Merge branch 'main' into dependabot/pip/dot-github/workflows/virtuale…

…nv-20.23.1

.github/workflows/release.yml

@@ -50,8 +50,8 @@ jobs:
         run: |
           set -o pipefail
           # Set git details
-          git config --global user.name "github-actions"
-          git config --global user.email "github-actions@github.com"
+          git config --global user.name "Erik Båvenstrand"
+          git config --global user.email "erik@bavenstrand.com"
           # Run semantic-release
           poetry run semantic-release publish -v DEBUG -D commit_author="github-actions <[email protected]>"
           output_value=$(poetry version | awk "{print $2}")

mleko/cache/cache_mixin.py

@@ -99,14 +99,24 @@ def _cached_execute(
         self,
         lambda_func: Callable[[], Any],
         cache_keys: list[Hashable | tuple[Any, BaseFingerprinter]],
+        cache_group: str | None = None,
         force_recompute: bool = False,
     ) -> Any:
         """Executes the given function, caching the results based on the provided cache keys and fingerprints.
 
+        Warning:
+            The cache group is used to group related cache keys together to prevent collisions between cache keys
+            originating from the same method. For example, if a method is called during the training and testing
+            phases of a machine learning pipeline, the cache keys for the training and testing phases should be
+            using different cache groups to prevent collisions between the cache keys for the two phases. Otherwise,
+            the later cache keys might overwrite the earlier cache entries.
+
         Args:
             lambda_func: A lambda function to execute.
             cache_keys: A list of cache keys that can be a mix of hashable values and tuples containing a value and a
                 BaseFingerprinter instance for generating fingerprints.
+            cache_group: A string representing the cache group, used to group related cache keys together when methods
+                are called independently.
             force_recompute: A boolean indicating whether to force recompute the result and update the cache, even if a
                 cached result is available.
 
@@ -116,7 +126,7 @@ def _cached_execute(
         """
         frame_qualname = get_frame_qualname(inspect.stack()[1])
         class_method_name = ".".join(frame_qualname.split(".")[-2:])
-        cache_key = self._compute_cache_key(cache_keys, frame_qualname)
+        cache_key = self._compute_cache_key(cache_keys, class_method_name, cache_group)
 
         if not force_recompute:
             output = self._load_from_cache(cache_key)
@@ -139,14 +149,22 @@ def _cached_execute(
         return self._load_from_cache(cache_key)
 
     def _compute_cache_key(
-        self, cache_keys: list[Hashable | tuple[Any, BaseFingerprinter]], frame_qualname: str
+        self,
+        cache_keys: list[Hashable | tuple[Any, BaseFingerprinter]],
+        class_method_name: str,
+        cache_group: str | None = None,
     ) -> str:
         """Computes the cache key based on the provided cache keys and the calling function's fully qualified name.
 
         Args:
             cache_keys: A list of cache keys that can be a mix of hashable values and tuples containing a value and a
                 BaseFingerprinter instance for generating fingerprints.
-            frame_qualname: The fully qualified name of the cached function stack frame.
+            class_method_name: A string of format "class.method" for class methods or "module.function" for
+                functions, representing the fully qualified name of the calling function or method.
+            cache_group: A string representing the cache group.
+
+        Raises:
+            ValueError: If the computed cache key is too long.
 
         Returns:
             A string representing the computed cache key, which is the MD5 hash of the fully qualified name of the
@@ -161,12 +179,22 @@ def _compute_cache_key(
             else:
                 values_to_hash.append(key)
 
-        data = pickle.dumps((frame_qualname, values_to_hash))
-
-        class_method_name = ".".join(frame_qualname.split(".")[-2:])
-        cache_key = f"{class_method_name}.{hashlib.md5(data).hexdigest()}"
+        data = pickle.dumps(values_to_hash)
+        cache_key_prefix = class_method_name
+        if cache_group is not None:
+            cache_key_prefix = f"{cache_key_prefix}.{cache_group}"
+
+        cache_key = f"{cache_key_prefix}.{hashlib.md5(data).hexdigest()}"
+        if len(cache_key) + 1 + len(self._cache_file_suffix) > 255:
+            raise ValueError(
+                f"The computed cache key is too long ({len(cache_key) + len(self._cache_file_suffix)} chars)."
+                "The maximum length of a cache key is 255 chars, and given the current class, the maximum "
+                "length of the provided cache_group is "
+                f"{255 - len(cache_key_prefix) - 32 - 1 - len(self._cache_file_suffix)} chars."
+                "Please reduce the length of the cache_group."
+            )
 
