Merge pull request #233 from thisisrohan/test

Added 'cull', 'binder' and 'Viewer1D'.

pysph/tools/binder.py

@@ -0,0 +1,206 @@
+"""Make a directory compatible with mybinder.org and ready for
+upload to a Github repo.
+"""
+
+from pysph.solver.utils import get_files, mkdir
+import os
+from shutil import copy
+import nbformat as nbf
+import argparse
+import sys
+import re
+import glob
+
+
+def find_viewer_type(path):
+    '''
+    Finds the type of viewer to use in the jupyter notebook.
+    Parses the log file at the file path and searches for
+    'dim=d', where 'dD' is taken to be the viewer type.
+
+    example: if 'dim=2', then what is returned is '2D'
+    '''
+
+    log_file_path = os.path.abspath(path) + '/*.log'
+    regex = r'dim=(\d)'
+
+    match_list = []
+    with open(glob.glob(log_file_path)[0], 'r') as file:
+        for line in file:
+            for match in re.finditer(regex, line, re.S):
+                match_text = match.group()
+                match_list.append(match_text)
+                if len(match_list) > 0:
+                    break
+            if len(match_list) > 0:
+                break
+    return match_list[0][-1] + 'D'
+
+
+def make_notebook(path, sim_name, config_dict={}):
+    '''
+    Makes a jupyter notebook to view simulation results stored in
+    a given directory
+
+    path: the directory conatining the output files
+
+    sim_name: name of the simulation
+              ex. 'cavity_output'
+
+    config_dict: configuration dictionary for the notbeook viewer [dict]
+                 ex. {'fluid': {'frame': 20}}
+    '''
+
+    viewer_type = find_viewer_type(path)
+    cell1_src = [
+        "import os\n",
+        "from pysph.tools.ipy_viewer import Viewer" + viewer_type
+    ]
+    cell2_src = [
+        "cwd = os.getcwd()"
+    ]
+    cell3_src = [
+        "viewer = Viewer" + viewer_type + "(cwd)\n",
+        "viewer.interactive_plot(" + str(config_dict) + ")"
+    ]
+
+    nb = nbf.v4.new_notebook()
+
+    nb.cells = [
+        nbf.v4.new_code_cell(source=cell1_src),
+        nbf.v4.new_code_cell(source=cell2_src),
+        nbf.v4.new_code_cell(source=cell3_src)
+    ]
+
+    nbf.write(
+        nb,
+        os.path.join(
+            path,
+            sim_name+'.ipynb'
+        )
+    )
+    return
+
+
+def find_sim_dirs(path, sim_paths_list=[]):
+    '''
+    Finds all the directories in a given directory that
+    contain pysph output files.
+    '''
+    path = os.path.abspath(path)
+    sim_files = get_files(path)
+    if len(sim_files) != 0:
+        sim_paths_list.append(path)
+    elif len(sim_files) == 0:
+        files = os.listdir(path)
+        files = [f for f in files if os.path.isdir(f)]
+        files = [os.path.abspath(f) for f in files if not f.startswith('.')]
+        for f in files:
+            sim_paths_list = find_sim_dirs(f, sim_paths_list)
+
+    return sim_paths_list
+
+
+def find_dir_size(path):
+    '''
+    Finds the size of a given directory.
+    '''
+    total_size = 0
+    for dir_path, dir_names, file_names in os.walk(path):
+        for f in file_names:
+            fp = os.path.join(dir_path, f)
+            if not os.path.islink(fp):
+                total_size += os.path.getsize(fp)
+
+    return total_size
+
+
+def make_binder(path):
+
+    src_path = os.path.abspath(path)
+
+    sim_paths_list = find_sim_dirs(src_path)
+
+    for path in sim_paths_list:
+        sim_name = os.path.split(path)[1]
+        make_notebook(path, sim_name)
+        if len(sim_paths_list) == 1 and sim_paths_list[0] == src_path:
+            files = os.listdir(src_path)
+            files = [os.path.join(src_path, f) for f in files]
+            mkdir(os.path.join(src_path, sim_name))
+            could_not_copy = []
+            for f in files:
+                try:
+                    copy(f, os.path.join(src_path, sim_name))
+                except BaseException as exc:
+                    could_not_copy.append([f, exc])
+                    continue
+                os.remove(f)
+            if len(could_not_copy) != 0:
+                print("Could not copy the following files:\n")
+                for f in could_not_copy:
+                    print('file: ', f[0])
+                    print('error: ', f[1], '\n')
+
+    with open(os.path.join(src_path, 'requirements.txt'), 'w') as file:
+        file.write(
+            "ipympl\n" +
+            "matplotlib\n" +
+            "ipyvolume\n" +
+            "numpy\n" +
+            "pytools\n" +
+            "-e git+https://github.com/pypr/compyle#egg=compyle\n" +
+            "-e git+https://github.com/pypr/pysph#egg=pysph"
+        )
+
+    with open(os.path.join(src_path, 'README.md'), 'w') as file:
+        file.write(
+            "# Title\n" +
+            "[![Binder](https://mybinder.org/badge_logo.svg)]" +
+            "(https://mybinder.org/v2/gh/user_name/repo_name/branch_name)" +
+            "\n" +
+            "[comment]: # (The above link is for repositories hosted " +
+            "on GitHub. For links corresponding to other hosting services, " +
+            "please visit https://mybinder.readthedocs.io)"
+        )
+
+
+def main(argv=None):
+    if argv is None:
+        argv = sys.argv[1:]
+
+    parser = argparse.ArgumentParser(
+        prog='binder',
+        description=__doc__,
+        add_help=False
+    )
+
+    parser.add_argument(
+        "-h",
+        "--help",
+        action="store_true",
+        default=False,
+        dest="help",
+        help="show this help message and exit"
+    )
+
+    parser.add_argument(
+        "src_path",
+        type=str,
+        nargs=1,
+        help="the directory containing the directories/files to be prepared"
+    )
+
+    if len(argv) > 0 and argv[0] in ['-h', '--help']:
+        parser.print_help()
+        sys.exit()
+
+    options, extra = parser.parse_known_args(argv)
+
+    src_path = options.src_path[0]
+
+    make_binder(src_path)
+
+
+if __name__ == '__main__':
+    main()

