Merge pull request #257 from galaxyproject/update_server_dependencies

Update server dependencies + improve development experience

.github/workflows/server-ci.yml

@@ -13,7 +13,7 @@ jobs:
   build:
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -29,12 +29,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements-dev.txt
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Lint with ruff
+        uses: chartboost/ruff-action@v1
       - name: Check mypy
         run: |
           mypy .

.vscode/extensions.json

@@ -0,0 +1,9 @@
+{
+    "recommendations": [
+        "charliermarsh.ruff",
+        "ms-python.python",
+        "ms-python.mypy-type-checker",
+        "esbenp.prettier-vscode",
+        "streetsidesoftware.code-spell-checker",
+    ]
+}

.vscode/settings.json.default

@@ -0,0 +1,35 @@
+{
+  "python.analysis.extraPaths": [
+    "server"
+  ],
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.fixAll": "explicit",
+      "source.organizeImports": "explicit"
+    },
+    "editor.defaultFormatter": "charliermarsh.ruff"
+  },
+  "python.languageServer": "Pylance",
+  "python.testing.pytestEnabled": true,
+  "cSpell.words": [
+    "anytree",
+    "galaxyls",
+    "galaxytool",
+    "galaxytools",
+    "lookpath",
+    "lsprotocol",
+    "lxml",
+    "nsmap",
+    "pygls"
+  ],
+  "[html]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode"
+  },
+  "[javascript]": {
+    "editor.defaultFormatter": "esbenp.prettier-vscode"
+  },
+  "[typescript]": {
+    "editor.defaultFormatter": "vscode.typescript-language-features"
+  }
+}

docs/CONTRIBUTING.md

@@ -144,7 +144,7 @@ If you are using `Windows` we recommend installing and using [WSL](https://docs.
 
 6. When you're done making changes, check that your changes pass ``style linter`` and the ``tests``.
     ```sh
-    flake8
+    ruff check
     pytest
     ```
 
@@ -184,6 +184,6 @@ Just have a little patience, if everything is in order your pull request will be
 
 
 # Style Guide
-Currently the style guide is only defined for the [Language Server](../server) which is writen in ``Python``.
+Currently the style guide is only defined for the [Language Server](../server) which is written in ``Python``.
 
-Basically you can rely on [flake8](https://pypi.org/project/flake8/) and [black](https://github.com/psf/black) (along with the configuration files provided in the project directory) to manage all the styling for you. If you installed the [development requirements](../requirements-dev.txt) you already have them installed :)
+Basically you can rely on [ruff](https://docs.astral.sh/ruff/) to manage all the styling for you. If you installed the [development requirements](../requirements-dev.txt) you already have them installed :)

server/galaxyls/server.py

@@ -1,12 +1,20 @@
-"""Galaxy Tools Language Server implementation
-"""
+"""Galaxy Tools Language Server implementation"""
 
-from typing import (
-    List,
-    Optional,
-)
+from typing import List, Optional
 
 from lsprotocol.types import (
+    INITIALIZED,
+    TEXT_DOCUMENT_CODE_ACTION,
+    TEXT_DOCUMENT_COMPLETION,
+    TEXT_DOCUMENT_DEFINITION,
+    TEXT_DOCUMENT_DID_CLOSE,
+    TEXT_DOCUMENT_DID_OPEN,
+    TEXT_DOCUMENT_DID_SAVE,
+    TEXT_DOCUMENT_DOCUMENT_LINK,
+    TEXT_DOCUMENT_DOCUMENT_SYMBOL,
+    TEXT_DOCUMENT_FORMATTING,
+    TEXT_DOCUMENT_HOVER,
+    WORKSPACE_DID_CHANGE_CONFIGURATION,
     CodeAction,
     CodeActionKind,
     CodeActionOptions,
@@ -26,33 +34,18 @@
     DocumentSymbol,
     DocumentSymbolParams,
     Hover,
-    INITIALIZED,
     InitializeParams,
     Location,
     MessageType,
-    TEXT_DOCUMENT_CODE_ACTION,
-    TEXT_DOCUMENT_COMPLETION,
-    TEXT_DOCUMENT_DEFINITION,
-    TEXT_DOCUMENT_DID_CLOSE,
-    TEXT_DOCUMENT_DID_OPEN,
-    TEXT_DOCUMENT_DID_SAVE,
-    TEXT_DOCUMENT_DOCUMENT_LINK,
-    TEXT_DOCUMENT_DOCUMENT_SYMBOL,
-    TEXT_DOCUMENT_FORMATTING,
-    TEXT_DOCUMENT_HOVER,
     TextDocumentIdentifier,
     TextDocumentPositionParams,
     TextEdit,
-    WORKSPACE_DID_CHANGE_CONFIGURATION,
     WorkspaceConfigurationParams,
 )
 from pygls.server import LanguageServer
 from pygls.workspace import Document
 