-        return cache_key
+        return f"{cache_key_prefix}.{hashlib.md5(data).hexdigest()}"
 
     def _read_cache_file(self, cache_file_path: Path) -> Any:
         """Reads the cache file from the specified path and returns the deserialized data.

mleko/cache/lru_cache_mixin.py

@@ -10,7 +10,7 @@
 
 import inspect
 import re
-from collections import OrderedDict
+from collections import OrderedDict, defaultdict
 from pathlib import Path
 from typing import Any
 
@@ -69,7 +69,7 @@ def __init__(self, cache_directory: str | Path, cache_file_suffix: str, cache_si
         """
         super().__init__(cache_directory, cache_file_suffix)
         self._cache_size = cache_size
-        self._cache: OrderedDict[str, bool] = OrderedDict()
+        self._cache: dict[str, OrderedDict[str, bool]] = defaultdict(OrderedDict)
         self._load_cache_from_disk()
 
     def _load_cache_from_disk(self) -> None:
@@ -79,23 +79,30 @@ def _load_cache_from_disk(self) -> None:
         """
         frame_qualname = get_frame_qualname(inspect.stack()[2])
         class_name = frame_qualname.split(".")[-2]
-        file_name_pattern = rf"{class_name}\.[a-zA-Z_][a-zA-Z0-9_]*\.[a-fA-F\d]{{32}}"
+        file_name_pattern = rf"{class_name}\.([a-zA-Z_][a-zA-Z0-9_]*)(\.[a-zA-Z_][a-zA-Z0-9_]*)?\.[a-fA-F\d]{{32}}"
+
         cache_files = [
             f
             for f in self._cache_directory.glob(f"*.{self._cache_file_suffix}")
             if re.search(file_name_pattern, str(f.stem))
         ]
         ordered_cache_files = sorted(cache_files, key=lambda x: x.stat().st_mtime)
+
         for cache_file in ordered_cache_files:
             cache_key_match = re.search(file_name_pattern, cache_file.stem)
-            cache_key = cache_key_match.group(0)  # type: ignore
-            if cache_key not in self._cache:
-                if len(self._cache) >= self._cache_size:
-                    oldest_key = next(iter(self._cache))
-                    del self._cache[oldest_key]
-                    for file in self._cache_directory.glob(f"{oldest_key}*.{self._cache_file_suffix}"):
-                        file.unlink()
-                self._cache[cache_key] = True
+            if cache_key_match:
+                method_name, cache_group = cache_key_match.groups()
+                group_identifier = method_name + cache_group if cache_group else method_name
+                cache_key = cache_key_match.group(0)
+
+                if cache_key not in self._cache[group_identifier]:
+                    if len(self._cache[group_identifier]) >= self._cache_size:
+                        oldest_key = next(iter(self._cache[group_identifier]))
+                        del self._cache[group_identifier][oldest_key]
+                        for file in self._cache_directory.glob(f"{oldest_key}*.{self._cache_file_suffix}"):
+                            file.unlink()
+
+                    self._cache[group_identifier][cache_key] = True
 
     def _load_from_cache(self, cache_key: str) -> Any | None:
         """Loads data from the cache based on the provided cache key and updates the LRU cache.
@@ -106,9 +113,11 @@ def _load_from_cache(self, cache_key: str) -> Any | None:
         Returns:
             The cached data if it exists, or None if there is no data for the given cache key.
         """
-        if cache_key in self._cache:
-            self._cache.move_to_end(cache_key)
-        return super()._load_from_cache(cache_key)
+        for group_identifier in self._cache.keys():
+            if cache_key in self._cache[group_identifier]:
+                self._cache[group_identifier].move_to_end(cache_key)
+            return super()._load_from_cache(cache_key)
+        return None
 