pysph/tools/cli.py

@@ -35,6 +35,16 @@ def run_tests(args):
     cmdline.main(args=argv)
 
 
+def make_binder(args):
+    from pysph.tools.binder import main
+    main(args)
+
+
+def cull_files(args):
+    from pysph.tools.cull import main
+    main(args)
+
+
 def main():
     parser = ArgumentParser(description=__doc__, add_help=False)
     parser.add_argument(
@@ -60,12 +70,28 @@ def main():
         add_help=False
     )
     vtk_out.set_defaults(func=output_vtk)
+
     tests = subparsers.add_parser(
         'test', help='Run entire PySPH test-suite',
         add_help=False
     )
     tests.set_defaults(func=run_tests)
 
+    binder = subparsers.add_parser(
+        'binder',
+        help='Make a mybinder.org compatible directory for upload to a ' +
+             'host repo',
+        add_help=False
+    )
+    binder.set_defaults(func=make_binder)
+
+    cull = subparsers.add_parser(
+        'cull',
+        help='Cull files in a given directory by a specified culling_factor',
+        add_help=False
+    )
+    cull.set_defaults(func=cull_files)
+
     if (len(sys.argv) == 1 or (len(sys.argv) > 1 and
                                sys.argv[1] in ['-h', '--help'])):
         parser.print_help()

pysph/tools/cull.py

@@ -0,0 +1,89 @@
+"""Culls files in a given directory, one in every 'c' files is spared.
+
+The specified directory can contain other directories that house the output
+ files; files in all these directories will be culled, sparing one in every
+ 'c' files. Note that DELETION IS PERMANENT.
+"""
+
+from pysph.tools.binder import find_sim_dirs, find_dir_size
+from pysph.solver.utils import get_files
+import os
+import sys
+import argparse
+
+
+def cull(src_path, c):
+
+    src_path = os.path.abspath(src_path)
+    sim_paths_list = find_sim_dirs(src_path)
+
+    initial_size = find_dir_size(src_path)
+
+    for path in sim_paths_list:
+        files = get_files(path)
+        l = len(files)
+        del_files = [
+            files[i] for i in set(range(l)) - set(range(0, l, c))
+        ]
+        if len(del_files) != 0:
+            for f in del_files:
+                os.remove(f)
+
+    final_size = find_dir_size(src_path)
+
+    print("Initial size of the directory was: "+str(initial_size)+" bytes")
+    print("Final size of the directory is: "+str(final_size)+" bytes")
+    return
+
+
+def main(argv=None):
+    if argv is None:
+        argv = sys.argv[1:]
+
+    parser = argparse.ArgumentParser(
+        prog='cull',
+        description=__doc__,
+        add_help=False
+    )
+
+    parser.add_argument(
+        "-h",
+        "--help",
+        action="store_true",
+        default=False,
+        dest="help",
+        help="show this help message and exit"
+    )
+
+    parser.add_argument(
+        "src_path",
+        metavar='src_path',
+        type=str,
+        nargs=1,
+        help="the directory containing the directories/files to be culled"
+    )
+
+    parser.add_argument(
+        "-c",
+        metavar='c',
+        type=int,
+        nargs=1,
+        default=2,
+        help="one in every 'c' files is spared, all remaining output " +
+             "files are deleted [default=2]"
+    )
+
+    if len(argv) > 0 and argv[0] in ['-h', '--help']:
+        parser.print_help()
+        sys.exit()
+
+    options, extra = parser.parse_known_args(argv)
+
+    src_path = options.src_path[0]
+    x = options.c[0]
+
+    cull(src_path, c)
+
+
+if __name__ == '__main__':
+    main()