Paul Eggert <eggert@HIDDEN>
to control <at> debbugs.gnu.org.
Full text available.Received: (at 42623) by debbugs.gnu.org; 30 Jul 2020 18:48:15 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Jul 30 14:48:15 2020 Received: from localhost ([127.0.0.1]:36719 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k1DbC-0006mH-VR for submit <at> debbugs.gnu.org; Thu, 30 Jul 2020 14:48:15 -0400 Received: from zimbra.cs.ucla.edu ([131.179.128.68]:42418) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <eggert@HIDDEN>) id 1k1DbB-0006m4-AV for 42623 <at> debbugs.gnu.org; Thu, 30 Jul 2020 14:48:14 -0400 Received: from localhost (localhost [127.0.0.1]) by zimbra.cs.ucla.edu (Postfix) with ESMTP id 0692B160065; Thu, 30 Jul 2020 11:48:07 -0700 (PDT) Received: from zimbra.cs.ucla.edu ([127.0.0.1]) by localhost (zimbra.cs.ucla.edu [127.0.0.1]) (amavisd-new, port 10032) with ESMTP id G9pnJNwESae6; Thu, 30 Jul 2020 11:48:06 -0700 (PDT) Received: from localhost (localhost [127.0.0.1]) by zimbra.cs.ucla.edu (Postfix) with ESMTP id 51080160084; Thu, 30 Jul 2020 11:48:06 -0700 (PDT) X-Virus-Scanned: amavisd-new at zimbra.cs.ucla.edu Received: from zimbra.cs.ucla.edu ([127.0.0.1]) by localhost (zimbra.cs.ucla.edu [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id 1bqJVawk8NwM; Thu, 30 Jul 2020 11:48:06 -0700 (PDT) Received: from [192.168.1.9] (cpe-75-82-69-226.socal.res.rr.com [75.82.69.226]) by zimbra.cs.ucla.edu (Postfix) with ESMTPSA id 2B592160065; Thu, 30 Jul 2020 11:48:06 -0700 (PDT) Subject: Re: bug#42623: fgrep -x -f problem To: Arthur Goldberg <artgoldberg@HIDDEN> References: <04c685c8-ddf7-52d3-5dcb-46ef67a1fa1a@HIDDEN> From: Paul Eggert <eggert@HIDDEN> Autocrypt: addr=eggert@HIDDEN; prefer-encrypt=mutual; keydata= LS0tLS1CRUdJTiBQR1AgUFVCTElDIEtFWSBCTE9DSy0tLS0tCgptUUlOQkV5QWNtUUJFQURB QXlIMnhvVHU3cHBHNUQzYThGTVpFb243NGRDdmM0K3ExWEEySjJ0QnkycHdhVHFmCmhweHhk R0E5Smo1MFVKM1BENGJTVUVnTjh0TFowc2FuNDdsNVhUQUZMaTI0NTZjaVNsNW04c0thSGxH 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<https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -4.1 (----) On 7/30/20 9:16 AM, Arthur Goldberg wrote: > fgrep -x -f dfba.py dfba.py > actual_output.txt That command works just fine for me with the file you attached. That is, this command: fgrep -x -f dfba.py dfba.py | cmp - dfba.py outputs nothing, as expected. This is on Ubuntu 18.04.4 which has fgrep 3.1 (same as what you have). I noticed that the file actual_output.txt that you attached had trailing CR at the end of each line, which would cause 'diff' to report a difference at any line. So perhaps the problem has to do with a Microsoft-oriented file system in your environment, or something like that.
bug-grep@HIDDEN:bug#42623; Package grep.
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To: bug-grep@HIDDEN
From: Arthur Goldberg <artgoldberg@HIDDEN>
Subject: fgrep -x -f problem
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Date: Thu, 30 Jul 2020 12:16:11 -0400
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This is a multi-part message in MIME format.
--------------E5D15685A8D8411705950180
Content-Type: text/plain; charset=utf-8; format=flowed
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Hi Gnu grep folks
I believe that
fgrep -x -f file file
should output the contents of `file`. However, it outputs something very
different for the attached file.
command:
fgrep -x -f dfba.py dfba.py > actual_output.txt
versions:
$ uname -a
Linux 8845f126fe89 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019
x86_64 x86_64 x86_64 GNU/Linux
$ fgrep --version
grep (GNU grep) 3.1
Copyright (C) 2017 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by Mike Haertel and others, see
<http://git.sv.gnu.org/cgit/grep.git/tree/AUTHORS>.
