Every time a bug is fixed, developers leave a trace – in the version database when they commit the fix, or in the bug database when they close the bug. In this chapter, we learn how to mine these repositories for past changes and bugs, and how to map them to individual modules and functions, highlighting those project components that have seen most changes and fixes over time.
Prerequisites
The history of any software project is a history of change. Any nontrivial project thus comes with a version database to organize and track changes; and possibly also with an issue database to organize and track issues.
Over time, these databases hold plenty of information about the project: Who changed what, when, and why? This information can be mined from existing databases and analyzed to answer questions such as
To answer such questions, we can mine change and bug histories for past changes and fixes. This involves digging through version databases such as git
and issue trackers such as RedMine or Bugzilla and extracting all their information. Fortunately for us, there is ready-made infrastructure for some of this.
PyDriller is a Python package for mining change histories. Its Repository
class takes a git
version repository and allows to access all the individual changes ("modifications"), together with committers, affected files, commit messages, and more.
To use Repository
, we need to pass it
git
repository; orgit
repository can be found.In general, cloning a git
repository locally (with git clone URL
) and then analyzing it locally will be faster and require less network resources.
Let us apply Repository
on the repository of this book. The function current_repo()
returns the directory in which a .git
subdirectory is stored – that is, the root of a cloned git
repository.
# ignore
from typing import Callable, Optional, Type, Tuple, Any
from typing import Dict, Union, Set, List
def current_repo() -> Optional[str]:
path = os.getcwd()
while True:
if os.path.exists(os.path.join(path, '.git')):
return os.path.normpath(path)
# Go one level up
new_path = os.path.normpath(os.path.join(path, '..'))
if new_path != path:
path = new_path
else:
return None
return None
current_repo()
'/Users/zeller/Projects/debuggingbook'
This gives us a repository miner for the book:
book_miner = Repository(current_repo(), to=datetime(2020, 10, 1))
The to
argument limits the range of time we want to look at.
You can also specify a URL instead, but this will access the repository via the network and generally be much slower.
DEBUGGINGBOOK_REMOTE_REPO = 'https://github.com/uds-se/debuggingbook.git'
# book_miner = Repository(DEBUGGINGBOOK_REMOTE_REPO)
# ignore
if 'CI' in os.environ:
# The CI git clone is shallow, so access full repo remotely
book_miner = Repository(DEBUGGINGBOOK_REMOTE_REPO,
to=datetime(2020, 10, 1))
traverse_commits()
is a generator that returns one commit after another. Let us fetch the very first commit made to the book:
book_commits = book_miner.traverse_commits()
book_first_commit = next(book_commits)
Each commit has a number of attributes telling us more about the commit.
[attr for attr in dir(book_first_commit) if not attr.startswith('_')]
['author', 'author_date', 'author_timezone', 'branches', 'committer', 'committer_date', 'committer_timezone', 'deletions', 'dmm_unit_complexity', 'dmm_unit_interfacing', 'dmm_unit_size', 'files', 'hash', 'in_main_branch', 'insertions', 'lines', 'merge', 'modified_files', 'msg', 'parents', 'project_name', 'project_path']
For instance, the msg
attribute lets us know about the commit message:
book_first_commit.msg
'first commit'
whereas the author
attribute gets us the name and email of the person who made the commit:
[attr for attr in dir(book_first_commit.author) if not attr.startswith('_')]
['email', 'name']
book_first_commit.author.name, book_first_commit.author.email
('Andreas Zeller', 'zeller@cispa.saarland')
A commit consists of multiple modifications to possibly multiple files. The commit modified_files
attribute returns a list of modifications.
book_first_commit.modified_files
[<pydriller.domain.commit.ModifiedFile at 0x1191673a0>]
For each modification, we can retrieve the files involved as well as several statistics:
[attr for attr in dir(book_first_commit.modified_files[0]) if not attr.startswith('_')]
['added_lines', 'change_type', 'changed_methods', 'complexity', 'content', 'content_before', 'deleted_lines', 'diff', 'diff_parsed', 'filename', 'language_supported', 'methods', 'methods_before', 'new_path', 'nloc', 'old_path', 'source_code', 'source_code_before', 'token_count']
Let us see which file was created with this modification:
book_first_commit.modified_files[0].new_path
'README.md'
The content
attribute holds the entire file contents after the modification.
print(book_first_commit.modified_files[0].content)
b'# debuggingbook\n'
We see that the debuggingbook
project started with a very simple commit, namely the addition of an (almost empty) README.md
file.
