poreflow 0.2.3__tar.gz

poreflow-0.2.3/.uv-cache/archive-v0/z45tL5TdILP1qJGGGgvg_/cmake/data/share/cmake-4.2/Modules/FortranCInterface/CMakeLists.txt

@@ -0,0 +1,141 @@
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file LICENSE.rst or https://cmake.org/licensing for details.
+
+cmake_minimum_required(VERSION ${CMAKE_VERSION})
+project(FortranCInterface C Fortran)
+include(${FortranCInterface_BINARY_DIR}/Input.cmake OPTIONAL)
+
+# Check if the C compiler supports '$' in identifiers.
+include(CheckSourceCompiles)
+check_source_compiles(C
+"extern int dollar$(void);
+int main() { return 0; }"
+C_SUPPORTS_DOLLAR)
+
+# List manglings of global symbol names to try.
+set(global_symbols
+  my_sub    # VisualAge
+  my_sub_   # GNU, Intel, HP, SunPro, PGI
+  my_sub__  # GNU g77
+  MY_SUB    # Intel on Windows
+  mysub     # VisualAge
+  mysub_    # GNU, Intel, HP, SunPro, PGI
+  MYSUB     # Intel on Windows
+  ${FortranCInterface_GLOBAL_SYMBOLS}
+  )
+list(REMOVE_DUPLICATES global_symbols)
+
+# List manglings of module symbol names to try.
+set(module_symbols
+  __my_module_MOD_my_sub  # GNU 4.3
+  __my_module_NMOD_my_sub # VisualAge
+  __my_module__my_sub     # GNU 4.2
+  __mymodule_MOD_mysub    # GNU 4.3
+  __mymodule_NMOD_mysub   # VisualAge
+  __mymodule__mysub       # GNU 4.2
+  my_module$my_sub        # HP
+  my_module_mp_my_sub_    # Intel
+  MY_MODULE_mp_MY_SUB     # Intel on Windows
+  my_module_my_sub_       # PGI
+  my_module_MP_my_sub     # NAG
+  mymodule$mysub          # HP
+  mysub$mymodule_         # Cray
+  my_sub$my_module_       # Cray
+  mymodule_mp_mysub_      # Intel
+  MYMODULE_mp_MYSUB       # Intel on Windows
+  mymodule_mysub_         # PGI
+  mymodule_MP_mysub       # NAG
+  _QMmy_modulePmy_sub     # LLVMFlang
+  _QMmymodulePmysub       # LLVMFlang
+  __module_my_module_my_sub # LFortran
+  __module_mymodule_mysub   # LFortran
+  ${FortranCInterface_MODULE_SYMBOLS}
+  )
+list(REMOVE_DUPLICATES module_symbols)
+
+# Note that some compiler manglings cannot be invoked from C:
+#   SunPro uses "my_module.my_sub_"
+#   PathScale uses "MY_SUB.in.MY_MODULE"
+
+# Add module symbols only with Fortran90.
+if(CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+  set(myfort_modules mymodule.f90 my_module.f90)
+  set(call_mod call_mod.f90)
+  set_property(SOURCE main.F PROPERTY COMPILE_DEFINITIONS CALL_MOD)
+else()
+  set(module_symbols)
+endif()
+
+# Generate C symbol sources.
+set(symbol_sources)
+if(NOT CMAKE_Fortran_COMPILER_ID MATCHES "^(PathScale)$")
+  # Provide mymodule_ and my_module_ init symbols because:
+  #  - PGI Fortran uses module init symbols
+  #  - Cray Fortran >= 7.3.2 uses module init symbols
+  # but not for:
+  #  - PathScale Fortran uses module init symbols but module symbols
+  #    use '.in.' so we cannot provide them anyway.
+  list(APPEND symbol_sources mymodule_.c my_module_.c MY_MODULE.c MYMODULE.c)
+endif()
+foreach(symbol IN LISTS global_symbols module_symbols)
+  # Skip symbols with '$' if C cannot handle them.
+  if(C_SUPPORTS_DOLLAR OR NOT "${symbol}" MATCHES "\\$")
+    if("${symbol}" MATCHES "SUB")
+      set(upper "-UPPER")
+    else()
+      set(upper)
+    endif()
+    string(REPLACE "$" "S" name "${symbol}")
+    set(source ${CMAKE_CURRENT_BINARY_DIR}/symbols/${name}${upper}.c)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/symbol.c.in ${source} @ONLY)
+    list(APPEND symbol_sources ${source})
+  endif()
+endforeach()
+
+# Provide symbols through Fortran.
+add_library(myfort STATIC mysub.f my_sub.f ${myfort_modules})
+
+# Provide symbols through C but fall back to Fortran.
+add_library(symbols STATIC ${symbol_sources})
+target_link_libraries(symbols PUBLIC myfort)
+
+# In case the Fortran compiler produces PIC by default make sure
+# the C compiler produces PIC even if it is not its default.
+set_property(TARGET symbols PROPERTY POSITION_INDEPENDENT_CODE 1)
+
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "LFortran")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL "0.55")
+    set(_LFORTRAN_SC_FLAG --separate-compilation)
+  else()
+    set(_LFORTRAN_SC_FLAG --generate-object-code)
+  endif()
+  add_compile_options(--implicit-interface ${_LFORTRAN_SC_FLAG})
+endif()
+
+# Require symbols through Fortran.
+add_executable(FortranCInterface main.F call_sub.f ${call_mod})
+target_link_libraries(FortranCInterface PUBLIC symbols)
+
+# If IPO is enabled here, GCC gfortran >= 12.0 will obfuscate
+# the strings of the return values in the compiled executable,
+# which we use to regex match against later.
+# The static libraries must be build with IPO and non-IPO objects,
+# as that will ensure the verify step will operate on IPO objects,
+# if requested by the system compiler flags.
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU" AND
+  CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
+  target_compile_options(FortranCInterface PRIVATE "-fno-lto")
+  if(NOT APPLE)
+    target_compile_options(myfort PRIVATE "-flto=auto" "-ffat-lto-objects")
+  endif()
+endif()
+if(CMAKE_C_COMPILER_ID STREQUAL "GNU" AND
+  CMAKE_C_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
+  if(NOT APPLE)
+    target_compile_options(symbols PRIVATE "-flto=auto" "-ffat-lto-objects")
+  endif()
+endif()
+
+file(GENERATE OUTPUT exe-$<CONFIG>.cmake CONTENT [[
+set(FortranCInterface_EXE "$<TARGET_FILE:FortranCInterface>")
+]])

