From 10e2f2e55f32cbca18d6f56d2a110f61a861d89f Mon Sep 17 00:00:00 2001 From: Antonio-JP Date: Wed, 26 Jun 2019 09:49:46 +0200 Subject: [PATCH] Adding extra files for distributing the package. --- .gitignore | 90 +++++ LICENSE | 674 ++++++++++++++++++++++++++++++++++++ Makefile | 60 +++- README.rst | 249 +++++++++++++ VERSION | 1 + ajpastor/dd_functions/ddFunction.py | 9 +- ajpastor/lazy/conversion.py | 8 +- ajpastor/operator/oreOperator.py | 8 +- setup.py | 53 ++- 9 files changed, 1123 insertions(+), 29 deletions(-) create mode 100644 LICENSE create mode 100644 README.rst create mode 100644 VERSION diff --git a/.gitignore b/.gitignore index fd20fdd..0ff8c7e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,92 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ *.pyc +*$py.class + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# IPython Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# dotenv +.env + +# virtualenv +venv/ +ENV/ + +# Spyder project settings +.spyderproject + +# Rope project settings +.ropeproject + +/.travis_ci_gh_pages_deploy_key +/.travis_ci_gh_pages_deploy_key.pub +/gh-pages + diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/Makefile b/Makefile index 7f61fe8..de6ab0c 100644 --- a/Makefile +++ b/Makefile @@ -1,11 +1,45 @@ SHELL:=/bin/bash + +# Package folder +PACKAGE = ajpastor BASE=ajpastor -ZIP=diff_defined_functions# ZIP name -VERSION=$(shell cat ./package-version.txt) -all: - sage -sh sage-pip-install . - +# change to your sage command if needed +SAGE = sage + +# zip name +ZIP=diff_defined_functions +# version short-cut +VERSION=$(shell cat ./VERSION) + + +# All command +all: install test + +# Installing commands +install: + $(SAGE) -pip install --upgrade --no-index -v . + +uninstall: + $(SAGE) -pip uninstall $(PACKAGE) + +develop: + $(SAGE) -pip install --upgrade -e . + +test: + $(SAGE) setup.py test + +# Documentation commands +coverage: + $(SAGE) -coverage $(PACKAGE)/* + +doc: + cd docs && $(SAGE) -sh -c "make html" + +doc-pdf: + cd docs && $(SAGE) -sh -c "make latexpdf" + +# Creating basic commands create: @echo "Creating main directories..." @mkdir -p ./$(BASE) @@ -13,21 +47,29 @@ create: @echo "from pkgutil import extend_path;" > ./$(BASE)/__init__.py @echo "__path__ = extend_path(__path__, __name__);" >> ./$(BASE)/__init__.py -zip: clean_pyc +# Zip commands +zip: clean-pyc @echo "Compressing the project into file" $(ZIP)".zip"... @rm -f ./releases/$(ZIP)__$(VERSION).zip @zip -r ./releases/$(ZIP)__$(VERSION).zip $(BASE) type SPKG.txt setup.py package-version.txt Makefile dependencies @cp ./releases/$(ZIP)__$(VERSION).zip ./releases/old/$(ZIP)__$(VERSION)__`date +'%y.%m.%d_%H:%M:%S'`.zip @cp ./releases/$(ZIP)__$(VERSION).zip ./releases/$(ZIP).zip -clean_pyc: +# Clean commands +clean: clean-pyc clean-doc + +clean-pyc: @echo "Cleaning the Python precompiled files (.pyc)" @find . -name "*.pyc" -exec rm {} + + +clean-doc: + cd docs && $(SAGE) -sh -c "make clean" +# git commands git: zip @echo "Pushing changes to public git repository" @git add -A @git commit @git push - - + +.PHONY: all install develop test coverage clean clean-doc doc doc-pdf diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..c2e94c8 --- /dev/null +++ b/README.rst @@ -0,0 +1,249 @@ +=================== +Sage Sample Package +=================== + +.. image:: https://mybinder.org/badge.svg + :target: https://mybinder.org/v2/gh/sagemath/sage_sample/master + +This package is designed as a simple `SageMath `_ package +example to serve as a good practice reference for package developers. We follow +python recommendations and adapt them to the SageMath community. You can find more +advanced documentation on python package creation on +`How To Package Your Python Code `_. + +This is still a work in progress. Once this example will have +stabilized, the plan is to make a +`cookie cutter `_ +template out of it. + +Installation +------------ + +Try the `demo `_ on binder +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Local install from source +^^^^^^^^^^^^^^^^^^^^^^^^^ + +Download the source from the git repository:: + + $ git