The attribute content_before
holds the previous source code. We see that it is None
– the file was just created.
print(book_first_commit.modified_files[0].content_before)
None
Let us have a look at the second commit. We see that it is much more substantial already.
book_second_commit = next(book_commits)
[m.new_path for m in book_second_commit.modified_files]
['Chapters.makefile', 'LICENSE.md', 'Makefile', 'README.md', 'debuggingbook.bib', 'ipypublish', 'ipypublish_plugins', 'notebooks/.ipynb_checkpoints/index-checkpoint.ipynb', 'notebooks/index.ipynb', 'utils']
We fetch the modification for the README.md
file:
readme_modification = [m for m in book_second_commit.modified_files if m.new_path == 'README.md'][0]
The content_before
attribute holds the previous version (which we already have seen):
print(str(readme_modification.content_before, 'utf8'))
# debuggingbook
The content
attribute holds the new version – now a complete "README" file. (Compare this first version to the current README text.)
print(str(readme_modification.content[:400], 'utf8'))
# About this Book __Welcome to "The Debugging Book"!__ Software has bugs, and finding bugs can involve lots of effort. This book addresses this problem by _automating_ software debugging, specifically by _locating errors and their causes automatically_. Recent years have seen the development of novel techniques that lead to dramatic improvements in test generation and software testing. They
The diff
attribute holds the differences between the old and the new version.
print(readme_modification.diff[:100])
@@ -1 +1,157 @@ -# debuggingbook + +# About this Book + +__Welcome to "The Debugging Book"!__ + +So
The diff_parsed
attribute even lists added and deleted lines:
readme_modification.diff_parsed['added'][:10]
[(1, ''), (2, '# About this Book'), (3, ''), (4, '__Welcome to "The Debugging Book"!__'), (5, ''), (6, 'Software has bugs, and finding bugs can involve lots of effort. This book addresses this problem by _automating_ software debugging, specifically by _locating errors and their causes automatically_. Recent years have seen the development of novel techniques that lead to dramatic improvements in test generation and software testing. They now are mature enough to be assembled in a book – even with executable code.'), (7, ''), (8, ''), (9, ''), (10, '## A Textbook for Paper, Screen, and Keyboard')]
With all this information, we can track all commits and modifications and establish statistics over which files were changed (and possibly even fixed) most. This is what we will do in the next section.
# ignore
del book_miner # Save a bit of memory
We start with a simple ChangeCounter
class that, given a repository, counts for each file how frequently it was changed.
We represent file names as nodes – a tuple $(f_1, f_2, ..., f_n)$ that denotes a hierarchy: Each $f_i$ is a directory holding $f_{i+1}$, with $f_n$ being the actual file. Here is what this notebook looks as a node:
tuple('debuggingbook/notebooks/ChangeCounter.ipynb'.split('/'))
('debuggingbook', 'notebooks', 'ChangeCounter.ipynb')
Node = Tuple
The constructor takes the repository to be analyzed and sets the internal counters.
class ChangeCounter:
"""Count the number of changes for a repository."""
def __init__(self, repo: str, *,
filter: Optional[Callable[[Commit], bool]] = None,
log: bool = False,
**kwargs: Any) -> None:
"""
Constructor.
`repo` is a git repository (as URL or directory).
`filter` is a predicate that takes a modification and returns True
if it should be considered (default: consider all).
`log` turns on logging if set.
`kwargs` are passed to the `Repository()` constructor.
"""
self.repo = repo
self.log = log
if filter is None:
def filter(m: ModifiedFile) -> bool:
return True
assert filter is not None
self.filter = filter
# A node is an tuple (f_1, f_2, f_3, ..., f_n) denoting
# a folder f_1 holding a folder f_2 ... holding a file f_n.
# Mapping node -> #of changes
self.changes: Dict[Node, int] = defaultdict(int)
# Mapping node -> list of commit messages
self.messages: Dict[Node, List[str]] = defaultdict(list)
# Mapping node -> last size seen
self.sizes: Dict[Node, Union[int, float]] = {}
self.mine(**kwargs)
The method mine()
does all the heavy lifting of mining. It retrieves all commits and all modifications from the repository, passing the modifications through the update_stats()
method.
class ChangeCounter(ChangeCounter):
def mine(self, **kwargs: Any) -> None:
"""Gather data from repository. To be extended in subclasses."""
miner = Repository(self.repo, **kwargs)
for commit in miner.traverse_commits():
try:
self.mine_commit(commit)
except GitCommandError as err:
# Warn about failing git commands, but continue
warnings.warn("Cannot mine commit " + repr(commit.hash) + '\n' + str(err))
except (ValueError, TypeError) as err:
warnings.warn("Cannot mine commit " + repr(commit.hash) + '\n' + str(err))
raise err
def mine_commit(self, commit: Commit) -> None:
for m in commit.modified_files:
m.committer = commit.committer
m.committer_date = commit.committer_date
m.msg = commit.msg
if self.include(m):
self.update_stats(m)
The include()
method allows filtering modifications. For simplicity, we copy the most relevant attributes of the commit over to the modification, such that the filter can access them, too.
class ChangeCounter(ChangeCounter):
def include(self, m: ModifiedFile) -> bool:
"""
Return True if the modification `m` should be included
(default: the `filter` predicate given to the constructor).
