From 68ad184e40ac383abead7bda6a5fa7ec68bbc431 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:21:42 +0000 Subject: [PATCH 01/13] docs(medcat-trainer): Migrate docs to Mkdocs. Update Navigation and more details --- medcat-trainer/.readthedocs.yaml | 22 +- medcat-trainer/docs/Makefile | 20 - medcat-trainer/docs/annotator_guide.md | 3 + medcat-trainer/docs/conf.py | 88 --- medcat-trainer/docs/{main.md => index.md} | 8 +- medcat-trainer/docs/index.rst | 31 -- medcat-trainer/docs/installation.md | 11 + medcat-trainer/docs/make.bat | 35 -- medcat-trainer/docs/pyproject.toml | 19 + medcat-trainer/docs/uv.lock | 620 ++++++++++++++++++++++ medcat-trainer/mkdocs.yml | 62 +++ 11 files changed, 733 insertions(+), 186 deletions(-) delete mode 100644 medcat-trainer/docs/Makefile delete mode 100644 medcat-trainer/docs/conf.py rename medcat-trainer/docs/{main.md => index.md} (82%) delete mode 100644 medcat-trainer/docs/index.rst delete mode 100644 medcat-trainer/docs/make.bat create mode 100644 medcat-trainer/docs/pyproject.toml create mode 100644 medcat-trainer/docs/uv.lock create mode 100644 medcat-trainer/mkdocs.yml diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index 4bea1918f..ce6bbae71 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -5,13 +5,19 @@ version: 2 build: - os: ubuntu-20.04 + os: "ubuntu-24.04" tools: - python: "3.9" + python: "3.13" + jobs: + pre_create_environment: + - cd docs + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + create_environment: + - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" + install: + - cd docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen -sphinx: - configuration: medcat-trainer/docs/conf.py - -python: - install: - - requirements: medcat-trainer/docs/requirements.txt +mkdocs: + configuration: mkdocs.yml \ No newline at end of file diff --git a/medcat-trainer/docs/Makefile b/medcat-trainer/docs/Makefile deleted file mode 100644 index d4bb2cbb9..000000000 --- a/medcat-trainer/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/medcat-trainer/docs/annotator_guide.md b/medcat-trainer/docs/annotator_guide.md index 32e659031..686441ad1 100644 --- a/medcat-trainer/docs/annotator_guide.md +++ b/medcat-trainer/docs/annotator_guide.md @@ -71,6 +71,9 @@ The sidebar shows details for the currently selected concept, including: If enabled by project settings, a **Comment** field is also available. +!!! tip + If the details are not showing in the sidebar after you've selected one, the issue is likely with an unfinished Project setup. See the section for "Concept lookup index (Solr import)" in the [Project Creation and Management Guide](project_admin.md) for details. + ## Meta annotations and relations Depending on project configuration: diff --git a/medcat-trainer/docs/conf.py b/medcat-trainer/docs/conf.py deleted file mode 100644 index bdd55355a..000000000 --- a/medcat-trainer/docs/conf.py +++ /dev/null @@ -1,88 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -import os -import sys -sys.path.insert(0, os.path.abspath('.')) - - -# -- Project information ----------------------------------------------------- - -project = 'MedCATtrainer' -copyright = '2022, CogStack Org' -author = 'CogStack Org' - -# The full version, including alpha/beta/rc tags -release = 'latest' - - -# -- General configuration --------------------------------------------------- - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - 'sphinx_rtd_theme', - 'sphinx.ext.autodoc', - 'myst_parser', - 'sphinx.ext.inheritance_diagram', - 'autoapi.extension', -] - -autoapi_type = 'python' -autoapi_dirs = ['../webapp/api/api'] -autodoc_typehints = 'description' -autoapi_template_dir = '_templates/autoapi_templates' - - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - -source_suffix = { - '.rst': 'restructuredtext', - '.txt': 'markdown', - '.md': 'markdown', -} - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'sphinx_rtd_theme' - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -html_css_files = [ - 'css/overrides.css' -] - -def autoapi_skip_member(app, what, name, obj, skip, options): - # skip: - # log class attributes - # 'private' methods, attributes, functions - exclude = (what == 'attribute' and name == 'log') or \ - (name.startswith('_') and not name.startswith('__')) - return