poreflow-0.2.3/.uv-cache/archive-v0/z45tL5TdILP1qJGGGgvg_/cmake/data/share/cmake-4.2/Modules/FortranCInterface/Verify/CMakeLists.txt

@@ -0,0 +1,35 @@
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file LICENSE.rst or https://cmake.org/licensing for details.
+
+cmake_minimum_required(VERSION ${CMAKE_VERSION})
+project(VerifyFortranC C Fortran)
+
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "LFortran")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL "0.55")
+    set(_LFORTRAN_SC_FLAG --separate-compilation)
+  else()
+    set(_LFORTRAN_SC_FLAG --generate-object-code)
+  endif()
+  add_compile_options("$<$<COMPILE_LANGUAGE:Fortran>:${_LFORTRAN_SC_FLAG}>")
+endif()
+
+option(VERIFY_CXX "Whether to verify C++ and Fortran" OFF)
+if(VERIFY_CXX)
+  enable_language(CXX)
+  set(VerifyCXX VerifyCXX.cxx)
+  add_definitions(-DVERIFY_CXX)
+endif()
+
+include(FortranCInterface)
+
+FortranCInterface_HEADER(VerifyFortran.h SYMBOLS VerifyFortran)
+include_directories(${VerifyFortranC_BINARY_DIR})
+
+add_library(VerifyFortran STATIC VerifyFortran.f)
+add_executable(VerifyFortranC main.c VerifyC.c ${VerifyCXX})
+target_link_libraries(VerifyFortranC VerifyFortran)
+
+if(NOT VERIFY_CXX)
+  # The entry point (main) is defined in C; link with the C compiler.
+  set_property(TARGET VerifyFortranC PROPERTY LINKER_LANGUAGE C)
+endif()

poreflow-0.2.3/.uv-cache/archive-v0/z45tL5TdILP1qJGGGgvg_/cmake/data/share/cmake-4.2/Modules/IntelVSImplicitPath/CMakeLists.txt

