get-quick-list.py script is feature complete
This commit is contained in:
Axel Kohlmeyer
@ -4,151 +4,275 @@ Find all example input files containing commands changed in this branch versus d
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Companion script to run_tests.py regression tester.
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"""
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import os, re, sys
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from glob import glob
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import subprocess
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import os, re, sys, subprocess
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from pathlib import Path
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# infer top level lammps dir
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if sys.version_info < (3,5):
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raise BaseException("Must use at least Python 3.5")
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# infer top level LAMMPS dir
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LAMMPS_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), '..', '..'))
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# get list of changed files relative to the develop branch from git
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output = None
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try:
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output = subprocess.run('git diff --diff-filter=MA --name-status develop',
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shell=True, capture_output=True)
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except:
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pass
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# ----------------------------------------------------------------------
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# collect header files to check for styles
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headers = []
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if output:
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for changed in output.stdout.decode().split():
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if (changed == 'A') or (changed == 'M'): continue
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if not changed.startswith('src/'): continue
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if changed.endswith('.h'): headers.append(changed)
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if changed.endswith('.cpp'): headers.append(changed.replace('.cpp','.h'))
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def changed_files_from_git(branch='develop'):
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"""
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Return list of changed file from git.
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# now loop over header files, search for XxxxStyle() macros and append style name
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command = []
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atom = []
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compute = []
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fix = []
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pair = []
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body = []
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bond = []
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angle = []
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dihedral = []
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improper = []
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kspace = []
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dump = []
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region = []
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integrate = []
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minimize = []
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This function queries git to return the list of changed files on
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the current branch relative to a given branch (default is 'develop').
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style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
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upper = re.compile("[A-Z]+")
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gpu = re.compile("(.+)/gpu$")
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intel = re.compile("(.+)/intel$")
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kokkos = re.compile("(.+)/kk$")
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kokkos_skip = re.compile("(.+)/kk/(host|device)$")
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omp = re.compile("(.+)/omp$")
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opt = re.compile("(.+)/opt$")
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removed = re.compile("(.*)Deprecated$")
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param branch: branch to compare with
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type branch: string
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return: path names of files with changes relative to the repository root
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rtype: list of strings
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"""
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for file in headers:
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with open(file) as f:
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for line in f:
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matches = style_pattern.findall(line)
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for m in matches:
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# skip over internal styles w/o explicit documentation
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style = m[1]
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if upper.match(style):
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continue
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# get list of changed files relative to the develop branch from git
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output = None
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try:
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output = subprocess.run('git diff --diff-filter=MA --name-status develop',
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shell=True, capture_output=True)
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except:
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pass
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# skip over suffix styles:
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suffix = kokkos_skip.match(style)
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if suffix:
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continue
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suffix = gpu.match(style)
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if suffix:
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continue
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suffix = intel.match(style)
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if suffix:
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continue
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suffix = kokkos.match(style)
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if suffix:
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continue
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suffix = omp.match(style)
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if suffix:
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continue
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suffix = opt.match(style)
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if suffix:
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continue
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deprecated = removed.match(m[2])
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if deprecated:
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continue
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# collect header files to check for styles
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# - skip files that don't end in '.h' or '.cpp'
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# - skip paths that don't start with 'src/'
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# - replace '.cpp' with '.h' w/o checking it exists
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headers = []
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# output will have a letter 'A' or 'M' for added or modified files followed by pathname
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# append iterms to list and return it
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if output:
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for changed in output.stdout.decode().split():
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if (changed == 'A') or (changed == 'M'): continue
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if not changed.startswith('src/'): continue
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if changed.endswith('.h'): headers.append(changed)
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if changed.endswith('.cpp'): headers.append(changed.replace('.cpp','.h'))
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return headers
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# register style and suffix flags
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if m[0] == 'Angle':
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angle.append(style)
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elif m[0] == 'Atom':
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atom.append(style)
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elif m[0] == 'Body':
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register_style(body,style,info)
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elif m[0] == 'Bond':
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bond.applend(style)
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elif m[0] == 'Command':
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command.append(style)
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elif m[0] == 'Compute':
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compute.append(style)
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elif m[0] == 'Dihedral':
