Merge pull request #22 from bjodah/more-sym

Bump CI image, use sym

.drone.sec

@@ -1 +1 @@
-eyJhbGciOiJSU0EtT0FFUCIsImVuYyI6IkExMjhHQ00ifQ.RxcFQnm0aBsJCz8bgQj_zrSLCFgkvwrGGlRu8aUH2J74zDsuaXZIpnhEgtpMv6RX_kqudaofSMe_euEl-c24By4N4QE1me7UpnPDRkuLYmWl8xl2Klot0rqXKNhZO7A0KQVWdtuVNPH8MxZUwjY18VkhAa1jJLuvTKIEaxzF-1WUMFbmVnhgFGOzkQJXZQDax8RP1cF-t6B7fXFUBkphjRlfSG1dEGhSqtFOeLv-TJ2pCNBbNQrfDbYxd8yVtHABvbzezpaVBZhc5AEUleNv7s7bmn2yXD-BsVPWSEF5ksLekXEgKft-DsyiU2bF1d2aSoixgWZ-DTqubMy65VjhTQ.y03vzHCHgFhpsVFy.p3tAhOXZ3rfxWInB3ajy0z9XP7XH-r54tSH7OXvG_9COIt-a4Ej_hal3Pb0EMNCintIvgsn44cfE_V-4YIhmp8Dhv6u9ZwSAVC_7OKt4wG6GTX2FF_gN6KU-BhSfnoBtJrq0P3T4wr1Gu_3dvZN9quURLY-4wd8E-svXTBetfqfJgMjCKys0q2MRCf51OJyOio4OPP98UcWnzi27.HP0QWTXM5o_2lVZ8UDqPDw
+eyJhbGciOiJSU0EtT0FFUCIsImVuYyI6IkExMjhHQ00ifQ.AhUu4693LswxH_s88tvpvB2V2z0ql2NWLzlyb9aybs8LEip3FjeGedMMK3uYSb_SoakPIgOeBqsfWVeXyQV9wV8lV2yv_8F2gNx9ccDtzoXzfkakUA3rEelEkpE9MdI2_GOnn4J3Y0niNiAUZLBRgrp2vQa3xOUKyM1cKAmYO-T7B380LG_weB2KfiOqLiTItCwloSZGpQ6tzQ_-3ola5OKdK5tNPZF7lyXCTahuCEuQFFrJ9IcGjq9yuJ3qG0uRSV9Lp7y2Toyiua35wBt8ZLjFTiONOvlSqNpA9oMM6I1QRr6XOB2KFRMt0HQKYHnXMY3hdA67O51A4bMNTqhw6w.1RlrqyEuqdjcKg9_.pUYfpYMfGl0UpYmZ0UuXbjvthQs13RQ7cHiK_TbN6eyuR49snGr-8rVxKTOZpbZp9LLa-GIhYGTIKNOjtUvSCm_wJFlSSZoikt78FdOmgKRfSZAzlJ6IoOv6-9fEKd48C9_grap7m1Dssjb6Z36HW8XK5t6MValR4Bfk1gQF1X2tPwaU8aPL7gsZ0HUjqxdPobgwVI6TP-6eAliJpZg.ECsKZKJClxiqVbXfpeKwhw

.drone.yml

@@ -1,15 +1,12 @@
 build:
- image: bjodah/bjodahimg:latest
+ image: bjodah/bjodahimg16:v1.2
  environment:
  - PYNLEQ2_NLEQ2_ROOT_URL=$$PYNLEQ2_NLEQ2_ROOT_URL
  commands:
- - python2.7 -m pip install --user pynleq2
- - python3.4 -m pip install --user pynleq2
+ - (cd /; python2 -m pip install --user pynleq2)
+ - (cd /; python3 -m pip install --user pynleq2)
  - export PYNLEQ2_NLEQ2_ROOT_URL=""
  - ./scripts/ci.sh pyneqsys
- - (cd examples/; ipython2 nbconvert --to=html --debug --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=300 *.ipynb)
- - (cd examples/; ../scripts/render_index.sh *.html)
- - ./scripts/generate_docs.sh
  - ./scripts/prepare_deploy.sh
 
 deploy:

