Add pre-commit that use black and flake8

.gitignore

@@ -2,4 +2,5 @@
 *.code-workspace
 *.pyc
 dist
-*.egg-info
+*.egg-info
\ No newline at end of file
+__pycache__

.hooks/pre-commit

+#!/usr/bin/env python
+"""File generated by pre-commit: https://pre-commit.com"""
+from __future__ import print_function
+
+import distutils.spawn
+import os
+import subprocess
+import sys
+
+# work around https://github.com/Homebrew/homebrew-core/issues/30445
+os.environ.pop('__PYVENV_LAUNCHER__', None)
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+Z40 = '0' * 40
+ID_HASH = '138fd403232d2ddd5efb44317e38bf03'
+# start templated
+CONFIG = '.pre-commit-config.yaml'
+HOOK_TYPE = 'pre-commit'
+INSTALL_PYTHON = '/home/rplanel/.virtualenvs/crispr-bact/bin/python3'
+SKIP_ON_MISSING_CONFIG = False
+# end templated
+
+
+class EarlyExit(RuntimeError):
+    pass
+
+
+class FatalError(RuntimeError):
+    pass
+
+
+def _norm_exe(exe):
+    """Necessary for shebang support on windows.
+
+    roughly lifted from `identify.identify.parse_shebang`
+    """
+    with open(exe, 'rb') as f:
+        if f.read(2) != b'#!':
+            return ()
+        try:
+            first_line = f.readline().decode('UTF-8')
+        except UnicodeDecodeError:
+            return ()
+
+        cmd = first_line.split()
+        if cmd[0] == '/usr/bin/env':
+            del cmd[0]
+        return tuple(cmd)
+
+
+def _run_legacy():
+    if __file__.endswith('.legacy'):
+        raise SystemExit(
+            "bug: pre-commit's script is installed in migration mode\n"
+            'run `pre-commit install -f --hook-type {}` to fix this\n\n'
+            'Please report this bug at '
+            'https://github.com/pre-commit/pre-commit/issues'.format(
+                HOOK_TYPE,
+            ),
+        )
+
+    if HOOK_TYPE == 'pre-push':
+        stdin = getattr(sys.stdin, 'buffer', sys.stdin).read()
+    else:
+        stdin = None
+
+    legacy_hook = os.path.join(HERE, '{}.legacy'.format(HOOK_TYPE))
+    if os.access(legacy_hook, os.X_OK):
+        cmd = _norm_exe(legacy_hook) + (legacy_hook,) + tuple(sys.argv[1:])
+        proc = subprocess.Popen(cmd, stdin=subprocess.PIPE if stdin else None)
+        proc.communicate(stdin)
+        return proc.returncode, stdin
+    else:
+        return 0, stdin
+
+
+def _validate_config():
+    cmd = ('git', 'rev-parse', '--show-toplevel')
+    top_level = subprocess.check_output(cmd).decode('UTF-8').strip()
+    cfg = os.path.join(top_level, CONFIG)
+    if os.path.isfile(cfg):
+        pass
+    elif SKIP_ON_MISSING_CONFIG or os.getenv('PRE_COMMIT_ALLOW_NO_CONFIG'):
+        print(
+            '`{}` config file not found. '
+            'Skipping `pre-commit`.'.format(CONFIG),
+        )
+        raise EarlyExit()
+    else:
+        raise FatalError(
+            'No {} file was found\n'
+            '- To temporarily silence this, run '
+            '`PRE_COMMIT_ALLOW_NO_CONFIG=1 git ...`\n'
+            '- To permanently silence this, install pre-commit with the '
+            '--allow-missing-config option\n'
+            '- To uninstall pre-commit run '
+            '`pre-commit uninstall`'.format(CONFIG),
+        )
+
+
+def _exe():
+    with open(os.devnull, 'wb') as devnull:
+        for exe in (INSTALL_PYTHON, sys.executable):
+            try:
+                if not subprocess.call(
+                        (exe, '-c', 'import pre_commit.main'),
+                        stdout=devnull, stderr=devnull,
+                ):
+                    return (exe, '-m', 'pre_commit.main', 'run')
+            except OSError:
+                pass
+
+    if distutils.spawn.find_executable('pre-commit'):
+        return ('pre-commit', 'run')
+
+    raise FatalError(
+        '`pre-commit` not found.  Did you forget to activate your virtualenv?',
+    )
+
+
+def _rev_exists(rev):
+    return not subprocess.call(('git', 'rev-list', '--quiet', rev))
+
+
+def _pre_push(stdin):
+    remote = sys.argv[1]
+
+    opts = ()
+    for line in stdin.decode('UTF-8').splitlines():
+        _, local_sha, _, remote_sha = line.split()
+        if local_sha == Z40:
+            continue
+        elif remote_sha != Z40 and _rev_exists(remote_sha):
+            opts = ('--origin', local_sha, '--source', remote_sha)
+        else:
+            # ancestors not found in remote
+            ancestors = subprocess.check_output((
+                'git', 'rev-list', local_sha, '--topo-order', '--reverse',
+                '--not', '--remotes={}'.format(remote),
+            )).decode().strip()
+            if not ancestors:
+                continue
+            else:
+                first_ancestor = ancestors.splitlines()[0]
+                cmd = ('git', 'rev-list', '--max-parents=0', local_sha)
+                roots = set(subprocess.check_output(cmd).decode().splitlines())
+                if first_ancestor in roots:
+                    # pushing the whole tree including root commit
+                    opts = ('--all-files',)
+                else:
+                    cmd = ('git', 'rev-parse', '{}^'.format(first_ancestor))
+                    source = subprocess.check_output(cmd).decode().strip()
+                    opts = ('--origin', local_sha, '--source', source)
+
+    if opts:
+        return opts
+    else:
+        # An attempt to push an empty changeset
+        raise EarlyExit()
+
+
+def _opts(stdin):
+    fns = {
+        'prepare-commit-msg': lambda _: ('--commit-msg-filename', sys.argv[1]),
+        'commit-msg': lambda _: ('--commit-msg-filename', sys.argv[1]),
+        'pre-commit': lambda _: (),
+        'pre-push': _pre_push,
+    }
+    stage = HOOK_TYPE.replace('pre-', '')
+    return ('--config', CONFIG, '--hook-stage', stage) + fns[HOOK_TYPE](stdin)
+
+
+if sys.version_info < (3, 7):  # https://bugs.python.org/issue25942
+    def _subprocess_call(cmd):  # this is the python 2.7 implementation
+        return subprocess.Popen(cmd).wait()
+else:
+    _subprocess_call = subprocess.call
+
+
+def main():
+    retv, stdin = _run_legacy()
+    try:
+        _validate_config()
+        return retv | _subprocess_call(_exe() + _opts(stdin))
+    except EarlyExit:
+        return retv
+    except FatalError as e:
+        print(e.args[0])
+        return 1
+    except KeyboardInterrupt:
+        return 1
+
+
+if __name__ == '__main__':
+    exit(main())

