Update the Readme file.
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epsi-builds/msspec_python3/pipeline/head This commit looks good
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I updated the information in the Readme file to provide detailed steps to build msspec with GNU make.
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README.md
126
README.md
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@ -4,68 +4,134 @@ Introduction
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This is the Python MsSpec version with support for Python 3.x and dynamic memory allocation for Phagen and Spec
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Installation of the devel package
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=================================
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To work with the git repository
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===============================
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Requirements
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------------
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You can clone this repository onto your local computer using git
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To compile MsSpec shared libraries, you need:
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- Python >= 3.6
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- gfortran compiler
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- cairo library (runtime files and header files)
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Depending on your OS and Python version, you may need all the requirements (runtime libraries
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and header files) to build wxPython (please consult your distribution's package list for the
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appropriate package names) and their dependencies:
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- python-dev (for your version of python)
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- gtk (preferably version 3, but depends on your needs)
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- gstreamer
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- gstreamer-plugins-base
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- glut
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- libwebkitgtk (matching your gtk version)
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- libjpeg
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- libpng
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- libtiff
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- libsdl
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- libnotify
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- libsm
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You also need a tool to create and manage Python virtual environments. For now only
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*virtualenv* is supported. So if you plan to install msspec with the one-step command,
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you need to install it.
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Fetching the code
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-----------------
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You first need to clone the devel branch with either 2 commands below:
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```Bash
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git clone https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git
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git checkout devel
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```
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This will create a folder named "msspec_python3" with all the source code inside.
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You can also clone the development branch:
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```Bash
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git clone --branch devel https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git
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```
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This will create a msspec\_python3 folder with a local copy of the repository.
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It is higly recommended to work in a Python virtual environment.
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To create one, you can use:
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One step install
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----------------
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The command below will do all the stuff to install msspec in its dedicated Python
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virtual environment provided all the above requirements are fullfilled
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```Bash
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virtualenv --python=python3 msspec_venv
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cd msspec_python3
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make devel
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```
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or
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This will:
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- Create a Python virtual environment in the "\_venv" folder inside the msspec\_python3 folder.
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- Install all the required Python packages in this virtual environment.
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- Install (or even maybe build) wxPython for your OS and Python version in this virtual environment.
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- Build the msspec shared librarires.
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- Install msspec in *edit mode* in this virtual environment.
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You can tweak the process by specifying space separated key=value pairs on the command line.
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Allowed keys are:
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- PYTHON, to give the executable name of the python interpreter to use rather than the default (python)
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- VERBOSE, set to 1 if you want the install process to be more verbose
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- NO\_VENV, set to 1 to not create a virtual environment
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- VENV\_PATH, specify the path to a virtual environment root folder
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- DEBUG, set to 1 to add debugging symbols
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- BUILDDIR, to set a different name than the default to store building artifacts (./build)
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- FC, the Fortran compiler to use (gfortran)
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- F2PY
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Work with msspec
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----------------
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All you need to do each time you want to work with msspec is activating the virtual environment.
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For example, if *virtualenv* was used to create the virtual environment:
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```Bash
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virtualenv --python=python3 --system-site-packages msspec_venv
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source msspec_python3/_venv/bin/activate
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```
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to activate the virtual environment (if you are in the folder where you created "msspec\_venv"):
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Then you can launch your script with
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```Bash
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source ./msspec_venv/bin/activate
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python myscript.py
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```
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Now you can build the program, go in the source folder
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See the online [tutorials](https://msspec.cnrs.fr/tutorials/index.html) for more information on how to use msspec.
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When you're done, you can deactivate the virtual environment with
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```Bash
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cd msspec_python3/src
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deactivate
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```
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Install the python package dependencies.
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Uninstall MsSpec
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----------------
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```Bash
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pip install -r setup_requirements.txt
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pip install -r requirements.txt
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```
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When Installed in "devel mode", nothing is created outside the msspec\_python3 folder, so you just have to remove
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that folder to get rid of msspec on your computer
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You need to compile the fortran libs. This is done by the scons (Software Construction) program
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```Bash
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scons
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```
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Manual control over the install
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-------------------------------
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Finally, install the package in develop mode:
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If for any reason you want to control each step of the building process (for example you do not have *virtualenv* but you
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are using *conda*), here is how:
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```Bash
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pip install -e .