exclude - - -def setup(app): - """Add autoapi-skip-member.""" - app.connect('autoapi-skip-member', autoapi_skip_member) diff --git a/medcat-trainer/docs/main.md b/medcat-trainer/docs/index.md similarity index 82% rename from medcat-trainer/docs/main.md rename to medcat-trainer/docs/index.md index e06bd377f..1f9a8a07d 100644 --- a/medcat-trainer/docs/main.md +++ b/medcat-trainer/docs/index.md @@ -1,4 +1,4 @@ -# Medical oncept Annotation Tool Trainer +# Medical MedCAToncept Annotation Tool Trainer MedCATtrainer is a web application for creating, validating, and improving MedCAT concept annotation models on biomedical or clinical text. @@ -27,9 +27,9 @@ review-only workflows (collect annotations without changing the model). ## Typical workflow 1. Install and configure MedCATtrainer. -2. Create users and upload model artifacts (Model Pack or CDB/Vocab). -3. Create a project and assign annotators. -4. Annotate and submit documents. +2. Create users and upload model artifacts (Model Pack or CDB/Vocab). [Administrator Setup](admin_setup.md) +3. Create a project and assign annotators. [Annotation Project Creation and Management](project_admin.md) +4. Annotate and submit documents. [Annotator Guide](annotator_guide.md) 5. Export annotations and evaluate with the metrics tools. ## Documentation map diff --git a/medcat-trainer/docs/index.rst b/medcat-trainer/docs/index.rst deleted file mode 100644 index b7758d22c..000000000 --- a/medcat-trainer/docs/index.rst +++ /dev/null @@ -1,31 +0,0 @@ -.. MedCATtrainer documentation master file, created by - sphinx-quickstart on Fri Feb 18 17:02:13 2022. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to MedCATtrainer's documentation! -========================================= - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - main.md - installation.md - admin_setup.md - project_admin.md - project_group_admin.md - demo_page.md - annotator_guide.md - meta_annotations.md - advanced_usage.md - maintenance.md - client.md - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/medcat-trainer/docs/installation.md b/medcat-trainer/docs/installation.md index 2eda1c2a9..89b91396d 100644 --- a/medcat-trainer/docs/installation.md +++ b/medcat-trainer/docs/installation.md @@ -1,5 +1,12 @@ # Installation +The steps to setup Medcat trainer are as follows: +1. Run MedCAT Trainer with Docker or Helm +2. Setup the Administrator user with [Administrator Setup](admin_setup.md) +3. Configure annotations Projects + +This page details the initial running of the application. + MedCATtrainer is packaged as a Docker Compose deployment with three core services: @@ -61,6 +68,7 @@ Host-level Compose variables (for example port overrides) can be set by copying | Variable | Description | |---|---| +| `CSRF_TRUSTED_ORIGINS` | Allowed origins to access the admin panel. Mandatory to set if you expose the app over a different URL or port (default `'http://127.0.0.1:8001', 'http://localhost:8001'`). | | `MCTRAINER_PORT` | Host port for the web UI/API (default `8001`). | | `SOLR_PORT` | Host port for Solr admin (default `8983`). | | `MEDCAT_CONFIG_FILE` | MedCAT config file path inside the container. | @@ -129,3 +137,6 @@ An example compose file is available at startup logs. - **Concept picker empty**: confirm Solr is running and concepts were imported for the selected CDB. + +# Next Steps +Now that medcat trainer is installed and running, proceed to [Administrator Setup](admin_setup.md) to create the Admin user. \ No newline at end of file diff --git a/medcat-trainer/docs/make.bat b/medcat-trainer/docs/make.bat deleted file mode 100644 index 8084272b4..000000000 --- a/medcat-trainer/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/medcat-trainer/docs/pyproject.toml b/medcat-trainer/docs/pyproject.toml new file mode 100644 index 000000000..9eb98e729 --- /dev/null +++ b/medcat-trainer/docs/pyproject.toml @@ -0,0 +1,19 @@ +[project] +name = "cogstack-documentation" +version = "0.1.0" +description = "CogStack Documentation" +readme = "README.md" +requires-python = ">=3.10" +dependencies = [ + "mkdocs-material>=9.7.0", + "termynal>=0.13.1", +] + +[project.optional-dependencies] +dev = [ + "ruff>=0.12.11", +] + +[tool.ruff] +line-length = 120 + diff --git a/medcat-trainer/docs/uv.lock b/medcat-trainer/docs/uv.lock