CHANGES.rst

@@ -1,3 +1,7 @@
+unreleased
+==========
+- Rely on ``sym`` package.
+
 v0.4.2
 ======
 - Support for chained solvers

conda-recipe/meta.yaml

@@ -1,32 +1,46 @@
+{% set name = "pyneqsys" %}
+{% set version = "0.5.0.git" %}
+
 package:
- name: pyneqsys
- version: 0.4.0.git
+ name: {{ name|lower }}
+ version: {{ version }}
 
 source:
- path: ../
+ git_url: ../
 
 build:
  number: 0
+ script: python setup.py install --single-version-externally-managed --record record.txt
 
 requirements:
  build:
  - python
- - numpy
+ - setuptools
  run:
  - python
  - numpy
- - sympy
  - scipy
- - pyodesys
+ - sym
+ - sympy
+ - symcxx
+ - python-symengine
+ - pysym
 
 test:
  imports:
- - pyneqsys
+ - {{ name }}
  requires:
- - nose
+ - pytest
  commands:
- - nosetests pyneqsys
+ - pytest --pyargs {{ name }}
 
 about:
- home: https://github.com/bjodah/pyneqsys
- license: BSD
+ home: https://github.com/bjodah/{{ name }}
+ license: BSD 2-Clause
+ license_file: LICENSE
+ summary: 'Solve symbolically defined systems of non-linear equations numerically.'
+ doc_url: https://bjodah.github.io/{{ name }}/latest
+
+extra:
+ recipe-maintainers:
+ - bjodah

pyneqsys/__init__.py

@@ -1,21 +1,21 @@
 # -*- coding: utf-8 -*-
 """
-Package for solving of symbolic systems of non-linear equations numerically.
+Package for numerically solving symbolically defined systems of non-linear equations.
 
 pyneqsys ties computer algebra systems like:
 
 - SymPy
 - symengine
-- symcxx
+- SymCXX
 
 and numerical solvers such as:
 
 - MINPACK in SciPy
 - NLEQ2 in pynleq2
 - KINSOL in pykinsol
 
-in addition pyneqsys provides abstraction classes for e.g. having
-conditional equations in a system.
+together. In addition ``pyneqsys`` provides helper classes for
+handling e.g. conditional equations in a system.
 """
 
 from __future__ import absolute_import

pyneqsys/_release.py

@@ -1 +1 @@
-__version__ = '0.4.0.git'
+__version__ = '0.5.0.git'

pyneqsys/symbolic.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 from sym import Backend
-from pyodesys.util import banded_jacobian, check_transforms
+from sym.util import banded_jacobian, check_transforms
 
 from .core import NeqSys, _ensure_3args
 

scripts/check_clean_repo_on_master.sh

@@ -7,3 +7,12 @@ if [[ ! -z $(git status -s) ]]; then
  echo "'git status' show there are some untracked/uncommited changes. Aborting..."
  exit 1
 fi
+if grep -e "^v" CHANGES.rst >/dev/null; then
+ if ! grep -e "^$1" CHANGES.rst >/dev/null; then
+ >&2 echo "CHANGES.rst does not contain an entry for: $1"
+ exit 1
+ fi
+else
+ >&2 echo "CHANGES.rst does not start with v*"
+ exit 1
+fi

scripts/ci.sh

@@ -4,18 +4,19 @@ if [[ "$CI_BRANCH" =~ ^v[0-9]+.[0-9]?* ]]; then
  eval export ${PKG_NAME^^}_RELEASE_VERSION=\$CI_BRANCH
  echo ${CI_BRANCH} | tail -c +2 > __conda_version__.txt
 fi
-for PY in python2.7 python3.4; do
- $PY -m pip install https://github.com/bjodah/sym/archive/master.zip # until sym > 0.1.2
- $PY -m pip install --upgrade sympy==1.0
-done
-python2.7 setup.py sdist
-(cd dist/; python2.7 -m pip install $PKG_NAME-$(python ../setup.py --version).tar.gz)
-(cd dist/; python3.4 -m pip install $PKG_NAME-$(python ../setup.py --version).tar.gz)
-(cd /; python2.7 -m pytest --pyargs $PKG_NAME)
-(cd /; python3.4 -m pytest --pyargs $PKG_NAME)
-python2.7 -m pip install --user -e .[all] pysym pykinsol git+https://github.com/bjodah/cyipopt.git
-python3.4 -m pip install --user -e .[all] pysym pykinsol git+https://github.com/bjodah/cyipopt.git
-PYTHONPATH=$(pwd) PYTHON=python2.7 ./scripts/run_tests.sh
-PYTHONPATH=$(pwd) PYTHON=python3.4 ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html
+git archive -o /tmp/$PKG_NAME.zip HEAD # test pip installable zip (symlinks break)
+python3 -m pip install /tmp/$PKG_NAME.zip
+
+python2 setup.py sdist # test pip installable sdist (checks MANIFEST.in)
+(cd dist/; python2 -m pip install $PKG_NAME-$(python2 ../setup.py --version).tar.gz)
+(cd /; python2 -m pytest --pyargs $PKG_NAME)
+
+python2 -m pip install --user -e .[all] pysym pykinsol git+https://github.com/bjodah/cyipopt.git
+python3 -m pip install --user -e .[all] pysym pykinsol git+https://github.com/bjodah/cyipopt.git
+PYTHONPATH=$(pwd) PYTHON=python2 ./scripts/run_tests.sh
+PYTHONPATH=$(pwd) PYTHON=python3 ./scripts/run_tests.sh --cov $PKG_NAME --cov-report html
 ./scripts/coverage_badge.py htmlcov/ htmlcov/coverage.svg
 ! grep "DO-NOT-MERGE!" -R . --exclude ci.sh
+
+./scripts/render_notebooks.sh
+./scripts/generate_docs.sh

scripts/generate_docs.sh

@@ -11,10 +11,16 @@
 NARGS=$#
 PKG=$(find . -maxdepth 2 -name __init__.py -print0 | xargs -0 -n1 dirname | xargs basename)
 AUTHOR=$(head -n 1 AUTHORS)
-sphinx-apidoc --full --force -A "$AUTHOR" --module-first --doc-version=$(python setup.py --version) -F -o doc $PKG/ $PKG/tests/
+sphinx-apidoc --full --force -A "$AUTHOR" --module-first --doc-version=$(python setup.py --version) -F -o doc $PKG/ $(find . -type d -name tests)
+sed -i "s/chempy's/ChemPy's/g" doc/index.rst
 #sed -i 's/Contents/.. include:: ..\/README.rst\n\nContents/g' doc/index.rst
-echo ".. include:: ../README.rst" >>doc/index.rst
-sed -i "s/'sphinx.ext.viewcode',/'sphinx.ext.viewcode',\n 'sphinx.ext.autosummary',\n 'numpydoc',/g" doc/conf.py
+#echo ".. include:: ../README.rst" >>doc/index.rst
+cat <<EOF >>doc/index.rst
+Overview
+========
+$(tail -n+3 README.rst)
+EOF
+sed -i "s/'sphinx.ext.viewcode',/'sphinx.ext.viewcode',\n 'sphinx.ext.autosummary',\n 'sphinx.ext.mathjax',\n 'numpydoc',/g" doc/conf.py
 sed -i "s/alabaster/sphinx_rtd_theme/g" doc/conf.py
 if [[ $NARGS -eq 3 ]]; then
 cat <<EOF>>doc/conf.py

scripts/post_release.sh

@@ -8,15 +8,28 @@ SERVER=$2
 GITHUBUSER=$3
 PKG=$(find . -maxdepth 2 -name __init__.py -print0 | xargs -0 -n1 dirname | xargs basename)
 PKG_UPPER=$(echo $PKG | tr '[:lower:]' '[:upper:]')
-MD5=$(md5sum dist/${PKG}-$VERSION.tar.gz | cut -f1 -d' ')
+SDIST_FILE=dist/${PKG}-$VERSION.tar.gz
+if [[ ! -f "$SDIST_FILE" ]]; then
+ >&2 echo "Nonexistent file $SDIST_FILE"
+ exit 1
+fi
+SHA256=$(openssl sha256 "$SDIST_FILE" | cut -f2 -d' ')
+if [[ -d "dist/conda-recipe-$VERSION" ]]; then
+ rm -r "dist/conda-recipe-$VERSION"
+fi
 cp -r conda-recipe/ dist/conda-recipe-$VERSION
-sed -i -E -e "s/version:(.+)/version: $VERSION/" -e "s/path:(.+)/fn: $PKG-$VERSION.tar.gz\n url: https:\/\/github.com\/$GITHUBUSER\/$PKG\/releases\/download\/v$VERSION\/$PKG-$VERSION.tar.gz\n md5: $MD5/" dist/conda-recipe-$VERSION/meta.yaml
-
-env ${PKG_UPPER}_RELEASE_VERSION=v$VERSION python setup.py upload_sphinx
+sed -i -E \
+ -e "s/\{\% set version(.+)/\{\% set version = \"$VERSION\" \%\}\n\{\% set sha256 = \"$SHA256\" \%\}/" \
+ -e "s/git_url:(.+)/fn: \{\{ name \}\}-\{\{ version \}\}.tar.gz\n url: https:\/\/pypi.io\/packages\/source\/\{\{ name\[0\] \}\}\/\{\{ name \}\}\/\{\{ name \}\}-\{\{ version \}\}.tar.gz\n sha256: \{\{ sha256 \}\}/" \
+ dist/conda-recipe-$VERSION/meta.yaml
+
+./scripts/update-gh-pages.sh v$VERSION
 