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```
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- Create a virtual environment or use an existing one and activate it
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- Install the list of requirements that are listed in the src/pip.freeze file
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- Install wxPython
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- Build the msspec shared librarires with the command "make pybinding"
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- Install the msspec Python package with "pip install -e src/"
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That's all. All you need to do each time you want to work with msspec is activating the virtual environment
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The last step can be replaced by adding the src/ path to your PYTHONPATH, but bear in mind that the package will then
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be also visible to other virtual environments no matter they fit the msspec requirements.
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@ -1,60 +0,0 @@
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VERSION:=$(shell python -c "import msspec; print(msspec.__version__)")
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VERBOSE:=0
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ifeq ($(VERBOSE),0)
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SUPPRESS_OUPUT:=1>/dev/null 2>/dev/null
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MAKEFLAGS += --no-print-directory --silent
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else
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SUPPRESS_OUPUT:=
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endif
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install: sdist
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@echo "Installing the newly created Python package..."
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@pip install dist/msspec-*.tar.gz $(SUPPRESS_OUPUT)
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sdist: install_deps
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@echo "Creating Python source distribution..."
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# Create the source distrib
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@python setup.py sdist $(SUPPRESS_OUPUT)
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install_deps: pybinding
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@echo "Installing Python dependencies..."
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# Install dependencies with pip
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@pip install --upgrade -r requirements.txt $(SUPPRESS_OUPUT)
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pybinding:
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@echo "Building Python binding for phagen and spec..."
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@+$(MAKE) -C msspec/spec/fortran pybinding $(SUPPRESS_OUPUT)
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@+$(MAKE) -C msspec/phagen/fortran pybinding $(SUPPRESS_OUPUT)
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results: msspec/results.txt
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msspec/results.txt: pybinding
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@echo "Generating results for unittests"
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@coverage run --source=./ --omit=msspec/es/*,msspec/msspecgui/* msspec/create_tests_results.py 1>/dev/null
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# create the html coverage report
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@coverage html -d ../doc/source/htmlcov
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@rm .coverage
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tests: pybinding
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@echo "Runing unittests"
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@python -m msspec.tests 1>/dev/null
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clean:
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@echo "Cleaning all..."
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@find ./ -type f -name '*.pyc' -exec rm -f {} +
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@find ./ -type d -name '__pycache__' -exec rm -rf {} +
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@+$(MAKE) -C msspec/spec/fortran clean $(SUPPRESS_OUPUT)
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@+$(MAKE) -C msspec/phagen/fortran clean $(SUPPRESS_OUPUT)
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# remove previous sdist
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@rm -rf dist
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@rm -rf *.egg*
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purge: clean
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@echo "Removing also shared objects..."
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@find ./ -type f -name '*.so' -exec rm -f {} +
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help:
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@echo "help message"
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125
src/SConstruct
125
src/SConstruct
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@ -1,125 +0,0 @@
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import os
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import subprocess
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import datetime
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from pkg_resources import parse_version
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from setuptools_scm import get_version
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###############################################################################
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def filtered_glob(env, pattern, omit=[],
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ondisk=True, source=False, strings=False):
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return list(filter(
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lambda f: os.path.basename(f.path) not in omit,
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env.Glob(pattern)))
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# Create a builder for f2py
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def f2py_generator(source, target, env, for_signature):
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suffix = ".so"
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main = source[0]
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objects = " ".join(o.get_path() for o in source[1:] if str(o).endswith('.o'))
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moduledir = os.path.dirname(target[0].abspath)
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modulefile = str(target[0])
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modulename = modulefile.replace(suffix, '').replace('/', '.')
