Slope

.gitmodules

@@ -1,3 +1,9 @@
 [submodule "travis-tools"]
 	path = travis-tools
 	url = https://github.com/matthew-brett/travis-tools.git
+[submodule "R-software"]
+	path = R-software
+	url = https://github.com/selective-inference/R-software
+[submodule "C-software"]
+	path = C-software
+	url = https://github.com/selective-inference/C-software

.travis.yml

@@ -1,7 +1,9 @@
 language: python
+dist: trusty
 python:
   - 2.7
-  - 3.3
+  - 3.4
+  - 3.5
 notifications:
   email: false
 addons:
@@ -13,29 +15,90 @@ env:
     global:
         # Maximal dependencies
         - DEPENDS="cython numpy scipy matplotlib"
+matrix:
+  include:
+    - python: 3.5
+      env:
+        - RUN_R_TESTS=1
+    - python: 2.7
+      env:
+        - RUN_R_TESTS=1
+    # Testing without matplotlib
+    - python: 2.7
+      env:
+        - DEPENDS="cython numpy scipy"
+    # Documentation doctests
+    - python: 2.7
+      env:
+        - DOC_DOC_TEST=1
+    # Setup.py install
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=setup
+    - python: 2.7
+      env:
+        # Sdist install should collect all dependencies
+        - INSTALL_TYPE=sdist
+        - DEPENDS="cython numpy scipy"
+    - python: 2.7
+      env:
+        # Wheel install should collect all dependencies
+        - INSTALL_TYPE=wheel
+        - DEPENDS="cython numpy scipy"
+    - python: 2.7
+      env:
+        - INSTALL_TYPE=requirements
+        - DEPENDS=
 before_install:
   - source travis-tools/utils.sh
   - travis_before_install
   # Install regreg 
-  - python -c "import numpy; print(numpy.version.version)"
   - git clone https://github.com/jonathan-taylor/regreg.git
   - cd regreg
   - pip install -r requirements.txt
   - pip install -e .
   - cd ..
+  - sudo apt-get install software-properties-common
+  - sudo add-apt-repository -y ppa:marutter/c2d4u
+  - sudo add-apt-repository -y ppa:marutter/rrutter
+  - sudo apt-get update
+  - sudo apt-get install -y r-base r-base-dev r-cran-devtools r-cran-rcpp
+
+
 install:
   # Install selection
-  - pip install -r requirements.txt
-  - pip install -e .
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then 
+      pip install  -r requirements.txt -c constraints.txt; 
+    else
+      pip install  -r requirements.txt; 
+    fi
+  - git submodule init
+  - git submodule update
+  - cd R-software
+  - git submodule init
+  - git submodule update
+  - Rscript -e "library(Rcpp); Rcpp::compileAttributes('selectiveInference')"
+  - sudo Rscript -e "install.packages(c('glmnet', 'intervals', 'adaptMCMC'), repos='http://cloud.r-project.org')"
+  - sudo R CMD INSTALL selectiveInference
+  - cd ..
+  - python -c "from statsmodels.api import PHReg"
   - travis_install $INSTALL_TYPE
+
 # command to run tests, e.g. python setup.py test
 script:
+
     - pip install nose
+    # No figure windows for mpl; quote to hide : from travis-ci yaml parsing
+    - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then 
+        pip install  -r doc-requirements.txt -c constraints.txt; 
+      else
+        pip install  -r doc-requirements.txt; 
+      fi
     # Change into an innocuous directory and find tests from installation
     - mkdir for_testing
     - cd for_testing
-    # No figure windows for mpl; quote to hide : from travis-ci yaml parsing
     - 'echo "backend : agg" > matplotlibrc'
+
     # Doctests only on platforms that have compatible fp output
     - if [ `uname` == "Darwin" ] ||
       [ "${TRAVIS_PYTHON_VERSION:0:1}" == "3" ]; then
@@ -45,6 +108,11 @@ script:
       cp ../.coveragerc .;
       COVER_ARGS="--with-coverage --cover-package selection";
       fi
-    - env USE_SMALL_SAMPLES=1 SET_SEED=1 nosetests $DOCTEST_ARGS --verbose $COVER_ARGS selection
+    - |
+      if [ "$RUN_R_TESTS" ]; then
+        nosetests -v ../selection/algorithms/tests/test_compareR.py
+      else 
+        env USE_SMALL_SAMPLES=1 USE_TEST_SEED=1 nosetests $DOCTEST_ARGS --verbose $COVER_ARGS selection
+      fi
 after_success:
     - if [ "${COVERAGE}" == "1" ]; then coveralls; fi