-from galaxyls.config import (
-    CompletionMode,
-    GalaxyToolsConfiguration,
-)
+from galaxyls.config import CompletionMode, GalaxyToolsConfiguration
 from galaxyls.constants import Commands
 from galaxyls.services.language import GalaxyToolLanguageService
 from galaxyls.services.validation import DocumentValidator

server/galaxyls/services/completion.py

@@ -1,9 +1,9 @@
 """Module in charge of the auto-completion feature."""
 
 from typing import (
-    cast,
     List,
     Optional,
+    cast,
 )
 
 from lsprotocol.types import (
@@ -22,6 +22,7 @@
     XmlCDATASection,
     XmlElement,
 )
+
 from ..config import CompletionMode
 from ..types import AutoCloseTagResult
 from .context import XmlContext

server/galaxyls/services/context.py

@@ -1,9 +1,9 @@
 """This module provides a service to determine position context inside an XML document."""
 
 from typing import (
-    cast,
     List,
     Optional,
+    cast,
 )
 
 from lsprotocol.types import (

server/galaxyls/services/language.py

@@ -42,6 +42,7 @@
     RefactorMacrosService,
 )
 from galaxyls.services.tools.testing import ToolTestsDiscoveryService
+
 from ..config import CompletionMode
 from ..types import (
     GeneratedSnippetResult,

server/galaxyls/services/tools/document.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 from typing import (
-    cast,
     Dict,
     List,
     Optional,
+    cast,
 )
 
 from anytree import find  # type: ignore

server/galaxyls/services/tools/generators/command.py

@@ -1,9 +1,9 @@
 from typing import (
-    cast,
     List,
     Optional,
     Tuple,
     Union,
+    cast,
 )
 
 from anytree import PreOrderIter  # type: ignore

server/galaxyls/services/tools/generators/snippets.py

@@ -3,11 +3,11 @@
     abstractmethod,
 )
 from typing import (
-    cast,
     List,
     Optional,
     Tuple,
     Union,
+    cast,
 )
 
 from galaxy.util import xml_macros
@@ -43,7 +43,7 @@ def generate_snippet(self) -> GeneratedSnippetResult:
         if is_error:
             return GeneratedSnippetResult.as_error(result)
         insert_position = self._find_snippet_insert_position()
-        if type(insert_position) == Range:
+        if type(insert_position) is Range:
             insert_position = cast(Range, insert_position)
             return GeneratedSnippetResult(result, insert_position.start, insert_position)
         insert_position = cast(Position, insert_position)

server/galaxyls/services/tools/generators/tests.py

@@ -1,9 +1,9 @@
 from typing import (
-    cast,
     List,
     Optional,
     Tuple,
     Union,
+    cast,
 )
 
