Repository: iterative/dvc

Issue:
optimize dvcignore
From https://github.com/iterative/dvc/pull/3867 it is apparent that we need to bench dvcignore and research if anything else there requires optimization. A user (@courentin ) reported that something simple like
```
data/something
bash_projects
mlruns
notebooks
externals
examples
.circleci
.vscode
.pytest_cache
wandb
```
takes a significant time.

- [ ] add benchmark for this to dvc-bench project


Discussion:
Looked at this and I see several issues with code, most of which also affect performance:

1. `DvcIgnore*` classes designed around using them in `walk()`, which leads to excessively complex code handling check for full path.
2. All the complexity above is added to `CleanTree`, which makes it go into `DvcIgnore*` domain. It should really look like:
    ```python
    def isfile(self, path):
        return self.tree.isfile(path) and not self.dvcignore.match_file(path)
    ```
3. `DvcIgnore*` hierarchy forces sequential check against all rules and regexes. This might be optimized by constructing single structure, i.e. a big regex or a prefix tree. This is complicated by the fact that dvcignores may contain negations though.
4. `pathspec` library also checks against all regexes sequentially, which adds to 3.
5. **High level issue**. I suspect that we recheck files found via walk, so we run ignores twice. It needs to be estimated whether this is an issue.
Thank you @Suor 

It seems consistent with what I experienced. The more I add lines in `.dvcignore`, the slowest `dvc status` is.
> Looked at this and I see several issues with code, most of which also affect performance:
> 
> 1. `DvcIgnore*` classes designed around using them in `walk()`, which leads to excessively complex code handling check for full path.
> 2. All the complexity above is added to `CleanTree`, which makes it go into `DvcIgnore*` domain. It should really look like:
>    ```python
>    def isfile(self, path):
>        return self.tree.isfile(path) and not self.dvcignore.match_file(path)
>    ```
> 3. `DvcIgnore*` hierarchy forces sequential check against all rules and regexes. This might be optimized by constructing single structure, i.e. a big regex or a prefix tree. This is complicated by the fact that dvcignores may contain negations though.
> 4. `pathspec` library also checks against all regexes sequentially, which adds to 3.
> 5. **High level issue**. I suspect that we recheck files found via walk, so we run ignores twice. It needs to be estimated whether this is an issue.

@Suor 
I also have an interest in this issue and had looked into the code. And here is my solution to some of the issues above:
1. For point (1), `walk()` should use information from `DvcIgnore`. For example,  exiting the `.git` directory at the beginning of the iteration.
2. For point (3), according to [this article](https://www.freecodecamp.org/news/regex-was-taking-5-days-flashtext-does-it-in-15-minutes-55f04411025f/), tried tree or automaton would only perform better if the number of ignored-expressions was greater than several hundred. 
3. For point (4), In `pathspec`  
```python
	matched = False
	for pattern in patterns:
		if pattern.include is not None:
			if file in pattern.match((file,)):
				matched = pattern.include
	return matched
```
It should stop if any of the patterns matched the file. 
@courentin
And I think this is the main reason that It gets slower as the ignore list grows. 

I'd like to try to solve these points this weekend.
@karajan1001 
1. There is no issue with walk, the ignored dir won't we traversed. The issue is when we need to check whether `some/path/abc/file.txt` is ignored we need to build all of its parents and test them in an unnatural way.

> It should stop if any of the patterns matched the file.

So for very common case that file is not ignored it will match it against all of those.
> 1. There is no issue with walk, the ignored dir won't we traversed. The issue is when we need to check whether `some/path/abc/file.txt` is ignored we need to build all of its parents and test them in an unnatural way.

Thank you
Dos `Dvcignore` support expressions like `../*.csv` which influences files outside the current path?


Haha, underrated the difficulty of it. Only written the benchmark (https://github.com/iterative/dvc-bench/pull/30).



> 5\. **High level issue**. I suspect that we recheck files found via walk, so we run ignores twice. It needs to be estimated whether this is an issue.