Thanks
Arthur
--
Arthur Goldberg
https://www.linkedin.com/in/arthurgoldberg
artgoldberg@HIDDEN
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--------------E5D15685A8D8411705950180
Content-Type: text/x-python-script; charset=UTF-8; x-mac-type="0"; x-mac-creator="0";
name="dfba.py"
Content-Transfer-Encoding: 7bit
Content-Disposition: attachment;
filename="dfba.py"
import conv_opt
from de_sim.simulation_object import SimulationObject
from wc_sim import message_types
from wc_sim.config import core as config_core_multialgorithm
from wc_sim.multialgorithm_errors import DynamicMultialgorithmError, MultialgorithmError
from wc_sim.species_populations import TempPopulationsLSP
from wc_sim.submodels.dynamic_submodel import DynamicSubmodel
from wc_utils.util.list import det_dedupe
class OdeSubmodel(DynamicSubmodel):
messages_sent = [message_types.RunOde]
event_handlers = [(message_types.RunOde, 'handle_RunOde_msg')]
def __init__(self, id, dynamic_model, reactions, species, dynamic_compartments,
local_species_population, ode_time_step, options=None):
if not isinstance(ode_time_step, (float, int)):
raise MultialgorithmError(f"OdeSubmodel {self.id}: ode_time_step must be a number but is "
f"{ode_time_step}")
if ode_time_step <= 0:
raise MultialgorithmError("ode_time_step must be positive, but is {}".format(ode_time_step))
self.ode_time_step = ode_time_step
self.options = options
# log initialization data
self.log_with_time("init: id: {}".format(id))
self.log_with_time("init: time_step: {}".format(str(ode_time_step)))
### dFBA specific code ###
# AG: let's use lower_with_under naming for instance variables
# AG: see https://google.github.io/styleguide/pyguide.html
self.metabolismProductionReaction = None
self.exchangedSpecies = None
self.thermodynamicBounds = None
self.exchangeRateBounds = None
self.defaultOdeBound = 1e15
### AG: should be size of # of reactions, I believe
self.reactionFluxes = np.zeros(0)
self.set_up_ode_submodel()
self.set_up_optimizations()
def set_up_ode_submodel(self):
""" Set up a DFBA submodel, by converting to a linear programming matrix """
ode_species = []
for idx, rxn in enumerate(self.reactions):
for species_coefficient in rxn.participants:
species_id = species_coefficient.species.gen_id()
ode_species.append(species_id)
self.ode_species_ids = det_dedupe(ode_species)
### dFBA specific code ###
# AG: TODO
# Reuse my code to convert reactions to conv_opt variables
# Create a dictionary that maps variables to reactions
# Create a dictionary that maps species to a dictionary that maps variables to species stoichiometric coefficient
# Reuse my code to set up the objective function in conv_opt format
self.schedule_next_FBA_analysis()
def schedule_next_ode_analysis(self):
""" Schedule the next analysis by this FBA submodel.
"""
self.send_event(self.ode_time_step, self, message_types.RunOde())
def set_up_optimizations(self):
""" To improve performance, pre-compute and pre-allocate some data structures """
# make fixed set of species ids used by this OdeSubmodel
self.ode_species_ids_set = set(self.ode_species_ids)
# pre-allocate dict of adjustments used to pass changes to LocalSpeciesPopulation
self.adjustments = {species_id: None for species_id in self.ode_species_ids}
# pre-allocate numpy arrays for populations
self.num_species = len(self.ode_species_ids)
self.populations = np.zeros(self.num_species)
def current_species_populations(self):
""" Obtain the current populations of species modeled by this FBA
The current populations are written into `self.populations`.
"""
pops_dict = self.local_species_population.read(self.time, self.ode_species_ids_set, round=False)
for idx, species_id in enumerate(self.ode_species_ids):
self.populations[idx] = pops_dict[species_id]
def run_ode_solver(self):
""" Run the FBA solver for one time step """
### dFBA specific code ###
# AG: TODO
# AG: do the bounds come from rate laws? I thought they would come from Reaction flux bounds in
# wc_lang.core.Reaction.flux_min and wc_lang.core.Reaction.flux_max
# Eval rate laws and set as bounds
# Set bounds of exchange reactions
# Maximize objective function and retrieve the reaction fluxes
# If no solution is found, raise error
self.current_species_populations()
# Calculate the adjustment for each species as sum over reactions of reaction flux * stoichiometry / ode_time_step
# Check that the adjustment will not cause a species population to become negative
# AG: I think that negative populations will need to generate an error
# the only other possibility would be to reduce the time step such that populations
# stay positive, subject to a minimum time step
# If it becomes negative, then change the adjustment so that the species population is zero
### store results in local_species_population ###
self.local_species_population.adjust_continuously(self.time, self.adjustments)
# flush expressions that depend on species and reactions modeled by this FBA submodel from cache
# AG: we can rename "ode_flush_after_populations_change" to
# "continuous_submodel_flush_after_populations_change" and use it both here and in odes.py
self.dynamic_model.ode_flush_after_populations_change(self.id) # will add this method to dynamic_components.py
def handle_RunOde_msg(self):
""" Handle an event containing a RunOde message
Args:
event (:obj:`Event`): a simulation event
"""
self.run_ode_solver()
self.schedule_next_ode_analysis()
--------------E5D15685A8D8411705950180--
Arthur Goldberg <artgoldberg@HIDDEN>:bug-grep@HIDDEN.
Full text available.bug-grep@HIDDEN:bug#42623; Package grep.
Full text available.
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997 nCipher Corporation Ltd,
1994-97 Ian Jackson.