new file mode 100644 index 000000000..4feaaa650 --- /dev/null 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search.highlight + - search.share + - search.suggest + - toc.follow + - attr_list + +repo_url: https://github.com/CogStack/cogstack-nlp +repo_name: cogstack-nlp + +docs_dir: docs + +nav: + - Home: index.md + - Getting started: + - Installation: installation.md + - Demo: demo_page.md + - User guide: + - Annotator Guide: annotator_guide.md + - Administratiors Guide: + - Administrator setup: admin_setup.md + - Annotation Project admin: project_admin.md + - Annotation Project group admin: project_group_admin.md + - Meta annotations: meta_annotations.md + - Reference: + - Advanced usage: advanced_usage.md + - Maintenance: maintenance.md + - Client API: client.md + +plugins: + - search + - termynal + +markdown_extensions: + - admonition + - attr_list + - pymdownx.details + - pymdownx.superfences + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg From 902a760dcabe236c6ed2b9309f11142360ae0d8f Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:24:36 +0000 Subject: [PATCH 02/13] docs(medcat-trainer): Update Readthedocs --- medcat-trainer/.readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index ce6bbae71..39c3277dd 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -17,7 +17,7 @@ build: create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: - - cd docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen + - cd medcat-trainer/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: configuration: mkdocs.yml \ No newline at end of file From f3fe1afed1314393cc0717e37cb95c13dc4035e5 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:25:10 +0000 Subject: [PATCH 03/13] docs(medcat-trainer): Update Readthedocs --- medcat-trainer/.readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index 39c3277dd..f834247a2 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -10,7 +10,7 @@ build: python: "3.13" jobs: pre_create_environment: - - cd docs + - cd medcat-trainer/docs - asdf plugin add uv - asdf install uv latest - asdf global uv latest From 531a01374240f83d11e65d3e2468bdcb25f259dc Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:25:59 +0000 Subject: [PATCH 04/13] docs(medcat-trainer): Update Readthedocs --- medcat-trainer/.readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index f834247a2..9769fa4f7 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -17,7 +17,7 @@ build: create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: - - cd medcat-trainer/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen + - cd medcat-trainer && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: configuration: mkdocs.yml \ No newline at end of file From a80d6f8e1300e3c0719852b1efc9556a9273d549 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:30:24 +0000 Subject: [PATCH 05/13] docs(medcat-trainer): Move all markdown files to docs folder --- medcat-trainer/.readthedocs.yaml | 4 ++-- .../docs/{ => docs}/_static/css/overrides.css | 0 .../_static/img/add-annotation-concept-pick.png | Bin .../_static/img/add-annotation-concept.png | Bin .../{ => docs}/_static/img/add-annotation-menu.png | Bin .../_static/img/add-annotation-select-concept.png | Bin .../{ => docs}/_static/img/add-annotation-text.png | Bin .../{ => docs}/_static/img/add-new-meta-task.png | Bin .../docs/{ => docs}/_static/img/add-new-users.png | Bin .../_static/img/add_project_annotate_entities.png | Bin .../docs/{ => docs}/_static/img/admin_page.png | Bin .../{ => docs}/_static/img/available-projects.png | Bin .../docs/{ => docs}/_static/img/cat-logo.png | Bin .../docs/{ => docs}/_static/img/cat-logo.svg | 0 .../docs/{ => docs}/_static/img/clone-projects.png | Bin .../_static/img/concepts-imported-status.png | Bin .../_static/img/delete-indexed-concepts.png | Bin .../docs/{ => docs}/_static/img/demo_interface.png | Bin .../docs/{ => docs}/_static/img/demo_tab.png | Bin .../docs/{ => docs}/_static/img/download-annos.png | Bin .../docs/{ => docs}/_static/img/help-button.png | Bin .../_static/img/home-screen-admin-options.png | Bin .../docs/{ => docs}/_static/img/import-concepts.png | Bin .../docs/{ => docs}/_static/img/login.png | Bin .../_static/img/main-annotation-interface.png | Bin .../docs/{ => docs}/_static/img/meta-task-form.png | Bin .../{ => docs}/_static/img/meta-tasks-interface.png | Bin .../docs/{ => docs}/_static/img/new_projects.png | Bin .../_static/img/pick-alternative-concept.png | Bin .../_static/img/project-groups-view-available.png | Bin .../{ => docs}/_static/img/project-groups-view.png | Bin .../_static/img/project_annotate_entities.png | Bin .../{ => docs}/_static/img/projects-in-group.png | Bin .../{ => docs}/_static/img/remove-default-user.png | Bin .../docs/{ => docs}/_static/img/reset-button.png | Bin .../docs/{ => docs}/_static/img/reset-projects.png | Bin .../docs/{ => docs}/_static/img/save_cdb.png | Bin .../{ => docs}/_static/img/select-concept-dbs.png | Bin .../_static/img/select-existing-project.png | Bin .../docs/{ => docs}/_static/img/select-tasks.png | Bin .../docs/{ => docs}/_static/img/summary-button.png | Bin .../docs/{ => docs}/_static/img/tick_mark.png | Bin .../docs/{ => docs}/_static/img/users-select.png | Bin medcat-trainer/docs/{ => docs}/admin_setup.md | 0 medcat-trainer/docs/{ => docs}/advanced_usage.md | 0 medcat-trainer/docs/{ => docs}/annotator_guide.md | 0 medcat-trainer/docs/{ => docs}/client.md | 0 medcat-trainer/docs/{ => docs}/demo_page.md | 0 medcat-trainer/docs/{ => docs}/index.md | 0 medcat-trainer/docs/{ => docs}/installation.md | 0 medcat-trainer/docs/{ => docs}/maintenance.md | 0 medcat-trainer/docs/{ => docs}/meta_annotations.md | 0 medcat-trainer/docs/{ => docs}/project_admin.md | 0 .../docs/{ => docs}/project_group_admin.md | 0 medcat-trainer/{ => docs}/mkdocs.yml | 0 medcat-trainer/docs/requirements.txt | 4 ---- 56 files changed, 2 insertions(+), 6 deletions(-) rename medcat-trainer/docs/{ => docs}/_static/css/overrides.css (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-annotation-concept-pick.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-annotation-concept.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-annotation-menu.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-annotation-select-concept.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-annotation-text.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-new-meta-task.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add-new-users.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/add_project_annotate_entities.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/admin_page.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/available-projects.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/cat-logo.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/cat-logo.svg (100%) rename medcat-trainer/docs/{ => docs}/_static/img/clone-projects.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/concepts-imported-status.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/delete-indexed-concepts.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/demo_interface.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/demo_tab.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/download-annos.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/help-button.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/home-screen-admin-options.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/import-concepts.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/login.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/main-annotation-interface.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/meta-task-form.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/meta-tasks-interface.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/new_projects.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/pick-alternative-concept.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/project-groups-view-available.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/project-groups-view.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/project_annotate_entities.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/projects-in-group.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/remove-default-user.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/reset-button.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/reset-projects.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/save_cdb.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/select-concept-dbs.