MANIFEST.in

@@ -0,0 +1,10 @@
+include AUTHOR LICENSE Makefile* MANIFEST.in setup* README.*
+include Changelog TODO
+recursive-include doc *
+recursive-include tools *
+# setup utilities
+include setup_helpers.py
+include cythexts.py
+recursive-include fake_pyrex *
+include versioneer.py
+include selection/_version.py

constraints.txt

@@ -0,0 +1 @@
+rpy2<2.9

cythexts.py

@@ -1,7 +1,6 @@
 import os
 from os.path import splitext, sep as filesep, join as pjoin, relpath
 from hashlib import sha1
-from subprocess import check_call
 
 from distutils.command.build_ext import build_ext
 from distutils.command.sdist import sdist
@@ -95,6 +94,8 @@ def cyproc_exts(exts, cython_min_version,
         Can be ``build_ext`` input (if we have good c files) or cython
         ``build_ext`` if we have a good cython, or a class raising an informative
         error on ``run()``
+    need_cython : bool
+        True if we need Cython to build extensions, False otherwise.
     """
     if stamped_pyx_ok(exts, hash_stamps_fname):
         # Replace pyx with c files, use standard builder
@@ -107,29 +108,33 @@ def cyproc_exts(exts, cython_min_version,
                 else:
                     sources.append(source)
             mod.sources = sources
-        return build_ext
+        return build_ext, False
     # We need cython
     try:
         from Cython.Compiler.Version import version as cyversion
     except ImportError:
-        cython_ok = False
-    else:
-        cython_ok = LooseVersion(cyversion) >= cython_min_version
-    if cython_ok:
+        return derror_maker(build_ext,
+                            'Need cython>={0} to build extensions '
+                            'but cannot import "Cython"'.format(
+                            cython_min_version)), True
+    if LooseVersion(cyversion) >= cython_min_version:
         from Cython.Distutils import build_ext as extbuilder
-        return extbuilder
+        return extbuilder, True
     return derror_maker(build_ext,
-                        'Need cython>=%s to build extensions'
-                        % cython_min_version)
+                        'Need cython>={0} to build extensions'
+                        'but found cython version {1}'.format(
+                        cython_min_version, cyversion)), True
 
 
-def build_stamp(pyxes):
+def build_stamp(pyxes, include_dirs=()):
     """ Cythonize files in `pyxes`, return pyx, C filenames, hashes
 
     Parameters
     ----------
     pyxes : sequence
         sequence of filenames of files on which to run Cython
+    include_dirs : sequence
+        Any extra include directories in which to find Cython files.
 
     Returns
     -------
@@ -139,11 +144,17 @@ def build_stamp(pyxes):
         hash>; "c_filename", <c filemane>; "c_hash", <c file SHA1 hash>.
     """
     pyx_defs = {}
+    from Cython.Compiler.Main import compile
+    from Cython.Compiler.CmdLine import parse_command_line
+    includes = sum([['--include-dir', d] for d in include_dirs], [])
     for source in pyxes:
         base, ext = splitext(source)
         pyx_hash = sha1(open(source, 'rt').read()).hexdigest()
         c_filename = base + '.c'
-        check_call('cython ' + source, shell=True)
+        options, sources = parse_command_line(includes + [source])
+        result = compile(sources, options)
+        if result.num_errors > 0:
+            raise RuntimeError('Cython failed to compile ' + source)
         c_hash = sha1(open(c_filename, 'rt').read()).hexdigest()
         pyx_defs[source] = dict(pyx_hash=pyx_hash,
                                 c_filename=c_filename,
@@ -173,22 +184,19 @@ def write_stamps(pyx_defs, stamp_fname='pyx-stamps'):
                                            pyx_info['c_hash']))
 
