condense python requirements

ayendiki · May 5, 2021 · 6ed8901 · 6ed8901
1 parent 96dacda
commit 6ed8901
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Showing 5 changed files with 22 additions and 40 deletions.
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
@@ -17,21 +17,13 @@ install(PROGRAMS fspython DESTINATION bin)
 # install any package requirements
 if(INSTALL_PYTHON_DEPENDENCIES)
 
-  # packages not in requirements.txt (not needed for the FS module, but for other tools)
-  set(EXTRA_PACKAGES " \
-    tensorflow==2.4.1 \
-    h5py==2.10 \
-    git+git://github.com/adalca/pystrum.git@3befbd1166595476e8315fef99bea373bfdc302c \
-    git+git://github.com/adalca/neurite.git@ac74518f367113ddadca90b70acf12f6a8526839 \
-    git+git://github.com/voxelmorph/voxelmorph.git@80d0c489febfb4fa32b4a247629e79720fbb4c14"
-  )
-
   if(NOT DISTRIBUTE_FSPYTHON)
     set(PKG_TARGET "--target=${CMAKE_INSTALL_PREFIX}/python/packages")
   endif()
+
   install(CODE "
     message(STATUS \"Installing freesurfer python package dependencies\")
-    execute_process(COMMAND bash -c \"${CMAKE_INSTALL_PREFIX}/python/bin/python3 -m pip install --upgrade --disable-pip-version-check ${EXTRA_PACKAGES} -r ${CMAKE_CURRENT_SOURCE_DIR}/requirements.txt ${PKG_TARGET}\" RESULT_VARIABLE retcode)
+    execute_process(COMMAND bash -c \"${CMAKE_INSTALL_PREFIX}/python/bin/python3 -m pip install --upgrade --disable-pip-version-check ${EXTRA_PACKAGES} -r ${CMAKE_CURRENT_SOURCE_DIR}/requirements.txt -r ${CMAKE_CURRENT_SOURCE_DIR}/requirements-extra.txt ${PKG_TARGET}\" RESULT_VARIABLE retcode)
     if(NOT \${retcode} STREQUAL 0)
       message(FATAL_ERROR \"Could not install freesurfer python dependencies\")
     endif()

diff --git a/python/requirements-extra.txt b/python/requirements-extra.txt
@@ -0,0 +1,18 @@
+# extra packages required for FS DL utilities
+tensorflow==2.4.1
+h5py==2.10
+
+# these are also required for FS DL utilities, but we need some features
+# that haven't quite made it into the stable releases yet - this should be
+# updated once they do
+git+git://github.com/adalca/pystrum.git@3befbd1166595476e8315fef99bea373bfdc302c
+git+git://github.com/adalca/neurite.git@ac74518f367113ddadca90b70acf12f6a8526839
+git+git://github.com/voxelmorph/voxelmorph.git@80d0c489febfb4fa32b4a247629e79720fbb4c14
+
+# extra packages required for QA tools
+numpy
+scipy
+pandas
+matplotlib
+transforms3d
+scikit-image==0.16.2
diff --git a/qatools/CMakeLists.txt b/qatools/CMakeLists.txt
@@ -5,6 +5,8 @@ if(NOT INSTALL_PYTHON_DEPENDENCIES)
 endif()
 
 # run 'pip install' and direct package installs to freesufer/python/packages
+# requirements are currently defined by python/requirements-extra.txt
+
 install(CODE "
   message(STATUS \"Installing QA tools\")
   execute_process(COMMAND bash -c \"${PYTHON_EXECUTABLE} -m pip install ${CMAKE_CURRENT_SOURCE_DIR} --no-dependencies --upgrade --target=${CMAKE_INSTALL_PREFIX}/python/packages\" RESULT_VARIABLE retcode)
@@ -15,21 +17,3 @@ install(CODE "
 )
 
 install_pyscript(qatools.py)
-
-# install any package requirements
-if(INSTALL_PYTHON_DEPENDENCIES)
-  if(NOT DISTRIBUTE_FSPYTHON)
-    set(PKG_TARGET "--target=${CMAKE_INSTALL_PREFIX}/python/packages")
-  endif()
-  install(CODE "
-    message(STATUS \"Installing QA tools package dependencies\")
-    execute_process(COMMAND bash -c \"${CMAKE_INSTALL_PREFIX}/python/bin/python3 -m pip install -r ${CMAKE_CURRENT_SOURCE_DIR}/requirements.txt ${PKG_TARGET}\" RESULT_VARIABLE retcode)
-    if(NOT \${retcode} STREQUAL 0)
-      message(FATAL_ERROR \"Could not install QA tools dependencies\")
-    endif()
-    execute_process(COMMAND bash -c \"find ${CMAKE_INSTALL_PREFIX}/python/bin ! -name 'python3*' -type f -exec rm -f {} +\" RESULT_VARIABLE retcode)
-    if(NOT \${retcode} STREQUAL 0)
-      message(FATAL_ERROR \"Could not remove pip-installed scripts\")
-    endif()"
-  )
-endif()
diff --git a/qatools/requirements.txt b/qatools/requirements.txt
diff --git a/qatools/setup.py b/qatools/setup.py
@@ -26,10 +26,4 @@
     ],
     python_requires='>=3.5',
     keywords='Freesurfer',
-    # This field lists other packages that your project depends on to run.
-    # Any package you put here will be installed by pip when your project is
-    # installed, so they must be valid existing projects.
-    # For an analysis of "install_requires" vs pip's requirements files see:
-    # https://packaging.python.org/en/latest/requirements.html
-    install_requires=['numpy','scipy','pandas','matplotlib','transforms3d','scikit-image==0.16.2']
 )