Fixes #394: Update Python setup (#395)

* Fixes #394: Update Python setup

Now using setuptools instead of distutils to do the install. Most of the Python code runs without installing, with a note in the manual that it has to be added to the PYTHONPATH to work correctly. But a user is likely to run "Make Install" instead which will install the files to the relevant site_packages folder without needing to change the PYTHONPATH. So to better replicate this, we'll add "make install" to the CI testing and simplify the Makefile by removing the Python-specific make recipes. We'll also modify the manual to mention that setting the PYTHONPATH is not necessary after running make install.

---------

Co-authored-by: Ben Fulton <bfulton@imperial.ac.uk>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

.gitignore

@@ -85,9 +85,6 @@ tests/tools.mk
 tools/lib
 tools/version-info
 
-## Python
-python/setup.py
-
 ## Fortran files
 diagnostics/Diagnostic_Fields_New.F90
 preprocessor/check_options.F90

Makefile.in

@@ -213,26 +213,14 @@ fltools: fluidity_library
 manual:
 	@cd manual; $(MAKE)
 
-python_build:
-ifeq (@HAVE_PYTHON@,yes)
-	@echo "    MAKE python"
-	@cd python; python3 setup.py build > build.log 2>&1
-	@cd python/fluidity; find ../build/lib* -name '*.so' -exec ln -sf {} . \;
-endif
-
-python_clean:
-	@echo "    CLEAN python"
-	@cd python; rm -rf build
-	@cd python/fluidity; find . -type l -name '*.so' -exec rm -f {} \;
-
 .PHONY: scripts
 
 scripts:
 	@echo "INSTALL local scripts"
 	@cd tools ; $(MAKE) scripts
 
 fluidity_library: lib/lib$(FLUIDITY).a
-lib/lib$(FLUIDITY).a: $(OBJS) python_build sub_system scripts
+lib/lib$(FLUIDITY).a: $(OBJS) sub_system scripts
 	@echo "BUILD libfluidity"
 	@echo "    MKDIR lib"
 	@mkdir -p lib

configure

@@ -17484,7 +17484,7 @@ printf "%s\n" "$ac_cv_path_GREP" >&6; }
 
 
 
-ac_config_files="$ac_config_files Makefile debug/Makefile bathymetry/Makefile ocean_forcing/Makefile ocean_forcing/tests/Makefile sediments/Makefile population_balance/Makefile hyperlight/Makefile femtools/Makefile femtools/tests/Makefile forward_interfaces/Makefile horizontal_adaptivity/Makefile horizontal_adaptivity/tests/Makefile preprocessor/Makefile error_measures/Makefile error_measures/tests/Makefile parameterisation/Makefile parameterisation/tests/Makefile fldecomp/Makefile assemble/Makefile assemble/tests/Makefile diagnostics/Makefile main/Makefile tools/Makefile tools/version-info python/setup.py climatology/Makefile libmba2d/Makefile libmba3d/Makefile libjudy/Makefile libjudy/src/Makefile libjudy/src/JudyCommon/Makefile libjudy/src/Judy1/Makefile libjudy/src/JudyL/Makefile libjudy/src/JudySL/Makefile libjudy/src/JudyHS/Makefile libwm/Makefile libvtkfortran/Makefile tests/tools.mk"
+ac_config_files="$ac_config_files Makefile debug/Makefile bathymetry/Makefile ocean_forcing/Makefile ocean_forcing/tests/Makefile sediments/Makefile population_balance/Makefile hyperlight/Makefile femtools/Makefile femtools/tests/Makefile forward_interfaces/Makefile horizontal_adaptivity/Makefile horizontal_adaptivity/tests/Makefile preprocessor/Makefile error_measures/Makefile error_measures/tests/Makefile parameterisation/Makefile parameterisation/tests/Makefile fldecomp/Makefile assemble/Makefile assemble/tests/Makefile diagnostics/Makefile main/Makefile tools/Makefile tools/version-info climatology/Makefile libmba2d/Makefile libmba3d/Makefile libjudy/Makefile libjudy/src/Makefile libjudy/src/JudyCommon/Makefile libjudy/src/Judy1/Makefile libjudy/src/JudyL/Makefile libjudy/src/JudySL/Makefile libjudy/src/JudyHS/Makefile libwm/Makefile libvtkfortran/Makefile tests/tools.mk"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure

configure.in

@@ -1859,7 +1859,6 @@ AC_CONFIG_FILES([Makefile
           main/Makefile
           tools/Makefile
           tools/version-info
-          python/setup.py
           climatology/Makefile
           libmba2d/Makefile
       	  libmba3d/Makefile

docker/actions/Dockerfile.actions.noble

@@ -32,6 +32,7 @@ RUN test -z "$(git status --porcelain */Makefile.dependencies)"
 RUN make
 RUN make fltools
 RUN make manual
+RUN sudo make install
 
 # Python module 'assess' is required for some longtests
 RUN python3 -m pip install --break-system-packages assess

manual/examples.tex

@@ -175,7 +175,8 @@ \subsection{Results}
 
 Alternatively the results can be plotted using python. An example python script using pylab and the
 vtktools python module, is provided with this example. The vtktools module is located in
-\texttt{\fluiditysourcepath/python/}; this path needs to be added to the \texttt{PYTHONPATH} environment
+\texttt{\fluiditysourcepath/python/}. It will be available in the default Python installation after
+fluidity is installed; alternatively, this path can be added to the \texttt{PYTHONPATH} environment
 variable.
 
 As can be seen in the numerical result using the CG method leads, to over and

manual/python.tex

@@ -33,9 +33,10 @@ \section{System requirements}
 \lstinline[language=Bash]+python-numpy+ package.
 
 \fluidity\ also requires access to its own Python modules which are stored in
-the python directory in the \fluidity\ source tree. To ensure that these are
-visible to \fluidity\ at runtime, users should add this directory to the
-\lstinline[language=Bash]+PYTHONPATH+ environment variable. For example:\
+the python directory in the \fluidity\ source tree. These will be installed
+to the default Python installation along with Fluidity, but users can add this
+directory to the \lstinline[language=Bash]+PYTHONPATH+ environment variable.
+For example:\
 \begin{lstlisting}[language=Bash]
 export PYTHONPATH=<my_fluidity>/python/:$PYTHONPATH
 \end{lstlisting}%$

python/pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "fluidity"
+version = "0.2"
+description = "Fluidity python files"
+requires-python = ">=3.8"
+authors = [
+    {name = "Patrick Farrell"},
+    {name = "Stephan Kramer"}
+]
+maintainers = [
+    {name = "Ben Fulton"},
+]
+license = {text = "See LICENSE file"}
+classifiers = [
+    "Development Status :: 5 - Production",
+    "Intended Audience :: Science/Research",
+    "License :: Other/Proprietary License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+
+[project.urls]
+Homepage = "https://fluidity-project.org"
+Documentation = "https://figshare.com/articles/journal_contribution/Fluidity_Manual/1387713?file=2031637"
+Repository = "https://github.com/FluidityProject/fluidity"
+Issues = "https://github.com/FluidityProject/fluidity/issues"
+
+[tool.setuptools]
+packages = ["fluidity", "fluidity.diagnostics"]
+py-modules = ["fluidity_tools", "vtktools"]
+
+[tool.setuptools.package-dir]
+fluidity = "fluidity"

python/setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()