Remove the test directory after successful test run

Fixes #23

.editorconfig

@@ -0,0 +1,13 @@
+root = true
+
+[*]
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.{py,pyx,pxd,pxi,yml,h}]
+indent_size = 4
+indent_style = space
+
+[ext/*.{c,cpp,h}]
+indent_size = 4
+indent_style = tab

.gitignore

@@ -0,0 +1,2 @@
+.bitrot.db
+.bitrot.sha512

Ånnóying 𝚏Ⅰlęnąme by Łukasz

@@ -0,0 +1 @@
+This is a form of testing strange encodings.

LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2013 Łukasz Langa
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

@@ -2,8 +2,8 @@
 bitrot
 ======
 
-Detects bit rotten files on the hard drive to save your precious photo and
+Detects bit rotten files on the hard drive to save your precious photo
-music collection from slow decay.
+and music collection from slow decay.
 
 Usage
 -----
@@ -12,30 +12,163 @@ Go to the desired directory and simply invoke::
 
   $ bitrot
 
-This will start digging through your directory structure recursively indexing
+This will start digging through your directory structure recursively
-all files found. The index is stored in a ``.bitrot.db`` file which is a SQLite
+indexing all files found. The index is stored in a ``.bitrot.db`` file
-3 database.
+which is a SQLite 3 database.
 
-Next time you run ``bitrot`` it will add new files and update the index for
+Next time you run ``bitrot`` it will add new files and update the index
-files with a changed modification date. Most importantly however, it will
+for files with a changed modification date. Most importantly however, it
-report all errors, e.g. files that changed on the hard drive but still have the
+will report all errors, e.g. files that changed on the hard drive but
-same modification date.
+still have the same modification date.
 
-All paths stored in ``.bitrot.db`` are relative so it's safe to rescan a folder
+All paths stored in ``.bitrot.db`` are relative so it's safe to rescan
-after moving it to another drive.
+a folder after moving it to another drive. Just remember to move it in
+a way that doesn't touch modification dates. Otherwise the checksum
+database is useless.
 
 Performance
 -----------
 
-Obviously depends on how fast the underlying drive is. No rigorous performance
+Obviously depends on how fast the underlying drive is.  Historically
-tests have been done. For informational purposes, on my typical 5400 RPM laptop
+the script was single-threaded because back in 2013 checksum
-hard drive scanning a 60+ GB music library takes around 15 minutes. On an OCZ
+calculations on a single core still outran typical drives, including
-Vertex 3 SSD drive ``bitrot`` is able to scan a 100 GB Aperture library in
+the mobile SSDs of the day.  In 2020 this is no longer the case so the
-under 10 minutes. Both tests on HFS+.
+script now uses a process pool to calculate SHA1 hashes and perform
+`stat()` calls.
+
+No rigorous performance tests have been done.  Scanning a ~1000 file
+directory totalling ~5 GB takes 2.2s on a 2018 MacBook Pro 15" with
+a AP0512M SSD.  Back in 2013, that same feat on a 2015 MacBook Air with
+a SM0256G SSD took over 20 seconds.
+
+On that same 2018 MacBook Pro 15", scanning a 60+ GB music library takes
+24 seconds.  Back in 2013, with a typical 5400 RPM laptop hard drive
+it took around 15 minutes.  How times have changed!
+
+Tests
+-----
+
+There's a simple but comprehensive test scenario using
+`pytest <https://pypi.org/p/pytest>`_ and
+`pytest-order <https://pypi.org/p/pytest-order>`_.
+
+Install::
+
+  $ python3 -m venv .venv
+  $ . .venv/bin/activate
+  (.venv)$ pip install -e .[test]
+
+Run::
+
+  (.venv)$ pytest -x
+  ==================== test session starts ====================
+  platform darwin -- Python 3.10.12, pytest-7.4.0, pluggy-1.2.0
+  rootdir: /Users/ambv/Documents/Python/bitrot
+  plugins: order-1.1.0
+  collected 12 items
+
+  tests/test_bitrot.py ............                      [100%]
+
+  ==================== 12 passed in 15.05s ====================
 
 Change Log
 ----------
 
+1.0.1
+~~~~~
+
+* officially remove Python 2 support that was broken since 1.0.0
+  anyway; now the package works with Python 3.8+ because of a few
+  features
+
+1.0.0
+~~~~~
+
+* significantly sped up execution on solid state drives by using
+  a process pool executor to calculate SHA1 hashes and perform `stat()`
+  calls; use `-w1` if your runs on slow magnetic drives were
+  negatively affected by this change
+
+* sped up execution by pre-loading all SQLite-stored hashes to memory
+  and doing comparisons using Python sets
+
+* all UTF-8 filenames are now normalized to NFKD in the database to
+  enable cross-operating system checks
+
+* the SQLite database is now vacuumed to minimize its size
+
+* bugfix: additional Python 3 fixes when Unicode names were encountered
+
+0.9.2
+~~~~~
+
+* bugfix: one place in the code incorrectly hardcoded UTF-8 as the
+  filesystem encoding
+
+0.9.1
+~~~~~
+
+* bugfix: print the path that failed to decode with FSENCODING
+
+* bugfix: when using -q, don't hide warnings about files that can't be
+  statted or read
+
+* bugfix: -s is no longer broken on Python 3
+
+0.9.0
+~~~~~
+
+* bugfix: bitrot.db checksum checking messages now obey --quiet
+
+* Python 3 compatibility
+
+0.8.0
+~~~~~
+
+* bitrot now keeps track of its own database's bitrot by storing
+  a checksum of .bitrot.db in .bitrot.sha512
+
+* bugfix: now properly uses the filesystem encoding to decode file names
+  for use with the .bitrotdb database. Report and original patch by
+  pallinger.
+
+0.7.1
+~~~~~
+
+* bugfix: SHA1 computation now works correctly on Windows; previously
+  opened files in text-mode. This fix will change hashes of files
+  containing some specific bytes like 0x1A.
+
+0.7.0
+~~~~~
+
+* when a file changes or is renamed, the timestamp of the last check is
+  updated, too
+
+* bugfix: files that disappeared during the run are now properly ignored
+
+* bugfix: files that are locked or with otherwise denied access are
+  skipped. If they were read before, they will be considered "missing"
+  in the report.
+
+* bugfix: if there are multiple files with the same content in the
+  scanned directory tree, renames are now handled properly for them
+
+* refactored some horrible code to be a little less horrible
+
+0.6.0
+~~~~~
+
+* more control over performance with ``--commit-interval`` and
+  ``--chunk-size`` command-line arguments
+
+* bugfix: symbolic links are now properly skipped (or can be followed if
+  ``--follow-links`` is passed)
+
+* bugfix: files that cannot be opened are now gracefully skipped
+
+* bugfix: fixed a rare division by zero when run in an empty directory
+
 0.5.1
 ~~~~~
 
@@ -44,8 +177,9 @@ Change Log
 0.5.0
 ~~~~~
 
