[med-svn] [python-cobra] 03/03: Drop obsolete patch
Afif Elghraoui
afif at moszumanska.debian.org
Wed Oct 18 02:37:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository python-cobra.
commit 9ae42477a86421f1ddc6a7c1842b1cbb3b640a57
Author: Afif Elghraoui <afif at debian.org>
Date: Tue Oct 17 22:36:05 2017 -0400
Drop obsolete patch
---
debian/patches/exclude-pytest-benchmark.patch | 258 --------------------------
debian/patches/series | 1 -
2 files changed, 259 deletions(-)
diff --git a/debian/patches/exclude-pytest-benchmark.patch b/debian/patches/exclude-pytest-benchmark.patch
deleted file mode 100644
index 49e748f..0000000
--- a/debian/patches/exclude-pytest-benchmark.patch
+++ /dev/null
@@ -1,258 +0,0 @@
-Description: Remove benchmark functions from test suite
- We would not have run the benchmarks during the build and CI.
- However, we would still need python-pytest-benchmark in order to specify
- skipping the benchmarks. Because of #846045, we can't do that successfully,
- so I resort to just removing the code that would be skipped.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
---- python-cobra.orig/cobra/test/test_model.py
-+++ python-cobra/cobra/test/test_model.py
-@@ -61,22 +61,6 @@
- fake_gene.name = "foo_gene"
- assert reaction.gene_name_reaction_rule == fake_gene.name
-
-- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_add_metabolite_benchmark(self, model, benchmark, solver):
-- reaction = model.reactions.get_by_id("PGI")
-- many_metabolites = dict((m, 1) for m in model.metabolites[0:50])
--
-- def add_remove_metabolite():
-- reaction.add_metabolites(many_metabolites)
-- if not getattr(model, 'solver', None):
-- solver_dict[solver].create_problem(model)
-- for m, c in many_metabolites.items():
-- try:
-- reaction.pop(m.id)
-- except KeyError:
-- pass
-- benchmark(add_remove_metabolite)
--
- def test_add_metabolite(self, model):
- reaction = model.reactions.get_by_id("PGI")
- reaction.add_metabolites({model.metabolites[0]: 1})
-@@ -103,10 +87,6 @@
- assert len(reaction._metabolites) == 1
-
- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_subtract_metabolite_benchmark(self, model, benchmark, solver):
-- benchmark(self.test_subtract_metabolite, model, solver)
--
-- @pytest.mark.parametrize("solver", list(solver_dict))
- def test_subtract_metabolite(self, model, solver):
- reaction = model.reactions.get_by_id("PGI")
- reaction.subtract_metabolites(reaction.metabolites)
-@@ -229,25 +209,6 @@
- class TestCobraModel:
- """test core cobra functions"""
-
-- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_add_remove_reaction_benchmark(self, model, benchmark, solver):
-- metabolite_foo = Metabolite("test_foo")
-- metabolite_bar = Metabolite("test_bar")
-- metabolite_baz = Metabolite("test_baz")
-- actual_metabolite = model.metabolites[0]
-- dummy_reaction = Reaction("test_foo_reaction")
-- dummy_reaction.add_metabolites({metabolite_foo: -1,
-- metabolite_bar: 1,
-- metabolite_baz: -2,
-- actual_metabolite: 1})
--
-- def benchmark_add_reaction():
-- model.add_reaction(dummy_reaction)
-- if not getattr(model, 'solver', None):
-- solver_dict[solver].create_problem(model)
-- model.remove_reactions([dummy_reaction], delete=False)
-- benchmark(benchmark_add_reaction)
--
- def test_add_reaction(self, model):
- old_reaction_count = len(model.reactions)
- old_metabolite_count = len(model.metabolites)
-@@ -397,22 +358,6 @@
- for reaction in gene_reactions:
- assert target_gene not in reaction.genes
-
-- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_copy_benchmark(self, model, solver, benchmark):
-- def _():
-- model.copy()
-- if not getattr(model, 'solver', None):
-- solver_dict[solver].create_problem(model)
-- benchmark(_)
--
-- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_copy_benchmark_large_model(self, large_model, solver, benchmark):
-- def _():
-- large_model.copy()
-- if not getattr(large_model, 'solver', None):
-- solver_dict[solver].create_problem(large_model)
-- benchmark(_)
--
- def test_copy(self, model):
- """modifying copy should not modify the original"""
- # test that deleting reactions in the copy does not change the
-@@ -427,9 +372,6 @@
- assert old_reaction_count == len(model.reactions)
- assert len(model.reactions) != len(model_copy.reactions)
-
-- def test_deepcopy_benchmark(self, model, benchmark):
-- benchmark(deepcopy, model)
--
- def test_deepcopy(self, model):
- """Reference structures are maintained when deepcopying"""
- model_copy = deepcopy(model)
-@@ -465,16 +407,6 @@
- # 'check not dangling metabolites when running Model.add_reactions
- assert len(orphan_metabolites) == 0
-
-- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_change_objective_benchmark(self, model, benchmark, solver):
-- atpm = model.reactions.get_by_id("ATPM")
--
-- def benchmark_change_objective():
-- model.objective = atpm.id
-- if not getattr(model, 'solver', None):
-- solver_dict[solver].create_problem(model)
-- benchmark(benchmark_change_objective)
--
- def test_change_objective(self, model):
- biomass = model.reactions.get_by_id("Biomass_Ecoli_core")
- atpm = model.reactions.get_by_id("ATPM")
---- python-cobra.orig/cobra/test/test_flux_analysis.py
-+++ python-cobra/cobra/test/test_flux_analysis.py
-@@ -44,10 +44,6 @@
- """Test the simulation functions in cobra.flux_analysis"""
-
- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_pfba_benchmark(self, large_model, benchmark, solver):
-- benchmark(optimize_minimal_flux, large_model, solver=solver)
--
-- @pytest.mark.parametrize("solver", list(solver_dict))
- def test_pfba(self, model, solver):
- optimize_minimal_flux(model, solver=solver)
- abs_x = [abs(i) for i in model.solution.x]
-@@ -96,13 +92,6 @@
- optimize_minimal_flux(model, solver=solver)
- model.reactions.ATPM.lower_bound = atpm
-
-- def test_single_gene_deletion_fba_benchmark(self, large_model, benchmark):
-- genes = ['b0511', 'b2521', 'b0651', 'b2502', 'b3132', 'b1486', 'b3384',
-- 'b4321', 'b3428', 'b2789', 'b0052', 'b0115',
-- 'b2167', 'b0759', 'b3389', 'b4031', 'b3916', 'b2374', 'b0677',
-- 'b2202']
-- benchmark(single_gene_deletion, large_model, gene_list=genes)
--
- def test_single_gene_deletion_fba(self, model):
- # expected knockouts for textbook model
- growth_dict = {"b0008": 0.87, "b0114": 0.80, "b0116": 0.78,
-@@ -114,15 +103,6 @@
- assert statuses[gene] == 'optimal'
- assert abs(rates[gene] - expected_value) < 0.01
-
-- def test_single_gene_deletion_moma_benchmark(self, large_model, benchmark):
-- try:
-- get_solver_name(qp=True)
-- except SolverNotFound:
-- pytest.skip("no qp support")
-- genes = ['b1764', 'b0463', 'b1779', 'b0417']
-- benchmark(single_gene_deletion, large_model, gene_list=genes,
-- method="moma")
--
- def test_single_gene_deletion_moma(self, model):
- try:
- get_solver_name(qp=True)
-@@ -140,11 +120,6 @@
- assert statuses[gene] == 'optimal'
- assert abs(rates[gene] - expected_value) < 0.01
-
-- def test_single_gene_deletion_benchmark(self, large_model, benchmark):
-- reactions = ['CDPMEK', 'PRATPP', 'HISTD', 'PPCDC']