     def _save_to_cache(self, cache_key: str, output: Any) -> None:
         """Saves the given data to the cache using the provided cache key, updating the LRU cache accordingly.
@@ -119,13 +128,22 @@ def _save_to_cache(self, cache_key: str, output: Any) -> None:
             cache_key: A string representing the cache key.
             output: The data to be saved to the cache.
         """
-        if cache_key not in self._cache:
-            if len(self._cache) >= self._cache_size:
-                oldest_key = next(iter(self._cache))
-                del self._cache[oldest_key]
-                for file in self._cache_directory.glob(f"{oldest_key}*.{self._cache_file_suffix}"):
-                    file.unlink()
-            self._cache[cache_key] = True
-        else:
-            self._cache.move_to_end(cache_key)
-        super()._save_to_cache(cache_key, output)
+        cache_key_match = re.match(
+            r"[a-zA-Z_][a-zA-Z0-9_]*\.([a-zA-Z_][a-zA-Z0-9_]*)(\.[a-zA-Z_][a-zA-Z0-9_]*)?\.[a-fA-F\d]{32}", cache_key
+        )
+        if cache_key_match:
+            method_name, cache_group = cache_key_match.groups()
+            group_identifier = method_name + cache_group if cache_group else method_name
+
+            if cache_key not in self._cache[group_identifier]:
+                if len(self._cache[group_identifier]) >= self._cache_size:
+                    oldest_key = next(iter(self._cache[group_identifier]))
+                    del self._cache[group_identifier][oldest_key]
+                    for file in self._cache_directory.glob(f"{oldest_key}*.{self._cache_file_suffix}"):
+                        file.unlink()
+
+                self._cache[group_identifier][cache_key] = True
+            else:
+                self._cache[group_identifier].move_to_end(cache_key)
+
+            super()._save_to_cache(cache_key, output)

mleko/dataset/convert/base_converter.py

@@ -26,11 +26,14 @@ def __init__(self, cache_directory: str | Path, cache_size: int):
         LRUCacheMixin.__init__(self, cache_directory, self._cache_file_suffix, cache_size)
 
     @abstractmethod
-    def convert(self, file_paths: list[Path] | list[str], force_recompute: bool = False) -> vaex.DataFrame:
+    def convert(
+        self, file_paths: list[Path] | list[str], cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Abstract method to convert the input file paths to the desired output format.
 
         Args:
             file_paths: A list of input file paths to be converted.
+            cache_group: The cache group to use.
             force_recompute: If set to True, forces recomputation and ignores the cache.
 
         Returns:

mleko/dataset/convert/csv_to_vaex_converter.py

@@ -117,7 +117,9 @@ def __init__(
         self._num_workers = num_workers
         self._random_state = random_state
 
-    def convert(self, file_paths: list[Path] | list[str], force_recompute: bool = False) -> vaex.DataFrame:
+    def convert(
+        self, file_paths: list[Path] | list[str], cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Converts a list of CSV files to Arrow format and returns a `vaex` dataframe joined from the converted data.
 
         The method takes care of caching, and results will be reused accordingly unless `force_recompute`
@@ -131,6 +133,7 @@ def convert(self, file_paths: list[Path] | list[str], force_recompute: bool = Fa
 
         Args:
             file_paths: A list of file paths to be converted.
+            cache_group: The cache group to use.
             force_recompute: If set to True, forces recomputation and ignores the cache.
 
         Returns:
@@ -149,6 +152,7 @@ def convert(self, file_paths: list[Path] | list[str], force_recompute: bool = Fa
                 self._downcast_float,
                 (file_paths, CSVFingerprinter(n_rows=100_000 // len(file_paths))),
             ],
+            cache_group=cache_group,
             force_recompute=force_recompute,
         )
 

mleko/dataset/feature_select/base_feature_selector.py

@@ -65,11 +65,14 @@ def __init__(
         self._ignore_features: tuple[str, ...] = tuple(ignore_features) if ignore_features is not None else tuple()
 
     @abstractmethod
-    def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = False) -> vaex.DataFrame:
+    def select_features(
+        self, dataframe: vaex.DataFrame, cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Selects features from the given DataFrame.
 
         Args:
             dataframe: DataFrame from which to select features.
+            cache_group: The cache group to use.
             force_recompute: Whether to force the feature selector to recompute its output, even if it already exists.
 