@Suor, According to @courentin 's call graph in #3867 it only runs once.
@efiop @pared 
I have a question how could I test unmerged changes using `dvc-bench`.
@karajan1001 
Prepared PR explaining this in README, please take a look and review:
https://github.com/iterative/dvc-bench/pull/41
> Dos Dvcignore support expressions like ../*.csv which influences files outside the current path?

@karajan1001 No, same as gitignore, it cannot look back in the tree.
> README

Thank you
@pared Should we keep this open or are we fully done here?
@efiop sorry, autoclose. Seems to me we should leave it open. The issue potentially is still present in the case of multiple `dvcignore` files. Also, points noted by @Suor (https://github.com/iterative/dvc/issues/3869#issuecomment-635854916) still need to be addressed.

EDIT:
#3967 addresses 2 points out of 5 (addressed points are 3 and 4)

Resolving patch:
diff --git a/dvc/ignore.py b/dvc/ignore.py
--- a/dvc/ignore.py
+++ b/dvc/ignore.py
@@ -6,8 +6,10 @@
 from funcy import cached_property
 from pathspec.patterns import GitWildMatchPattern
 from pathspec.util import normalize_file
+from pygtrie import StringTrie
 
 from dvc.path_info import PathInfo
+from dvc.pathspec_math import merge_patterns
 from dvc.scm.tree import BaseTree
 from dvc.system import System
 from dvc.utils import relpath
@@ -23,25 +25,33 @@ def __call__(self, root, dirs, files):
 
 
 class DvcIgnorePatterns(DvcIgnore):
-    def __init__(self, ignore_file_path, tree):
-        assert os.path.isabs(ignore_file_path)
+    def __init__(self, pattern_list, dirname):
+
+        self.pattern_list = pattern_list
+        self.dirname = dirname
+        self.prefix = self.dirname + os.sep
 
-        self.ignore_file_path = ignore_file_path
-        self.dirname = os.path.normpath(os.path.dirname(ignore_file_path))
+        regex_pattern_list = map(
+            GitWildMatchPattern.pattern_to_regex, pattern_list
+        )
 
+        self.ignore_spec = [
+            (ignore, re.compile("|".join(item[0] for item in group)))
+            for ignore, group in groupby(regex_pattern_list, lambda x: x[1])
+            if ignore is not None
+        ]
+
+    @classmethod
+    def from_files(cls, ignore_file_path, tree):
+        assert os.path.isabs(ignore_file_path)
+        dirname = os.path.normpath(os.path.dirname(ignore_file_path))
         with tree.open(ignore_file_path, encoding="utf-8") as fobj:
-            path_spec_lines = fobj.readlines()
-            regex_pattern_list = map(
-                GitWildMatchPattern.pattern_to_regex, path_spec_lines
-            )
-            self.ignore_spec = [
-                (ignore, re.compile("|".join(item[0] for item in group)))
-                for ignore, group in groupby(
-                    regex_pattern_list, lambda x: x[1]
-                )
-                if ignore is not None
+            path_spec_lines = [
+                line for line in map(str.strip, fobj.readlines()) if line
             ]
 
+        return cls(path_spec_lines, dirname)
+
     def __call__(self, root, dirs, files):
         files = [f for f in files if not self.matches(root, f)]
         dirs = [d for d in dirs if not self.matches(root, d, True)]
@@ -51,11 +61,10 @@ def __call__(self, root, dirs, files):
     def matches(self, dirname, basename, is_dir=False):
         # NOTE: `relpath` is too slow, so we have to assume that both
         # `dirname` and `self.dirname` are relative or absolute together.
-        prefix = self.dirname + os.sep
         if dirname == self.dirname:
             path = basename
-        elif dirname.startswith(prefix):
-            rel = dirname[len(prefix) :]
+        elif dirname.startswith(self.prefix):
+            rel = dirname[len(self.prefix) :]
             # NOTE: `os.path.join` is ~x5.5 slower
             path = f"{rel}{os.sep}{basename}"
         else:
@@ -79,13 +88,47 @@ def ignore(self, path, is_dir):
         return result
 
     def __hash__(self):
-        return hash(self.ignore_file_path)
+        return hash(self.dirname + ":" + "\n".join(self.pattern_list))
 
     def __eq__(self, other):
         if not isinstance(other, DvcIgnorePatterns):
             return NotImplemented
+        return (self.dirname == other.dirname) & (
+            self.pattern_list == other.pattern_list
+        )
+
+    def __bool__(self):
+        return bool(self.pattern_list)
 