 # Specific for this project:
 scp -r dist/conda-recipe-$VERSION/ $PKG@$SERVER:~/public_html/conda-recipes/
-scp dist/${PKG}-$VERSION.tar.gz $PKG@$SERVER:~/public_html/releases/
+scp "$SDIST_FILE" "$PKG@$SERVER:~/public_html/releases/"
 for CONDA_PY in 2.7 3.4 3.5; do
- ssh $PKG@$SERVER "source /etc/profile; conda-build --python $CONDA_PY ~/public_html/conda-recipes/conda-recipe-$VERSION/"
+ for CONDA_NPY in 1.11; do
+ ssh $PKG@$SERVER "source /etc/profile; conda-build --python $CONDA_PY --numpy $CONDA_NPY ~/public_html/conda-recipes/conda-recipe-$VERSION/"
+ done
 done

scripts/release.sh

@@ -1,36 +1,51 @@
-#!/bin/bash -xe
+#!/bin/bash -xeu
 # Usage:
 #
-# $ ./scripts/release.sh v1.2.3 ~/anaconda2/bin
-# $ ./scripts/release.sh v1.2.3 ~/anaconda2/bin upstream
+# $ ./scripts/release.sh v1.2.3 ~/anaconda2/bin myserver.example.com GITHUB_USER GITHUB_REPO
 #
 
 if [[ $1 != v* ]]; then
  echo "Argument does not start with 'v'"
  exit 1
 fi
-if [[ $# == 3 ]]; then
- REMOTE=origin
-else
- REMOTE=$4
-fi
 VERSION=${1#v}
+CONDA_PATH=$2
+SERVER=$3
+find . -type f -iname "*.pyc" -exec rm {} +
+find . -type f -iname "*.o" -exec rm {} +
+find . -type f -iname "*.so" -exec rm {} +
+find . -type d -name "__pycache__" -exec rmdir {} +
 ./scripts/check_clean_repo_on_master.sh
 cd $(dirname $0)/..
 # PKG will be name of the directory one level up containing "__init__.py" 
 PKG=$(find . -maxdepth 2 -name __init__.py -print0 | xargs -0 -n1 dirname | xargs basename)
+! grep --include "*.py" "will_be_missing_in='$VERSION'" -R $PKG/ # see deprecation()
 PKG_UPPER=$(echo $PKG | tr '[:lower:]' '[:upper:]')
 ./scripts/run_tests.sh
 env ${PKG_UPPER}_RELEASE_VERSION=v$VERSION python setup.py sdist
-env ${PKG_UPPER}_RELEASE_VERSION=v$VERSION ./scripts/generate_docs.sh
+if [[ -e ./scripts/generate_docs.sh ]]; then
+ env ${PKG_UPPER}_RELEASE_VERSION=v$VERSION ./scripts/generate_docs.sh # $4 ${5:-$PKG} v$VERSION
+fi
 for CONDA_PY in 2.7 3.4 3.5; do
- PATH=$2:$PATH ./scripts/build_conda_recipe.sh v$VERSION --python $CONDA_PY
+ for CONDA_NPY in 1.11; do
+ continue # we build the conda recipe on another host for now..
+ PATH=$CONDA_PATH:$PATH ./scripts/build_conda_recipe.sh v$VERSION --python $CONDA_PY --numpy $CONDA_NPY
+ done
 done
 
