diff --git a/.hooks/pre-commit b/.hooks/pre-commit
deleted file mode 100755
index e206cfbe424d6b1409434282ad245c40756baa68..0000000000000000000000000000000000000000
--- a/.hooks/pre-commit
+++ /dev/null
@@ -1,195 +0,0 @@
-#!/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())
diff --git a/README.md b/README.md
index 4441a6392fa820cb9065f718b2ba1c40fc6129a8..a40e33be7696d684af6113f7e823287136b2755d 100644
--- a/README.md
+++ b/README.md
@@ -164,3 +164,37 @@ CGTTTGAGGAGATCCACAAAATTAT 732 -1.2437430146548256 CP027060.1
CATGAATGGTATAAACCGGCGTGCC 680 -0.8043242669169294 CP027060.1
```
+
+## Contributing
+
+### Create a virtualenv
+
+```console
+$ virtualenv -p pyton3.7 .venv
+$ . .venv/bin/activate
+$ pip install poetry
+```
+
+### Install crisprbact dependencies
+
+```console
+$ poetry install
+```
+
+### Install hooks
+
+```console
+$ pre-commit install
+```
+
+
+<!--
+### Change hooks
+
+
+```console
+$ git config --unset-all core.hooksPath
+$ pre-commit install
+$ cp .git/hooks/pre-commit .hooks/pre-commit
+$ git config core.hooksPath .hooks/
+``` -->