-        return self.ignore_file_path == other.ignore_file_path
+
+class DvcIgnorePatternsTrie(DvcIgnore):
+    trie = None
+
+    def __init__(self):
+        if self.trie is None:
+            self.trie = StringTrie(separator=os.sep)
+
+    def __call__(self, root, dirs, files):
+        ignore_pattern = self[root]
+        if ignore_pattern:
+            return ignore_pattern(root, dirs, files)
+        return dirs, files
+
+    def __setitem__(self, root, ignore_pattern):
+        base_pattern = self[root]
+        common_dirname, merged_pattern = merge_patterns(
+            base_pattern.dirname,
+            base_pattern.pattern_list,
+            ignore_pattern.dirname,
+            ignore_pattern.pattern_list,
+        )
+        self.trie[root] = DvcIgnorePatterns(merged_pattern, common_dirname)
+
+    def __getitem__(self, root):
+        ignore_pattern = self.trie.longest_prefix(root)
+        if ignore_pattern:
+            return ignore_pattern.value
+        return DvcIgnorePatterns([], root)
 
 
 class DvcIgnoreDirs(DvcIgnore):
@@ -127,14 +170,19 @@ def __init__(self, tree, root_dir):
             DvcIgnoreDirs([".git", ".hg", ".dvc"]),
             DvcIgnoreRepo(),
         }
-        for root, dirs, files in self.tree.walk(self.root_dir):
-            self._update(root)
-            dirs[:], files[:] = self(root, dirs, files)
-
-    def _update(self, dirname):
+        ignore_pattern_trie = DvcIgnorePatternsTrie()
+        for root, dirs, _ in self.tree.walk(self.root_dir):
+            ignore_pattern = self._get_ignore_pattern(root)
+            if ignore_pattern:
+                ignore_pattern_trie[root] = ignore_pattern
+                self.ignores.add(ignore_pattern_trie)
+            dirs[:], _ = self(root, dirs, [])
+
+    def _get_ignore_pattern(self, dirname):
         ignore_file_path = os.path.join(dirname, DvcIgnore.DVCIGNORE_FILE)
         if self.tree.exists(ignore_file_path):
-            self.ignores.add(DvcIgnorePatterns(ignore_file_path, self.tree))
+            return DvcIgnorePatterns.from_files(ignore_file_path, self.tree)
+        return None
 