 from lsprotocol.types import (
@@ -32,7 +32,6 @@
     HAS_TEXT,
     INPUTS,
     LINE,
-    N,
     NAME,
     OPTION,
     OUTPUT,
@@ -48,6 +47,7 @@
     TOOL,
     TYPE,
     VALUE,
+    N,
 )
 from galaxyls.services.tools.document import GalaxyToolXmlDocument
 from galaxyls.services.tools.generators.snippets import SnippetGenerator

server/galaxyls/services/tools/inputs.py

@@ -1,12 +1,12 @@
 from typing import (
-    cast,
     List,
     Optional,
+    cast,
 )
 
 from anytree import (  # type: ignore
-    find,
     NodeMixin,
+    find,
 )
 
 from galaxyls.services.tools.constants import (

server/galaxyls/services/tools/linting.py

@@ -1,14 +1,14 @@
 from typing import (
-    cast,
     List,
+    cast,
 )
 
 from galaxy.tool_util.lint import (
-    lint_xml_with,
     LintContext,
     LintLevel,
     LintMessage,
     XMLLintMessageXPath,
+    lint_xml_with,
 )
 from lsprotocol.types import (
     Diagnostic,

server/galaxyls/services/xml/document.py

@@ -1,9 +1,9 @@
 from typing import (
     Any,
-    cast,
     Dict,
     List,
     Optional,
+    cast,
 )
 
 from anytree.search import findall  # type: ignore
@@ -16,6 +16,7 @@
 from pygls.workspace import Document
 
 from galaxyls.constants import DEFAULT_DOCUMENT_RANGE
+
 from .nodes import (
     XmlContainerNode,
     XmlElement,
@@ -70,7 +71,7 @@ def root(self) -> Optional[XmlElement]:
         if len(self.children) == 0:
             return None
         try:
-            return next(child for child in self.children if type(child) == XmlElement)
+            return next(child for child in self.children if type(child) is XmlElement)
         except StopIteration:
             return None
 

server/galaxyls/services/xml/nodes.py

@@ -3,11 +3,11 @@
     abstractmethod,
 )
 from typing import (
-    cast,
     Dict,
     List,
     Optional,
     Tuple,
+    cast,
 )
 
 from anytree import NodeMixin  # type: ignore
@@ -423,7 +423,7 @@ def get_children_with_name(self, name: str) -> List["XmlElement"]:
 
     def get_cdata_section(self) -> Optional["XmlCDATASection"]:
         """Gets the CDATA node inside this element or None if it doesn't have a CDATA section."""
-        return next((node for node in self.children if type(node) == XmlCDATASection), None)
+        return next((node for node in self.children if type(node) is XmlCDATASection), None)
 
 
 class XmlCDATASection(XmlContainerNode):

server/galaxyls/services/xml/parser.py

@@ -1,26 +1,15 @@
-""" This code is based on the Eclipse/Lemminx XML language server implementation:
+"""This code is based on the Eclipse/Lemminx XML language server implementation:
 https://github.com/eclipse/lemminx/tree/master/org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/dom
 
 Only the minimum subset of the XML dialect used by Galaxy tool wrappers is supported.
 """
 
-from typing import (
-    cast,
-    Optional,
-)
+from typing import Optional, cast
 
 from pygls.workspace import Document
 
 from .document import XmlDocument
-from .nodes import (
-    XmlAttribute,
-    XmlCDATASection,
-    XmlComment,
-    XmlContent,
-    XmlElement,
-    XmlProcessingInstruction,
-    XmlSyntaxNode,
-)
+from .nodes import XmlAttribute, XmlCDATASection, XmlComment, XmlContent, XmlElement, XmlProcessingInstruction, XmlSyntaxNode
 from .scanner import XmlScanner
 from .types import TokenType
 
@@ -31,7 +20,6 @@ class XmlDocumentParser:
     If the document is incomplete or malformed, the parser will try to recover
     the syntax tree in those cases without altering the original offsets of the nodes."""
 
-    # flake8: noqa: C901
     def parse(self, document: Document) -> XmlDocument:
         """Parses the given text document and returns the resulting syntax tree as
         a XmlDocument.