clone https://github.com/sagemath/sage_sample.git + +Change to the root directory and run:: + + $ sage -pip install --upgrade --no-index -v . + +For convenience this package contains a `makefile `_ with this +and other often used commands. Should you wish too, you can use the +shorthand:: + + $ make install + +Install from PyPI +^^^^^^^^^^^^^^^^^^ + +sage_sample is distributed on PyPI. You can install it with the command:: + + $ sage -pip install sage_sample + +Distribute via PyPI +^^^^^^^^^^^^^^^^^^^ + +To distribute your own package on PyPI, you will need an account on +`pypi.org `_ (maybe at first on +`test.pypi.org `_). + +You also need to install setuptools, wheel and twine:: + + $ pip install --upgrade setuptools wheel twine + +If the README file is in Markdown format, you need to install cmarkgfm as well:: + + $ pip install --upgrade cmarkgfm + +Then you can generate the distribution package via:: + + $ python setup.py sdist bdist_wheel + +*NB:* if the package is both Python 2 and Python 3 compatible, use instead:: + + $ python setup.py sdist bdist_wheel --universal + +Check that everything is all right:: + + $ twine check dist/* + +Upload the package to the test PyPI repository:: + + $ twine upload --repository-url https://test.pypi.org/legacy/ dist/* + +Check the package install in Sage:: + + $ sage -pip install -i https://test.pypi.org/simple sage_sample + +And later, upload your distribution to the real PyPI [optionally sign it with GPG]:: + + $ twine upload [-s] dist/* + + +Usage +----- + +Once the package is installed, you can use it in Sage with:: + + sage: from sage_sample import answer_to_ultimate_question + sage: answer_to_ultimate_question() + 42 + +See also the `demo notebook `_. + +Setup +------ + +All packaging setup is done through ``setup.py``. To create your own package +follow the strcuture of the file and change the parameters accordingly. + +Source code +----------- + +All source code is stored in the folder ``sage_sample`` using the same name as the +package. This is not mandatory but highly recommended for clarity. All source folder +must contain a ``__init__.py`` file with needed includes. + +Tests +----- + +This package is configured for tests written in the documentation +strings, also known as ``doctests``. For examples, see this +`source file `_. See also +`SageMath's coding conventions and best practices document `_. +With additional configuration, it would be possible to include unit +tests as well. + +Once the package is installed, one can use the SageMath test system +configured in ``setup.py`` to run the tests:: + + $ sage setup.py test + +This is just calling ``sage -t`` with appropriate flags. + +Shorthand:: + + $ make test + +Documentation +------------- + +The documentation of the package can be generated using Sage's +``Sphinx`` installation:: + + $ cd docs + $ sage -sh -c "make html" + +Shorthand:: + + $ make doc + +For this to work on your own package, make sure you follow the same +structure as we do here: + +* Create a ``docs`` folder containing the exact same ``Makefile`` and a ``source`` + folder. +* Copy and paste the ``docs/source/conf.py`` file from this package and update + the few project specific variables at the beginning of the file. +* Create an ``index.rst`` file as well as a ``.rst`` file for each + module you want on the documentation. + +Travis CI integration +--------------------- + +.. image:: https://travis-ci.org/sagemath/sage_sample.svg?branch=master + :target: https://travis-ci.org/sagemath/sage_sample + +Scripts that run ``make test`` on various SageMath versions on the +Travis CI system are included. +https://docs.travis-ci.com/user/for-beginners explains how to enable +automatic Travis CI builds for your GitHub-hosted project. + +The scripts download and install binary releases (7.1-7.4) from a +SageMath mirror. Edit ``.travis-install.sh`` if some optional or +experimental SageMath packages need to be installed prior to running +your package. Edit ``.travis.yml`` to change the list of SageMath +versions used. + +Automatically deploying documentation to GitHub pages using