-* ``--test`` command-line argument for testing the state without updating the
+* ``--test`` command-line argument for testing the state without
-  database on disk (works for testing databases you don't have write access to)
+  updating the database on disk (works for testing databases you don't
+  have write access to)
 
 * size of the data read is reported upon finish
 
@@ -56,19 +190,22 @@ Change Log
 
 * renames are now reported as such
 
-* all non-regular files (e.g. symbolic links, pipes, sockets) are now skipped
+* all non-regular files (e.g. symbolic links, pipes, sockets) are now
+  skipped
 
 * progress presented in percentage
 
 0.3.0
 ~~~~~
 
-* ``--sum`` command-line argument for easy comparison of multiple databases
+* ``--sum`` command-line argument for easy comparison of multiple
+  databases
 
 0.2.1
 ~~~~~
 
-* fixed regression from 0.2.0 where new files caused a ``KeyError`` exception
+* fixed regression from 0.2.0 where new files caused a ``KeyError``
+  exception
 
 0.2.0
 ~~~~~
@@ -85,4 +222,15 @@ Change Log
 Authors
 -------
 
-Glued together by `Łukasz Langa <mailto:lukasz@langa.pl>`_.
+Glued together by `Łukasz Langa <mailto:lukasz@langa.pl>`_. Multiple
+improvements by
+`Ben Shepherd <mailto:bjashepherd@gmail.com>`_,
+`Jean-Louis Fuchs <mailto:ganwell@fangorn.ch>`_,
+`Marcus Linderoth <marcus@thingsquare.com>`_,
+`p1r473 <mailto:subwayjared@gmail.com>`_,
+`Peter Hofmann <mailto:scm@uninformativ.de>`_,
+`Phil Lundrigan <mailto:philipbl@cs.utah.edu>`_,
+`Reid Williams <rwilliams@ideo.com>`_,
+`Stan Senotrusov <senotrusov@gmail.com>`_,
+`Yang Zhang <mailto:yaaang@gmail.com>`_, and
+`Zhuoyun Wei <wzyboy@wzyboy.org>`_.

bin/bitrot

@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Copyright (C) 2013 by Łukasz Langa
-# 
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
-
-from bitrot import run_from_command_line
-run_from_command_line()

pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm[toml]"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "bitrot"
+authors = [
+    {name = "Łukasz Langa", email = "lukasz@langa.pl"},
+]
+description = "Detects bit rotten files on the hard drive to save your precious photo and music collection from slow decay."
+readme = "README.rst"
+requires-python = ">=3.8"
+keywords = ["file", "checksum", "database"]
+license = {text = "MIT"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Topic :: System :: Filesystems",
+    "Topic :: System :: Monitoring",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+
+]
+dependencies = []
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-order"]
+
+[project.scripts]
+bitrot = "bitrot:run_from_command_line"
+
+[tool.setuptools_scm]
+tag_regex = "^(?P<version>v\\d+(?:\\.\\d+){0,2}[^\\+]*)(?:\\+.*)?$"

setup.py

@@ -1,76 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Copyright (C) 2013 by Łukasz Langa
-# 
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-
-import os
-import sys
-from setuptools import setup, find_packages
-
-reload(sys)
-sys.setdefaultencoding('utf8')
-
-current_dir = os.path.abspath(os.path.dirname(__file__))
-ld_file = open(os.path.join(current_dir, 'README.rst'))
-try:
-    long_description = ld_file.read()
-finally:
-    ld_file.close()
-# We let it die a horrible tracebacking death if reading the file fails.
-# We couldn't sensibly recover anyway: we need the long description.
-
-sys.path.insert(0, current_dir + os.sep + 'src')
-from bitrot import VERSION
-release = ".".join(str(num) for num in VERSION)
-
-setup(
-    name = 'bitrot',
-    version = release,
-    author = 'Łukasz Langa',
-    author_email = 'lukasz@langa.pl',
-    description = ("Detects bit rotten files on the hard drive to save your "
-                   "precious photo and music collection from slow decay."),
-    long_description = long_description,
-    url = 'https://github.com/ambv/bitrot/',
-    keywords = 'file checksum database',
-    platforms = ['any'],
-    license = 'MIT',
-    package_dir = {'': 'src'},
-    packages = find_packages('src'),
-    py_modules = ['bitrot'],
-    scripts = ['bin/bitrot'],
-    include_package_data = True,
-    zip_safe = False, # if only because of the readme file
-    install_requires = [
-    ],
-
-    classifiers = [
-        'Development Status :: 3 - Alpha',
-        'License :: OSI Approved :: MIT License',
-        'Natural Language :: English',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 2 :: Only',
-        'Programming Language :: Python',
-        'Topic :: System :: Filesystems',
-        'Topic :: System :: Monitoring',
-        'Topic :: Software Development :: Libraries :: Python Modules',
-        ]
-    )

src/bitrot.py

@@ -1,8 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 
 # Copyright (C) 2013 by Łukasz Langa
-# 
+
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
 # in the Software without restriction, including without limitation the rights
@@ -21,14 +20,12 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
-from __future__ import absolute_import
+from __future__ import annotations
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
 
 import argparse
 import atexit
 import datetime
+import errno
 import hashlib
 import os
 import shutil
@@ -36,24 +33,48 @@ import sqlite3
 import stat
 import sys
 import tempfile
+import time
+import unicodedata
+
+from concurrent.futures import ProcessPoolExecutor, as_completed
+from multiprocessing import freeze_support
+from importlib.metadata import version, PackageNotFoundError
 
 
-CHUNK_SIZE = 16384
+DEFAULT_CHUNK_SIZE = 16384  # block size in HFS+; 4X the block size in ext4
 DOT_THRESHOLD = 200
-VERSION = (0, 5, 1)