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/select-existing-project.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/select-tasks.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/summary-button.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/tick_mark.png (100%) rename medcat-trainer/docs/{ => docs}/_static/img/users-select.png (100%) rename medcat-trainer/docs/{ => docs}/admin_setup.md (100%) rename medcat-trainer/docs/{ => docs}/advanced_usage.md (100%) rename medcat-trainer/docs/{ => docs}/annotator_guide.md (100%) rename medcat-trainer/docs/{ => docs}/client.md (100%) rename medcat-trainer/docs/{ => docs}/demo_page.md (100%) rename medcat-trainer/docs/{ => docs}/index.md (100%) rename medcat-trainer/docs/{ => docs}/installation.md (100%) rename medcat-trainer/docs/{ => docs}/maintenance.md (100%) rename medcat-trainer/docs/{ => docs}/meta_annotations.md (100%) rename medcat-trainer/docs/{ => docs}/project_admin.md (100%) rename medcat-trainer/docs/{ => docs}/project_group_admin.md (100%) rename medcat-trainer/{ => docs}/mkdocs.yml (100%) delete mode 100644 medcat-trainer/docs/requirements.txt diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index 9769fa4f7..e4f0e3a7e 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -17,7 +17,7 @@ build: create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: - - cd medcat-trainer && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen + - cd medcat-trainer/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: - configuration: mkdocs.yml \ No newline at end of file + configuration: docs/mkdocs.yml \ No newline at end of file diff --git a/medcat-trainer/docs/_static/css/overrides.css b/medcat-trainer/docs/docs/_static/css/overrides.css similarity index 100% rename from medcat-trainer/docs/_static/css/overrides.css rename to medcat-trainer/docs/docs/_static/css/overrides.css diff --git a/medcat-trainer/docs/_static/img/add-annotation-concept-pick.png b/medcat-trainer/docs/docs/_static/img/add-annotation-concept-pick.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-annotation-concept-pick.png rename to medcat-trainer/docs/docs/_static/img/add-annotation-concept-pick.png diff --git a/medcat-trainer/docs/_static/img/add-annotation-concept.png b/medcat-trainer/docs/docs/_static/img/add-annotation-concept.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-annotation-concept.png rename to medcat-trainer/docs/docs/_static/img/add-annotation-concept.png diff --git a/medcat-trainer/docs/_static/img/add-annotation-menu.png b/medcat-trainer/docs/docs/_static/img/add-annotation-menu.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-annotation-menu.png rename to medcat-trainer/docs/docs/_static/img/add-annotation-menu.png diff --git a/medcat-trainer/docs/_static/img/add-annotation-select-concept.png b/medcat-trainer/docs/docs/_static/img/add-annotation-select-concept.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-annotation-select-concept.png rename to medcat-trainer/docs/docs/_static/img/add-annotation-select-concept.png diff --git a/medcat-trainer/docs/_static/img/add-annotation-text.png b/medcat-trainer/docs/docs/_static/img/add-annotation-text.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-annotation-text.png rename to medcat-trainer/docs/docs/_static/img/add-annotation-text.png diff --git a/medcat-trainer/docs/_static/img/add-new-meta-task.png b/medcat-trainer/docs/docs/_static/img/add-new-meta-task.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-new-meta-task.png rename to medcat-trainer/docs/docs/_static/img/add-new-meta-task.png diff --git a/medcat-trainer/docs/_static/img/add-new-users.png b/medcat-trainer/docs/docs/_static/img/add-new-users.png similarity index 100% rename from medcat-trainer/docs/_static/img/add-new-users.png rename to medcat-trainer/docs/docs/_static/img/add-new-users.png diff --git a/medcat-trainer/docs/_static/img/add_project_annotate_entities.png b/medcat-trainer/docs/docs/_static/img/add_project_annotate_entities.png similarity index 100% rename from medcat-trainer/docs/_static/img/add_project_annotate_entities.png rename to medcat-trainer/docs/docs/_static/img/add_project_annotate_entities.png diff --git a/medcat-trainer/docs/_static/img/admin_page.png