GNU logs - #42623, boring messages

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Subject: bug#42623: fgrep -x -f problem
Resent-From: Arthur Goldberg <artgoldberg@HIDDEN>
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From: Arthur Goldberg <artgoldberg@HIDDEN>
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Date: Thu, 30 Jul 2020 12:16:11 -0400
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--------------E5D15685A8D8411705950180
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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--

Message sent:

Content-Disposition: inline
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X-Loop: help-debbugs@HIDDEN
From: help-debbugs@HIDDEN (GNU bug Tracking System)
To: Arthur Goldberg <artgoldberg@HIDDEN>
Subject: bug#42623: Acknowledgement (fgrep -x -f problem)
Message-ID: <handler.42623.B.159613194221549.ack <at> debbugs.gnu.org>
References: <04c685c8-ddf7-52d3-5dcb-46ef67a1fa1a@HIDDEN>
X-Gnu-PR-Message: ack 42623
X-Gnu-PR-Package: grep
Reply-To: 42623 <at> debbugs.gnu.org
Date: Thu, 30 Jul 2020 18:00:02 +0000

Thank you for filing a new bug report with debbugs.gnu.org.

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has been received.

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42623: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D42623
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Subject: bug#42623: fgrep -x -f problem
Resent-From: Paul Eggert <eggert@HIDDEN>
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Resent-Sender: help-debbugs@HIDDEN
To: Arthur Goldberg <artgoldberg@HIDDEN>
Cc: 42623 <at> debbugs.gnu.org
References: <04c685c8-ddf7-52d3-5dcb-46ef67a1fa1a@HIDDEN>
From: Paul Eggert <eggert@HIDDEN>
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Organization: UCLA Computer Science Department
Message-ID: <39288803-4a20-2aa5-a7da-ad19c9507064@HIDDEN>
Date: Thu, 30 Jul 2020 11:48:05 -0700
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Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org
Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>

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.

Message received at control <at> debbugs.gnu.org:

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Subject: some more wishlist bugs and moreinfo tags
To: control <at> debbugs.gnu.org
References: <c61dffe5-af26-8a6b-6bdd-330fe1b7cfd5@HIDDEN>
 <CMM.0.96.0.1455644062.beebe@HIDDEN>
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Organization: UCLA Computer Science Department
Message-ID: <24c615d9-dced-b04a-821d-7fb925c6a48e@HIDDEN>
Date: Mon, 21 Sep 2020 12:47:14 -0700
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severity 32704 wishlist
severity 40395 wishlist
severity 42245 wishlist
tags 42419 + moreinfo
tags 42623 + moreinfo
severity 42762 wishlist

Last modified: Mon, 21 Sep 2020 20:00:02 UTC

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.