-- benchmark(single_reaction_deletion, large_model,
-- reaction_list=reactions)
--
- def test_single_reaction_deletion(self, model):
- expected_results = {'FBA': 0.70404, 'FBP': 0.87392, 'CS': 0,
- 'FUM': 0.81430, 'GAPD': 0, 'GLUDy': 0.85139}
-@@ -169,12 +144,6 @@
- assert abs(matrix1[i][j] - matrix2[i][j]) < 10 ** -places
-
- @pytest.mark.skipif(numpy is None, reason="double deletions require numpy")
-- def test_double_gene_deletion_benchmark(self, large_model, benchmark):
-- genes = ["b0726", "b4025", "b0724", "b0720", "b2935", "b2935", "b1276",
-- "b1241"]
-- benchmark(double_gene_deletion, large_model, gene_list1=genes)
--
-- @pytest.mark.skipif(numpy is None, reason="double deletions require numpy")
- def test_double_gene_deletion(self, model):
- genes = ["b0726", "b4025", "b0724", "b0720", "b2935", "b2935", "b1276",
- "b1241"]
-@@ -216,11 +185,6 @@
- self.compare_matrices(growth_list, solution["data"])
-
- @pytest.mark.parametrize("solver", list(solver_dict))
-- def test_flux_variability_benchmark(self, large_model, benchmark, solver):
-- benchmark(flux_variability_analysis, large_model, solver=solver,
-- reaction_list=large_model.reactions[1::3])
--
-- @pytest.mark.parametrize("solver", list(solver_dict))
- def test_flux_variability(self, model, fva_results, solver):
- if solver == "esolver":
- pytest.skip("esolver too slow...")
-@@ -271,10 +235,6 @@
- test_model.add_reactions([EX_A, DM_C, v1, v2, v3])
- return test_model
-
-- def test_loopless_benchmark(self, benchmark):
-- test_model = self.construct_ll_test_model()
-- benchmark(lambda: construct_loopless_model(test_model).optimize())
--
- def test_loopless(self):
- try:
- get_solver_name(mip=True)
-@@ -330,12 +290,6 @@
- assert {i[0].id for i in result} == {"SMILEY_EX_b", "SMILEY_EX_c"}
-
- @pytest.mark.skipif(numpy is None, reason="phase plane require numpy")
-- def test_phenotype_phase_plane_benchmark(self, model, benchmark):
-- benchmark(calculate_phenotype_phase_plane,
-- model, "EX_glc__D_e", "EX_o2_e",
-- reaction1_npoints=20, reaction2_npoints=20)
--
-- @pytest.mark.skipif(numpy is None, reason="phase plane require numpy")
- def test_phenotype_phase_plane(self, model):
- data = calculate_phenotype_phase_plane(
- model, "EX_glc__D_e", "EX_o2_e",
---- python-cobra.orig/cobra/test/test_io.py
-+++ python-cobra/cobra/test/test_io.py
-@@ -188,14 +188,6 @@
- self.extra_comparisons(name, test_model, reread_model)
-
-
--def test_benchmark_read(data_directory, benchmark):
-- benchmark(io.sbml3.read_sbml_model, join(data_directory, 'mini_fbc2.xml'))
--
--
--def test_benchmark_write(model, benchmark):
-- benchmark(io.sbml3.write_sbml_model, model, join(gettempdir(), "-bench"))
--
--
- @pytest.mark.parametrize("trial", trials)
- def test_validate(trial, data_directory):
- if trial.validation_function is None:
---- python-cobra.orig/cobra/test/__init__.py
-+++ python-cobra/cobra/test/__init__.py
-@@ -2,7 +2,6 @@
- from cobra.io import read_sbml_model
- try:
- import pytest
-- import pytest_benchmark
- except ImportError:
- pytest = None
- try:
-@@ -44,6 +43,6 @@
- """
- if pytest:
- return pytest.main(
-- ['--pyargs', 'cobra', '--benchmark-skip', '-v', '-rs']) == 0
-+ ['--pyargs', 'cobra', '-v', '-rs']) == 0
- else:
- raise ImportError('missing package pytest required for testing')
diff --git a/debian/patches/series b/debian/patches/series
index 0987c97..d86c913 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
mathjax.patch
-exclude-pytest-benchmark.patch
--
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