Travis CI +--------------------------------------------------------------------- + +* First do the steps described above to enable Travis CI integration + of your GitHub-hosted project. + +* If you don't already have GitHub pages for your project: Create and + checkout a branch ``gh-pages`` in your repository and put an empty + file ``.nojekyll`` in it (see + https://help.github.com/articles/files-that-start-with-an-underscore-are-missing/). + Then commit it and push it to GitHub:: + + $ git clone --single-branch --depth 1 https://github.com/USER/PROJECT.git gh-pages + $ cd gh-pages + $ git checkout --orphan gh-pages + $ git rm -rf . + $ touch .nojekyll + $ git add .nojekyll + $ git commit -m "Initial commit" + $ git push -u origin gh-pages + $ cd .. + +* (Back in your working copy:) Generate a new ssh key pair with an + empty passphrase:: + + $ ssh-keygen -t dsa -f .travis_ci_gh_pages_deploy_key + +* Add the public ssh key (contents of the file + ``.travis_ci_gh_pages_deploy_key.pub``) to your GitHub repository + as a deploy key (Settings/Deploy keys/Add deploy key). + Title: Key for deploying documentation to GitHub pages. + Check Allow write access. + +* Install the Travis CI command-line client from + https://github.com/travis-ci/travis.rb:: + + $ gem install travis + +* Log in to Travis CI using your GitHub credentials:: + + $ travis login + +* Encrypt the private ssh key, add the decryption keys + as secure environment variables to Travis CI, and + add code to ``.travis.yml`` to decrypt it:: + + $ travis encrypt-file .travis_ci_gh_pages_deploy_key --add before_script + +* Add the encrypted private ssh key to the repository:: + + $ git add .travis_ci_gh_pages_deploy_key.enc + +* Have git ignore the other keys (and the gh-pages directory):: + + $ echo >> .gitignore + $ echo "/.travis_ci_gh_pages_deploy_key" >> .gitignore + $ echo "/.travis_ci_gh_pages_deploy_key.pub" >> .gitignore + $ echo "/gh-pages" >> .gitignore + $ git add .gitignore + +* Optionally, edit ``.travis.yml`` to adjust variables ``DEPLOY_DOC_...`` + +* Commit all changes to GitHub. The Travis CI build should then run + automatically and deploy it:: + + $ git add .travis.yml + $ git commit -m "Deploy built documentation to GitHub" + $ git push + +* The deployed documentation will be available at: + https://USER.github.io/PROJECT/ + This can be customized by changing ``DEPLOY_DOC_TO_DIRECTORY=/`` + to another directory in ``.travis.yml`` + For example, setting ``DEPLOY_DOC_TO_DIRECTORY=doc/html`` will make + the deployed documentation available at: + https://USER.github.io/PROJECT/doc/html/ diff --git a/VERSION b/VERSION new file mode 100644 index 0000000..5a2a580 --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +0.6 diff --git a/ajpastor/dd_functions/ddFunction.py b/ajpastor/dd_functions/ddFunction.py index 3e10024..32fd7e3 100644 --- a/ajpastor/dd_functions/ddFunction.py +++ b/ajpastor/dd_functions/ddFunction.py @@ -412,10 +412,12 @@ class DDRing (Ring_w_Sequence, IntegralDomain): except: pass; if(F is None): - raise TypeError("Incompatible original structures:\n\t- %s\n\t- %s" %(pself, pS)); + return None; + #raise TypeError("Incompatible original structures:\n\t- %s\n\t- %s" %(pself, pS)); if(not F in IntegralDomains()): - raise TypeError("Pushout of the original structures is not an integral domain:\n\t- %s" %F); + return None; + #raise TypeError("Pushout of the original structures is not an integral domain:\n\t- %s" %F); if(not F.is_field()): F = F.fraction_field(); @@ -423,7 +425,8 @@ class DDRing (Ring_w_Sequence, IntegralDomain): polys = {str(el[0 ]):el[1 ] for el in gens_self['algebraic']} for el in gens_S['algebraic']: if(polys.get(str(el[0 ]), el[1 ]) != el[1 ]): - raise TypeError("Incompatible names in algebraic extensions:\n\t- %s\n\t- %s" %(el,(el[0 ],polys[str(el[0 ])]))); + return None; + #raise TypeError("Incompatible names in algebraic extensions:\n\t- %s\n\t- %s" %(el,(el[0 ],polys[str(el[0 ])]))); polys[str(el[0 ])] = el[1 ]; sorted_names = sorted(polys); diff --git a/ajpastor/lazy/conversion.py b/ajpastor/lazy/conversion.py index 81a8eab..9049049 