         Raises:

mleko/dataset/feature_select/composite_feature_selector.py

@@ -78,11 +78,14 @@ def __init__(
         super().__init__(cache_directory, None, None, cache_size)
         self._feature_selectors = tuple(feature_selectors)
 
-    def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = False) -> vaex.DataFrame:
+    def select_features(
+        self, dataframe: vaex.DataFrame, cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Selects the features from the DataFrame.
 
         Args:
             dataframe: DataFrame from which the features will be selected.
+            cache_group: The cache group to use for caching.
             force_recompute: If True, the features will be recomputed even if they are cached.
 
         Returns:
@@ -91,6 +94,7 @@ def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = Fal
         return self._cached_execute(
             lambda_func=lambda: self._select_features(dataframe),
             cache_keys=[self._fingerprint(), (dataframe, VaexFingerprinter())],
+            cache_group=cache_group,
             force_recompute=force_recompute,
         )
 

mleko/dataset/feature_select/invariance_feature_selector.py

@@ -66,11 +66,14 @@ def __init__(
         """
         super().__init__(cache_directory, features, ignore_features, cache_size)
 
-    def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = False) -> vaex.DataFrame:
+    def select_features(
+        self, dataframe: vaex.DataFrame, cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Selects features based on invariance.
 
         Args:
             dataframe: The DataFrame to select features from.
+            cache_group: The cache group to use for caching.
             force_recompute: Whether to force recompute the selected features.
 
         Returns:
@@ -82,6 +85,7 @@ def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = Fal
                 self._fingerprint(),
                 (dataframe, VaexFingerprinter()),
             ],
+            cache_group=cache_group,
             force_recompute=force_recompute,
         )
 

mleko/dataset/feature_select/missing_rate_feature_selector.py

@@ -69,13 +69,16 @@ def __init__(
         super().__init__(cache_directory, features, ignore_features, cache_size)
         self._missing_rate_threshold = missing_rate_threshold
 
-    def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = False) -> vaex.DataFrame:
+    def select_features(
+        self, dataframe: vaex.DataFrame, cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Selects features based on the missing rate.
 
         Will cache the result of the feature selection.
 
         Args:
             dataframe: The DataFrame to select features from.
+            cache_group: The cache group to use.
             force_recompute: Whether to force recompute the feature selection.
 
         Returns:
@@ -84,6 +87,7 @@ def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = Fal
         return self._cached_execute(
             lambda_func=lambda: self._select_features(dataframe),
             cache_keys=[self._fingerprint(), (dataframe, VaexFingerprinter())],
+            cache_group=cache_group,
             force_recompute=force_recompute,
         )
 

mleko/dataset/feature_select/pearson_correlation_feature_selector.py

@@ -72,11 +72,14 @@ def __init__(
         super().__init__(cache_directory, features, ignore_features, cache_size)
         self._correlation_threshold = correlation_threshold
 
-    def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = False) -> vaex.DataFrame:
+    def select_features(
+        self, dataframe: vaex.DataFrame, cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Selects features based on the Pearson correlation.
 
         Args:
             dataframe: The DataFrame to select features from.
+            cache_group: The cache group to use.
             force_recompute: Whether to force recompute the selected features.
 
         Returns:
@@ -85,6 +88,7 @@ def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = Fal
         return self._cached_execute(
             lambda_func=lambda: self._select_features(dataframe),
             cache_keys=[self._fingerprint(), (dataframe, VaexFingerprinter())],
+            cache_group=cache_group,
             force_recompute=force_recompute,
         )
 

mleko/dataset/feature_select/variance_feature_selector.py

@@ -72,11 +72,14 @@ def __init__(
         super().__init__(cache_directory, features, ignore_features, cache_size)
         self._variance_threshold = variance_threshold
 
-    def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = False) -> vaex.DataFrame:
+    def select_features(
+        self, dataframe: vaex.DataFrame, cache_group: str | None = None, force_recompute: bool = False
+    ) -> vaex.DataFrame:
         """Selects features based on the variance.
 
         Args:
             dataframe: The DataFrame to select features from.
+            cache_group: The cache group to use.
             force_recompute: Whether to force recompute the selected features.
 
         Returns:
@@ -88,6 +91,7 @@ def select_features(self, dataframe: vaex.DataFrame, force_recompute: bool = Fal
                 self._fingerprint(),
                 (dataframe, VaexFingerprinter()),
             ],
+            cache_group=cache_group,
             force_recompute=force_recompute,
         )