Fix #1076: suppress NumPy division warnings from analysis classes (#1079

) * Fix 1076 by suppressing 2 types of NumPy warnings in selected analysis classes. * Satisfy mypy re: KnowledgeBaseEcoli has no attribute "compartments". mypy can't track the reflection like `setattr(self, attr_name, rows)` used in `KnowledgeBaseEcoli`.
CovertLab · Jun 2, 2021 · aaf6646 · aaf6646
1 parent 8b3d11d
commit aaf6646
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Showing 28 changed files with 68 additions and 3 deletions.
diff --git a/models/ecoli/analysis/analysisPlot.py b/models/ecoli/analysis/analysisPlot.py
@@ -14,8 +14,9 @@
 import os
 
 import matplotlib as mp
-
 from matplotlib import pyplot as plt
+import numpy as np
+
 from wholecell.utils import memory_debug, parallelization
 from wholecell.utils import filepath as fp
 
@@ -33,6 +34,10 @@ class AnalysisPlot(metaclass=abc.ABCMeta):
 		cpus: allotted number of CPU cores; default (0) => all available cores
 	"""
 
+	#: Whether to suppress NumPy "divide" and "invalid" warnings like Theano
+	#: used to do. Override this in subclasses as needed.
+	_suppress_numpy_warnings = False
+
 	def __init__(self, cpus=0):
 		self.cpus = parallelization.cpus(cpus)
 		self._axeses = {}
@@ -98,14 +103,21 @@ def do_plot(self, inputDir, plotOutDir, plotOutFileName, simDataFile,
 	def plot(self, inputDir, plotOutDir, plotOutFileName, simDataFile,
 			validationDataFile, metadata):
 		"""Public method to set up, make a plot, and cleanup."""
+		def do_plot():
+			self.do_plot(inputDir, plotOutDir, plotOutFileName, simDataFile,
+						 validationDataFile, metadata)
+
 		if not os.path.isdir(inputDir):
 			raise RuntimeError('Input directory ({}) does not currently exist.'
 				.format(inputDir))
 		fp.makedirs(plotOutDir)
 
 		with memory_debug.detect_leaks(), mp.rc_context():
-			self.do_plot(inputDir, plotOutDir, plotOutFileName, simDataFile,
-				validationDataFile, metadata)
+			if self._suppress_numpy_warnings:
+				with np.errstate(divide='ignore'), np.errstate(invalid='ignore'):
+					do_plot()
+			else:
+				do_plot()
 
 		self._axeses = {}
 

diff --git a/models/ecoli/analysis/cohort/centralCarbonMetabolismCorrelationTimeCourse.py b/models/ecoli/analysis/cohort/centralCarbonMetabolismCorrelationTimeCourse.py
@@ -19,6 +19,8 @@
 
 
 class Plot(cohortAnalysisPlot.CohortAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, variantDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		plt.figure(figsize = (8.5, 11))
 

diff --git a/models/ecoli/analysis/cohort/kinetics_flux_comparison.py b/models/ecoli/analysis/cohort/kinetics_flux_comparison.py
@@ -28,6 +28,8 @@
 
 
 class Plot(cohortAnalysisPlot.CohortAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, variantDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		# Get all cells
 		ap = AnalysisPaths(variantDir, cohort_plot = True)

diff --git a/models/ecoli/analysis/cohort/promoter_probabilities.py b/models/ecoli/analysis/cohort/promoter_probabilities.py
@@ -17,6 +17,8 @@
 
 
 class Plot(cohortAnalysisPlot.CohortAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, variantDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:
 			sim_data = pickle.load(f)

diff --git a/models/ecoli/analysis/multigen/centralCarbonMetabolismCorrelationTimeCourse.py b/models/ecoli/analysis/multigen/centralCarbonMetabolismCorrelationTimeCourse.py
@@ -20,6 +20,8 @@
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		validation_data = cPickle.load(open(validationDataFile, "rb"))
 		sim_data = cPickle.load(open(simDataFile, "rb"))

diff --git a/models/ecoli/analysis/multigen/charging_molecules.py b/models/ecoli/analysis/multigen/charging_molecules.py
@@ -85,6 +85,8 @@ def post_plot_formatting(ax, division_times, y_label, draw_horizontal=None, y_li
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:
 			sim_data = cPickle.load(f)

diff --git a/models/ecoli/analysis/multigen/growthAffectingPolymerases.py b/models/ecoli/analysis/multigen/growthAffectingPolymerases.py
@@ -16,6 +16,8 @@
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		ap = AnalysisPaths(seedOutDir, multi_gen_plot = True)
 

diff --git a/models/ecoli/analysis/multigen/kineticsFluxComparison.py b/models/ecoli/analysis/multigen/kineticsFluxComparison.py
@@ -32,6 +32,8 @@
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		# Get all cells
 		ap = AnalysisPaths(seedOutDir, multi_gen_plot = True)

diff --git a/models/ecoli/analysis/multigen/replication.py b/models/ecoli/analysis/multigen/replication.py
@@ -15,6 +15,8 @@
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		sim_data = cPickle.load(open(simDataFile, "rb"))
 		genomeLength = len(sim_data.process.replication.genome_sequence)

diff --git a/models/ecoli/analysis/multigen/ribosomeProduction.py b/models/ecoli/analysis/multigen/ribosomeProduction.py
@@ -16,6 +16,8 @@
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		ap = AnalysisPaths(seedOutDir, multi_gen_plot = True)
 

diff --git a/models/ecoli/analysis/multigen/tf_binding.py b/models/ecoli/analysis/multigen/tf_binding.py
@@ -65,6 +65,8 @@ def subplot(gs, legend, title, tf_id, gene_id, t, active, bound, inactive, promo
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:
 			sim_data = pickle.load(f)

