Merge pull request #254 from galaxyproject/prepare_patch_0.12.1

Prepare patch 0.12.1
galaxyproject · May 18, 2024 · c0a0f51 · c0a0f51
2 parents 14d8d61 + 38f69a0
commit c0a0f51
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Showing 19 changed files with 55 additions and 28 deletions.
diff --git a/.github/workflows/client-ci.yml b/.github/workflows/client-ci.yml
@@ -9,7 +9,7 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest]
         python-version: ["3.8", "3.11"]
     runs-on: ${{ matrix.os }}
     defaults:

diff --git a/README.md b/README.md
@@ -40,6 +40,7 @@ This project has the following main goals:
   - [Improved macros support](#improved-macros-support)
   - [Extract macro](#extract-macro)
   - [Full Galaxy tool linter integration](#document-validation)
+  - [Document Outline](#document-outline) _New feature!_ ✨
 
 # Getting Started
 
@@ -153,3 +154,9 @@ There are also a lot of features around macros auto-completion. You can now navi
 You can select (a complete) XML element and then extract it to a local macro (directly in the tool wrapper) or into an external macro file. If there are several imported macro files, you can choose where to put them or if there is no imported file it will be created and imported directly.
 
 ![Demo feature expanded macros](../assets/feature.extract.macro.gif)
+
+## Document Outline
+
+You can now see a document outline of the currently opened tool document. This is especially useful when working with large tool documents. You can navigate to the different sections of the document in a quick and convenient way.
+
+![Demo feature document outline](../assets/feature.document.outline.gif)
diff --git a/client/CHANGELOG.md b/client/CHANGELOG.md
@@ -1,5 +1,16 @@
 # Galaxy Tools (VS Code Extension) Changelog
 
+## [0.12.1] - 2024-05-18
+
+### Added
+
+- Option to skip future server install confirmations ([#252](https://github.com/galaxyproject/galaxy-language-server/pull/252)).
+
+### Changed
+
+-   Updated Galaxy Language Server [v0.12.1](./server/CHANGELOG.md#0121)
+
+
 ## [0.12.0] - 2023-10-14
 
 ### Added

diff --git a/client/package-lock.json b/client/package-lock.json
diff --git a/client/package.json b/client/package.json
@@ -5,7 +5,7 @@
   "author": "davelopez",
   "publisher": "davelopez",
   "license": "Apache-2.0",
-  "version": "0.12.0",
+  "version": "0.12.1",
   "preview": true,
   "repository": {
     "type": "git",

diff --git a/client/src/constants.ts b/client/src/constants.ts
@@ -3,7 +3,7 @@ export namespace Constants {
     export const LS_VENV_NAME = "glsenv";
     export const GALAXY_LS_PACKAGE = "galaxy-language-server";
     export const GALAXY_LS = "galaxyls";
-    export const GALAXY_LS_VERSION = "0.12.0";
+    export const GALAXY_LS_VERSION = "0.12.1";
     export const LANGUAGE_ID = "galaxytool";
     export const TOOL_DOCUMENT_EXTENSION = "xml";
 

diff --git a/server/CHANGELOG.md b/server/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Galaxy Language Server Changelog
 
+## [0.12.1] - 2024-05-18
+
+### Changed
+
+- Update internal dependencies to support new Galaxy (24.0.2) XSD definitions.
+
+
 ## [0.12.0] - 2023-10-14
 
 ### Added

diff --git a/server/galaxyls/constants.py b/server/galaxyls/constants.py
@@ -1,4 +1,5 @@
 """This module contains definitions for constants used by the Galaxy Tools Language Server."""
+
 from lsprotocol.types import (
     Position,
     Range,

diff --git a/server/galaxyls/server.py b/server/galaxyls/server.py
@@ -1,5 +1,6 @@
 """Galaxy Tools Language Server implementation
 """
+
 from typing import (
     List,
     Optional,
@@ -280,7 +281,7 @@ def generate_expanded_command(server: GalaxyToolsLanguageServer, parameters: Com
     document = server.workspace.get_document(params.uri)
     if document and DocumentValidator.is_tool_document(document):
         return server.service.macro_expander.generate_expanded_from(document.path)
-    return GeneratedExpandedDocument(error_message=f"The document {document.filename} is not a valid Galaxy Tool wrapper.")
+    return GeneratedExpandedDocument(errorMessage=f"The document {document.filename} is not a valid Galaxy Tool wrapper.")
 