+IGNORED_FILE_SYSTEM_ERRORS = {errno.ENOENT, errno.EACCES}
+FSENCODING = sys.getfilesystemencoding()
+try:
+    VERSION = version("bitrot")
+except PackageNotFoundError:
+    VERSION = "1.0.1"
 
 
-def sha1(path):
+def normalize_path(path):
+    path_uni = path.decode(FSENCODING)
+    if FSENCODING in ('utf-8', 'UTF-8'):
+        return unicodedata.normalize('NFKD', path_uni)
+
+    return path_uni
+
+
+def sha1(path, chunk_size):
     digest = hashlib.sha1()
-    with open(path) as f:
+    with open(path, 'rb') as f:
-        d = f.read(CHUNK_SIZE)
+        d = f.read(chunk_size)
         while d:
             digest.update(d)
-            d = f.read(CHUNK_SIZE)
+            d = f.read(chunk_size)
     return digest.hexdigest()
 
 
+def ts():
+    return datetime.datetime.utcnow().strftime('%Y-%m-%d %H:%M:%S%z')
+
+
 def get_sqlite3_cursor(path, copy=False):
+    path = path.decode(FSENCODING)
     if copy:
         if not os.path.exists(path):
             raise ValueError("error: bitrot database at {} does not exist."
@@ -70,111 +91,282 @@ def get_sqlite3_cursor(path, copy=False):
     conn = sqlite3.connect(path)
     atexit.register(conn.close)
     cur = conn.cursor()
-    for name, in cur.execute('SELECT name FROM sqlite_master'):
+    tables = set(t for t, in cur.execute('SELECT name FROM sqlite_master'))
-        if name == 'bitrot':
+    if 'bitrot' not in tables:
-            break
-    else:
         cur.execute('CREATE TABLE bitrot (path TEXT PRIMARY KEY, '
                     'mtime INTEGER, hash TEXT, timestamp TEXT)')
+    if 'bitrot_hash_idx' not in tables:
+        cur.execute('CREATE INDEX bitrot_hash_idx ON bitrot (hash)')
+    atexit.register(conn.commit)
     return conn
 
 
-def run(verbosity=1, test=False):
+def list_existing_paths(directory, expected=(), ignored=(), follow_links=False):
-    current_dir = b'.'   # sic, relative path
+    """list_existing_paths(b'/dir') -> ([path1, path2, ...], total_size)
-    bitrot_db = os.path.join(current_dir, b'.bitrot.db')
+
-    conn = get_sqlite3_cursor(bitrot_db, copy=test)
+    Returns a tuple with a set of existing files in `directory` and its subdirectories
+    and their `total_size`. If directory was a bytes object, so will be the returned
+    paths.
+
+    Doesn't add entries listed in `ignored`.  Doesn't add symlinks if
+    `follow_links` is False (the default).  All entries present in `expected`
+    must be files (can't be directories or symlinks).
+    """
+    paths = set()
+    total_size = 0
+    for path, _, files in os.walk(directory):
+        for f in files:
+            p = os.path.join(path, f)
+            try:
+                p_uni = p.decode(FSENCODING)
+            except UnicodeDecodeError:
+                binary_stderr = getattr(sys.stderr, 'buffer', sys.stderr)
+                binary_stderr.write(b"warning: cannot decode file name: ")
+                binary_stderr.write(p)
+                binary_stderr.write(b"\n")
+                continue
+
+            try:
+                if follow_links or p_uni in expected:
+                    st = os.stat(p)
+                else:
+                    st = os.lstat(p)
+            except OSError as ex:
+                if ex.errno not in IGNORED_FILE_SYSTEM_ERRORS:
+                    raise
+            else:
+                if not stat.S_ISREG(st.st_mode) or p in ignored:
+                    continue
+                paths.add(p)
+                total_size += st.st_size
+    return paths, total_size
+
+
+def compute_one(path, chunk_size):
+    """Return a tuple with (unicode path, size, mtime, sha1). Takes a binary path."""
+    p_uni = normalize_path(path)
+    try:
+        st = os.stat(path)
+    except OSError as ex:
+        if ex.errno in IGNORED_FILE_SYSTEM_ERRORS:
+            # The file disappeared between listing existing paths and
+            # this run or is (temporarily?) locked with different
+            # permissions. We'll just skip it for now.
+            print(
+                '\rwarning: `{}` is currently unavailable for '
+                'reading: {}'.format(
+                    p_uni, ex,
+                ),
+                file=sys.stderr,
+            )
+            raise BitrotException
+
+        raise   # Not expected? https://github.com/ambv/bitrot/issues/
+
+    try:
+        new_sha1 = sha1(path, chunk_size)
+    except (IOError, OSError) as e:
+        print(
+            '\rwarning: cannot compute hash of {} [{}]'.format(
+                p_uni, errno.errorcode[e.args[0]],
+            ),
+            file=sys.stderr,
+        )
+        raise BitrotException
+
+    return p_uni, st.st_size, int(st.st_mtime), new_sha1
+
+
+class BitrotException(Exception):
+    pass
+
+
+class Bitrot(object):
+    def __init__(
+        self, verbosity=1, test=False, follow_links=False, commit_interval=300,
+        chunk_size=DEFAULT_CHUNK_SIZE, workers=os.cpu_count(),
+    ):
+        self.verbosity = verbosity
+        self.test = test
+        self.follow_links = follow_links
+        self.commit_interval = commit_interval
+        self.chunk_size = chunk_size
+        self._last_reported_size = ''
+        self._last_commit_ts = 0
+        self.pool = ProcessPoolExecutor(max_workers=workers)
+
+    def maybe_commit(self, conn):
+        if time.time() < self._last_commit_ts + self.commit_interval:
+            # no time for commit yet!
+            return
+
+        conn.commit()
+        self._last_commit_ts = time.time()
+
+    def run(self):
+        check_sha512_integrity(verbosity=self.verbosity)
+
+        bitrot_db = get_path()
+        bitrot_sha512 = get_path(ext=b'sha512')
+        try:
+            conn = get_sqlite3_cursor(bitrot_db, copy=self.test)
+        except ValueError:
+            raise BitrotException(
+                2,
+                'No database exists so cannot test. Run the tool once first.',
+            )
+
         cur = conn.cursor()
         new_paths = []
         updated_paths = []
         renamed_paths = []
-    error_count = 0
+        errors = []
-    total_size = 0
         current_size = 0
-    last_reported_size = ''
+        missing_paths = self.select_all_paths(cur)
-    missing_paths = set()
+        hashes = self.select_all_hashes(cur)
-    cur.execute('SELECT path FROM bitrot')
+        paths, total_size = list_existing_paths(
-    row = cur.fetchone()
+            b'.', expected=missing_paths, ignored={bitrot_db, bitrot_sha512},
-    while row:
+            follow_links=self.follow_links,
-        missing_paths.add(row[0])
-        row = cur.fetchone()
-    paths = []
-    for path, _, files in os.walk(current_dir):
-        for f in files:
-            p = os.path.join(path, f)
-            st = os.stat(p)
-            if not stat.S_ISREG(st.st_mode) or p == bitrot_db:
-                continue
-            paths.append(p)
-            total_size += st.st_size
-    paths.sort()
-    for p in paths:
-        st = os.stat(p)
-        new_mtime = int(st.st_mtime)
-        current_size += st.st_size
-        if verbosity:
-            size_fmt = '\r{:>6.1%}'.format(current_size/total_size)
-            if size_fmt != last_reported_size:
-                sys.stdout.write(size_fmt)
-                sys.stdout.flush()
-                last_reported_size = size_fmt
-        new_sha1 = sha1(p)
-        update_ts = datetime.datetime.utcnow().strftime(
-            '%Y-%m-%d %H:%M:%S%z'
         )
-        p_uni = p.decode('utf8')
+        paths_uni = set(normalize_path(p) for p in paths)
+        futures = [self.pool.submit(compute_one, p, self.chunk_size) for p in paths]
+
+        for future in as_completed(futures):
+            try:
+                p_uni, new_size, new_mtime, new_sha1 = future.result()
+            except BitrotException:
+                continue
+
+            current_size += new_size
+            if self.verbosity:
+                self.report_progress(current_size, total_size)
+
+            if p_uni not in missing_paths:
+                # We are not expecting this path, it wasn't in the database yet.
+                # It's either new or a rename. Let's handle that.
+                stored_path = self.handle_unknown_path(
+                    cur, p_uni, new_mtime, new_sha1, paths_uni, hashes
+                )
+                self.maybe_commit(conn)
+                if p_uni == stored_path:
+                    new_paths.append(p_uni)
                     missing_paths.discard(p_uni)
-        cur.execute('SELECT mtime, hash, timestamp FROM bitrot WHERE '
+                else:
-                    'path=?', (p_uni,))
-        row = cur.fetchone()
-        if not row:
-            cur.execute('SELECT mtime, path, timestamp FROM bitrot WHERE '
-                        'hash=?', (new_sha1,))
-            rows = cur.fetchall()
-            for row in rows:
-                stored_mtime, stored_path, update_ts = row
-                if not os.path.exists(stored_path):
                     renamed_paths.append((stored_path, p_uni))
                     missing_paths.discard(stored_path)
-                    cur.execute('UPDATE bitrot SET mtime=?, path=?, '
-                                'timestamp=? WHERE hash=?',
-                                (new_mtime, p_uni, update_ts, new_sha1))
-                    conn.commit()
-                    break
-            else:
-                new_paths.append(p)
-                cur.execute('INSERT INTO bitrot VALUES (?, ?, ?, ?)',
-                    (p_uni, new_mtime, new_sha1, update_ts))
-                conn.commit()
                 continue
-        stored_mtime, stored_sha1, update_ts = row
+
+            # At this point we know we're seeing an expected file.
+            missing_paths.discard(p_uni)
+            cur.execute('SELECT mtime, hash, timestamp FROM bitrot WHERE path=?',
+                        (p_uni,))
+            row = cur.fetchone()
+            if not row:
+                print(
+                    '\rwarning: path disappeared from the database while running:',
+                    p_uni,
+                    file=sys.stderr,
+                )
+                continue
+
+            stored_mtime, stored_sha1, stored_ts = row
             if int(stored_mtime) != new_mtime:
-            updated_paths.append(p)
+                updated_paths.append(p_uni)
                 cur.execute('UPDATE bitrot SET mtime=?, hash=?, timestamp=? '
                             'WHERE path=?',
-                        (new_mtime, new_sha1, update_ts, p_uni))
+                            (new_mtime, new_sha1, ts(), p_uni))
-            conn.commit()
+                self.maybe_commit(conn)
-        elif stored_sha1 != new_sha1:
+                continue
-            error_count += 1
+
-            print('\rerror: SHA1 mismatch for {}: expected {}, got {}.'
+            if stored_sha1 != new_sha1:
-                  ' Original info from {}.'.format(
+                errors.append(p_uni)
-                        p, stored_sha1, new_sha1, update_ts
+                print(
+                    '\rerror: SHA1 mismatch for {}: expected {}, got {}.'
+                    ' Last good hash checked on {}.'.format(
+                        p_uni, stored_sha1, new_sha1, stored_ts
                     ),
                     file=sys.stderr,