@@ -0,0 +1,7 @@
+cmake_minimum_required(VERSION ${CMAKE_VERSION})
+project(IntelFortranImplicit Fortran)
+add_custom_command(
+  OUTPUT output.cmake
+  COMMAND ${CMAKE_COMMAND} -P ${IntelFortranImplicit_SOURCE_DIR}/detect.cmake
+  )
+add_library(FortranLib hello.f output.cmake)

poreflow-0.2.3/.uv-cache/wheels-v6/pypi/cmake/4.2.1-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64/cmake/data/share/cmake-4.2/Modules/FortranCInterface/CMakeLists.txt

@@ -0,0 +1,141 @@
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file LICENSE.rst or https://cmake.org/licensing for details.
+
+cmake_minimum_required(VERSION ${CMAKE_VERSION})
+project(FortranCInterface C Fortran)
+include(${FortranCInterface_BINARY_DIR}/Input.cmake OPTIONAL)
+
+# Check if the C compiler supports '$' in identifiers.
+include(CheckSourceCompiles)
+check_source_compiles(C
+"extern int dollar$(void);
+int main() { return 0; }"
+C_SUPPORTS_DOLLAR)
+
+# List manglings of global symbol names to try.
+set(global_symbols
+  my_sub    # VisualAge
+  my_sub_   # GNU, Intel, HP, SunPro, PGI
+  my_sub__  # GNU g77
+  MY_SUB    # Intel on Windows
+  mysub     # VisualAge
+  mysub_    # GNU, Intel, HP, SunPro, PGI
+  MYSUB     # Intel on Windows
+  ${FortranCInterface_GLOBAL_SYMBOLS}
+  )
+list(REMOVE_DUPLICATES global_symbols)
+
+# List manglings of module symbol names to try.
+set(module_symbols
+  __my_module_MOD_my_sub  # GNU 4.3
+  __my_module_NMOD_my_sub # VisualAge
+  __my_module__my_sub     # GNU 4.2
+  __mymodule_MOD_mysub    # GNU 4.3
+  __mymodule_NMOD_mysub   # VisualAge
+  __mymodule__mysub       # GNU 4.2
+  my_module$my_sub        # HP
+  my_module_mp_my_sub_    # Intel
+  MY_MODULE_mp_MY_SUB     # Intel on Windows
+  my_module_my_sub_       # PGI
+  my_module_MP_my_sub     # NAG
+  mymodule$mysub          # HP
+  mysub$mymodule_         # Cray
+  my_sub$my_module_       # Cray
+  mymodule_mp_mysub_      # Intel
+  MYMODULE_mp_MYSUB       # Intel on Windows
+  mymodule_mysub_         # PGI
+  mymodule_MP_mysub       # NAG
+  _QMmy_modulePmy_sub     # LLVMFlang
+  _QMmymodulePmysub       # LLVMFlang
+  __module_my_module_my_sub # LFortran
+  __module_mymodule_mysub   # LFortran
+  ${FortranCInterface_MODULE_SYMBOLS}
+  )
+list(REMOVE_DUPLICATES module_symbols)
+
+# Note that some compiler manglings cannot be invoked from C:
+#   SunPro uses "my_module.my_sub_"
+#   PathScale uses "MY_SUB.in.MY_MODULE"
+
+# Add module symbols only with Fortran90.
+if(CMAKE_Fortran_COMPILER_SUPPORTS_F90)
+  set(myfort_modules mymodule.f90 my_module.f90)
+  set(call_mod call_mod.f90)
+  set_property(SOURCE main.F PROPERTY COMPILE_DEFINITIONS CALL_MOD)
+else()
+  set(module_symbols)
+endif()
+
+# Generate C symbol sources.
+set(symbol_sources)
+if(NOT CMAKE_Fortran_COMPILER_ID MATCHES "^(PathScale)$")
+  # Provide mymodule_ and my_module_ init symbols because:
+  #  - PGI Fortran uses module init symbols
+  #  - Cray Fortran >= 7.3.2 uses module init symbols
+  # but not for:
+  #  - PathScale Fortran uses module init symbols but module symbols
+  #    use '.in.' so we cannot provide them anyway.
+  list(APPEND symbol_sources mymodule_.c my_module_.c MY_MODULE.c MYMODULE.c)
+endif()
+foreach(symbol IN LISTS global_symbols module_symbols)
+  # Skip symbols with '$' if C cannot handle them.
+  if(C_SUPPORTS_DOLLAR OR NOT "${symbol}" MATCHES "\\$")
+    if("${symbol}" MATCHES "SUB")
+      set(upper "-UPPER")
+    else()
+      set(upper)
+    endif()
+    string(REPLACE "$" "S" name "${symbol}")
+    set(source ${CMAKE_CURRENT_BINARY_DIR}/symbols/${name}${upper}.c)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/symbol.c.in ${source} @ONLY)
+    list(APPEND symbol_sources ${source})
+  endif()
+endforeach()
+
+# Provide symbols through Fortran.
+add_library(myfort STATIC mysub.f my_sub.f ${myfort_modules})
+
+# Provide symbols through C but fall back to Fortran.
+add_library(symbols STATIC ${symbol_sources})
+target_link_libraries(symbols PUBLIC myfort)
+
+# In case the Fortran compiler produces PIC by default make sure
+# the C compiler produces PIC even if it is not its default.
+set_property(TARGET symbols PROPERTY POSITION_INDEPENDENT_CODE 1)
+
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "LFortran")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL "0.55")
+    set(_LFORTRAN_SC_FLAG --separate-compilation)
+  else()
+    set(_LFORTRAN_SC_FLAG --generate-object-code)
+  endif()
+  add_compile_options(--implicit-interface ${_LFORTRAN_SC_FLAG})
+endif()
+
+# Require symbols through Fortran.
+add_executable(FortranCInterface main.F call_sub.f ${call_mod})
+target_link_libraries(FortranCInterface PUBLIC symbols)
+
+# If IPO is enabled here, GCC gfortran >= 12.0 will obfuscate
+# the strings of the return values in the compiled executable,
+# which we use to regex match against later.
+# The static libraries must be build with IPO and non-IPO objects,
+# as that will ensure the verify step will operate on IPO objects,
+# if requested by the system compiler flags.
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU" AND
+  CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
+  target_compile_options(FortranCInterface PRIVATE "-fno-lto")
+  if(NOT APPLE)
+    target_compile_options(myfort PRIVATE "-flto=auto" "-ffat-lto-objects")
+  endif()
+endif()
+if(CMAKE_C_COMPILER_ID STREQUAL "GNU" AND
+  CMAKE_C_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
+  if(NOT APPLE)
+    target_compile_options(symbols PRIVATE "-flto=auto" "-ffat-lto-objects")
+  endif()
+endif()
+
+file(GENERATE OUTPUT exe-$<CONFIG>.cmake CONTENT [[
+set(FortranCInterface_EXE "$<TARGET_FILE:FortranCInterface>")
+]])

