11_add_module(pyamplitudes amplitudes_py.cc)
+Python_add_library(pyamplitudes amplitudes_py.cc)
+target_link_libraries(pyamplitudes PRIVATE mspass ${Boost_LIBRARIES} pybind11::headers)
 set_target_properties(pyamplitudes PROPERTIES OUTPUT_NAME "amplitudes")
 
-pybind11_add_module(pydeconvolution deconvolution_py.cc)
-target_link_libraries(pydeconvolution PRIVATE mspass ${Boost_LIBRARIES})
+#pybind11_add_module(pydeconvolution deconvolution_py.cc)
+Python_add_library(pydeconvolution deconvolution_py.cc)
+target_link_libraries(pydeconvolution PRIVATE mspass ${Boost_LIBRARIES} pybind11::headers)
 set_target_properties(pydeconvolution PROPERTIES OUTPUT_NAME "deconvolution")
 
 if(DEFINED CMAKE_LIBRARY_OUTPUT_DIRECTORY)

cxx/python/io/CMakeLists.txt

@@ -1,19 +1,19 @@
 include_directories(
   ${MSEED_INCLUDE_DIR}
   ${pylib11_INCLUDE_DIRS}
-  ${PYTHON_INCLUDE_DIRS}
+  ${Python_INCLUDE_DIRS}
   ${PROJECT_SOURCE_DIR}/include
   ${PROJECT_SOURCE_DIR}
   ${PROJECT_BINARY_DIR}/include
   ${Boost_INCLUDE_DIRS}
 )
 
 #add_library(mspasspython STATIC ${sources_python})
-#target_link_libraries(mspasspython PRIVATE mspass ${PYTHON_LIBRARIES})
+#target_link_libraries(mspasspython PRIVATE mspass ${Python_LIBRARIES})
 
-pybind11_add_module(pyio io_py.cc)
-
-target_link_libraries(pyio PRIVATE mspass ${MSEED_LIBRARIES})
+#pybind11_add_module(pyio io_py.cc)
+Python_add_library(pyio io_py.cc)
+target_link_libraries(pyio PRIVATE mspass ${MSEED_LIBRARIES} ${Boost_LIBRARIES} pybind11::headers)
 set_target_properties(pyio PROPERTIES OUTPUT_NAME "io")
 if(DEFINED CMAKE_LIBRARY_OUTPUT_DIRECTORY)
   set_target_properties(pyio PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/ccore)

cxx/python/io/io_py.cc

@@ -70,7 +70,7 @@ PYBIND11_MODULE(io,m){
     "Builds an index for a miniseed file returning std::pair with index and ErrorLogger object",
     py::return_value_policy::copy,
     py::arg("file"),
-    py::arg("segment") = false,
+    py::arg("segment") = true,
     py::arg("verbose") = false
     )
   ;

cxx/python/seismic/CMakeLists.txt

@@ -2,17 +2,17 @@ include_directories(
   ${Boost_INCLUDE_DIRS}
   ${GSL_INCLUDE_DIRS}
   ${pylib11_INCLUDE_DIRS}
-  ${PYTHON_INCLUDE_DIRS}
+  ${Python_INCLUDE_DIRS}
   ${PROJECT_SOURCE_DIR}/include
   ${PROJECT_SOURCE_DIR}
   ${PROJECT_BINARY_DIR}/include)
 
 #add_library(mspasspython STATIC ${sources_python})
-#target_link_libraries(mspasspython PRIVATE mspass ${PYTHON_LIBRARIES})
+#target_link_libraries(mspasspython PRIVATE mspass ${Python_LIBRARIES})
 
-pybind11_add_module(pyseismic seismic_py.cc)
-
-target_link_libraries(pyseismic PRIVATE mspass ${Boost_LIBRARIES})
+#pybind11_add_module(pyseismic seismic_py.cc)
+Python_add_library(pyseismic seismic_py.cc)
+target_link_libraries(pyseismic PRIVATE mspass ${Boost_LIBRARIES} pybind11::headers)
 set_target_properties(pyseismic PROPERTIES OUTPUT_NAME "seismic")
 if(DEFINED CMAKE_LIBRARY_OUTPUT_DIRECTORY)
   set_target_properties(pyseismic PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/ccore)