diff --git a/models/ecoli/analysis/multigen/transcriptionFrequency.py b/models/ecoli/analysis/multigen/transcriptionFrequency.py
@@ -22,6 +22,8 @@
 
 
 class Plot(multigenAnalysisPlot.MultigenAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		# Get all cells
 		ap = AnalysisPaths(seedOutDir, multi_gen_plot = True)

diff --git a/models/ecoli/analysis/single/allReactionFluxes.py b/models/ecoli/analysis/single/allReactionFluxes.py
@@ -25,6 +25,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time")
 		fbaResults = TableReader(os.path.join(simOutDir, "FBAResults"))

diff --git a/models/ecoli/analysis/single/cell_wall_expression.py b/models/ecoli/analysis/single/cell_wall_expression.py
@@ -52,6 +52,8 @@
 }
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName,
 				simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:

diff --git a/models/ecoli/analysis/single/centralCarbonMetabolismCorrelationTimeCourse.py b/models/ecoli/analysis/single/centralCarbonMetabolismCorrelationTimeCourse.py
@@ -19,6 +19,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		validation_data = cPickle.load(open(validationDataFile, "rb"))
 		sim_data = cPickle.load(open(simDataFile, "rb"))

diff --git a/models/ecoli/analysis/single/compartment_mass_fraction_summary.py b/models/ecoli/analysis/single/compartment_mass_fraction_summary.py
@@ -30,6 +30,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(
 			self, simOutDir, plotOutDir, plotOutFileName,
 			simDataFile, validationDataFile, metadata):

diff --git a/models/ecoli/analysis/single/cotranscriptional_translation.py b/models/ecoli/analysis/single/cotranscriptional_translation.py
@@ -23,6 +23,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:
 			sim_data = cPickle.load(f)

diff --git a/models/ecoli/analysis/single/equilibriumComparison.py b/models/ecoli/analysis/single/equilibriumComparison.py
@@ -19,6 +19,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		# Load data from KB
 		sim_data = cPickle.load(open(simDataFile, "rb"))

diff --git a/models/ecoli/analysis/single/flagella_expression.py b/models/ecoli/analysis/single/flagella_expression.py
@@ -56,6 +56,8 @@
 }
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:
 			sim_data = pickle.load(f)

diff --git a/models/ecoli/analysis/single/inter_rnap_distance.py b/models/ecoli/analysis/single/inter_rnap_distance.py
@@ -22,6 +22,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:
 			sim_data = cPickle.load(f)

diff --git a/models/ecoli/analysis/single/kineticsFluxComparison.py b/models/ecoli/analysis/single/kineticsFluxComparison.py
@@ -31,6 +31,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		sim_data = cPickle.load(open(simDataFile, 'rb'))
 

diff --git a/models/ecoli/analysis/single/kineticsFluxComparisonKcatOnly.py b/models/ecoli/analysis/single/kineticsFluxComparisonKcatOnly.py
@@ -18,6 +18,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		# read constraint data
 		enzymeKineticsReader = TableReader(os.path.join(simOutDir, "EnzymeKinetics"))

diff --git a/models/ecoli/analysis/single/outer_membrane_expression.py b/models/ecoli/analysis/single/outer_membrane_expression.py
@@ -81,6 +81,8 @@
 }
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName,
 				simDataFile, validationDataFile, metadata):
 		with open(simDataFile, 'rb') as f:

diff --git a/models/ecoli/analysis/single/transcriptional_attenuation.py b/models/ecoli/analysis/single/transcriptional_attenuation.py
@@ -23,6 +23,8 @@
 
 
 class Plot(singleAnalysisPlot.SingleAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		# Listeners used
 		transcription_reader = TableReader(os.path.join(simOutDir, 'TranscriptElongationListener'))

diff --git a/models/ecoli/analysis/variant/growthConditionComparison.py b/models/ecoli/analysis/variant/growthConditionComparison.py
@@ -22,6 +22,8 @@
 
 
 class Plot(variantAnalysisPlot.VariantAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, inputDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		ap = AnalysisPaths(inputDir, variant_plot = True)
 		all_cells = ap.get_cells()

diff --git a/models/ecoli/analysis/variant/metabolism_kinetic_objective_weight.py b/models/ecoli/analysis/variant/metabolism_kinetic_objective_weight.py
@@ -33,6 +33,7 @@
 	]  # type: Sequence
 
 
+@np.errstate(invalid='ignore')  # "invalid value encountered in true_divide" in its own process
 def analyze_variant(args):
 	# type: (Tuple[int, AnalysisPaths, List[str], np.ndarray, List[bool]]) -> tuple
 	'''

diff --git a/models/ecoli/analysis/variant/remove_aa_inhibition.py b/models/ecoli/analysis/variant/remove_aa_inhibition.py
@@ -99,6 +99,8 @@ def heatmap(gs, aa_idx, data, enzyme_order):
 
 
 class Plot(variantAnalysisPlot.VariantAnalysisPlot):
+	_suppress_numpy_warnings = True
+
 	def do_plot(self, inputDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
 		ap = AnalysisPaths(inputDir, variant_plot=True)
 		variants = ap.get_variants()

diff --git a/reconstruction/ecoli/knowledge_base_raw.py b/reconstruction/ecoli/knowledge_base_raw.py
@@ -118,6 +118,8 @@ class KnowledgeBaseEcoli(object):
 	""" KnowledgeBaseEcoli """
 
 	def __init__(self):
+		self.compartments = []  # mypy can't track setattr(self, attr_name, rows)
+
 		# Load raw data from TSV files
 		for filename in LIST_OF_DICT_FILENAMES:
 			self._load_tsv(FLAT_DIR, os.path.join(FLAT_DIR, filename))