New recipes

.gitignore

@@ -1 +1,2 @@
 opt
+recipes/50_chemreac/chemreac/chemreac-0.6.0.git/

README.rst

@@ -30,8 +30,14 @@ now when I try to build e.g. sundials
 
 it will use the conda package built in the previous step.
 
-And that is it. Built packages are then found under ``./opt/miniconda/conda-bld/linux-64`` which may then be
-uploaded manually to anaconda.org using the anaconda tool.
-
+And that is it. Built packages are then found under ``./opt/miniconda/conda-bld/linux-64``.
 Note that the ``./opt`` dir may grow quite large over time, and you will need to remove it if there has
 been a new docker image published by ContinuumIO in between your builds.
+
+
+The built packages are then uploaded manually to anaconda.org using the ``anaconda`` tool.
+To test the anaconda.org/chemreac repo another script is provided:
+
+::
+
+   $ ./test_anaconda_chemreac.sh

build_all.sh → _build_all.sh

@@ -22,11 +22,11 @@ for PKG in $PKGS; do
         conda build ./$PKG
     elif [[ $PKG == recipes/30_* ]] || [[ $PKG == recipes/50_* ]]; then
         for PY in 2.7 3.4 3.5; do
-            for NPY in 1.10; do
+            for NPY in 1.11; do
                 conda build --python $PY --numpy $NPY ./$PKG
             done
         done
-    elif [[ $PKG == recipes/40_* ]]; then
+    elif [[ $PKG == recipes/4?_* ]]; then
         NPY=1.10
         for PY in 2.7 3.4 3.5; do
             conda build --python $PY ./$PKG

_entrypoint.sh

@@ -0,0 +1,5 @@
+#!/bin/bash -x
+echo "show_channel_urls: true" >>~/.condarc
+cd $(dirname $0)
+./_build_all.sh $@
+

_run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+conda install -c chemreac chemreac pytest
+py.test --pyargs chemreac

orchestrate_all.sh

@@ -10,4 +10,4 @@ cp -r /opt/* /new_opt/
 EOF
 fi
 
-start_cpp98.sh --rm -v /home/bjorn/vc/chemreac_anaconda:/home/dev/chemreac_anaconda -v $BASE_PATH/opt:/opt ./chemreac_anaconda/entrypoint.sh $@
+start_cpp98.sh --rm -v /home/bjorn/vc/chemreac_anaconda:/home/dev/chemreac_anaconda -v $BASE_PATH/opt:/opt ./chemreac_anaconda/_entrypoint.sh $@

recipes/10_non-python/10_lapack/build.sh

@@ -1,8 +1,11 @@
 mkdir build
 cd build
 
+# CMAKE_INSTALL_LIBDIR="lib" suppresses CentOS default of lib64 (conda expects lib)
+
 cmake \
   -DCMAKE_INSTALL_PREFIX=$PREFIX \
+  -DCMAKE_INSTALL_LIBDIR="lib" \
   -DBUILD_TESTING=OFF \
   -DBUILD_SHARED_LIBS=ON \
   -DLAPACKE=ON \

recipes/10_non-python/10_lapack/meta.yaml

@@ -8,15 +8,15 @@ source:
   sha1: 7e993de16d80d52b22b6093465eeb90c93c7a2e7
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:
     - cmake
     # - gcc
 
-  # run:
-  #   - libgcc
+  run:
+    - libgcc
 
 about:
   home: http://www.netlib.org/lapack

recipes/10_non-python/20_gsl/meta.yaml

@@ -16,7 +16,7 @@ requirements:
     - lapack
 
   run:
-    # - libgcc
+    - libgcc
     - lapack
 
 about:

recipes/10_non-python/30_sundials/meta.yaml

@@ -18,7 +18,7 @@ requirements:
     - lapack
 
   run:
-    # - libgcc
+    - libgcc
     - lapack
 
 test:

recipes/30_python-numpy/block_diag_ilu/meta.yaml

@@ -1,24 +1,22 @@
 package:
-    name: block_diag_ilu
-    version: 0.2.1
+  name: block_diag_ilu
+  version: 0.2.2
 