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dihedral.append(style)
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elif m[0] == 'Dump':
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dump.append(style)
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elif m[0] == 'Fix':
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fix.append(style)
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elif m[0] == 'Improper':
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improper.append(style)
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elif m[0] == 'Integrate':
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integrate.append(style)
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elif m[0] == 'KSpace':
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kspace.append(style)
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elif m[0] == 'Minimize':
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minimize.append(style)
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elif m[0] == 'Pair':
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pair.append(style)
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elif m[0] == 'Region':
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region.append(style)
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else:
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pass
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# ----------------------------------------------------------------------
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if len(command):
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print("Commands: ", '|'.join(command))
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if len(atom):
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print("Atom styles: ", '|'.join(atom))
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if len(compute):
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print("Compute styles: ", '|'.join(compute))
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if len(fix):
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print("Fix styles: ", '|'.join(fix))
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if len(pair):
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print("Pair styles: ", '|'.join(pair))
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if len(body):
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print("Body styles: ", '|'.join(body))
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if len(bond):
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print("Bond styles: ", '|'.join(bond))
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if len(angle):
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print("Angle styles: ", '|'.join(angle))
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if len(dihedral):
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print("Dihedral styles: ", '|'.join(dihedral))
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if len(improper):
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print("Improper styles: ", '|'.join(improper))
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if len(kspace):
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print("Kspace styles: ", '|'.join(kspace))
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if len(dump):
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print("Dump styles: ", '|'.join(dump))
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if len(region):
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print("Region styles: ", '|'.join(region))
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if len(integrate):
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print("Integrate styles: ", '|'.join(integrate))
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if len(minimize):
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print("Minimize styles: ", '|'.join(minimize))
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def get_command_from_header(headers, topdir="."):
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"""
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Loop over list of header files and extract style names, if present.
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LAMMPS commands have macros XxxxStyle() that connects a string with a class.
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We search the header files for those macros, extract the string and append
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it to a list in a dictionary of different types of styles. We skip over known
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suffixes and deprecated commands.
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param headers: header files to check for commands
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type headers:
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return: dictionary with lists of style names
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rtype: dict
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"""
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styles = {}
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styles['command'] = []
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styles['atom'] = []
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styles['compute'] = []
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styles['fix'] = []
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styles['pair'] = []
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styles['body'] = []
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styles['bond'] = []
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styles['angle'] = []
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styles['dihedral'] = []
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styles['improper'] = []
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styles['kspace'] = []
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styles['dump'] = []
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styles['region'] = []
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styles['integrate'] = []
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styles['minimize'] = []
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# some regex
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style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)")
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upper = re.compile("[A-Z]+")
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gpu = re.compile("(.+)/gpu$")
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intel = re.compile("(.+)/intel$")
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kokkos = re.compile("(.+)/kk$")
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kokkos_skip = re.compile("(.+)/kk/(host|device)$")
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omp = re.compile("(.+)/omp$")
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opt = re.compile("(.+)/opt$")
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removed = re.compile("(.*)Deprecated$")
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for file in headers:
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# don't fail if file is not present
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try:
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with open(os.path.join(topdir,file)) as f:
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for line in f:
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matches = style_pattern.findall(line)
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for m in matches:
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# skip over internal styles w/o explicit documentation
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style = m[1]
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if upper.match(style):
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continue
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# skip over suffix styles:
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suffix = kokkos_skip.match(style)
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if suffix:
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continue
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suffix = gpu.match(style)
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if suffix:
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continue
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suffix = intel.match(style)
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if suffix:
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continue
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suffix = kokkos.match(style)
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if suffix:
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continue
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suffix = omp.match(style)
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if suffix:
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continue
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suffix = opt.match(style)
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if suffix:
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continue
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deprecated = removed.match(m[2])
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if deprecated:
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continue
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# register style and suffix flags
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if m[0] == 'Angle':
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styles['angle'].append(style)
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elif m[0] == 'Atom':
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styles['atom'].append(style)
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elif m[0] == 'Body':
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styles['body'].append(style)
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elif m[0] == 'Bond':
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styles['bond'].applend(style)
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elif m[0] == 'Command':
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styles['command'].append(style)
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elif m[0] == 'Compute':
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styles['compute'].append(style)
