Test against latest upstream versions (#168)

* Test against latest upstream versions * set CC & CXX env vars * Add suitesparse to CPATH * forgot CPATH * another PulpSolverError * PulpSolverError from pulp * python -> python3
bjodah · May 29, 2020 · 379e140 · 379e140
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commit 379e140
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Showing 5 changed files with 38 additions and 30 deletions.
diff --git a/.drone.yml b/.drone.yml
@@ -3,7 +3,6 @@ pipeline:
     image: drillster/drone-volume-cache
     restore: true
     mount:
-#      - ./ci-cache/sund-3.2.1
       - ./ci-cache/pyusrb
       - ./ci-cache/conda_packages
       - ./ci-cache/pip_cache
@@ -12,16 +11,17 @@ pipeline:
     ttl: 90  # liftetime in days
 
   install:
-    image: bjodah/bjodahimg18dev:v4.0.1
+    image: bjodah/bjodahimg20dev:v1.2.0
     environment:
-      - CPLUS_INCLUDE_PATH=/opt/boost_1_72_p/include
-      - SUNDBASE=/opt/sundials-5.1.0-klu-lapack
+      - CC=gcc-10
+      - CXX=g++-10
+      - CPLUS_INCLUDE_PATH=/opt/boost_1_73_p/include
+      - SUNDBASE=/opt/sundials-5.3.0-klu-lapack
+      - CPATH=/usr/include/suitesparse  # sunlinsol_klu.h includes "klu.h"
     commands:
-#      - export SUNDBASE=$(pwd)/ci-cache/sund-3.2.1
       - export PYTHONUSERBASE=$(pwd)/ci-cache/pyusrb
-#      - if [ ! -d $SUNDBASE ]; then .ci/get_sundials.sh 3.2.1 $SUNDBASE -DLAPACK_ENABLE:BOOL=ON -DSUNDIALS_INDEX_SIZE=32 $SUNDBASE; fi
       - if [ ! -d $PYTHONUSERBASE ]; then mkdir -p $PYTHONUSERBASE; fi
-      - export CPATH=$SUNDBASE/include
+      - export CPATH=$SUNDBASE/include:$CPATH
       - export LIBRARY_PATH=$SUNDBASE/lib
       - export LD_LIBRARY_PATH=$SUNDBASE/lib
       - python3 -m pip install --cache-dir ./ci-cache/pip_cache --user -e .[all]
@@ -33,14 +33,17 @@ pipeline:
       - cp dist/chempy-* deploy/public_html/branches/${DRONE_BRANCH}/
 
   test-suite:
-    image: bjodah/bjodahimg18dev:v4.0.1
+    image: bjodah/bjodahimg20dev:v1.2.0
     group: testing
     environment:
-      - CPLUS_INCLUDE_PATH=/opt/boost_1_72_p/include
-      - SUNDBASE=/opt/sundials-5.1.0-klu-lapack
+      - CC=gcc-10
+      - CXX=g++-10
+      - CPLUS_INCLUDE_PATH=/opt/boost_1_73_p/include
+      - SUNDBASE=/opt/sundials-5.3.0-klu-lapack
+      - CPATH=/usr/include/suitesparse  # sunlinsol_klu.h includes "klu.h"
     commands:
       - export PYTHONUSERBASE=$(pwd)/ci-cache/pyusrb
-      - export CPATH=$SUNDBASE/include
+      - export CPATH=$SUNDBASE/include:$CPATH
       - export LIBRARY_PATH=$SUNDBASE/lib
       - export LD_LIBRARY_PATH=$SUNDBASE/lib
       - bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
@@ -56,11 +59,11 @@ pipeline:
       - bash -c "source /tmp/test_git_archive/bin/activate; pip install --cache-dir ./ci-cache/pip_cache chempy-head.zip pytest; pytest --pyargs chempy"
 
   render-notebooks:
-    image: bjodah/bjodahimg18dev:v4.0.1
+    image: bjodah/bjodahimg20dev:v1.2.0
     group: testing
     environment:
       - CHEMPY_DEPRECATION_FILTER=ignore
-      - SUNDBASE=/opt/sundials-5.1.0-klu-lapack
+      - SUNDBASE=/opt/sundials-5.3.0-klu-lapack
     commands:
       - export PYTHONUSERBASE=$(pwd)/ci-cache/pyusrb
       - export CPATH=$SUNDBASE/include
@@ -73,7 +76,7 @@ pipeline:
       - cp -r index.* examples/ "deploy/public_html/branches/${DRONE_BRANCH}"
 
 #  conda-recipe:
-#    image: bjodah/bjodahimg18dev:v4.0.1
+#    image: bjodah/bjodahimg20dev:v1.2.0
 #    group: testing
 #    commands:
 #      - export CONDA_PKGS_DIRS=$(pwd)/ci-cache/conda_packages
@@ -83,10 +86,10 @@ pipeline:
 #      - (cd $CONDA_PKGS_DIRS; find . -maxdepth 1 -type d -not -path . -not -path .. | xargs rm -r)
 
   compile-documentation:
-    image: bjodah/bjodahimg18dev:v4.0.1
+    image: bjodah/bjodahimg20dev:v1.2.0
     environment:
       - CHEMPY_DEPRECATION_FILTER=ignore
-      - SUNDBASE=/opt/sundials-5.1.0-klu-lapack
+      - SUNDBASE=/opt/sundials-5.3.0-klu-lapack
     commands:
       - export PYTHONUSERBASE=$(pwd)/ci-cache/pyusrb
       - export CPATH=$SUNDBASE/include

diff --git a/README.rst b/README.rst
@@ -7,7 +7,7 @@ ChemPy
 .. image:: https://img.shields.io/pypi/v/chempy.svg
    :target: https://pypi.python.org/pypi/chempy
    :alt: PyPI version
-.. image:: https://img.shields.io/badge/python-3.6,3.7-blue.svg
+.. image:: https://img.shields.io/badge/python-3.7,3.8-blue.svg
    :target: https://www.python.org/
    :alt: Python version
 .. image:: https://img.shields.io/pypi/l/chempy.svg
@@ -102,8 +102,8 @@ Note that this option will install the following libraries
 