     def __call__(self, root, dirs, files):
         for ignore in self.ignores:
diff --git a/dvc/pathspec_math.py b/dvc/pathspec_math.py
new file mode 100644
--- /dev/null
+++ b/dvc/pathspec_math.py
@@ -0,0 +1,85 @@
+# Path Specification Pattern Math
+# Including changing base dir of path specification patterns and merging
+# of two path specification patterns with different base
+# All the operations follow the documents of `gitignore`
+import os
+
+from pathspec.util import normalize_file
+
+
+def _not_ignore(rule):
+    return (True, rule[1:]) if rule.startswith("!") else (False, rule)
+
+
+def _is_comment(rule):
+    return rule.startswith("#")
+
+
+def _remove_slash(rule):
+    if rule.startswith("\\"):
+        return rule[1:]
+    return rule
+
+
+def _match_all_level(rule):
+    if rule[:-1].find("/") >= 0 and not rule.startswith("**/"):
+        if rule.startswith("/"):
+            rule = rule[1:]
+        return False, rule
+    if rule.startswith("**/"):
+        rule = rule[3:]
+    return True, rule
+
+
+def change_rule(rule, rel):
+    rule = rule.strip()
+    if _is_comment(rule):
+        return rule
+    not_ignore, rule = _not_ignore(rule)
+    match_all, rule = _match_all_level(rule)
+    rule = _remove_slash(rule)
+    if not match_all:
+        rule = f"/{rule}"
+    else:
+        rule = f"/**/{rule}"
+    if not_ignore:
+        rule = f"!/{rel}{rule}"
+    else:
+        rule = f"/{rel}{rule}"
+    rule = normalize_file(rule)
+    return rule
+
+
+def _change_dirname(dirname, pattern_list, new_dirname):
+    if new_dirname == dirname:
+        return pattern_list
+    rel = os.path.relpath(dirname, new_dirname)
+    if rel.startswith(".."):
+        raise ValueError("change dirname can only change to parent path")
+
+    return [change_rule(rule, rel) for rule in pattern_list]
+
+
+def merge_patterns(prefix_a, pattern_a, prefix_b, pattern_b):
+    """
+    Merge two path specification patterns.
+
+    This implementation merge two path specification patterns on different
+    bases. It returns the longest common parent directory, and the patterns
+    based on this new base directory.
+    """
+    if not pattern_a:
+        return prefix_b, pattern_b
+    elif not pattern_b:
+        return prefix_a, pattern_a
+
+    longest_common_dir = os.path.commonpath([prefix_a, prefix_b])
+    new_pattern_a = _change_dirname(prefix_a, pattern_a, longest_common_dir)
+    new_pattern_b = _change_dirname(prefix_b, pattern_b, longest_common_dir)
+
+    if len(prefix_a) < len(prefix_b):
+        merged_pattern = new_pattern_a + new_pattern_b
+    else:
+        merged_pattern = new_pattern_b + new_pattern_a
+
+    return longest_common_dir, merged_pattern


Test patch:
diff --git a/tests/func/test_ignore.py b/tests/func/test_ignore.py
--- a/tests/func/test_ignore.py
+++ b/tests/func/test_ignore.py
@@ -8,6 +8,7 @@
     DvcIgnore,
     DvcIgnoreDirs,
     DvcIgnorePatterns,
+    DvcIgnorePatternsTrie,
     DvcIgnoreRepo,
 )
 from dvc.repo import Repo
@@ -98,12 +99,19 @@ def test_ignore_collecting_dvcignores(tmp_dir, dvc, dname):
 
