make the whole project more python idiomatic

* rename src directory to allocbench
* make global variable names UPPERCASE
* format a lot of code using yapf
* use lowercase ld_preload and ld_library_path as Allocator members
* name expected Errors 'err' and don't raise a new Exception
* disable some pylint messages

1 files changed, 0 insertions, 108 deletions

diff --git a/src/benchmarks/raxmlng.py b/src/benchmarks/raxmlng.py
deleted file mode 100644
index ef77d2d..0000000
--- a/src/benchmarks/raxmlng.py
+++ /dev/null
@@ -1,108 +0,0 @@
-# Copyright 2018-2019 Florian Fischer <florian.fl.fischer@fau.de>
-#
-# This file is part of allocbench.
-#
-# allocbench is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# allocbench is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with allocbench.  If not, see <http://www.gnu.org/licenses/>.
-"""Definition of the RAxML-ng benchmark"""
-
-import os
-import re
-
-from src.artifact import GitArtifact
-from src.benchmark import Benchmark
-import src.plots as plt
-from src.util import print_info, run_cmd
-
-RUNTIME_RE = re.compile("Elapsed time: (?P<runtime>(\\d*.\\d*)) seconds")
-
-
-class BenchmarkRaxmlng(Benchmark):
-    """RAxML-ng benchmark
-    """
-    def __init__(self):
-        name = "raxmlng"
-
-        super().__init__(name)
-
-        self.cmd = (
-            f"raxml-ng --msa {self.build_dir}/data/prim.phy --model GTR+G"
-            " --redo --threads 2 --seed 2")
-
-    def prepare(self):
-        super().prepare()
-
-        if os.path.exists(self.build_dir):
-            return
-
-        raxmlng_sources = GitArtifact("raxml-ng",
-                                      "https://github.com/amkozlov/raxml-ng")
-        raxmlng_version = "0.9.0"
-        raxmlng_dir = os.path.join(self.build_dir, "raxml-ng-git")
-        raxmlng_builddir = os.path.join(raxmlng_dir, "build")
-        self.results["facts"]["versions"]["raxml-ng"] = raxmlng_version
-        raxmlng_sources.provide(raxmlng_version, raxmlng_dir)
-
-        # Create builddir
-        os.makedirs(raxmlng_builddir, exist_ok=True)
-
-        # building raxml-ng
-        run_cmd(["cmake", ".."], cwd=raxmlng_builddir)
-        run_cmd(["make"], cwd=raxmlng_builddir)
-
-        # create symlinks
-        for exe in ["raxml-ng"]:
-            src = os.path.join(raxmlng_dir, "bin", exe)
-            dest = os.path.join(self.build_dir, exe)
-            os.link(src, dest)
-
-        raxmlng_data = GitArtifact("raxml-ng-data",
-                                   "https://github.com/amkozlov/ng-tutorial")
-        raxmlng_data_dir = os.path.join(self.build_dir, "data")
-        raxmlng_data.provide("f8f0b6a057a11397b4dad308440746e3436db8b4",
-                             raxmlng_data_dir)
-
-    def cleanup(self):
-        for direntry in os.listdir():
-            if direntry.startswith("prim.raxml"):
-                os.remove(direntry)
-
-    @staticmethod
-    def process_output(result, stdout, stderr, allocator, perm):
-        result["runtime"] = RUNTIME_RE.search(stdout).group("runtime")
-
-    def summary(self):
-        plt.plot(self,
-                 "{runtime}",
-                 plot_type='bar',
-                 fig_options={
-                    'ylabel': 'runtime in s',
-                    'title': 'raxml-ng tree inference benchmark',
-                 },
-                 file_postfix="runtime")
-
-        plt.export_stats_to_dataref(self, "runtime")
-
-        plt.plot(self,
-                 "{VmHWM}",
-                 plot_type='bar',
-                 fig_options={
-                     'ylabel': 'VmHWM in KB',
-                     'title': 'raxml-ng memusage',
-                 },
-                 file_postfix="memusage")
-
-        plt.export_stats_to_dataref(self, "VmHWM")
-
-
-raxmlng = BenchmarkRaxmlng()