                 )
+
         for path in missing_paths:
             cur.execute('DELETE FROM bitrot WHERE path=?', (path,))
+
         conn.commit()
+
+        if not self.test:
+            cur.execute('vacuum')
+
+        if self.verbosity:
             cur.execute('SELECT COUNT(path) FROM bitrot')
             all_count = cur.fetchone()[0]
-    if verbosity:
+            self.report_done(
+                total_size,
+                all_count,
+                len(errors),
+                new_paths,
+                updated_paths,
+                renamed_paths,
+                missing_paths,
+            )
+
+        update_sha512_integrity(verbosity=self.verbosity)
+
+        if errors:
+            raise BitrotException(
+                1, 'There were {} errors found.'.format(len(errors)), errors,
+            )
+
+    def select_all_paths(self, cur):
+        """Return a set of all distinct paths in the bitrot database.
+
+        The paths are Unicode and are normalized if FSENCODING was UTF-8.
+        """
+        result = set()
+        cur.execute('SELECT path FROM bitrot')
+        row = cur.fetchone()
+        while row:
+            result.add(row[0])
+            row = cur.fetchone()
+        return result
+
+    def select_all_hashes(self, cur):
+        """Return a dict where keys are hashes and values are sets of paths.
+
+        The paths are Unicode and are normalized if FSENCODING was UTF-8.
+        """
+        result = {}
+        cur.execute('SELECT hash, path FROM bitrot')
+        row = cur.fetchone()
+        while row:
+            rhash, rpath = row
+            result.setdefault(rhash, set()).add(rpath)
+            row = cur.fetchone()
+        return result
+
+    def report_progress(self, current_size, total_size):
+        size_fmt = '\r{:>6.1%}'.format(current_size/(total_size or 1))
+        if size_fmt == self._last_reported_size:
+            return
+
+        sys.stdout.write(size_fmt)
+        sys.stdout.flush()
+        self._last_reported_size = size_fmt
+
+    def report_done(
+        self, total_size, all_count, error_count, new_paths, updated_paths,
+        renamed_paths, missing_paths):
+        """Print a report on what happened.  All paths should be Unicode here."""
         print('\rFinished. {:.2f} MiB of data read. {} errors found.'
             ''.format(total_size/1024/1024, error_count))
-        if verbosity == 1:
+        if self.verbosity == 1:
-            print('{} entries in the database, {} new, {} updated, '
+            print(
-                  '{} renamed, {} missing.'.format(all_count, len(new_paths),
+                '{} entries in the database, {} new, {} updated, '
-                      len(updated_paths), len(renamed_paths), len(missing_paths)
+                '{} renamed, {} missing.'.format(
-            ))
+                    all_count, len(new_paths), len(updated_paths),
-        elif verbosity > 1:
+                    len(renamed_paths), len(missing_paths),
+                ),
+            )
+        elif self.verbosity > 1:
             print('{} entries in the database.'.format(all_count), end=' ')
             if new_paths:
                 print('{} entries new:'.format(len(new_paths)))
@@ -190,7 +382,12 @@ def run(verbosity=1, test=False):
                 print('{} entries renamed:'.format(len(renamed_paths)))
                 renamed_paths.sort()
                 for path in renamed_paths:
-                    print(' from', path[0], 'to', path[1])
+                    print(
+                        ' from',
+                        path[0],
+                        'to',
+                        path[1],
+                    )
             if missing_paths:
                 print('{} entries missing:'.format(len(missing_paths)))
                 missing_paths = sorted(missing_paths)
@@ -198,53 +395,196 @@ def run(verbosity=1, test=False):
                     print(' ', path)
             if not any((new_paths, updated_paths, missing_paths)):
                 print()
-        if test:
+        if self.test and self.verbosity:
             print('warning: database file not updated on disk (test mode).')
-    if error_count:
+
-        sys.exit(1)
+    def handle_unknown_path(self, cur, new_path, new_mtime, new_sha1, paths_uni, hashes):
+        """Either add a new entry to the database or update the existing entry
+        on rename.
+
+        `cur` is the database cursor. `new_path` is the new Unicode path.
+        `paths_uni` are Unicode paths seen on disk during this run of Bitrot.
+        `hashes` is a dictionary selected from the database, keys are hashes, values
+        are sets of Unicode paths that are stored in the DB under the given hash.
+
+        Returns `new_path` if the entry was indeed new or the `old_path` (e.g.
+        outdated path stored in the database for this hash) if there was a rename.
+        """
+
+        for old_path in hashes.get(new_sha1, ()):
+            if old_path not in paths_uni:
+                # File of the same hash used to exist but no longer does.
+                # Let's treat `new_path` as a renamed version of that `old_path`.
+                cur.execute(
+                    'UPDATE bitrot SET mtime=?, path=?, timestamp=? WHERE path=?',
+                    (new_mtime, new_path, ts(), old_path),
+                )
+                return old_path
+
+        else:
+            # Either we haven't found `new_sha1` at all in the database, or all
+            # currently stored paths for this hash still point to existing files.
+            # Let's insert a new entry for what appears to be a new file.
+            cur.execute(