     assert len(dvc.tree.dvcignore.ignores) == 3
     assert DvcIgnoreDirs([".git", ".hg", ".dvc"]) in dvc.tree.dvcignore.ignores
+    ignore_pattern_trie = None
+    for ignore in dvc.tree.dvcignore.ignores:
+        if isinstance(ignore, DvcIgnorePatternsTrie):
+            ignore_pattern_trie = ignore
+
+    assert ignore_pattern_trie is not None
     assert (
-        DvcIgnorePatterns(
+        DvcIgnorePatterns.from_files(
             os.fspath(top_ignore_file), WorkingTree(dvc.root_dir)
         )
-        in dvc.tree.dvcignore.ignores
+        == ignore_pattern_trie[os.fspath(ignore_file)]
     )
+
     assert any(
         i for i in dvc.tree.dvcignore.ignores if isinstance(i, DvcIgnoreRepo)
     )
@@ -236,3 +244,102 @@ def test_ignore_directory(tmp_dir, dvc):
     assert _files_set("dir", dvc.tree) == {
         "dir/{}".format(DvcIgnore.DVCIGNORE_FILE),
     }
+
+
+def test_multi_ignore_file(tmp_dir, dvc, monkeypatch):
+    tmp_dir.gen({"dir": {"subdir": {"should_ignore": "1", "not_ignore": "1"}}})
+    tmp_dir.gen(DvcIgnore.DVCIGNORE_FILE, "dir/subdir/*_ignore")
+    tmp_dir.gen({"dir": {DvcIgnore.DVCIGNORE_FILE: "!subdir/not_ignore"}})
+
+    assert _files_set("dir", dvc.tree) == {
+        "dir/subdir/not_ignore",
+        "dir/{}".format(DvcIgnore.DVCIGNORE_FILE),
+    }
+
+
+def test_pattern_trie_tree(tmp_dir, dvc):
+    tmp_dir.gen(
+        {
+            "top": {
+                "first": {
+                    DvcIgnore.DVCIGNORE_FILE: "a\nb\nc",
+                    "middle": {
+                        "second": {
+                            DvcIgnore.DVCIGNORE_FILE: "d\ne\nf",
+                            "bottom": {},
+                        }
+                    },
+                },
+            },
+            "other": {DvcIgnore.DVCIGNORE_FILE: "1\n2\n3"},
+        }
+    )
+    ignore_pattern_trie = None
+    for ignore in dvc.tree.dvcignore.ignores:
+        if isinstance(ignore, DvcIgnorePatternsTrie):
+            ignore_pattern_trie = ignore
+            break
+
+    assert ignore_pattern_trie is not None
+    ignore_pattern_top = ignore_pattern_trie[os.fspath(tmp_dir / "top")]
+    ignore_pattern_other = ignore_pattern_trie[os.fspath(tmp_dir / "other")]
+    ignore_pattern_first = ignore_pattern_trie[
+        os.fspath(tmp_dir / "top" / "first")
+    ]
+    ignore_pattern_middle = ignore_pattern_trie[
+        os.fspath(tmp_dir / "top" / "first" / "middle")
+    ]
+    ignore_pattern_second = ignore_pattern_trie[
+        os.fspath(tmp_dir / "top" / "first" / "middle" / "second")
+    ]
+    ignore_pattern_bottom = ignore_pattern_trie[
+        os.fspath(tmp_dir / "top" / "first" / "middle" / "second" / "bottom")
+    ]
+    assert not ignore_pattern_top
+    assert (
+        DvcIgnorePatterns([], os.fspath(tmp_dir / "top")) == ignore_pattern_top
+    )
+    assert (
+        DvcIgnorePatterns(["1", "2", "3"], os.fspath(tmp_dir / "other"))
+        == ignore_pattern_other
+    )
+    assert (
+        DvcIgnorePatterns(
+            ["a", "b", "c"], os.fspath(tmp_dir / "top" / "first")
+        )
+        == ignore_pattern_first
+    )
+    assert (
+        DvcIgnorePatterns(
+            ["a", "b", "c"], os.fspath(tmp_dir / "top" / "first")
+        )
+        == ignore_pattern_middle
+    )
+    assert (
+        DvcIgnorePatterns(
+            [
+                "a",
+                "b",
+                "c",
+                "/middle/second/**/d",
+                "/middle/second/**/e",
+                "/middle/second/**/f",
+            ],
+            os.fspath(tmp_dir / "top" / "first"),
+        )
+        == ignore_pattern_second
+    )
+    assert (
+        DvcIgnorePatterns(
+            [
+                "a",
+                "b",
+                "c",
+                "/middle/second/**/d",
+                "/middle/second/**/e",
+                "/middle/second/**/f",
+            ],
+            os.fspath(tmp_dir / "top" / "first"),
+        )
+        == ignore_pattern_bottom
+    )
diff --git a/tests/unit/test_ignore.py b/tests/unit/test_ignore.py
--- a/tests/unit/test_ignore.py
+++ b/tests/unit/test_ignore.py
@@ -9,7 +9,7 @@
 def mock_dvcignore(dvcignore_path, patterns):
     tree = MagicMock()
     with patch.object(tree, "open", mock_open(read_data="\n".join(patterns))):
-        ignore_patterns = DvcIgnorePatterns(dvcignore_path, tree)
+        ignore_patterns = DvcIgnorePatterns.from_files(dvcignore_path, tree)
 