poreflow-0.2.3/.uv-cache/wheels-v6/pypi/cmake/4.2.1-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64/cmake/data/share/cmake-4.2/Modules/FortranCInterface/Verify/CMakeLists.txt

@@ -0,0 +1,35 @@
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file LICENSE.rst or https://cmake.org/licensing for details.
+
+cmake_minimum_required(VERSION ${CMAKE_VERSION})
+project(VerifyFortranC C Fortran)
+
+if(CMAKE_Fortran_COMPILER_ID STREQUAL "LFortran")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL "0.55")
+    set(_LFORTRAN_SC_FLAG --separate-compilation)
+  else()
+    set(_LFORTRAN_SC_FLAG --generate-object-code)
+  endif()
+  add_compile_options("$<$<COMPILE_LANGUAGE:Fortran>:${_LFORTRAN_SC_FLAG}>")
+endif()
+
+option(VERIFY_CXX "Whether to verify C++ and Fortran" OFF)
+if(VERIFY_CXX)
+  enable_language(CXX)
+  set(VerifyCXX VerifyCXX.cxx)
+  add_definitions(-DVERIFY_CXX)
+endif()
+
+include(FortranCInterface)
+
+FortranCInterface_HEADER(VerifyFortran.h SYMBOLS VerifyFortran)
+include_directories(${VerifyFortranC_BINARY_DIR})
+
+add_library(VerifyFortran STATIC VerifyFortran.f)
+add_executable(VerifyFortranC main.c VerifyC.c ${VerifyCXX})
+target_link_libraries(VerifyFortranC VerifyFortran)
+
+if(NOT VERIFY_CXX)
+  # The entry point (main) is defined in C; link with the C compiler.
+  set_property(TARGET VerifyFortranC PROPERTY LINKER_LANGUAGE C)
+endif()

poreflow-0.2.3/.uv-cache/wheels-v6/pypi/cmake/4.2.1-py3-none-manylinux2014_aarch64.manylinux_2_17_aarch64/cmake/data/share/cmake-4.2/Modules/IntelVSImplicitPath/CMakeLists.txt