+                'INSERT INTO bitrot VALUES (?, ?, ?, ?)',
+                (new_path, new_mtime, new_sha1, ts()),
+            )
+            return new_path
+
+def get_path(directory=b'.', ext=b'db'):
+    """Compose the path to the selected bitrot file."""
+    return os.path.join(directory, b'.bitrot.' + ext)
 
 
-def stable_sum():
+def stable_sum(bitrot_db=None):
-    current_dir = b'.'   # sic, relative path
+    """Calculates a stable SHA512 of all entries in the database.
-    bitrot_db = os.path.join(current_dir, b'.bitrot.db')
+
+    Useful for comparing if two directories hold the same data, as it ignores
+    timing information."""
+    if bitrot_db is None:
+        bitrot_db = get_path()
     digest = hashlib.sha512()
     conn = get_sqlite3_cursor(bitrot_db)
     cur = conn.cursor()
     cur.execute('SELECT hash FROM bitrot ORDER BY path')
     row = cur.fetchone()
     while row:
-        digest.update(row[0])
+        digest.update(row[0].encode('ascii'))
         row = cur.fetchone()
     return digest.hexdigest()
 
 
+def check_sha512_integrity(verbosity=1):
+    sha512_path = get_path(ext=b'sha512')
+    if not os.path.exists(sha512_path):
+        return
+
+    if verbosity:
+        print('Checking bitrot.db integrity... ', end='')
+        sys.stdout.flush()
+    with open(sha512_path, 'rb') as f:
+        old_sha512 = f.read().strip()
+    bitrot_db = get_path()
+    digest = hashlib.sha512()
+    with open(bitrot_db, 'rb') as f:
+        digest.update(f.read())
+    new_sha512 = digest.hexdigest().encode('ascii')
+    if new_sha512 != old_sha512:
+        if verbosity:
+            if len(old_sha512) == 128:
+                print(
+                    "error: SHA512 of the file is different, bitrot.db might "
+                    "be corrupt.",
+                )
+            else:
+                print(
+                    "error: SHA512 of the file is different but bitrot.sha512 "
+                    "has a suspicious length. It might be corrupt.",
+                )
+            print(
+                "If you'd like to continue anyway, delete the .bitrot.sha512 "
+                "file and try again.",
+                file=sys.stderr,
+            )
+        raise BitrotException(
+            3, 'bitrot.db integrity check failed, cannot continue.',
+        )
+
+    if verbosity:
+        print('ok.')
+
+def update_sha512_integrity(verbosity=1):
+    old_sha512 = 0
+    sha512_path = get_path(ext=b'sha512')
+    if os.path.exists(sha512_path):
+        with open(sha512_path, 'rb') as f:
+            old_sha512 = f.read().strip()
+    bitrot_db = get_path()
+    digest = hashlib.sha512()
+    with open(bitrot_db, 'rb') as f:
+        digest.update(f.read())
+    new_sha512 = digest.hexdigest().encode('ascii')
+    if new_sha512 != old_sha512:
+        if verbosity:
+            print('Updating bitrot.sha512... ', end='')
+            sys.stdout.flush()
+        with open(sha512_path, 'wb') as f:
+            f.write(new_sha512)
+        if verbosity:
+            print('done.')
+
 def run_from_command_line():
+    global FSENCODING
+
+    freeze_support()
+
     parser = argparse.ArgumentParser(prog='bitrot')
-    parser.add_argument('-q', '--quiet', action='store_true',
+    parser.add_argument(
+        '-l', '--follow-links', action='store_true',
+        help='follow symbolic links and store target files\' hashes. Once '
+             'a path is present in the database, it will be checked against '
+             'changes in content even if it becomes a symbolic link. In '
+             'other words, if you run `bitrot -l`, on subsequent runs '
+             'symbolic links registered during the first run will be '
+             'properly followed and checked even if you run without `-l`.')
+    parser.add_argument(
+        '-q', '--quiet', action='store_true',
         help='don\'t print anything besides checksum errors')
-    parser.add_argument('-s', '--sum', action='store_true',
+    parser.add_argument(
+        '-s', '--sum', action='store_true',
         help='using only the data already gathered, return a SHA-512 sum '
              'of hashes of all the entries in the database. No timestamps '
              'are used in calculation.')
-    parser.add_argument('-v', '--verbose', action='store_true',
+    parser.add_argument(
+        '-v', '--verbose', action='store_true',
         help='list new, updated and missing entries')
-    parser.add_argument('-t', '--test', action='store_true',
+    parser.add_argument(
+        '-t', '--test', action='store_true',
         help='just test against an existing database, don\'t update anything')
-    parser.add_argument('--version', action='version',
+    parser.add_argument(
-        version='%(prog)s {}.{}.{}'.format(*VERSION))
+        '--version', action='version',
+        version=f"%(prog)s {VERSION}")
+    parser.add_argument(
+        '--commit-interval', type=float, default=300,
+        help='min time in seconds between commits '
+             '(0 commits on every operation)')
+    parser.add_argument(
+        '-w', '--workers', type=int, default=os.cpu_count(),
+        help='run this many workers (use -w1 for slow magnetic disks)')
+    parser.add_argument(
+        '--chunk-size', type=int, default=DEFAULT_CHUNK_SIZE,
+        help='read files this many bytes at a time')
+    parser.add_argument(
+        '--fsencoding', default='',
+        help='override the codec to decode filenames, otherwise taken from '
+             'the LANG environment variables')
     args = parser.parse_args()
     if args.sum:
         try:
             print(stable_sum())