     return ignore_patterns
 
diff --git a/tests/unit/test_pathspec_math.py b/tests/unit/test_pathspec_math.py
new file mode 100644
--- /dev/null
+++ b/tests/unit/test_pathspec_math.py
@@ -0,0 +1,72 @@
+import pytest
+
+from dvc.pathspec_math import _change_dirname
+
+
+@pytest.mark.parametrize(
+    "patterns, dirname, changed",
+    [
+        # A line starting with # serves as a comment.
+        ("#comment", "/dir", "#comment"),
+        # Put a backslash ("\") in front of the first hash for patterns that
+        # begin with a hash.
+        ("\\#hash", "/dir", "/dir/**/#hash"),
+        ("\\#hash", "/#dir", "/#dir/**/#hash"),
+        # Trailing spaces are ignored unless they are quoted with
+        # backslash ("\").
+        (" space", "/dir", "/dir/**/space"),
+        ("\\ space", "/dir", "/dir/**/ space"),
+        # An optional prefix "!" which negates the pattern;
+        ("!include", "/dir", "!/dir/**/include"),
+        # Put a backslash ("\") in front of the first "!" for patterns that
+        # begin with a literal "!", for example, "\!important!.txt".
+        ("\\!important!.txt", "/dir", "/dir/**/!important!.txt"),
+        # If there is a separator at the beginning or middle (or both) of the
+        # pattern, then the pattern is relative to the directory level of the
+        # particular .gitignore file itself.
+        ("/separator.txt", "/dir", "/dir/separator.txt"),
+        ("subdir/separator.txt", "/dir", "/dir/subdir/separator.txt"),
+        # Otherwise the pattern may also match at any level below
+        # the .gitignore level.
+        ("no_sep", "/dir", "/dir/**/no_sep"),
+        # If there is a separator at the end of the pattern then the pattern
+        # will only match directories, otherwise the pattern can match both
+        # files and directories.
+        ("doc/fortz/", "/dir", "/dir/doc/fortz/"),
+        ("fortz/", "/dir", "/dir/**/fortz/"),
+        # An asterisk "*" matches anything except a slash.
+        ("*aste*risk*", "/dir", "/dir/**/*aste*risk*"),
+        # The character "?" matches any one character except "/".
+        ("?fi?le?", "/dir", "/dir/**/?fi?le?"),
+        # The range notation, e.g. [a-zA-Z], can be used to match one of the
+        # characters in a range. See fnmatch(3) and the FNM_PATHNAME flag
+        # for a more detailed description.
+        ("[a-zA-Z]file[a-zA-Z]", "/dir", "/dir/**/[a-zA-Z]file[a-zA-Z]"),
+        # Two consecutive asterisks ("**") in patterns matched against full
+        # pathname may have special meaning:
+        # A leading "**" followed by a slash means match in all directories.
+        # For example, "**/foo" matches file or directory "foo" anywhere,
+        # the same as pattern "foo".
+        ("**/foo", "/dir", "/dir/**/foo"),
+        # "**/foo/bar" matches file or directory "bar" anywhere that is
+        # directly under directory "foo".
+        ("**/foo/bar", "/dir", "/dir/**/foo/bar"),
+        # A trailing "/**" matches everything inside.
+        # For example, "abc/**" matches all files inside directory "abc",
+        # relative to the location of the .gitignore file, with infinite depth.
+        ("abc/**", "/dir", "/dir/abc/**"),
+        # A slash followed by two consecutive asterisks then a slash matches
+        # zero or more directories. For example, "a/**/b"
+        # matches "a/b", "a/x/b", "a/x/y/b" and so on.
+        ("a/**/b", "/dir", "/dir/a/**/b"),
+        # Other consecutive asterisks are considered regular asterisks and
+        # will match according to the previous rules.
+        ("/***.txt", "/dir", "/dir/***.txt"),
+        ("data/***", "/dir", "/dir/data/***"),
+        ("***/file.txt", "/dir", "/dir/***/file.txt"),
+        ("***file", "/dir", "/dir/**/***file"),
+        ("a/***/b", "/dir", "/dir/a/***/b"),
+    ],
+)
+def test_dvcignore_pattern_change_dir(tmp_dir, patterns, dirname, changed):
+    assert _change_dirname(dirname, [patterns], "/") == [changed]