Add spaCy NLP tool and data manager#8006
Open
ksuderman wants to merge 10 commits into
Open
Conversation
- spaCy tool wrapper for fast, production-ready NLP - 25+ languages with multiple model sizes (sm/md/lg/trf) - Core annotations: tokenization, POS, NER, dependency parsing - Enhanced JSON output with is_alpha, is_stop attributes - Python 3.12 compatible - Data manager for automated model downloads via pip - 70+ models across 25+ languages - Comprehensive tests with planemo validation - Memory efficient and optimized for speed Tool: spacy_nlp (v3.8.11+galaxy4) Data Manager: data_manager_spacy_models Categories: Text Manipulation, Natural Language Processing
Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
SaimMomin12
reviewed
May 21, 2026
| @@ -0,0 +1,152 @@ | |||
| <tool id="data_manager_spacy_models" name="spaCy Language Models" version="3.8.11.1" tool_type="manage_data" profile="24.1"> | |||
Contributor
There was a problem hiding this comment.
Suggested change
| <tool id="data_manager_spacy_models" name="spaCy Language Models" version="3.8.11.1" tool_type="manage_data" profile="24.1"> | |
| <tool id="data_manager_spacy_models" name="spaCy Language Models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@"> |
Perhaps defining TOKENS and defining them here?
Comment on lines
+1
to
+4
| <tool id="spacy_nlp" name="spaCy NLP Annotators" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.1"> | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">3.8.11</token> | ||
| <token name="@VERSION_SUFFIX@">4</token> |
Contributor
There was a problem hiding this comment.
Suggested change
| <tool id="spacy_nlp" name="spaCy NLP Annotators" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.1"> | |
| <macros> | |
| <token name="@TOOL_VERSION@">3.8.11</token> | |
| <token name="@VERSION_SUFFIX@">4</token> | |
| <tool id="spacy_nlp" name="spaCy NLP Annotators" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE@"> | |
| <macros> | |
| <token name="@TOOL_VERSION@">3.8.11</token> | |
| <token name="@VERSION_SUFFIX@">4</token> | |
| <token name="@PROFILE@">25.0</token> |
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test> |
Contributor
There was a problem hiding this comment.
Suggested change
| <test> | |
| <test expect_num_outputs="1"> |
Applies to all tests
Comment on lines
+62
to
+65
| <assert_contents> | ||
| <has_text text=""text""/> | ||
| <has_text text=""tokens""/> | ||
| <has_text text="John"/> |
Contributor
There was a problem hiding this comment.
Can we have more specific assertions here?
RZ9082
reviewed
May 21, 2026
Member
There was a problem hiding this comment.
Please place in a sub-directory called data_manager
Member
There was a problem hiding this comment.
This also goes to data_manager sub-directory
Member
There was a problem hiding this comment.
Is it possible to write some tests for the DM?
- Fix remote repository URLs in both tool and data manager .shed.yml files - Standardize versioning with @Profile@ token and update to profile 25.0 - Change VERSION_SUFFIX from 4 to 0 for initial release - Add expect_num_outputs="1" to all test cases - Update citation to DOI format (10.5281/zenodo.10009823) - Remove unnecessary README.md from data manager - Reorganize data manager files into data_manager/ subdirectory structure All changes address reviewer feedback from SaimMomin12 and RZ9082
Removed unused imports for Path and DocBin.
…am help, fix parse/NER and language-count claims, align citation DOI, fold README into help Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Test plan
🤖 Generated with Claude Code