#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2019, by the GROMACS development team, led by
+# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# Stub file for future higher-level CMake management. Ultimately, we want to
# drive building and testing from the repository-level CMake configuration, but
-# in the initial packaging, tests are somewhat manual and installation of the
-# Python package is driven through the setup.py file in src.
+# in the initial packaging, tests are somewhat manual and Python package
+# installation is driven through the setup.py file in src.
#
-# To be driven by a higher-level CMake configuration, a CMakeLists.txt file at this level would
+# Terminology note:
+# * A "Python package" is a directory that can be imported as a Python module
+# by the Python interpreter using the `import packagename` syntax.
+# * A "distribution archive" is a file in any of several distribution
+# formats (including archive files of specified directory structures)
+# that a Python package management tool or framework
+# (e.g. pypi.org, ``pip``, the ``setuptools`` module)
+# knows how to download, upload, or install
+# (building, if necessary, in the case of a source distribution).
+# * Here, the verb "to package" means to produce a package distribitution archive.
+# This terminology is used because
+# * The verb "to produce a package distribution archive" is awkward to conjugate.
+# * "To build a package" is otherwise ambiguous.
+# * Here, the meaning of "install" varies with context. In the context of CMake
+# or a build system like ``make``, "install" refers to the build system target
+# or command. In the context of a Python package or Python tool, "install"
+# refers to the managed installation of a Python package from a distribution
+# archive to a "site-packages" directory for the Python environment.
+# Note: a (valid and complete) Python does not need to be "installed" to be
+# usable, such as if the ``import`` and dependencies can be resolved with the
+# current ``PYTHONPATH`` environment variable or after ``sys.path.append()``.
+# * "To build a package" means to create a package from sources that may need
+# to be configured or compiled before the package can be imported. Reference
+# the ``distutils`` ``build`` and ``build_ext`` commands.
+#
+# For basic building and testing of the Python package, we don't necessarily
+# need to create a distribution archive or install the Python package outside
+# of the build tree. We can use a CMake ExternalProject to build and install the
+# ``_gmxapi`` binary extension module from `python_packaging/src` into the main
+# project build tree (note ``ExternalProject_add()`` option ``INSTALL_DIR``).
+# If avoiding Python packaging tools in this way, the Python source files (``.py`` files)
+# will have to be copied explicitly in additional CMake ``install(FILES)`` directives,
+# and the ExternalProject installation directory will have to be added to the
+# PYTHONPATH environment variable where the package needs to be available.
+#
+# Note that a binary distribution needs to be built for a specific major and minor
+# Python release, and is often sensitive to a particular Python distribution or
+# packaging system. Instead, we can build `gmxapi` source distributions during
+# the CMake build phase at the GROMACS project level. These source distributions
+# can be installed into the GROMACS installation path or uploaded to, .e.g,
+# PyPI.org so that the binary extension is built in the context of a specific
+# (system or user) GROMACS installation and (user) Python environment. For a
+# system-wide Python environment, the package needs to be built and installed
+# (to the ``site-packages`` directory) for each supported Python interpreter.
+# ``setup.py`` can just be invoked with different Python interpreters.
+#
+# To drive the packaging of a Python package distribution archive
+# by a higher-level CMake configuration, a CMakeLists.txt file at this level would
# 1. configure: copy the contents of `src` to the build directory, potentially
# configuring version info and CMakeToolchain for GROMACS
# 2. build: run (cd $CMAKE_CURRENT_BINARY_DIR/src && python setup.py sdist),
# 2. create and activate a Python venv in the build dir
# 3. `pip install <the_sdist_archive_file>` into the venv
# 4. run `pytest copy_of_src/test`
+
+set(PYBIND11_PYTHON_VERSION "3")
+add_subdirectory(src)
+add_subdirectory(sample_restraint)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff