feature/require minimum bioio-base for plugins

bioio/plugins.py

@@ -2,22 +2,28 @@
 # -*- coding: utf-8 -*-
 
 import os
+import re
 import sys
 from datetime import datetime
 from pathlib import Path
 
+import semver
+
 if sys.version_info < (3, 10):
-    from importlib_metadata import EntryPoint, entry_points
+    from importlib_metadata import EntryPoint, entry_points, requires
 else:
-    from importlib.metadata import entry_points, EntryPoint
+    from importlib.metadata import entry_points, EntryPoint, requires
 
-from typing import Dict, List, NamedTuple, Optional
+from typing import Dict, List, NamedTuple, Optional, Tuple
 
 from bioio_types.reader import Reader
 from bioio_types.reader_metadata import ReaderMetadata
 
 ###############################################################################
 
+BIOIO_DIST_NAME = "bioio"
+BIOIO_BASE_DIST_NAME = "bioio-types"  # TODO: Rename to bioio-base
+
 
 class PluginEntry(NamedTuple):
     entrypoint: EntryPoint
@@ -53,24 +59,105 @@ def add_plugin(pluginentry: PluginEntry) -> None:
         insert_sorted_by_timestamp(pluginlist, pluginentry)
 
 
+def get_dependency_version_range_for_distribution(
+    distribution_name: str, dependency_name: str
+) -> Tuple[Optional[str], Optional[str]]:
+    """
+    Retrieves the minimum and maximum versions of the dependency as specified
+    by the given distribution.
+    `None` as the minimum or maximum represents no minimum or maximum (respectively)
+    """
+    all_distribution_deps = requires(distribution_name) or []
+    matching_distribution_deps = [
+        dep for dep in all_distribution_deps if dep.startswith(dependency_name)
+    ]
+    if len(matching_distribution_deps) != 1:
+        raise ValueError(
+            f"Expected to find 1 `{dependency_name}` dependency for "
+            f"`{distribution_name}`, instead found {len(matching_distribution_deps)}"
+        )
+
+    # Versions from importlib are formatted like "<dependency name> (<0.19,>=0.18)"
+    # so this regex needs to find the inner part of the parentheses to get the
+    # version specifications
+    version_specification_match = re.findall(r"\(.*?\)", matching_distribution_deps[0])
+
+    minimum_dependency_version = None
+    maximum_dependency_version = None
+    if version_specification_match:
+        # A distribution can specify a minimum and maximum (or force an exact) version
+        # so multiple versions need to be parsed here
+        version_specifications = version_specification_match[0].split(",")
+        for version_specification in version_specifications:
+            version = "".join(
+                [
+                    char
+                    for char in version_specification
+                    if char.isnumeric() or char == "."
+                ]
+            )
+
+            # Unfortunately not all versions are specified in full SemVer format
+            # and instead can be like "0.19" and the "semver" package does not
+            # handle these well so we can just fill in the missing .0
+            # to make 0.19 -> 0.19.0
+            while version.count(".") < 2:
+                version += ".0"
+
+            if "<" in version_specification or "==" in version_specification:
+                maximum_dependency_version = version
+
+            if ">" in version_specification or "==" in version_specification:
+                minimum_dependency_version = version
+
+    return minimum_dependency_version, maximum_dependency_version
+
+
 def get_plugins() -> List[PluginEntry]:
     plugins = entry_points(group="bioio.readers")
+    (
+        min_compatible_bioio_base_version,
+        _,
+    ) = get_dependency_version_range_for_distribution(
+        BIOIO_DIST_NAME, BIOIO_BASE_DIST_NAME
+    )
     for plugin in plugins:
-        # ReaderMetadata knows how to instantiate the actual Reader
-        reader_meta = plugin.load().ReaderMetadata
-        if plugin.dist is not None:
-            files = plugin.dist.files
-            if files is not None:
-                firstfile = files[0]
-                timestamp = os.path.getmtime(Path(firstfile.locate()).parent)
-            else:
-                print(f"No files found for plugin: '{plugin}'")
+        (
+            _,
+            max_bioio_base_version_for_plugin,
+        ) = get_dependency_version_range_for_distribution(
+            plugin.name, BIOIO_BASE_DIST_NAME
+        )
+        if (
+            min_compatible_bioio_base_version is not None
+            and max_bioio_base_version_for_plugin is not None
+            and semver.compare(
+                max_bioio_base_version_for_plugin,
+                min_compatible_bioio_base_version,
+            )
+            < 0
+        ):
+            print(
+                f"Plugin `{plugin.name}` does not meet "
+                f"minimum `{BIOIO_BASE_DIST_NAME}` of "
+                f"{min_compatible_bioio_base_version}, ignoring"
+            )
         else:
-            print(f"Could not find distribution for plugin: '{plugin}'")
-            timestamp = 0.0
+            # ReaderMetadata knows how to instantiate the actual Reader
+            reader_meta = plugin.load().ReaderMetadata
+            if plugin.dist is not None:
+                files = plugin.dist.files
+                if files is not None:
+                    firstfile = files[0]
+                    timestamp = os.path.getmtime(Path(firstfile.locate()).parent)
+                else:
+                    print(f"No files found for plugin: '{plugin}'")
+            else:
+                print(f"Could not find distribution for plugin: '{plugin}'")
+                timestamp = 0.0
 
-        # Add plugin entry
-        add_plugin(PluginEntry(plugin, reader_meta, timestamp))
+            # Add plugin entry
+            add_plugin(PluginEntry(plugin, reader_meta, timestamp))
 
     return plugin_cache
 

pyproject.toml

@@ -28,7 +28,8 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-  "bioio-types",
+  "bioio-types>=0.0.2",
+  "semver>=3.0.1",
 ]
 
 [project.urls]