separate cli and lib

pairtools/__init__.py

@@ -1,129 +1,15 @@
-# -*- coding: utf-8 -*-
 """
 pairtools
 ~~~~~~~~~
 
 CLI tools to process mapped Hi-C data
 
-:copyright: (c) 2017-2021 Open2C
+:copyright: (c) 2017-2022 Open2C
 :author: Open2C
 :license: MIT
 
 """
 
-__version__ = "0.3.1-dev.1"
+__version__ = "1.0.0-dev1"
 
-
-import click
-import functools
-import sys
-
-CONTEXT_SETTINGS = {
-    "help_option_names": ["-h", "--help"],
-}
-
-
-@click.version_option(version=__version__)
-@click.group(context_settings=CONTEXT_SETTINGS)
-@click.option(
-    "--post-mortem", help="Post mortem debugging", is_flag=True, default=False
-)
-@click.option(
-    "--output-profile",
-    help="Profile performance with Python cProfile and dump the statistics "
-    "into a binary file",
-    type=str,
-    default="",
-)
-def cli(post_mortem, output_profile):
-    """Flexible tools for Hi-C data processing.
-
-    All pairtools have a few common options, which should be typed _before_
-    the command name.
-
-    """
-    if post_mortem:
-        import traceback
-
-        try:
-            import ipdb as pdb
-        except ImportError:
-            import pdb
-
-        def _excepthook(exc_type, value, tb):
-            traceback.print_exception(exc_type, value, tb)
-            print()
-            pdb.pm()
-
-        sys.excepthook = _excepthook
-
-    if output_profile:
-        import cProfile
-        import atexit
-
-        pr = cProfile.Profile()
-        pr.enable()
-
-        def _atexit_profile_hook():
-            pr.disable()
-            pr.dump_stats(output_profile)
-
-        atexit.register(_atexit_profile_hook)
-
-
-def common_io_options(func):
-    @click.option(
-        "--nproc-in",
-        type=int,
-        default=3,
-        show_default=True,
-        help="Number of processes used by the auto-guessed input decompressing command.",
-    )
-    @click.option(
-        "--nproc-out",
-        type=int,
-        default=8,
-        show_default=True,
-        help="Number of processes used by the auto-guessed output compressing command.",
-    )
-    @click.option(
-        "--cmd-in",
-        type=str,
-        default=None,
-        help="A command to decompress the input file. "
-        "If provided, fully overrides the auto-guessed command. "
-        "Does not work with stdin and pairtools parse. "
-        "Must read input from stdin and print output into stdout. "
-        "EXAMPLE: pbgzip -dc -n 3",
-    )
-    @click.option(
-        "--cmd-out",
-        type=str,
-        default=None,
-        help="A command to compress the output file. "
-        "If provided, fully overrides the auto-guessed command. "
-        "Does not work with stdout. "
-        "Must read input from stdin and print output into stdout. "
-        "EXAMPLE: pbgzip -c -n 8",
-    )
-    @functools.wraps(func)
-    def wrapper(*args, **kwargs):
-        return func(*args, **kwargs)
-
-    return wrapper
-
-
-from .pairtools_dedup import dedup
-from .pairtools_sort import sort
-from .pairtools_flip import flip
-from .pairtools_merge import merge
-from .pairtools_markasdup import markasdup
-from .pairtools_select import select
-from .pairtools_split import split
-from .pairtools_restrict import restrict
-from .pairtools_phase import phase
-from .pairtools_parse import parse
-from .pairtools_parse2 import parse2
-from .pairtools_stats import stats
-from .pairtools_sample import sample
-from .pairtools_filterbycov import filterbycov
+# from . import lib

pairtools/__main__.py

@@ -1,4 +1,4 @@
-from . import cli
+from .cli import cli
 
 if __name__ == "__main__":
-    cli()
+    cli()

pairtools/cli/__init__.py

@@ -0,0 +1,118 @@
+# -*- coding: utf-8 -*-
+
+import click
+import functools
+import sys
+from .. import __version__
+
+CONTEXT_SETTINGS = {
+    "help_option_names": ["-h", "--help"],
+}
+
+
+@click.version_option(version=__version__)
+@click.group(context_settings=CONTEXT_SETTINGS)
+@click.option(
+    "--post-mortem", help="Post mortem debugging", is_flag=True, default=False
+)
+@click.option(
+    "--output-profile",
+    help="Profile performance with Python cProfile and dump the statistics "
+    "into a binary file",
+    type=str,
+    default="",
+)
+def cli(post_mortem, output_profile):
+    """Flexible tools for Hi-C data processing.
+
+    All pairtools have a few common options, which should be typed _before_
+    the command name.
+
+    """
+    if post_mortem:
+        import traceback
+
+        try:
+            import ipdb as pdb
+        except ImportError:
+            import pdb
+
+        def _excepthook(exc_type, value, tb):
+            traceback.print_exception(exc_type, value, tb)
+            print()
+            pdb.pm()
+
+        sys.excepthook = _excepthook
+
+    if output_profile:
+        import cProfile
+        import atexit
+
+        pr = cProfile.Profile()
+        pr.enable()
+
+        def _atexit_profile_hook():
+            pr.disable()
+            pr.dump_stats(output_profile)
+
+        atexit.register(_atexit_profile_hook)
+
+
+def common_io_options(func):
+    @click.option(
+        "--nproc-in",
+        type=int,
+        default=3,
+        show_default=True,
+        help="Number of processes used by the auto-guessed input decompressing command.",
+    )
+    @click.option(
+        "--nproc-out",
+        type=int,
+        default=8,
+        show_default=True,
+        help="Number of processes used by the auto-guessed output compressing command.",
+    )
+    @click.option(
+        "--cmd-in",
+        type=str,
+        default=None,
+        help="A command to decompress the input file. "
+        "If provided, fully overrides the auto-guessed command. "
+        "Does not work with stdin and pairtools parse. "
+        "Must read input from stdin and print output into stdout. "
+        "EXAMPLE: pbgzip -dc -n 3",
+    )
+    @click.option(
+        "--cmd-out",
+        type=str,
+        default=None,
+        help="A command to compress the output file. "
+        "If provided, fully overrides the auto-guessed command. "
+        "Does not work with stdout. "
+        "Must read input from stdin and print output into stdout. "
+        "EXAMPLE: pbgzip -c -n 8",
+    )
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
+from . import (
+    dedup,
+    sort,
+    flip,
+    merge,
+    markasdup,
+    select,
+    split,
+    restrict,
+    phase,
+    parse,
+    parse2,
+    stats,
+    sample,
+    filterbycov,
+)