 - `pygslodeiv2 <https://github.com/bjodah/pygslodeiv2>`_: solving initial value problems, requires GSL_. (>=1.16).
 - `pyodeint <https://github.com/bjodah/pyodeint>`_: solving initial value problems, requires boost_ (>=1.65.0).
-- `pycvodes <https://github.com/bjodah/pycvodes>`_: solving initial value problems, requires SUNDIALS_ (>=2.7.0).
-- `pykinsol <https://github.com/bjodah/pykinsol>`_: solving non-linear root-finding, requires SUNDIALS_ (>=2.7.0).
+- `pycvodes <https://github.com/bjodah/pycvodes>`_: solving initial value problems, requires SUNDIALS_ (>=5.3.0).
+- `pykinsol <https://github.com/bjodah/pykinsol>`_: solving non-linear root-finding, requires SUNDIALS_ (>=5.3.0).
 - `pycompilation <https://github.com/bjodah/pycompilation>`_: python front-end for calling compilers, requires gcc/clang/icpc.
 - `pycodeexport <https://github.com/bjodah/pycodeexport>`_: package for code-generation, used when generating C++ code.
 

diff --git a/chempy/tests/test_chemistry.py b/chempy/tests/test_chemistry.py
@@ -340,17 +340,23 @@ def test_balance_stoichiometry__simple():
     assert p2 == {'Na2O': 1, 'CO2': 1}
 
 
-@requires('sympy')
+@requires('sympy', 'pulp')
 @pytest.mark.parametrize('underdet', [False, None, True])
 def test_balance_stoichiometry__impossible(underdet):
-    from pulp.solvers import PulpSolverError
+    try:
+        from pulp import PulpSolverError
+    except ModuleNotFoundError:
+        from pulp.solvers import PulpSolverError  # older version of PuLP
     with pytest.raises((ValueError, PulpSolverError)):
         r1, p1 = balance_stoichiometry({'CO'}, {'CO2'}, underdetermined=underdet)
 
 
 @requires('sympy', 'pulp')
 def test_balance_stoichiometry__underdetermined():
-    from pulp.solvers import PulpSolverError
+    try:
+        from pulp import PulpSolverError
+    except ModuleNotFoundError:
+        from pulp.solvers import PulpSolverError  # older version of PuLP
 
     with pytest.raises(ValueError):
         balance_stoichiometry({'C2H6', 'O2'}, {'H2O', 'CO2', 'CO'}, underdetermined=False)

diff --git a/scripts/coverage_badge.py b/scripts/coverage_badge.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 """

diff --git a/setup.py b/setup.py
@@ -73,9 +73,8 @@ def _path_under_setup(*args):
     'Topic :: Scientific/Engineering :: Chemistry',
     'Programming Language :: Python',
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.5',
-    'Programming Language :: Python :: 3.6',
     'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.8',
 ]
 
 with io.open(_path_under_setup(pkg_name, '__init__.py'), 'rt', encoding='utf-8') as f:
@@ -88,9 +87,9 @@ def _path_under_setup(*args):
 _author, _author_email = open(_path_under_setup('AUTHORS'), 'rt').readline().split('<')
 
 extras_req = {
-    'integrators': ['pyodeint>=0.10.1', 'pycvodes>=0.11.9', 'pygslodeiv2>=0.9.1'],
-    'solvers': ['pykinsol>=0.1.3'],
-    'native': ['pycompilation>=0.4.3', 'pycodeexport>=0.1.2', 'appdirs'],
+    'integrators': ['pyodeint>=0.10.4', 'pycvodes>=0.13.1', 'pygslodeiv2>=0.9.4'],
+    'solvers': ['pykinsol>=0.1.5'],
+    'native': ['pycompilation>=0.4.9', 'pycodeexport>=0.1.2', 'appdirs'],
     'docs': ['Sphinx', 'sphinx_rtd_theme', 'numpydoc'],
     'plotting': ['bokeh>=0.13.0', 'ipywidgets'],
     'testing': ['pytest>=3.9', 'pytest-cov', 'pytest-flakes', 'pytest-pep8', 'rstcheck']
@@ -112,12 +111,12 @@ def _path_under_setup(*args):
     install_requires=[
         'numpy>1.11.3', 'scipy>=1.0.1', 'matplotlib>=2.2.3',
         'sympy>=1.1.1,!=1.2', 'quantities>=0.12.1', 'pyneqsys>=0.5.5',
-        'pyodesys>=0.12.5' if sys.version_info[0] >= 3 else 'pyodesys<0.12',
+        'pyodesys>=0.13.1' if sys.version_info[0] >= 3 else 'pyodesys<0.12',
         'pyparsing>=2.0.3', 'sym>=0.3.4', 'jupyter', 'pulp>=1.6.8',
         'dot2tex>=2.11.3'
     ],
     extras_require=extras_req,
-    python_requires='>=3.6'
+    python_requires='>=3.7'
 )
 
 if __name__ == '__main__':