 
-def find_pyx(root_dir=None):
+def find_pyx(root_dir):
     """ Recursively find files with extension '.pyx' starting at `root_dir`
 
     Parameters
     ----------
-    root_dir : None or str, optional
-        Directory from which to search for pyx files.  If None, use current
-        working directory.
+    root_dir : str
+        Directory from which to search for pyx files.
 
     Returns
     -------
     pyxes : list
         list of filenames relative to `root_dir`
     """
-    if root_dir is None:
-        root_dir = os.getcwd()
     pyxes = []
     for dirpath, dirnames, filenames in os.walk(root_dir):
         for filename in filenames:
@@ -199,7 +207,8 @@ def find_pyx(root_dir=None):
     return pyxes
 
 
-def get_pyx_sdist(sdist_like=sdist, hash_stamps_fname='pyx-stamps'):
+def get_pyx_sdist(sdist_like=sdist, hash_stamps_fname='pyx-stamps',
+                  include_dirs=()):
     """ Add pyx->c conversion, hash recording to sdist command `sdist_like`
 
     Parameters
@@ -210,6 +219,8 @@ def get_pyx_sdist(sdist_like=sdist, hash_stamps_fname='pyx-stamps'):
     hash_stamps_fname : str, optional
         filename to which to write hashes of pyx / py and c files.  Default is
         ``pyx-stamps``
+    include_dirs : sequence
+        Any extra include directories in which to find Cython files.
 
     Returns
     -------
@@ -240,7 +251,7 @@ def make_distribution(self):
                     base, ext = splitext(source)
                     if ext in ('.pyx', '.py'):
                         pyxes.append(source)
-            self.pyx_defs = build_stamp(pyxes)
+            self.pyx_defs = build_stamp(pyxes, include_dirs)
             for pyx_fname, pyx_info in self.pyx_defs.items():
                 self.filelist.append(pyx_info['c_filename'])
             sdist_like.make_distribution(self)
@@ -254,7 +265,8 @@ def make_release_tree(self, base_dir, files):
     return PyxSDist
 
 
-def build_stamp_source(root_dir=None, stamp_fname='pyx-stamps'):
+def build_stamp_source(root_dir=None, stamp_fname='pyx-stamps',
+                       include_dirs=None):
     """ Build cython c files, make stamp file in source tree `root_dir`
 
     Parameters
@@ -264,7 +276,13 @@ def build_stamp_source(root_dir=None, stamp_fname='pyx-stamps'):
         working directory.
     stamp_fname : str, optional
         Filename for stamp file we will write
+    include_dirs : None or sequence
+        Any extra Cython include directories
     """
+    if root_dir is None:
+        root_dir = os.getcwd()
+    if include_dirs is None:
+        include_dirs = [pjoin(root_dir, 'src')]
     pyxes = find_pyx(root_dir)
-    pyx_defs = build_stamp(pyxes)
+    pyx_defs = build_stamp(pyxes, include_dirs=include_dirs)
     write_stamps(pyx_defs, stamp_fname)

dev-requirements.txt

@@ -0,0 +1,4 @@
+# Requirements for developing regreg
+# Check these dependencies against regreg/info.py
+-r requirements.txt
+nose

doc-requirements.txt

@@ -0,0 +1,9 @@
+# Requirements for building docs
+# Check these dependencies against doc/conf.py
+-r dev-requirements.txt
+sphinx>=1.4
+numpydoc
+matplotlib
+texext
+nb2plots
+rpy2