To be overloaded in subclasses.
"""
return self.filter(m)
For each such node, update_stats()
then invokes update_size()
, update_changes()
, and update_elems()
.
class ChangeCounter(ChangeCounter):
def update_stats(self, m: ModifiedFile) -> None:
"""
Update counters with modification `m`.
Can be extended in subclasses.
"""
if not m.new_path:
return
node = tuple(m.new_path.split('/'))
self.update_size(node, len(m.content) if m.content else 0)
self.update_changes(node, m.msg)
self.update_elems(node, m)
update_size()
simply saves the last size of the item being modified. Since we progress from first to last commit, this reflects the size of the newest version.
class ChangeCounter(ChangeCounter):
def update_size(self, node: Tuple, size: int) -> None:
"""
Update counters for `node` with `size`.
Can be extended in subclasses.
"""
self.sizes[node] = size
update_changes()
increases the counter changes
for the given node node
, and adds the current commit message commit_msg
to its list. This makes
size
a mapping of nodes to their sizechanges
a mapping of nodes to the number of changes they have seencommit_msg
a mapping of nodes to the list of commit messages that have affected them.class ChangeCounter(ChangeCounter):
def update_changes(self, node: Tuple, commit_msg: str) -> None:
"""
Update stats for `node` changed with `commit_msg`.
Can be extended in subclasses.
"""
self.changes[node] += 1
self.messages[node].append(commit_msg)
The update_elems()
method is reserved for later use, when we go and count fine-grained changes.
class ChangeCounter(ChangeCounter):
def update_elems(self, node: Tuple, m: ModifiedFile) -> None:
"""
Update counters for subelements of `node` with modification `m`.
To be defined in subclasses.
"""
pass
Let us put ChangeCounter
to action – on the current (debuggingbook) repository.
DEBUGGINGBOOK_REPO = current_repo()
DEBUGGINGBOOK_REPO
'/Users/zeller/Projects/debuggingbook'
The function debuggingbook_change_counter
instantiates a ChangeCounter
class (or any subclass) with the debuggingbook repository, mining all the counters as listed above. Since mining all history takes quite some time, its parameter start_date
allows to set a starting date (default: March 1, 2021); changes before that date will be ignored.
DEBUGGINGBOOK_START_DATE: datetime = datetime(2021, 3, 1)
NUM_WORKERS = 4 # Number of threads to be run in parallel
def debuggingbook_change_counter(
cls: Type,
start_date: datetime = DEBUGGINGBOOK_START_DATE) -> Any:
"""
Instantiate a ChangeCounter (sub)class `cls` with the debuggingbook repo.
Only mines changes after `start_date` (default: DEBUGGINGBOOK_START_DATE)
"""
def filter(m: ModifiedFile) -> bool:
"""
Do not include
* the `docs/` directory; it only holds generated Web pages
* the `notebooks/shared/` package; this is infrastructure
* the `synopsis` pictures; these are all generated
"""
return (m.new_path and
not m.new_path.startswith('docs/') and
not m.new_path.startswith('notebooks/shared/') and
'-synopsis-' not in m.new_path)
return cls(DEBUGGINGBOOK_REPO,
filter=filter,
since=start_date,
num_workers=NUM_WORKERS)
Let us set change_counter
to this ChangeCounter
instance. This can take a few minutes.