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elif m[0] == 'Dihedral':
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styles['dihedral'].append(style)
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elif m[0] == 'Dump':
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styles['dump'].append(style)
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elif m[0] == 'Fix':
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styles['fix'].append(style)
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elif m[0] == 'Improper':
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styles['improper'].append(style)
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elif m[0] == 'Integrate':
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styles['integrate'].append(style)
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elif m[0] == 'KSpace':
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styles['kspace'].append(style)
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elif m[0] == 'Minimize':
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styles['minimize'].append(style)
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elif m[0] == 'Pair':
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styles['pair'].append(style)
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elif m[0] == 'Region':
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styles['region'].append(style)
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else:
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pass
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# header file not found or not readable
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except:
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pass
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return styles
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# ----------------------------------------------------------------------
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def make_regex(styles):
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"""Convert dictionary with styles into a regular expression to scan input files with
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This will construct a regular expression matching LAMMPS commands. Ignores continuation
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param styles: dictionary with style names
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type styles: dict
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return: compiled regular expression
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rtype: regex
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"""
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restring = "^\\s*("
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if len(styles['command']):
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restring += '(' + '|'.join(styles['command']) + ')|'
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if len(styles['atom']):
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restring += '(atom_style\\s+(' + '|'.join(styles['atom']) + '))|'
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if len(styles['compute']):
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restring += '(compute\\s+\\S+\\s+\\S+\\s+(' + '|'.join(styles['compute']) + '))|'
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if len(styles['fix']):
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restring += '(fix\\s+\\S+\\s+\\S+\\s+(' + '|'.join(styles['fix']) + '))|'
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if len(styles['pair']):
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restring += '(pair_style\\s+(' + '|'.join(styles['pair']) + '))|'
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if len(styles['body']):
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restring += '(atom_style\\s+body\\s+(' + '|'.join(styles['body']) + '))|'
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if len(styles['bond']):
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restring += '(bond_style\\s+(' + '|'.join(styles['bond']) + '))|'
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if len(styles['angle']):
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restring += '(angle_style\\s+(' + '|'.join(styles['angle']) + '))|'
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if len(styles['dihedral']):
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restring += '(dihedral_style\\s+(' + '|'.join(styles['dihedral']) + '))|'
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if len(styles['improper']):
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restring += '(improper_style\\s+(' + '|'.join(styles['improper']) + '))|'
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if len(styles['kspace']):
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restring += '(kspace_style\\s+(' + '|'.join(styles['kspace']) + '))|'
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if len(styles['dump']):
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restring += '(dump\\s+\\S+\\s+\\S+\\s+(' + '|'.join(styles['dump']) + '))|'
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if len(styles['region']):
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restring += '(region\\s+(' + '|'.join(styles['region']) + '))|'
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if len(styles['integrate']):
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restring += '(run_style\\s+(' + '|'.join(styles['integrate']) + '))|'
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if len(styles['minimize']):
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restring += '(min_style\\s+(' + '|'.join(styles['minimize']) + '))|'
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# replace last (pipe) character with closing parenthesis
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length = len(restring)
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restring = restring[:length-1] + ')'
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# return compiled regex or None
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if length > 5:
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return re.compile(restring)
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else:
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return None
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# ----------------------------------------------------------------------
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def get_examples_using_styles(regex, examples='examples'):
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"""
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Loop through LAMMPS examples tree and find all files staring with 'in.'
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that have at least one line matching the regex.
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param regex: pattern matching LAMMPS commands
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type regex: compiled regex
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param example: path where to start looking for examples recursively
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type example: string
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return: list of matching example inputs
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rtype: list of strings
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"""
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inputs = []
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for filename in Path(examples).rglob('in.*'):
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with open(filename) as f:
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for line in f:
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matches = regex.match(line)
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if matches:
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inputs.append(filename)
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break
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return inputs
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# ----------------------------------------------------------------------
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# ----------------------------------------------------------------------
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if __name__ == "__main__":
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headers = changed_files_from_git('develop')
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styles = get_command_from_header(headers, LAMMPS_DIR)
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inputs = get_examples_using_styles(make_regex(styles), os.path.join(LAMMPS_DIR,'examples'))
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print("Suggested inputs for testing:")
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for inp in inputs:
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print(inp)
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print("Found changes to the following styles:")
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print("Commands: ", styles['command'])
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print("Atom styles: ", styles['atom'])
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print("Compute styles: ", styles['compute'])
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print("Fix styles: ", styles['fix'])
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print("Pair styles: ", styles['pair'])
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print("Body styles: ", styles['body'])
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print("Bond styles: ", styles['bond'])
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print("Angle styles: ", styles['angle'])
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print("Dihedral styles: ", styles['dihedral'])
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print("Improper styles: ", styles['improper'])
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print("Kspace styles: ", styles['kspace'])
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print("Dump styles: ", styles['dump'])
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print("Region styles: ", styles['region'])
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print("Integrate styles: ", styles['integrate'])
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print("Minimize styles: ", styles['minimize'])
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Reference in New Issue
Block a user