 source:
-    fn: block_diag_ilu-0.2.1.tar.gz
-    url: https://pypi.python.org/packages/source/b/block_diag_ilu/block_diag_ilu-0.2.1.tar.gz#md5=c8ab75427ced5499be251cda0a701f89
-    md5: c8ab75427ced5499be251cda0a701f89
+  fn: block_diag_ilu-0.2.2.tar.gz
+  url: https://pypi.python.org/packages/source/b/block_diag_ilu/block_diag_ilu-0.2.2.tar.gz#md5=e3cafd56eacc7a2a924abd417362a024
+  md5: e3cafd56eacc7a2a924abd417362a024
 
 build:
-  number: 1
+  number: 2
 
 requirements:
   build:
-    # - gcc
     - python
     - numpy
     - cython
     - lapack
   run:
-    # - libgcc
     - python
     - numpy
     - lapack

recipes/30_python-numpy/block_diag_ilu/run_test.py

@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import io
 import os
 from block_diag_ilu import get_include
 assert os.listdir(get_include())[0] == 'block_diag_ilu.hpp'
 path = os.path.join(get_include(), 'block_diag_ilu.hpp')
-assert open(path, 'rt').readline().startswith('#pragma once')
+assert io.open(path, 'rt', encoding='utf-8').readline().startswith('#pragma once')

recipes/30_python-numpy/pycvodes/meta.yaml

@@ -1,33 +1,28 @@
 package:
   name: pycvodes
-  version: 0.4.1
+  version: 0.4.2
 
 source:
-  fn: pycvodes-0.4.1.tar.gz
-  url: https://pypi.python.org/packages/source/p/pycvodes/pycvodes-0.4.1.tar.gz#md5=17edc03854ecdfd092972b32787d4897
-  md5: 17edc03854ecdfd092972b32787d4897
+  fn: pycvodes-0.4.2.tar.gz
+  url: https://pypi.python.org/packages/source/p/pycvodes/pycvodes-0.4.2.tar.gz#md5=925f3fd6e9ab65ea258ff0277b8df1ca
+  md5: 925f3fd6e9ab65ea258ff0277b8df1ca
 
 build:
-  number: 1
+  number: 0
 
 requirements:
   build:
-    # - gcc
-    - python
-    - numpy
-    - sundials
+   - python
+   - numpy
+   - sundials
   run:
-    - python
-    - numpy
-    - sundials
-    # - libgcc
+   - python
+   - numpy
+   - sundials
+
 test:
   imports:
     - pycvodes
-    # requires:
-    #     - pytest
-    # commands:
-    #     - py.test --pyargs pycvodes  # https://github.com/conda/conda/issues/2075, https://github.com/pytest-dev/pytest/issues/1445
 
 about:
   home: https://github.com/bjodah/pycvodes

recipes/30_python-numpy/pygslodeiv2/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+CPLUS_INCLUDE_PATH=${PREFIX}/include ${PYTHON} setup.py build
+${PYTHON} setup.py install

recipes/30_python-numpy/pygslodeiv2/meta.yaml

@@ -0,0 +1,31 @@
+package:
+  name: pygslodeiv2
+  version: 0.5.2
+
+source:
+  fn: pygslodeiv2-0.5.2.tar.gz
+  url: https://pypi.python.org/packages/source/p/pygslodeiv2/pygslodeiv2-0.5.2.tar.gz#md5=6a141b1993396372063c54262c5a3a73
+  md5: 6a141b1993396372063c54262c5a3a73
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - python
+    - numpy
+    - gsl
+  run:
+    - numpy
+    - python
+    - gsl
+
+test:
+  imports:
+    - pygslodeiv2
+  requires:
+    - pytest
+
+about:
+  home: https://github.com/bjodah/pygslodeiv2
+  license: GNU GPL v3

recipes/30_python-numpy/pygslodeiv2/run_test.py

@@ -0,0 +1,2 @@
+import pytest
+pytest.main(['--pyargs', 'pygslodeiv2'])

recipes/30_python-numpy/pyodeint/build.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+export CPLUS_INCLUDE_PATH=$PREFIX/include:$CPLUS_INCLUDE_PATH
+
+${PYTHON} setup.py build
+${PYTHON} setup.py install