 
 @language_server.command(Commands.DISCOVER_TESTS_IN_WORKSPACE)

diff --git a/server/galaxyls/services/tools/document.py b/server/galaxyls/services/tools/document.py
@@ -6,7 +6,7 @@
     Optional,
 )
 
-from anytree import find
+from anytree import find  # type: ignore
 from lsprotocol.types import (
     Position,
     Range,

diff --git a/server/galaxyls/services/tools/generators/command.py b/server/galaxyls/services/tools/generators/command.py
@@ -6,7 +6,7 @@
     Union,
 )
 
-from anytree import PreOrderIter
+from anytree import PreOrderIter  # type: ignore
 from lsprotocol.types import (
     Position,
     Range,

diff --git a/server/galaxyls/services/tools/generators/snippets.py b/server/galaxyls/services/tools/generators/snippets.py
@@ -71,7 +71,7 @@ def _get_expanded_tool_document(self, tool_document: GalaxyToolXmlDocument) -> G
             try:
                 document = tool_document.document
                 expanded_tool_tree, _ = xml_macros.load_with_references(document.path)
-                expanded_tool_tree = cast(etree._ElementTree, expanded_tool_tree)
+                expanded_tool_tree = cast(etree._ElementTree, expanded_tool_tree)  # type: ignore
                 expanded_source = etree.tostring(expanded_tool_tree, encoding=str)
                 expanded_document = Document(uri=document.uri, source=expanded_source, version=document.version)
                 return GalaxyToolXmlDocument(expanded_document)

diff --git a/server/galaxyls/services/tools/inputs.py b/server/galaxyls/services/tools/inputs.py
@@ -4,7 +4,7 @@
     Optional,
 )
 
-from anytree import (
+from anytree import (  # type: ignore
     find,
     NodeMixin,
 )

diff --git a/server/galaxyls/services/xml/document.py b/server/galaxyls/services/xml/document.py
@@ -6,7 +6,7 @@
     Optional,
 )
 
-from anytree.search import findall
+from anytree.search import findall  # type: ignore
 from galaxy.util import xml_macros
 from lsprotocol.types import (
     Position,

diff --git a/server/galaxyls/services/xml/nodes.py b/server/galaxyls/services/xml/nodes.py
@@ -10,7 +10,7 @@
     Tuple,
 )
 
-from anytree import NodeMixin
+from anytree import NodeMixin  # type: ignore
 
 from galaxyls.services.xml.constants import UNDEFINED_OFFSET
 from galaxyls.services.xml.types import NodeType

diff --git a/server/galaxyls/services/xsd/types.py b/server/galaxyls/services/xsd/types.py
@@ -9,7 +9,7 @@
     Optional,
 )
 
-from anytree import (
+from anytree import (  # type: ignore
     findall,
     NodeMixin,
     RenderTree,

diff --git a/server/galaxyls/version.py b/server/galaxyls/version.py
@@ -1 +1 @@
-GLS_VERSION = "0.12.0"
+GLS_VERSION = "0.12.1"
diff --git a/server/requirements-dev.txt b/server/requirements-dev.txt
@@ -2,13 +2,13 @@
 # But imports the runtime ones too
 -r requirements.txt
 
-black==22.12.0
-flake8-bugbear==23.2.13
-flake8==6.0.0
-isort==5.12.0
-lxml-stubs==0.4.0
-mypy==1.0.1
-pytest-cov==4.0.0
-pytest-mock==3.10.0
-pytest==7.2.1
-types-setuptools==67.4.0.1
+black==24.4.2
+flake8-bugbear==24.4.26
+flake8==7.0.0
+isort==5.13.2
+lxml-stubs==0.5.1
+mypy==1.10.0
+pytest-cov==5.0.0
+pytest-mock==3.14.0
+pytest==8.2.0
+types-setuptools==69.5.0.20240518
diff --git a/server/requirements.txt b/server/requirements.txt
@@ -1,4 +1,4 @@
-pygls==1.1.1
-lxml==4.9.3
-anytree==2.10.0
-galaxy-tool-util==23.0.5
+pygls==1.3.1
+lxml==5.2.2
+anytree==2.12.1
+galaxy-tool-util==24.0.2