         except RuntimeError as e:
-            print(unicode(e).encode('utf8'), file=sys.stderr)
+            print(str(e).encode('utf8'), file=sys.stderr)
     else:
         verbosity = 1
         if args.quiet:
             verbosity = 0
         elif args.verbose:
             verbosity = 2
-        run(verbosity=verbosity, test=args.test)
+        bt = Bitrot(
+            verbosity=verbosity,
+            test=args.test,
+            follow_links=args.follow_links,
+            commit_interval=args.commit_interval,
+            chunk_size=args.chunk_size,
+            workers=args.workers,
+        )
+        if args.fsencoding:
+            FSENCODING = args.fsencoding
+        try:
+            bt.run()
+        except BitrotException as bre:
+            print('error:', bre.args[1], file=sys.stderr)
+            sys.exit(bre.args[0])
 
 
 if __name__ == '__main__':

tests/test_bitrot.py

@@ -0,0 +1,348 @@
+"""
+NOTE: those tests are ordered and require pytest-order to run correctly.
+"""
+
+from __future__ import annotations
+
+import getpass
+import os
+from pathlib import Path
+import shlex
+import shutil
+import subprocess
+import sys
+from textwrap import dedent
+
+import pytest
+
+
+TMP = Path("/tmp/")
+
+
+ReturnCode = int
+StdOut = list[str]
+StdErr = list[str]
+
+
+def bitrot(*args: str) -> tuple[ReturnCode, StdOut, StdErr]:
+    cmd = [sys.executable, "-m", "bitrot"]
+    cmd.extend(args)
+    res = subprocess.run(shlex.join(cmd), shell=True, capture_output=True)
+    stdout = (res.stdout or b"").decode("utf8")
+    stderr = (res.stderr or b"").decode("utf8")
+    return res.returncode, lines(stdout), lines(stderr)
+
+
+def bash(script, empty_dir: bool = False) -> bool:
+    username = getpass.getuser()
+    test_dir = TMP / f"bitrot-dir-{username}"
+    if empty_dir and test_dir.is_dir():
+        os.chdir(TMP)
+        shutil.rmtree(test_dir)
+    test_dir.mkdir(exist_ok=True)
+    os.chdir(test_dir)
+
+    preamble = """
+        set -euxo pipefail
+        LC_ALL=en_US.UTF-8
+        LANG=en_US.UTF-8
+        """
+
+    if script:
+        # We need to wait a second for modification timestamps to differ so that
+        # the ordering of the output stays the same every run of the tests.
+        preamble += """
+        sleep 1
+        """
+
+    script_path = TMP / "bitrot-test.bash"
+    script_path.write_text(dedent(preamble + script))
+    script_path.chmod(0o755)
+
+    out = subprocess.run(["bash", str(script_path)], capture_output=True)
+    if out.returncode:
+        print(f"Non-zero return code {out.returncode} when running {script_path}")
+        if out.stdout:
+            print(out.stdout)
+        if out.stderr:
+            print(out.stderr)
+        return False
+    return True
+
+
+def lines(s: str) -> list[str]:
+    r"""Only return non-empty lines that weren't killed by \r."""
+    return [
+        line.rstrip()
+        for line in s.splitlines(keepends=True)
+        if line and line.rstrip() and line[-1] != "\r"
+    ]
+
+
+@pytest.mark.order(1)
+def test_command_exists() -> None:
+    rc, out, err = bitrot("--help")
+    assert rc == 0
+    assert not err
+    assert out[0].startswith("usage:")
+
+    assert bash("", empty_dir=True)
+
+
+@pytest.mark.order(2)
+def test_new_files_in_a_tree_dir() -> None:
+    assert bash(
+        """
+        mkdir -p nonemptydirs/dir2/
+        touch nonemptydirs/dir2/new-file-{a,b}.txt
+        echo $RANDOM >> nonemptydirs/dir2/new-file-b.txt
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    # assert out[0] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[1] == "2 entries in the database. 2 entries new:"
+    assert out[2] == "  ./nonemptydirs/dir2/new-file-a.txt"
+    assert out[3] == "  ./nonemptydirs/dir2/new-file-b.txt"
+    assert out[4] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(3)
+def test_modified_files_in_a_tree_dir() -> None:
+    assert bash(
+        """
+        echo $RANDOM >> nonemptydirs/dir2/new-file-a.txt
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "2 entries in the database. 1 entries updated:"
+    assert out[3] == "  ./nonemptydirs/dir2/new-file-a.txt"
+    assert out[4] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(4)
+def test_renamed_files_in_a_tree_dir() -> None:
+    assert bash(
+        """
+        mv nonemptydirs/dir2/new-file-a.txt nonemptydirs/dir2/new-file-a.txt2
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "2 entries in the database. 1 entries renamed:"
+    o3 = " from ./nonemptydirs/dir2/new-file-a.txt to ./nonemptydirs/dir2/new-file-a.txt2"
+    assert out[3] == o3
+    assert out[4] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(5)
+def test_deleted_files_in_a_tree_dir() -> None:
+    assert bash(
+        """
+        rm  nonemptydirs/dir2/new-file-a.txt2
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "1 entries in the database. 1 entries missing:"
+    assert out[3] == "  ./nonemptydirs/dir2/new-file-a.txt2"
+    assert out[4] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(5)
+def test_new_files_and_modified_files_in_a_tree_dir() -> None:
+    assert bash(
+        """
+        for fil in {a,b,c,d,e,f,g}; do
+            echo $fil >> more-files-$fil.txt
+        done
+        echo $RANDOM >> nonemptydirs/dir2/new-file-b.txt
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "8 entries in the database. 7 entries new:"
+    assert out[3] == "  ./more-files-a.txt"
+    assert out[4] == "  ./more-files-b.txt"
+    assert out[5] == "  ./more-files-c.txt"
+    assert out[6] == "  ./more-files-d.txt"
+    assert out[7] == "  ./more-files-e.txt"
+    assert out[8] == "  ./more-files-f.txt"