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compiler = env['FORTRAN']
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cmd = f"$F2PY --fcompiler={compiler} "
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cmd += f" $F2PY_OPTS -m {modulename} -c {objects} {main}"
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cmd += f" && cp {'/'.join(modulename.split('.'))}.*.so {modulefile}"
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#cmd += " 1>/dev/null 2>/dev/null"
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return cmd
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def install_module(env, module):
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destdir = os.path.dirname(module[0].srcnode().abspath)
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env.Install(destdir, module)
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env.Alias('install', destdir)
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return None
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def version_action(target, source, env):
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with open(str(target[0]), 'w') as fd:
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v = get_version(root='../', relative_to='./', version_scheme="post-release")
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v = parse_version(v)
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if v._version.post[-1] == 0:
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version = v.base_version
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else:
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version = v.public
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fd.write(version + '\n')
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now = datetime.datetime.now().isoformat()
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fd.write(f'compiled on {now}\n')
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p = subprocess.run([env['FORTRAN'], "--version"], stdout=subprocess.PIPE)
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fd.write(p.stdout.decode('utf8'))
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f2py_bld = Builder(generator=f2py_generator)
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version_bld = Builder(action=version_action)
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# define the default build environment
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std = Environment(tools=['default', 'fortran'], F2PY_OPTS=[], LIBS=[])
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std.AddMethod(filtered_glob, "FilteredGlob")
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std.AddMethod(install_module, "InstallModule")
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std['BUILDERS']['F2py'] = f2py_bld
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std['BUILDERS']['Version'] = version_bld
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###############################################################################
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# Define the command line options
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AddOption('--dbg',
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dest='dbg',
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action='store_true',
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help='add debugging symbols')
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AddOption('--verbose',
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dest='verbose',
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action='store_true',
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help='add debugging symbols')
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AddOption('--compiler',
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dest='compiler',
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default='gfortran',
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choices=['gfortran', 'ifort'],
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help='The Fortran compiler to use')
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AddOption('--f2py_path',
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dest='f2py_path',
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default='f2py3',
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help='The full path to the f2py compiler')
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# define environments
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gfortran_env = std.Clone(tools=['gfortran'])
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#gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-O2', '-ffast-math', '-mcmodel=large', '-fdefault-real-8', '-fdefault-double-8'])
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gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-mcmodel=large'])
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ifort_env = std.Clone(tools=['ifort'])
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# parse options
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if GetOption('compiler') == 'gfortran':
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env = gfortran_env
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#env.Append(F2PY_OPTS='--opt=-O2')
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elif GetOption('compiler') == 'ifort':
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env = ifort_env
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f2py_path = GetOption('f2py_path')
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p = subprocess.run(['which', f2py_path], stdout=subprocess.PIPE)
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if p.returncode != 0:
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raise Exception('Invalid path for f2py compiler!')
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else:
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env.Append(F2PY=p.stdout.decode('utf8').strip())
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if GetOption('dbg'):
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flags = ['-g', '-Wall', '-Wextra', '-Warray-temporaries',
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'-Wconversion', '-fbacktrace', '-ffree-line-length-0',
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'-fcheck=all', '-ffpe-trap=zero,overflow,underflow,invalid,denormal',
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'-finit-real=nan']
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gfortran_env.Append(FORTRANFLAGS = flags,
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F2PY_OPTS = ['--noopt', '--debug-capi', '--debug', '--f77flags=-g -fcheck=all -fbacktrace -ffpe-trap=zero,overflow,underflow,invalid,denormal'])
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if GetOption('verbose'):
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env.Replace(FORTRANCOMSTR = "")
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Export('env')
