chore(medcat-gliner): CU-869c3bvm0 Migrate gliner implementation to public

.github/workflows/medcat-gliner_main.yml

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+name: MedCAT-Gliner-main
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - 'medcat-plugins/medcat-gliner/**'
+      - '.github/workflows/medcat-gliner**'
+  pull_request:
+    paths:
+      - 'medcat-plugins/medcat-gliner/**'
+      - '.github/workflows/medcat-gliner**'
+
+defaults:
+  run:
+    working-directory: ./medcat-plugins/medcat-gliner
+
+jobs:
+  tests:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: [ '3.10', '3.11', '3.12', '3.13' ]
+      max-parallel: 4
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          df -h # check spaces before
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]" --extra-index-url https://download.pytorch.org/whl/cpu/
+          df -h # check spaces after
+      - name: Check types
+        run: |
+          python -m mypy --follow-imports=normal src/medcat_gliner --follow-untyped-imports
+      - name: Lint
+        run: |
+          ruff check src/medcat_gliner --preview
+      - name: Test
+        run: |
+          python -m unittest discover
+
+  publish-to-test-PyPI:
+    runs-on: ubuntu-latest
+    needs: tests
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0        # fetch all history
+          fetch-tags: true      # fetch tags explicitly
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade build
+
+      - name: Set timestamp-based dev version
+        run: |
+          TS=$(date -u +"%Y%m%d%H%M%S")
+          echo "SETUPTOOLS_SCM_PRETEND_VERSION_FOR_MEDCAT_GLINER=0.2.2.dev${TS}" >> $GITHUB_ENV
+
+      - name: Install package in development mode
+        run: |
+          pip install -e .
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Publish distribution to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository_url: https://test.pypi.org/legacy/
+          packages_dir: medcat-plugins/medcat-gliner/dist
+

.github/workflows/medcat-gliner_release.yml

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+name: medcat-gliner release-build
+
+on:
+  push:
+    tags:
+      - 'medcat-gliner/v*.*.*'  
+
+permissions:
+  id-token: write
+
+defaults:
+  run:
+    working-directory: ./medcat-plugins/medcat-gliner
+
+jobs:
+  test-and-publish-to-PyPI:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v6
+
+      - name: Release Tag
+        # If GITHUB_REF=refs/tags/medcat-gliner/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt
+        run: echo "RELEASE_VERSION=${GITHUB_REF##refs/*/}" >> $GITHUB_ENV
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade build
+
+      - name: Install client package in development mode
+        run: |
+          pip install -e ".[dev]"
+
+      - name: Test
+        run: |
+          pytest tests
+
+      - name: Build client package
+        run: |
+          python -m build
+
+      - name: Publish production distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages_dir: medcat-plugins/medcat-gliner/dist

medcat-plugins/medcat-gliner/README.md

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+# MedCAT-gliner
+
+This provides [gliner](https://github.com/urchade/GLiNER) based NER step for MedCAT core library.
+
+# Usage
+
+First install from PyPI, e.g:
+```
+pip install medcat-gliner
+```
+Subsequently, if you have an existing model, you should be able to just change the NER component:
+```
+cat = CAT.load_model_pack("path/to/existing/model")
+# change component
+from medcat_gliner import GLiNERConfig
+cat.config.components.ner.comp_name = "gliner_ner"
+cat.config.components.ner.custom_cnf = GLiNERConfig()
+# recreate pipe with new NER component
+cat._recreate_pipe()
+# use as needed
+```
+
+## NER recall comparison (linkable SNOMED entities)
+
+The following results compare the existing NER (vocab based NER with spell checking) implementation with the gliner implementation when used as the NER component within MedCAT.
+Evaluation was performed on the **2023 SNOMED CT Linking Challenge** dataset.
+
+> **Important caveat**
+> This is **not a measure of general NER quality**.
+> Recall is computed only with respect to annotated, linkable SNOMED CT entities present in the linking dataset.
+> Mentions outside the annotation scope are treated as false positives by construction, so precision is not meaningful here.
+
+| Implementation         | True Positives | False Negatives | Recall | Runtime |
+| ---------------------- | -------------- | --------------- | ------ | ------- |
+| Vocab based NER        | 10,545         | 3,917           | 0.729  | ~5m 50s |
+| GliNER implementation  | 7,971          | 6,491           | 0.551  | ~34m    |
+
+As we can see, for this dataset, GliNER is significantly slower and performs worse than the standard vocab based implementation. This is likely because the vocab based NER step has been configured and tuned to work best within the MedCAT pipeline. It is likely that with additional tuning the GliNER implementation could perform as good or better than the vocab based linker does.

medcat-plugins/medcat-gliner/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel",  "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "medcat_gliner"
+dynamic = ["version"]
+description = ""
+readme = "README.md"
+license = { text = "Apache-2.0" }
+authors = [
+    { name="Mart Ratas", email="mart.ratas@kcl.ac.uk" }
+]
+requires-python = ">=3.10"
+
+keywords = ["NLP", "NER", "medical", "MedCAT", "gliner"]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "License :: OSI Approved :: Apache Software License"
+]
+
+dependencies = [
+    "medcat>=2.5",
+    "gliner",
+]
+
+[project.optional-dependencies]
+dev = [
+    "ruff",
+    "mypy",
+]
+
+# entry-points to add onto medcat
+[project.entry-points."medcat.plugins"]
+ner_gliner = "medcat_gliner"
+
+[project.urls]
+Homepage = "https://github.com/CogStack/medcat-ops/tree/main/medcat-gliner"
+Repository = "https://github.com/CogStack/medcat-ops/tree/main/medcat-gliner"
+Issues = "https://github.com/CogStack/medcat-ops/issues"
+
+[tool.setuptools_scm]
+root = ".."
+tag_regex = "^medcat-gliner/v(?P<version>[0-9]+(?:\\.[0-9]+)*)$"
+version_scheme = "post-release"
+local_scheme = "no-local-version"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"medcat_gliner" = ["py.typed"]

medcat-plugins/medcat-gliner/src/medcat_gliner/__init__.py

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+from .registration import do_registration as __register
+
+__register()