100644 --- a/ajpastor/lazy/conversion.py +++ b/ajpastor/lazy/conversion.py @@ -307,10 +307,12 @@ class ConversionSystem(object): if(len(variables) == 0): return self.base()(polynomial); - - return sum([self.base()(coefficients[i])*prod([self.map_of_vars()[str(v)]**monomials[i].degree(v) for v in variables],self.base().one()) for i in range(len(monomials))],self.base().zero()); + try: + return sum([self.base()(coefficients[i])*prod([self.map_of_vars()[str(v)]**monomials[i].degree(v) for v in variables],self.base().one()) for i in range(len(monomials))],self.base().zero()); + except Exception: + print "Error here"; - return self.base()(polynomial(**{str(v) : self.map_of_vars()[str(v)] for v in variables})); +# return self.base()(polynomial(**{str(v) : self.map_of_vars()[str(v)] for v in variables})); # multi = (len(variables) > _sage_const_1 ); # res = self.base().zero(); # for (k,v) in polynomial.dict().items(): diff --git a/ajpastor/operator/oreOperator.py b/ajpastor/operator/oreOperator.py index 08b15c2..450228e 100644 --- a/ajpastor/operator/oreOperator.py +++ b/ajpastor/operator/oreOperator.py @@ -179,13 +179,7 @@ class w_OreOperator(Operator): def _compute_derivative_solution(self): d = self.__oa.gen(); - try: - return w_OreOperator(self.base(), self.operator/d); - except ValueError: - c = self.getCoefficient(_sage_const_0 ); - dc = self.derivate()(c); - - return w_OreOperator(self.base(), ((c*d - dc)*self.operator)/d); + return w_OreOperator(self.base(), self.operator.annihilator_of_associate(d)); def _compute_integral_solution(self): return w_OreOperator(self.base(),self.operator.annihilator_of_integral()); diff --git a/setup.py b/setup.py index 48c6900..6d3d10c 100644 --- a/setup.py +++ b/setup.py @@ -1,12 +1,51 @@ -from distutils.core import setup +## -*- encoding: utf-8 -*- +import os; +import sys; +from setuptools import setup; +from codecs import open; # To open the README file with proper encoding +from setuptools.command.test import test as TestCommand; # for tests + +# Get information from separate files (README, VERSION) +def readfile(filename): + with open(filename, encoding='utf-8') as f: + return f.read() + +# For the tests +class SageTest(TestCommand): + def run_tests(self): + errno = os.system("sage -t --force-lib sage_sample") + if errno != 0: + sys.exit(1) setup( name = "ajpastor", - version = "0.5", - author = "Antonio Jimenez-Pastor", - author_email = "antonio.jimenez-pastor@dk-compmath.jku.at", - license = "GPL", - packages = ["ajpastor", "ajpastor.dd_functions", "ajpastor.operator", "ajpastor.lazy", "ajpastor.misc", "ajpastor.tests"] - ) + version = readfile("VERSION").strip(), # the VERSION file is shared with the documentation + description='Sage-based package for DD-finite functions', + #long_description = readfile("README.rst"), # get the long description from the README + # For a Markdown README replace the above line by the following two lines: + # long_description = readfile("README.md"), + # long_description_content_type="text/markdown", + url='https://www.dk-compmath.jku.at/Members/antonio/sage-package-dd_functions', + author='Antonio Jimenez-Pastor', + author_email='ajpastor@risc.uni-linz.ac.at', # choose a main contact email + license='GPLv3+', # This should be consistent with the LICENCE file + classifiers=[ + # How mature is this project? Common values are + # 3 - Alpha + # 4 - Beta + # 5 - Production/Stable + 'Development Status :: 3 - Alpha', + 'Intended Audience :: Science/Research', + 'Topic :: Software Development :: Build Tools', + 'Topic :: Scientific/Engineering :: Mathematics', + 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)', + 'Programming Language :: Python :: 2.7.15', + ], # classifiers list: https://pypi.python.org/pypi?%3Aaction=list_classifiers + keywords = "SageMath packaging", + packages = ["ajpastor", "ajpastor.dd_functions", "ajpastor.operator", "ajpastor.lazy", "ajpastor.misc", "ajpastor.tests"], + cmdclass = {'test': SageTest}, # adding a special setup command for tests + setup_requires = ['sage-package'], + install_requires = ['sage-package', 'sphinx'], +) -- 2.1.4