@@ -0,0 +1,7 @@
+cmake_minimum_required(VERSION ${CMAKE_VERSION})
+project(IntelFortranImplicit Fortran)
+add_custom_command(
+  OUTPUT output.cmake
+  COMMAND ${CMAKE_COMMAND} -P ${IntelFortranImplicit_SOURCE_DIR}/detect.cmake
+  )
+add_library(FortranLib hello.f output.cmake)

poreflow-0.2.3/CMakeLists.txt

@@ -0,0 +1,37 @@
+cmake_minimum_required(VERSION 3.15)
+project(poreflow_changepoint)
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Find Python
+find_package(Python 3.11 COMPONENTS Interpreter Development.Module REQUIRED)
+
+# Find NumPy
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -c "import numpy; print(numpy.get_include())"
+  OUTPUT_VARIABLE Python_NumPy_INCLUDE_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+# Fetch Eigen
+include(FetchContent)
+FetchContent_Declare(
+  Eigen3
+  GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+  GIT_TAG 3.4.0
+  GIT_SHALLOW TRUE
+)
+FetchContent_MakeAvailable(Eigen3)
+
+# Define the extension module
+python_add_library(_changepoint MODULE src/poreflow/feature_extraction/_changepoint.cpp)
+
+# Include directories
+target_include_directories(_changepoint PRIVATE 
+    ${Python_NumPy_INCLUDE_DIR}
+    ${Eigen3_SOURCE_DIR}
+)
+
+# Install location
+install(TARGETS _changepoint DESTINATION poreflow/feature_extraction)

poreflow-0.2.3/LICENSE.MD

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2025] [Xiuqi Chen]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

poreflow-0.2.3/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.2
+Name: poreflow
+Version: 0.2.3
+Summary: Python module for processing nanopore sequencing
+Keywords: nanopore,peptide,bioinformatics
+Author-Email: Xiuqi Chen <X.Chen-13@tudelft.nl>, Thijn Hoekstra <thijnhoekstra@gmail.com>
+License: MIT License
+         
+         Copyright (c) [2025] [Xiuqi Chen]
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy
+         of this software and associated documentation files (the "Software"), to deal
+         in the Software without restriction, including without limitation the rights
+         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+         copies of the Software, and to permit persons to whom the Software is
+         furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all
+         copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3.11
+Project-URL: Repository, https://gitlab.tudelft.nl/xiuqichen/poreFlow.git
+Project-URL: Issues, https://gitlab.tudelft.nl/xiuqichen/poreFlow/-/issues
+Requires-Python: >=3.11
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: pandas>=2.3.1
+Requires-Dist: tables>=3.10.1
+Requires-Dist: scikit-learn>=1.7.1
+Requires-Dist: matplotlib>=3.10.5
+Requires-Dist: plotly>=6.2.0
+Requires-Dist: h5py>=3.14.0
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: dash>=2.18.1
+Requires-Dist: dash-bootstrap-components>=1.6.0
+Requires-Dist: psutil>=7.1.3
+Description-Content-Type: text/markdown
+
+# PoreFlow
+> *Nanopore data analysis tools*
+
+PoreFlow is a fast, simple, and flexible set of tools for analysing raw nanopore sequencing data, 
+intended for use for research in the Cees Dekker lab (and beyond?). 
+
+Please see the [Documentation][PoreFlow] for an introductory tutorial and full user guide.
+
+## Features
+
+- Python API for storing measurement, event, and step data.
+- Event detection algorithm
+- Fast step detection algorithm written in C++
+- Support for reasarch .fast5 files, along with .dat files from the UTube device
+- Filter events with basic metrics and store metadata
+- Find DNA-peptide boundary with expected DNA sequence
+
+## If you need help with PoreFlow, do not hesitate to get in contact:
+- For questions, contact the authors in-person or via email
+- To report a bug or make a feature request, open an **[Issue]** on GitLab.
+
+## Links
+- [Official Documentation][PoreFlow]
+
+## Contributing to PoreFlow
+Please see the [Contributing Guide] for information on how you can help develop PoreFlow.
+
+
+## Authors
+Thijn Hoekstra, Xiuqi Chen
+
+## License
+[MIT license](https://gitlab.tudelft.nl/xiuqichen/poreFlow/LICENSE)
+
+<!-- Links -->
+[PoreFlow]: https://twhoekstra.github.io/poreFlow-docs/
+[Issue]: https://https://gitlab.tudelft.nl/xiuqichen/poreFlow/issues
+[Contributing Guide]: https://twhoekstra.github.io/poreFlow-docs/contributing/
+[PyPA Code of Conduct]: https://www.pypa.io/en/latest/code-of-conduct/

