This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository python-cobra.
commit c887cfb3f41793d7a5a2f51c38c55af658eec4ab Author: Afif Elghraoui <[email protected]> Date: Tue Mar 8 19:30:02 2016 -0800 Imported Upstream version 0.4.0+0 --- appveyor.yml | 26 +++++++++++--------- appveyor/build_glpk.py | 59 +++++++++++++++++++++++++++++++++++++++++++++ cobra/VERSION | 2 +- cobra/core/Reaction.py | 9 +++++++ cobra/test/flux_analysis.py | 6 ++--- cobra/test/unit_tests.py | 15 ++++++++++++ 6 files changed, 102 insertions(+), 15 deletions(-) diff --git a/appveyor.yml b/appveyor.yml index bbd790c..b2cfa53 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -5,41 +5,45 @@ environment: # /E:ON and /V:ON options are not enabled in the batch script intepreter # See: http://stackoverflow.com/a/13751649/163740 WITH_COMPILER: "cmd /E:ON /V:ON /C .\\appveyor\\run_with_env.cmd" - UCRT: " " matrix: - PYTHON: "C:\\Python27" - PYTHON_VERSION: "2.7.10" + PYTHON_VERSION: "2.7.11" PYTHON_ARCH: "32" - PYTHON: "C:\\Python34" - PYTHON_VERSION: "3.4.3" + PYTHON_VERSION: "3.4.4" + PYTHON_ARCH: "32" + + - PYTHON: "C:\\Python35" + PYTHON_VERSION: "3.5.1" PYTHON_ARCH: "32" - PYTHON: "C:\\Python27-x64" - PYTHON_VERSION: "2.7.10" + PYTHON_VERSION: "2.7.11" PYTHON_ARCH: "64" - PYTHON: "C:\\Python34-x64" - PYTHON_VERSION: "3.4.3" + PYTHON_VERSION: "3.4.4" PYTHON_ARCH: "64" - PYTHON: "C:\\Python35-x64" - PYTHON_VERSION: "3.5.0" + PYTHON_VERSION: "3.5.1" PYTHON_ARCH: "64" - UCRT: "UCRT" clone_depth: 25 init: - - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH% %UCRT%" + - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%bit" + +cache: + - glpk_build -> appveyor/build_glpk.py + install: - "powershell appveyor\\install.ps1" - ps: Start-FileDownload 'https://bitbucket.org/gutworth/six/raw/default/six.py' - # Download glpk.h and glpk.lib (separate files for 32/64 bit) - - ps: Start-FileDownload 'https://opencobra.github.io/pypi_cobrapy_travis/glpk.h' - - "appveyor DownloadFile https://opencobra.github.io/pypi_cobrapy_travis/glpk.lib%PYTHON_ARCH%%UCRT% -FileName glpk.lib" + - "%WITH_COMPILER% %PYTHON%/python appveyor/build_glpk.py" - "%PYTHON%/python -m pip install Cython" build: off diff --git a/appveyor/build_glpk.py b/appveyor/build_glpk.py new file mode 100644 index 0000000..38216ba --- /dev/null +++ b/appveyor/build_glpk.py @@ -0,0 +1,59 @@ +import os +import sys +import hashlib +import tarfile +import struct +import shutil +import setuptools.msvc9_support +try: + import urllib2 +except ImportError: # python 3 + import urllib.request as urllib2 + +# these need to be set to the latest glpk version +glpk_version = "4.57" +glpk_md5 = "237531a54f73155842f8defe51aedb0f" + +glpk_build_dir = "glpk_build/glpk-%s" % glpk_version +url = "http://ftp.gnu.org/gnu/glpk/glpk-%s.tar.gz"; % glpk_version +bitness = struct.calcsize("P") * 8 + + +def md5(fname): + hash = hashlib.md5() + with open(fname, "rb") as f: + for chunk in iter(lambda: f.read(4096), b""): + hash.update(chunk) + return hash.hexdigest() + + +def get_vcvarsall_cmd(): + py_ver = sys.version_info + if py_ver.major == 3 and py_ver.minor >= 5: + vc_ver = 14 + elif py_ver.major == 3 and py_ver.minor >= 3: + vc_ver = 10 + else: + vc_ver = 9 + vc_path = setuptools.msvc9_support.find_vcvarsall(vc_ver) + assert vc_path is not None + return '"%s" %s' % (vc_path, " amd64" if bitness == 64 else "") + + +if not os.path.isdir("glpk_build/"): + os.mkdir("glpk_build") +if not os.path.isdir(glpk_build_dir): + response = urllib2.urlopen(url) + with open("glpk-download.tar.gz", "wb") as outfile: + outfile.write(response.read()) + assert md5("glpk-download.tar.gz") == glpk_md5 + with tarfile.open("glpk-download.tar.gz") as infile: + infile.extractall("glpk_build") + +os.chdir("%s/w%d" % (glpk_build_dir, bitness)) +if not os.path.isfile("glpk.lib"): + shutil.copy2("config_VC", "config.h") + os.system(get_vcvarsall_cmd() + "& nmake /f Makefile_VC") +shutil.copy2("glpk.lib", "../../..") +os.chdir("../../..") +shutil.copy2(glpk_build_dir + "/src/glpk.h", ".") diff --git a/cobra/VERSION b/cobra/VERSION index a9e3532..1d0ba9e 100644 --- a/cobra/VERSION +++ b/cobra/VERSION @@ -1 +1 @@ -0.4.0b7 +0.4.0 diff --git a/cobra/core/Reaction.py b/cobra/core/Reaction.py index d8f80fc..1110599 100644 --- a/cobra/core/Reaction.py +++ b/cobra/core/Reaction.py @@ -40,6 +40,8 @@ def _is_positive(n): # precompiled regular expressions # Matches and/or in a gene reaction rule and_or_search = re.compile(r'\(| and| or|\+|\)', re.IGNORECASE) +uppercase_AND = re.compile(r'\bAND\b') +uppercase_OR = re.compile(r'\bOR\b') gpr_clean = re.compile(' {2,}') # This regular expression finds any single letter compartment enclosed in # square brackets at the beginning of the string. For example [c] : foo --> bar @@ -101,6 +103,13 @@ class Reaction(Object): try: _, gene_names = parse_gpr(self._gene_reaction_rule) except (SyntaxError, TypeError) as e: + if "AND" in new_rule or "OR" in new_rule: + warn("uppercase AND/OR found in rule '%s' for '%s'" % + (new_rule, repr(self))) + new_rule = uppercase_AND.sub("and", new_rule) + new_rule = uppercase_OR.sub("or", new_rule) + self.gene_reaction_rule = new_rule + return warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self))) tmp_str = and_or_search.sub('', self._gene_reaction_rule) diff --git a/cobra/test/flux_analysis.py b/cobra/test/flux_analysis.py index 4103cf0..0ba8cf1 100644 --- a/cobra/test/flux_analysis.py +++ b/cobra/test/flux_analysis.py @@ -173,7 +173,7 @@ class TestCobraFluxAnalysis(TestCase): try: solver = get_solver_name(mip=True) except: - self.skip("no MILP solver found") + self.skipTest("no MILP solver found") test_model = Model() test_model.add_metabolites(Metabolite("A")) test_model.add_metabolites(Metabolite("B")) @@ -203,7 +203,7 @@ class TestCobraFluxAnalysis(TestCase): try: solver = get_solver_name(mip=True) except: - self.skip("no MILP solver found") + self.skipTest("no MILP solver found") m = Model() m.add_metabolites(map(Metabolite, ["a", "b", "c"])) r = Reaction("EX_A") @@ -247,7 +247,7 @@ class TestCobraFluxAnalysis(TestCase): self.assertAlmostEqual(data.growth_rates.max(), 1.20898, places=4) self.assertAlmostEqual(abs(data.growth_rates[0, :]).max(), 0, places=4) if matplotlib is None: - self.skip("can't test plots without matplotlib") + self.skipTest("can't test plots without matplotlib") data.plot() # make a test suite to run all of the tests diff --git a/cobra/test/unit_tests.py b/cobra/test/unit_tests.py index f673d50..eb984e0 100644 --- a/cobra/test/unit_tests.py +++ b/cobra/test/unit_tests.py @@ -269,6 +269,21 @@ class TestReactions(CobraTestCase): reaction_gene = list(reaction.genes)[0] model_gene = model.genes.get_by_id(reaction_gene.id) self.assertIs(reaction_gene, model_gene) + # test ability to handle uppercase AND/OR + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + reaction.gene_reaction_rule = "(b1 AND b2) OR (b3 and b4)" + self.assertEqual(reaction.gene_reaction_rule, + "(b1 and b2) or (b3 and b4)") + self.assertEqual(len(reaction.genes), 4) + # ensure regular expressions correctly extract genes from malformed + # GPR string + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + reaction.gene_reaction_rule = "(a1 or a2" + self.assertEqual(len(reaction.genes), 2) + reaction.gene_reaction_rule = "(forT or " + self.assertEqual(len(reaction.genes), 1) def testGPR_modification(self): model = self.model -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