recipes/30_python-numpy/pyodeint/meta.yaml

@@ -0,0 +1,32 @@
+package:
+  name: pyodeint
+  version: 0.6.1
+
+source:
+  fn: pyodeint-0.6.1.tar.gz
+  url: https://pypi.python.org/packages/source/p/pyodeint/pyodeint-0.6.1.tar.gz#md5=0e6f000ea7b434de01f8bf502bb8f684
+  md5: 0e6f000ea7b434de01f8bf502bb8f684
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - python
+    - numpy
+    - boost ==1.57.0
+  run:
+    - numpy
+    - python
+
+test:
+  imports:
+    - pyodeint
+  requires:
+    - pytest
+  commands:
+    - python -m pytest --pyargs pyodeint
+
+about:
+  home: https://github.com/bjodah/pyodeint
+  license: Simplified BSD license

recipes/30_python-numpy/pyodeint/run_test.py

@@ -0,0 +1,2 @@
+import pytest
+pytest.main(['--pyargs', 'pyodeint'])

recipes/40_python/pycompilation/bld.bat

@@ -0,0 +1,9 @@
+xcopy /e "%RECIPE_DIR%\.." "%SRC_DIR%"
+"%PYTHON%" setup.py install
+if errorlevel 1 exit 1
+
+:: Add more build steps here, if they are necessary.
+
+:: See
+:: http://docs.continuum.io/conda/build.html
+:: for a list of environment variables that are set during the build process.

recipes/40_python/pycompilation/build.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+cp -r $RECIPE_DIR/.. $SRC_DIR
+$PYTHON setup.py install
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.

recipes/40_python/pycompilation/meta.yaml

@@ -0,0 +1,39 @@
+package:
+  name: pycompilation
+  version: "0.4.2"
+
+source:
+  fn: pycompilation-0.4.2.tar.gz
+  url: https://pypi.python.org/packages/source/p/pycompilation/pycompilation-0.4.2.tar.gz#md5=aa3a6466687111302ec415de815e2c44
+  md5: aa3a6466687111302ec415de815e2c44
+
+# build:
+  #preserve_egg_dir: True
+  #entry_points:
+    # Put any entry points (scripts to be generated automatically) here. The
+    # syntax is module:function.  For example
+    #
+    # - pycompilation = pycompilation:main
+    #
+    # Would create an entry point called pycompilation that calls pycompilation.main()
+
+
+  # If this is a new build for the same version, increment the build
+  # number. If you do not include this key, it defaults to 0.
+  # number: 1
+
+requirements:
+  build:
+    - python
+
+  run:
+    - python
+
+about:
+  home: https://github.com/bjodah/pycompilation
+  license:  BSD License
+  summary: 'Package for compilation (meta programming).'
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml

recipes/40_python/pyodesys/build.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+${PYTHON} setup.py build
+${PYTHON} setup.py install

recipes/40_python/pyodesys/meta.yaml

@@ -0,0 +1,34 @@
+package:
+  name: pyodesys
+  version: 0.5.1
+
+source:
+  fn: pyodesys-0.5.1.tar.gz
+  url: https://pypi.python.org/packages/source/p/pyodesys/pyodesys-0.5.1.tar.gz#md5=00c30f5e507c3b514055ee86087152dc
+  md5: 00c30f5e507c3b514055ee86087152dc
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - python
+  run:
+    - python
+    - numpy
+    - sympy
+    - scipy
+
+test:
+  imports:
+    - pyodesys
+  requires:
+    - pytest
+    - scipy
+    - pyodeint
+    - pygslodeiv2
+    - pycvodes
+
+about:
+  home: https://github.com/bjodah/pyodesys
+  license: BSD

recipes/40_python/pyodesys/run_test.py

@@ -0,0 +1,2 @@
+import pytest
+pytest.main(['--pyargs', 'pyodesys'])

recipes/42_python/pycodeexport/bld.bat

@@ -0,0 +1,8 @@
+"%PYTHON%" setup.py install
+if errorlevel 1 exit 1
+
+:: Add more build steps here, if they are necessary.
+
+:: See
+:: http://docs.continuum.io/conda/build.html
+:: for a list of environment variables that are set during the build process.

recipes/42_python/pycodeexport/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+export LIBRARY_PATH="$PREFIX/lib"
+export INCLUDE_PATH="$PREFIX/include"
+$PYTHON setup.py install
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.