poreflow-0.2.3/README.md

@@ -0,0 +1,39 @@
+# PoreFlow
+> *Nanopore data analysis tools*
+
+PoreFlow is a fast, simple, and flexible set of tools for analysing raw nanopore sequencing data, 
+intended for use for research in the Cees Dekker lab (and beyond?). 
+
+Please see the [Documentation][PoreFlow] for an introductory tutorial and full user guide.
+
+## Features
+
+- Python API for storing measurement, event, and step data.
+- Event detection algorithm
+- Fast step detection algorithm written in C++
+- Support for reasarch .fast5 files, along with .dat files from the UTube device
+- Filter events with basic metrics and store metadata
+- Find DNA-peptide boundary with expected DNA sequence
+
+## If you need help with PoreFlow, do not hesitate to get in contact:
+- For questions, contact the authors in-person or via email
+- To report a bug or make a feature request, open an **[Issue]** on GitLab.
+
+## Links
+- [Official Documentation][PoreFlow]
+
+## Contributing to PoreFlow
+Please see the [Contributing Guide] for information on how you can help develop PoreFlow.
+
+
+## Authors
+Thijn Hoekstra, Xiuqi Chen
+
+## License
+[MIT license](https://gitlab.tudelft.nl/xiuqichen/poreFlow/LICENSE)
+
+<!-- Links -->
+[PoreFlow]: https://twhoekstra.github.io/poreFlow-docs/
+[Issue]: https://https://gitlab.tudelft.nl/xiuqichen/poreFlow/issues
+[Contributing Guide]: https://twhoekstra.github.io/poreFlow-docs/contributing/
+[PyPA Code of Conduct]: https://www.pypa.io/en/latest/code-of-conduct/

poreflow-0.2.3/pyproject.toml

@@ -0,0 +1,69 @@
+[build-system]
+requires = ["scikit-build-core", "numpy"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "poreflow"
+dynamic = ["version"]
+authors = [
+    {name = "Xiuqi Chen", email = "X.Chen-13@tudelft.nl"},
+    {name = "Thijn Hoekstra", email = "thijnhoekstra@gmail.com"},
+]
+description = "Python module for processing nanopore sequencing"
+readme = "README.md"
+license = {file = "LICENSE.MD"}
+requires-python = ">=3.11"
+dependencies = [
+    "numpy>=2.2.6",
+    "scipy>=1.15.3",
+    "tqdm>=4.67.1",
+    "pandas>=2.3.1",
+    "tables>=3.10.1",
+    "scikit-learn>=1.7.1",
+    "matplotlib>=3.10.5",
+    "plotly>=6.2.0",
+    "h5py>=3.14.0",
+#    "dtw-python>=1.5.3",
+#    "torch>=2.6.0",
+    "seaborn>=0.13.2",
+#    "tslearn>=0.7.0",
+#    "pomegranate>=1.1.2",
+    "dash>=2.18.1",
+    "dash-bootstrap-components>=1.6.0",
+    "psutil>=7.1.3",
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Developers",
+  "Programming Language :: Python :: 3.11",
+]
+keywords = ["nanopore", "peptide", "bioinformatics", ]
+
+[project.scripts]
+poreflow = "poreflow.cli:main"
+
+[project.urls]
+Repository = "https://gitlab.tudelft.nl/xiuqichen/poreFlow.git"
+Issues = "https://gitlab.tudelft.nl/xiuqichen/poreFlow/-/issues"
+
+[tool.scikit-build]
+wheel.packages = ["src/poreflow", "src/fast5_research"]
+sdist.include = ["src/*", "LICENSE.MD", "pyproject.toml", "CMakeLists.txt", "README.md"]
+sdist.exclude = ["*"]
+
+[tool.scikit-build.metadata.version]
+provider = "scikit_build_core.metadata.regex"
+input = "src/poreflow/__init__.py"
+
+[dependency-groups]
+dev = [
+    "jupyterlab>=4.4.5",
+    "ipywidgets>=8.1.7",
+    "ipympl>=0.9.7",
+    "pytest>=8.3.3",
+    "pytest-cov>=6.0.0",
+    "ruff>=0.15.0",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"