From 6bda1ff037b8481ee49c0243a85cc34042a5b00a Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Thu, 5 Oct 2023 15:21:54 +0200 Subject: [PATCH] Remove numpy, replace by math module and pure python --- autosubmit/monitor/diagram.py | 50 +++++++++++++++++++++++------------ requeriments.txt | 1 - setup.py | 2 +- 3 files changed, 34 insertions(+), 19 deletions(-) diff --git a/autosubmit/monitor/diagram.py b/autosubmit/monitor/diagram.py index 6989ccf02..17fe9d789 100644 --- a/autosubmit/monitor/diagram.py +++ b/autosubmit/monitor/diagram.py @@ -17,20 +17,21 @@ # You should have received a copy of the GNU General Public License # along with Autosubmit. If not, see . -import matplotlib as mtp -import numpy as np +import itertools +import math import traceback +import matplotlib as mtp + mtp.use('Agg') import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec import matplotlib.patches as mpatches -# from autosubmit.experiment.statistics import ExperimentStats from autosubmit.statistics.statistics import Statistics from autosubmit.job.job import Job -from log.log import Log, AutosubmitCritical +from log.log import Log from datetime import datetime -from typing import List +from typing import List, Dict Log.get_logger("Autosubmit") @@ -41,6 +42,11 @@ MAX_NUM_PLOTS = 40 +def _seq(start, end, step): + """From: https://pynative.com/python-range-for-float-numbers/""" + sample_count = int(abs(end - start) / step) + return itertools.islice(itertools.count(start, step), sample_count) + def create_bar_diagram(experiment_id, jobs_list, general_stats, output_file, period_ini=None, period_fi=None, queue_time_fixes=None): # type: (str, List[Job], List[str], str, datetime, datetime, Dict[str, int]) -> None @@ -75,15 +81,15 @@ def create_bar_diagram(experiment_id, jobs_list, general_stats, output_file, per failed_jobs_dict = exp_stats.build_failed_jobs_only_list() # Stats variables definition - normal_plots_count = int(np.ceil(len(exp_stats.jobs_stat) / MAX_JOBS_PER_PLOT)) - failed_jobs_plots_count = int(np.ceil(len(failed_jobs_dict) / MAX_JOBS_PER_PLOT)) + normal_plots_count = int(math.ceil(len(exp_stats.jobs_stat) / MAX_JOBS_PER_PLOT)) + failed_jobs_plots_count = int(math.ceil(len(failed_jobs_dict) / MAX_JOBS_PER_PLOT)) except Exception as exp: print(exp) print((traceback.format_exc())) # Plotting total_plots_count = normal_plots_count + failed_jobs_plots_count - # num_plots = norma + # num_plots = norma # ind = np.arrange(int(MAX_JOBS_PER_PLOT)) width = 0.16 # Creating stats figure + sanity check @@ -110,22 +116,30 @@ def create_bar_diagram(experiment_id, jobs_list, general_stats, output_file, per l2 = min(int(plot * MAX_JOBS_PER_PLOT), len(exp_stats.jobs_stat)) if l2 - l1 <= 0: continue - ind = np.arange(l2 - l1) + ind = range(l2 - l1) + ind_width = [x + width for x in ind] + ind_width_3 = [x + width * 3 for x in ind] + ind_width_4 = [x + width * 4 for x in ind] # Building plot axis ax.append(fig.add_subplot(grid_spec[RATIO * plot - RATIO + 2:RATIO * plot + 1])) ax[plot - 1].set_ylabel('hours') - ax[plot - 1].set_xticks(ind + width) + ax[plot - 1].set_xticks(ind_width) ax[plot - 1].set_xticklabels( [job.name for job in jobs_list[l1:l2]], rotation='vertical') ax[plot - 1].set_title(experiment_id, fontsize=20) upper_limit = round(1.10 * exp_stats.max_time, 4) - ax[plot - 1].set_yticks(np.arange(0, upper_limit, round(upper_limit / 10, 4))) + step = round(upper_limit / 10, 4) + # Here we use ``upper_limit + step`` as np.arange is inclusive at the end, + # ``islice`` is not. + y_ticks = [round(x, 4) for x in _seq(0, upper_limit + step, step)] + # ax[plot - 1].set_yticks(np.arange(0, upper_limit, round(upper_limit / 10, 4))) + ax[plot - 1].set_yticks(y_ticks) ax[plot - 1].set_ylim(0, float(1.10 * exp_stats.max_time)) # Building reacts rects[0] = ax[plot - 1].bar(ind, exp_stats.queued[l1:l2], width, color='lightpink') - rects[1] = ax[plot - 1].bar(ind + width, exp_stats.run[l1:l2], width, color='green') - rects[2] = ax[plot - 1].bar(ind + width * 3, exp_stats.fail_queued[l1:l2], width, color='lightsalmon') - rects[3] = ax[plot - 1].bar(ind + width * 4, exp_stats.fail_run[l1:l2], width, color='salmon') + rects[1] = ax[plot - 1].bar(ind_width, exp_stats.run[l1:l2], width, color='green') + rects[2] = ax[plot - 1].bar(ind_width_3, exp_stats.fail_queued[l1:l2], width, color='lightsalmon') + rects[3] = ax[plot - 1].bar(ind_width_4, exp_stats.fail_run[l1:l2], width, color='salmon') rects[4] = ax[plot - 1].plot([0., width * 6 * MAX_JOBS_PER_PLOT], [exp_stats.threshold, exp_stats.threshold], "k--", label='wallclock sim') # Building legend @@ -142,16 +156,18 @@ def create_bar_diagram(experiment_id, jobs_list, general_stats, output_file, per l2 = min(int(j_plot * MAX_JOBS_PER_PLOT), len(job_names_in_failed)) if l2 - l1 <= 0: continue - ind = np.arange(l2 - l1) + ind = range(l2 - l1) + ind_width = [x + width for x in ind] + ind_width_2 = [x + width * 2 for x in ind] plot = i_plot + j_plot ax.append(fig.add_subplot(grid_spec[RATIO * plot - RATIO + 2:RATIO * plot + 1])) ax[plot - 1].set_ylabel('# failed attempts') - ax[plot - 1].set_xticks(ind + width) + ax[plot - 1].set_xticks(ind_width) ax[plot - 1].set_xticklabels([name for name in job_names_in_failed[l1:l2]], rotation='vertical') ax[plot - 1].set_title(experiment_id, fontsize=20) ax[plot - 1].set_ylim(0, float(1.10 * exp_stats.max_fail)) ax[plot - 1].set_yticks(range(0, exp_stats.max_fail + 2)) - failed_jobs_rects[0] = ax[plot - 1].bar(ind + width * 2, [exp_stats.failed_jobs_dict[name] for name in + failed_jobs_rects[0] = ax[plot - 1].bar(ind_width_2, [exp_stats.failed_jobs_dict[name] for name in job_names_in_failed[l1:l2]], width, color='red') except Exception as exp: print((traceback.format_exc())) diff --git a/requeriments.txt b/requeriments.txt index 15acaad8c..77c7bf345 100644 --- a/requeriments.txt +++ b/requeriments.txt @@ -8,7 +8,6 @@ configobj>=5.0.6 argparse>=1.4.0 python-dateutil>=2.8.2 matplotlib<3.6 -numpy<1.22 py3dotplus>=1.1.0 pyparsing>=3.0.7 mock>=4.0.3 diff --git a/setup.py b/setup.py index 9709769e2..16fdb0b4f 100644 --- a/setup.py +++ b/setup.py @@ -39,7 +39,7 @@ setup( url='http://www.bsc.es/projects/earthscience/autosubmit/', download_url='https://earth.bsc.es/wiki/doku.php?id=tools:autosubmit', keywords=['climate', 'weather', 'workflow', 'HPC'], - install_requires=['ruamel.yaml==0.17.21','cython','autosubmitconfigparser','bcrypt>=3.2','packaging>19','six>=1.10.0','configobj>=5.0.6','argparse>=1.4.0','python-dateutil>=2.8.2','matplotlib<3.6','numpy<1.22','py3dotplus>=1.1.0','pyparsing>=3.0.7','paramiko>=2.9.2','mock>=4.0.3','portalocker>=2.3.2,<=2.7.0','networkx==2.6.3','requests>=2.27.1','bscearth.utils>=0.5.2','cryptography>=36.0.1','setuptools>=60.8.2','xlib>=0.21','pip>=22.0.3','pythondialog','pytest','nose','coverage','PyNaCl>=1.5.0','Pygments','psutil'], + install_requires=['ruamel.yaml==0.17.21','cython','autosubmitconfigparser','bcrypt>=3.2','packaging>19','six>=1.10.0','configobj>=5.0.6','argparse>=1.4.0','python-dateutil>=2.8.2','matplotlib<3.6','py3dotplus>=1.1.0','pyparsing>=3.0.7','paramiko>=2.9.2','mock>=4.0.3','portalocker>=2.3.2,<=2.7.0','networkx==2.6.3','requests>=2.27.1','bscearth.utils>=0.5.2','cryptography>=36.0.1','setuptools>=60.8.2','xlib>=0.21','pip>=22.0.3','pythondialog','pytest','nose','coverage','PyNaCl>=1.5.0','Pygments','psutil'], classifiers=[ "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.9", -- GitLab