.pre-commit-config.yaml

+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+      - id: black
+        exclude: .hooks
+        language_version: python3.7
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.4.0
+    hooks:
+      - id: flake8
+        args: [--max-line-length=89]

crisprbact/__init__.py

-from .predict import on_target_predict
+from .predict import on_target_predict
\ No newline at end of file
+
+__all__ = ["on_target_predict"]

pyproject.toml

@@ -25,8 +25,9 @@ biopython = "^1.75"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"
-black = {version = "^18.3-alpha.0", allows-prereleases = true}
 flake8 = "^3.7"
+pre-commit = "^1.20.0"
+black = "^19.10b0"
 
 [tool.poetry.scripts]
 crisprbact= "crisprbact.cli:main"
@@ -35,3 +36,30 @@ crisprbact= "crisprbact.cli:main"
 requires = ["poetry>=0.12"]
 build-backend = "poetry.masonry.api"
 
+[tool.black]
+target-version = ['py37']
+include = '\.pyi?$'
+exclude = '''
+
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | \.hooks
+    | _build
+    | buck-out
+    | build
+    | dist
+  )/
+  | foo.py           # also separately exclude a file named foo.py in
+                     # the root of the project
+)
+'''
+
+[flake8]
+max-line-length = 89
+max-complexity = 18

tests/predict_test.py

-import pytest
 import crisprbact
 
 
@@ -11,7 +10,12 @@ def test_on_target_predict_empty():
 def test_on_target_predict_size_guide():
     size_guide = 20
     predicted_targets = crisprbact.on_target_predict(
-        "TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG"
+        """ TGCCTGTTTACGCGCCGATTGTTGCG
+        AGATTTGGACGGACGTTGACGGGG
+        TCTATACCTGCGACCCGCGTCAGG
+        TGCCCGATGCGAGGTTGTTGAAGT
+        CGATGTCCTACCAGGAAGCGATGG
+        AGCTTTCCTACTTCGGCG"""
     )
     guides = (predicted_target["guide"] for predicted_target in predicted_targets)
     for guide in guides:
@@ -27,4 +31,3 @@ def test_on_target_predict_size_guide():
         assert (
             start_val - pam_val == 2
         ), "the difference between start and pam position is different than 2"
-