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SConscript('msspec/spec/fortran/SConstruct', variant_dir='build/build_spec')
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SConscript('msspec/phagen/fortran/SConstruct', variant_dir='build/build_phagen')
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version_file = env.Version('VERSION', [])
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Depends(version_file, "install")
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@ -1,10 +0,0 @@
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Import('env')
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import os
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objects_src= ['phagen_scf_2.1_dp.f']
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objects = env.Object(objects_src)
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module = env.F2py('libphagen.so', ['main.f'] + objects, F2PYCOMSTR=">>")
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env.InstallModule(module)
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env.Alias('phagen', module)
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@ -1,71 +0,0 @@
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Import('env')
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import os
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# Configure the environment
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env_spec = env.Clone()
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cwd = Dir('.').get_abspath()
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env_spec.Append(FORTRANFLAGS=['-I' + cwd,'-J' + cwd])
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env_spec.Append(F2PY_OPTS=['-I' + cwd])
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# define sources
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dim_mod = ['memalloc/dim_mod.f']
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memalloc = ['memalloc/modules.f', 'memalloc/allocation.f']
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cluster_gen = Glob('cluster_gen/*.f')
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common_sub = Glob('common_sub/*.f')
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renormalization = Glob('renormalization/*.f')
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phd_se_noso_nosp_nosym = env_spec.FilteredGlob('phd_se_noso_nosp_nosym/*.f', omit=['main.f'])
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phd_mi_noso_nosp_nosym = env_spec.FilteredGlob('phd_mi_noso_nosp_nosym/*.f', omit=['main.f'])
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eig_common = Glob('eig/common/*.f')
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eig_mi = env_spec.FilteredGlob('eig/mi/*.f', omit=['main.f'])
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eig_pw = env_spec.FilteredGlob('eig/pw/*.f', omit=['main.f'])
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comp_curves = ['treatment/comp_curves.f']
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conf = Configure(env_spec, log_file='./config.log')
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if conf.CheckLib('lapack'):
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env_spec.Append(F2PY_OPTS = "-llapack")
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eig_mi = [f for f in eig_mi if str(f).find('lapack') == -1]
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phd_mi_noso_nosp_nosym = [f for f in phd_mi_noso_nosp_nosym if str(f).find('lapack') == -1]
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env_spec = conf.Finish()
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env_spec.Append(FORTRANFLAGS='-fno-automatic')
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# define objects
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dim_mod_obj = env_spec.Object(dim_mod)
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memalloc_obj = env_spec.Object(memalloc)
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cluster_gen_obj = env_spec.Object(cluster_gen)
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common_sub_obj = env_spec.Object(common_sub)
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renormalization_obj = env_spec.Object(renormalization)
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phd_se_noso_nosp_nosym_obj = env_spec.Object(phd_se_noso_nosp_nosym)
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phd_mi_noso_nosp_nosym_obj = env_spec.Object(phd_mi_noso_nosp_nosym)
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eig_common_obj = env_spec.Object(eig_common)
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eig_pw_obj = env_spec.Object(eig_pw)
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eig_mi_obj = env_spec.Object(eig_mi)
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comp_curves_obj = env_spec.Object(comp_curves)
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Requires(memalloc_obj, dim_mod_obj)
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# define Python extensions
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common_deps = dim_mod_obj + memalloc_obj + cluster_gen_obj + common_sub_obj
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deps = common_deps + renormalization_obj + phd_se_noso_nosp_nosym_obj
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phd_se_mod = env_spec.F2py('_phd_se_noso_nosp_nosym.so', ['phd_se_noso_nosp_nosym/main.f'] + deps)
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env_spec.InstallModule(phd_se_mod)
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deps = common_deps + renormalization_obj + phd_mi_noso_nosp_nosym_obj
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phd_mi_mod = env_spec.F2py('_phd_mi_noso_nosp_nosym.so', ['phd_mi_noso_nosp_nosym/main.f'] + deps)
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env_spec.InstallModule(phd_mi_mod)
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deps = common_deps + renormalization_obj + eig_common_obj + eig_mi_obj
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eig_mi_mod = env_spec.F2py('_eig_mi.so', ['eig/mi/main.f'] + deps)
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env_spec.InstallModule(eig_mi_mod)
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deps = common_deps + renormalization_obj + eig_common_obj + eig_pw_obj
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eig_pw_mod = env_spec.F2py('_eig_pw.so', ['eig/pw/main.f'] + deps)
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env_spec.InstallModule(eig_pw_mod)
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deps = comp_curves_obj
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comp_curve_mod = env_spec.F2py('_comp_curves.so', ['treatment/main.f'] + deps)
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env_spec.InstallModule(comp_curve_mod)
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# Alias
|
||||
env_spec.Alias('spec', [phd_se_mod, phd_mi_mod, eig_pw_mod, eig_mi_mod])
|
||||
|
||||
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Reference in New Issue