with Timer() as t:
change_counter = debuggingbook_change_counter(ChangeCounter)
t.elapsed_time()
120.80079912499059
The attribute changes
of our ChangeCounter
now is a mapping of nodes to the respective number of changes. Here are the first 10 entries:
list(change_counter.changes.keys())[:10]
[('notebooks', 'Slicer.ipynb'), ('.github', 'workflows', 'check-code.yml'), ('.github', 'workflows', 'check-notebooks.yml'), ('code', 'requirements.txt'), ('Chapters.makefile',), ('notebooks', 'ChangeDebugger.ipynb'), ('notebooks', 'DeltaDebugger.ipynb'), ('notebooks', 'Assertions.ipynb'), ('notebooks', 'ChangeCounter.ipynb'), ('notebooks', 'DDSetDebugger.ipynb')]
This is the number of changes to the Chapters.makefile
file which lists the book chapters:
change_counter.changes.get(('Chapters.makefile',), None)
30
The messages
attribute holds all the messages:
change_counter.messages.get(('Chapters.makefile',), None)
['New: publish DeltaDebugger', 'New release: ChangeDebugger', 'New: publish StatisticalDebugger', 'Made StatisticalDebugger visible', 'New: public chapter on dynamic invariants', 'New: publish DDSetDebugger', 'New: PerformanceDebugger goes live', 'New: Publish repair chapter', 'New chapter: Tracking', 'New: ChangeCounter is public', 'New: do not check types in fuzzingbook (yet)', 'New: release first chapters', "New: have a 'shared' directory for material shared between fuzzingbook and debuggingbook; avoid cross-project links", "New: 'make shared' syncs the 'shared' folder", 'New: can now run notebooks and check HTML as part of CI', 'New: Assertions is ready', "Fix: Mark 'Assertions' as new, too", 'New: publish Slicer', 'Fix: DEPENDENCIES_PART was missing in PUBLIC_CHAPTERS', 'New: (Incomplete) chapters on performance and concurrency debugging', 'New: moved StackInspector in its own module', "New: mark (pretty much) all chapters as 'ready'", 'Doc fix', 'New: checking types is now the default', 'New: illustrated code', 'New: Illustrated Code', 'New: efficient timeout handling', 'Fix: added default target', 'Fix: bad default target', 'No new chapters']
for node in change_counter.changes:
assert len(change_counter.messages[node]) == change_counter.changes[node]
The sizes
attribute holds the final size:
change_counter.sizes.get(('Chapters.makefile',), None)
3743
To explore the number of changes across all project files, we visualize them as a tree map. A tree map visualizes hierarchical data using nested rectangles. In our visualization, each directory is shown as a rectangle containing smaller rectangles. The size of a rectangle is relative to its size (in bytes); and the color of a rectangle is relative to the number of changes it has seen.
We use the easyplotly package to easily create a treemap.
The method map_node_sizes()
returns a size for the node – any number will do. By default, we use a logarithmic scale, such that smaller files are not totally visually eclipsed by larger files.
class ChangeCounter(ChangeCounter):
def map_node_sizes(self,scale: str = 'log') -> \
Dict[Node, Union[int, float]]:
"""
Return a mapping of nodes to sizes.
Can be overloaded in subclasses.
"""
if scale == 'log':
# Default: use log scale
return {node: math.log(size+1)
for node, size in self.sizes.items()}
elif scale == 'sqrt':
# Alternative: use sqrt size
return {node: math.sqrt(size)
for node, size in self.sizes.items()}
elif scale == 'abs':
# Alternative: use absolute size
return self.sizes
else:
raise ValueError(f"Unknown scale: {scale}; "
f"use one of [log, sqrt, abs]")
The method map_node_color()
returns a color for the node – again, as a number. The smallest and largest numbers returned indicate beginning and end in the given color scale, respectively.
class ChangeCounter(ChangeCounter):
def map_node_color(self, node: Node) -> Optional[int]:
"""
Return a color of the node, as a number.
Can be overloaded in subclasses.
"""
return self.changes.get(node)
The method map_node_text()
shows a text to be displayed in the rectangle; we set this to the number of changes.
class ChangeCounter(ChangeCounter):
def map_node_text(self, node: Node) -> Optional[str]:
"""
Return the text to be shown for the node (default: #changes).
Can be overloaded in subclasses.
"""
change = self.changes.get(node)
return str(change) if change is not None else None
The methods map_hoverinfo()
and map_colorscale()
set additional map parameters. For details, see the easyplotly documentation.
class ChangeCounter(ChangeCounter):
def map_hoverinfo(self) -> str:
"""
Return the text to be shown when hovering over a node.
To be overloaded in subclasses.
"""
return 'label+text'
def map_colorscale(self) -> str:
"""
Return the colorscale for the map. To be overloaded in subclasses.
"""
return 'YlOrRd'
With all this, the map()
function creates a tree map of the repository, using the easyplotly Treemap
constructor.
class ChangeCounter(ChangeCounter):
def map(self) -> go.Figure:
"""Produce an interactive tree map of the repository."""
treemap = ep.Treemap(
self.map_node_sizes(),
text=self.map_node_text,
hoverinfo=self.map_hoverinfo(),
marker_colors=self.map_node_color,
marker_colorscale=self.map_colorscale(),
root_label=self.repo,
branchvalues='total'
)
fig = go.Figure(treemap)
fig.update_layout(margin=dict(l=0, r=0, t=30, b=0))
return fig
This is what the tree map for debuggingbook
looks like.
change_counter = debuggingbook_change_counter(ChangeCounter)
change_counter.map()