-# All went well
+# All went well, add a tag and push it.
 git tag -a v$VERSION -m v$VERSION
-git push $REMOTE
-git push $REMOTE --tags
+git push
+git push --tags
 twine upload dist/${PKG}-$VERSION.tar.gz
 
-echo "Create a new release on github (with custom .tar.gz), then run ./scripts/post_release.sh ..."
+set +x
+echo ""
+echo " You may now create a new github release at with the tag \"v$VERSION\", here is a link:"
+echo " https://github.com/$4/${5:-$PKG}/releases/new "
+echo " name the release \"${PKG}-${VERSION}\", and don't foreget to manually attach the file:"
+echo " $(openssl sha256 $(pwd)/dist/${PKG}-${VERSION}.tar.gz)"
+echo " Then run:"
+echo ""
+echo " $ ./scripts/post_release.sh $1 $SERVER $4"
+echo ""

scripts/render_index.sh

@@ -20,11 +20,11 @@ for f in $@; do
  continue # don't include notebooks starting with underscore
  fi
  img=$(basename $f .html).png
- phantomjs $(unset CDPATH && cd "$(dirname "$0")" && echo $PWD)/rasterize.js $f $tmpdir/$img 1200px*900px
+ QT_QPA_PLATFORM=offscreen phantomjs $(unset CDPATH && cd "$(dirname "$0")" && echo $PWD)/rasterize.js $f $tmpdir/$img 1200px*900px
  convert $tmpdir/$img -resize 400x300 thumbs/$img
  cat <<EOF>>index.html
 <p style='text-align: center'>
-<a href='$f' style='ffont-ont-family: sans-serif'>
+<a href='$f' style='font-family: sans-serif'>
 <img src='thumbs/$img'><br>
 $f
 </a></p>

scripts/render_notebooks.sh

@@ -0,0 +1,4 @@
+#!/bin/bash -e
+cd examples/
+jupyter nbconvert --debug --to=html --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=300 *.ipynb
+../scripts/render_index.sh *.html

scripts/update-gh-pages.sh

@@ -0,0 +1,72 @@
+#!/bin/bash -x
+#
+# Usage:
+#
+# $ ./scripts/update-gh-pages.sh v0.6.0 origin
+#
+
+tag=${1:-master}
+remote=${2:-origin}
+
+ori_branch=$(git rev-parse --symbolic-full-name --abbrev-ref HEAD)
+tmpdir=$(mktemp -d)
+cleanup() {
+ rm -r $tmpdir
+}
+trap cleanup INT TERM
+
+cp -r doc/_build/html/ $tmpdir
+git ls-files --others | tar cf $tmpdir/untracked.tar -T -
+if [[ -d .gh-pages-skeleton ]]; then
+ cp -r .gh-pages-skeleton $tmpdir
+fi
+
+git checkout gh-pages
+if [[ $? -ne 0 ]]; then
+ git checkout --orphan gh-pages
+ if [[ $? -ne 0 ]]; then
+ >&2 echo "Failed to switch to 'gh-pages' branch."
+ cleanup
+ exit 1
+ fi
+ preexisting=0
+else
+ preexisting=1
+fi
+
+if [[ $preexisting == 1 ]]; then
+ while [[ "$(git log -1 --pretty=%B)" == Volatile* ]]; do
+ # overwrite previous docs
+ git reset --hard HEAD~1
+ done
+fi
+
+shopt -s extglob
+git clean -xfd
+if [[ $preexisting == 1 ]]; then
+ git rm -rf !(v*) > /dev/null
+fi
+cp -r $tmpdir/html/ $tag
+if [[ -d $tmpdir/.gh-pages-skeleton ]]; then
+ cp -r $tmpdir/.gh-pages-skeleton/. .
+fi
+if [[ "$tag" == v* ]]; then
+ ln -s $tag latest
+ commit_msg="Release docs for $tag"
+else
+ if [[ $preexisting == 1 ]]; then
+ commit_msg="Volatile ($tag) docs"
+ else
+ commit_msg="Initial commit"
+ fi
+fi
+git add -f . >/dev/null
+git commit -m "$commit_msg"
+if [[ $preexisting == 1 ]]; then
+ git push -f $remote gh-pages
+else
+ git push --set-upstream $remote gh-pages
+fi
+git checkout $ori_branch
+tar xf $tmpdir/untracked.tar
+cleanup