+    assert out[9] == "  ./more-files-g.txt"
+    assert out[10] == "1 entries updated:"
+    assert out[11] == "  ./nonemptydirs/dir2/new-file-b.txt"
+    assert out[12] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(6)
+def test_new_files_modified_deleted_and_moved_in_a_tree_dir() -> None:
+    assert bash(
+        """
+        for fil in {a,b,c,d,e,f,g}; do
+            echo $fil $RANDOM >> nonemptydirs/pl-more-files-$fil.txt
+        done
+        echo $RANDOM >> nonemptydirs/dir2/new-file-b.txt
+        mv more-files-a.txt more-files-a.txt2
+        rm more-files-g.txt
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "14 entries in the database. 7 entries new:"
+    assert out[3] == "  ./nonemptydirs/pl-more-files-a.txt"
+    assert out[4] == "  ./nonemptydirs/pl-more-files-b.txt"
+    assert out[5] == "  ./nonemptydirs/pl-more-files-c.txt"
+    assert out[6] == "  ./nonemptydirs/pl-more-files-d.txt"
+    assert out[7] == "  ./nonemptydirs/pl-more-files-e.txt"
+    assert out[8] == "  ./nonemptydirs/pl-more-files-f.txt"
+    assert out[9] == "  ./nonemptydirs/pl-more-files-g.txt"
+    assert out[10] == "1 entries updated:"
+    assert out[11] == "  ./nonemptydirs/dir2/new-file-b.txt"
+    assert out[12] == "1 entries renamed:"
+    assert out[13] == " from ./more-files-a.txt to ./more-files-a.txt2"
+    assert out[14] == "1 entries missing:"
+    assert out[15] == "  ./more-files-g.txt"
+    assert out[16] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(7)
+def test_new_files_modified_deleted_and_moved_in_a_tree_dir_2() -> None:
+    assert bash(
+        """
+        for fil in {a,b,c,d,e,f,g}; do
+            echo  $RANDOM >> nonemptydirs/pl2-more-files-$fil.txt
+        done
+        echo  $RANDOM >> nonemptydirs/pl-more-files-a.txt
+        mv nonemptydirs/pl-more-files-b.txt  nonemptydirs/pl-more-files-b.txt2
+        cp nonemptydirs/pl-more-files-g.txt  nonemptydirs/pl2-more-files-g.txt2
+        cp nonemptydirs/pl-more-files-d.txt  nonemptydirs/pl2-more-files-d.txt2
+        rm more-files-f.txt nonemptydirs/pl-more-files-c.txt
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "21 entries in the database. 9 entries new:"
+    assert out[3] == "  ./nonemptydirs/pl2-more-files-a.txt"
+    assert out[4] == "  ./nonemptydirs/pl2-more-files-b.txt"
+    assert out[5] == "  ./nonemptydirs/pl2-more-files-c.txt"
+    assert out[6] == "  ./nonemptydirs/pl2-more-files-d.txt"
+    assert out[7] == "  ./nonemptydirs/pl2-more-files-d.txt2"
+    assert out[8] == "  ./nonemptydirs/pl2-more-files-e.txt"
+    assert out[9] == "  ./nonemptydirs/pl2-more-files-f.txt"
+    assert out[10] == "  ./nonemptydirs/pl2-more-files-g.txt"
+    assert out[11] == "  ./nonemptydirs/pl2-more-files-g.txt2"
+    assert out[12] == "1 entries updated:"
+    assert out[13] == "  ./nonemptydirs/pl-more-files-a.txt"
+    assert out[14] == "1 entries renamed:"
+    o15 = " from ./nonemptydirs/pl-more-files-b.txt to ./nonemptydirs/pl-more-files-b.txt2"
+    assert out[15] == o15
+    assert out[16] == "2 entries missing:"
+    assert out[17] == "  ./more-files-f.txt"
+    assert out[18] == "  ./nonemptydirs/pl-more-files-c.txt"
+    assert out[19] == "Updating bitrot.sha512... done."
+
+
+@pytest.mark.order(8)
+def test_3278_files() -> None:
+    assert bash(
+        """
+        mkdir -p alotfiles/here; cd alotfiles/here
+        # create a 320KB file
+        dd if=/dev/urandom of=masterfile bs=1 count=327680
+        # split it in 3277 files (instantly) + masterfile = 3278
+        split -b 100 -a 10 masterfile
+        """
+    )
+    rc, out, err = bitrot()
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    o2 = "3299 entries in the database, 3278 new, 0 updated, 0 renamed, 0 missing."
+    assert out[2] == o2
+
+
+@pytest.mark.order(9)
+def test_3278_files_2() -> None:
+    assert bash(
+        """
+        mv alotfiles/here alotfiles/here-moved
+        """
+    )
+    rc, out, err = bitrot()
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    o2 = "3299 entries in the database, 0 new, 0 updated, 3278 renamed, 0 missing."
+    assert out[2] == o2
+
+
+@pytest.mark.order(10)
+def test_rotten_file() -> None:
+    assert bash(
+        """
+        touch non-rotten-file
+        dd if=/dev/zero of=rotten-file bs=1k count=1000 &>/dev/null
+        # let's make sure they share the same timestamp
+        touch -r non-rotten-file rotten-file
+        """
+    )
+    rc, out, err = bitrot("-v")
+    assert rc == 0
+    assert not err
+    assert out[0] == "Checking bitrot.db integrity... ok."
+    # assert out[1] == "Finished. 0.00 MiB of data read. 0 errors found."
+    assert out[2] == "3301 entries in the database. 2 entries new:"
+    assert out[3] == "  ./non-rotten-file"
+    assert out[4] == "  ./rotten-file"
+
+
+@pytest.mark.order(11)
+def test_rotten_file_2() -> None:
+    assert bash(
+        """
+        # modify the rotten file...
+        dd if=/dev/urandom of=rotten-file bs=1k count=10 seek=1k conv=notrunc &>/dev/null
+        # ...but revert the modification date
+        touch -r non-rotten-file rotten-file
+        """
+    )
+    rc, out, err = bitrot("-q")
+    assert rc == 1
+    assert not out
+    e = (
+        "error: SHA1 mismatch for ./rotten-file: expected"
+        " 8fee1653e234fee8513245d3cb3e3c06d071493e, got"
+    )
+    assert err[0].startswith(e)
+    assert err[1] == "error: There were 1 errors found."
+
+
+@pytest.mark.order("last")
+def test_cleanup() -> None:
+    username = getpass.getuser()
+    test_dir = TMP / f"bitrot-dir-{username}"
+    if test_dir.is_dir():
+        os.chdir(TMP)
+        shutil.rmtree(test_dir)