b/medcat-trainer/docs/docs/_static/img/admin_page.png similarity index 100% rename from medcat-trainer/docs/_static/img/admin_page.png rename to medcat-trainer/docs/docs/_static/img/admin_page.png diff --git a/medcat-trainer/docs/_static/img/available-projects.png b/medcat-trainer/docs/docs/_static/img/available-projects.png similarity index 100% rename from medcat-trainer/docs/_static/img/available-projects.png rename to medcat-trainer/docs/docs/_static/img/available-projects.png diff --git a/medcat-trainer/docs/_static/img/cat-logo.png b/medcat-trainer/docs/docs/_static/img/cat-logo.png similarity index 100% rename from medcat-trainer/docs/_static/img/cat-logo.png rename to medcat-trainer/docs/docs/_static/img/cat-logo.png diff --git a/medcat-trainer/docs/_static/img/cat-logo.svg b/medcat-trainer/docs/docs/_static/img/cat-logo.svg similarity index 100% rename from medcat-trainer/docs/_static/img/cat-logo.svg rename to medcat-trainer/docs/docs/_static/img/cat-logo.svg diff --git a/medcat-trainer/docs/_static/img/clone-projects.png b/medcat-trainer/docs/docs/_static/img/clone-projects.png similarity index 100% rename from medcat-trainer/docs/_static/img/clone-projects.png rename to medcat-trainer/docs/docs/_static/img/clone-projects.png diff --git a/medcat-trainer/docs/_static/img/concepts-imported-status.png b/medcat-trainer/docs/docs/_static/img/concepts-imported-status.png similarity index 100% rename from medcat-trainer/docs/_static/img/concepts-imported-status.png rename to medcat-trainer/docs/docs/_static/img/concepts-imported-status.png diff --git 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a/medcat-trainer/docs/_static/img/login.png b/medcat-trainer/docs/docs/_static/img/login.png similarity index 100% rename from medcat-trainer/docs/_static/img/login.png rename to medcat-trainer/docs/docs/_static/img/login.png diff --git a/medcat-trainer/docs/_static/img/main-annotation-interface.png b/medcat-trainer/docs/docs/_static/img/main-annotation-interface.png similarity index 100% rename from medcat-trainer/docs/_static/img/main-annotation-interface.png rename to medcat-trainer/docs/docs/_static/img/main-annotation-interface.png diff --git a/medcat-trainer/docs/_static/img/meta-task-form.png b/medcat-trainer/docs/docs/_static/img/meta-task-form.png similarity index 100% rename from medcat-trainer/docs/_static/img/meta-task-form.png rename to medcat-trainer/docs/docs/_static/img/meta-task-form.png diff --git a/medcat-trainer/docs/_static/img/meta-tasks-interface.png b/medcat-trainer/docs/docs/_static/img/meta-tasks-interface.png similarity index 100% rename from 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a/medcat-trainer/docs/_static/img/remove-default-user.png b/medcat-trainer/docs/docs/_static/img/remove-default-user.png similarity index 100% rename from medcat-trainer/docs/_static/img/remove-default-user.png rename to medcat-trainer/docs/docs/_static/img/remove-default-user.png diff --git a/medcat-trainer/docs/_static/img/reset-button.png b/medcat-trainer/docs/docs/_static/img/reset-button.png similarity index 100% rename from medcat-trainer/docs/_static/img/reset-button.png rename to medcat-trainer/docs/docs/_static/img/reset-button.png diff --git a/medcat-trainer/docs/_static/img/reset-projects.png b/medcat-trainer/docs/docs/_static/img/reset-projects.png similarity index 100% rename from medcat-trainer/docs/_static/img/reset-projects.png rename to medcat-trainer/docs/docs/_static/img/reset-projects.png diff --git a/medcat-trainer/docs/_static/img/save_cdb.png b/medcat-trainer/docs/docs/_static/img/save_cdb.png similarity index 100% rename from medcat-trainer/docs/_static/img/save_cdb.png rename to medcat-trainer/docs/docs/_static/img/save_cdb.png diff --git a/medcat-trainer/docs/_static/img/select-concept-dbs.png b/medcat-trainer/docs/docs/_static/img/select-concept-dbs.png similarity index 100% rename from medcat-trainer/docs/_static/img/select-concept-dbs.png rename to medcat-trainer/docs/docs/_static/img/select-concept-dbs.png diff --git a/medcat-trainer/docs/_static/img/select-existing-project.png b/medcat-trainer/docs/docs/_static/img/select-existing-project.png similarity index 100% rename from medcat-trainer/docs/_static/img/select-existing-project.png rename to medcat-trainer/docs/docs/_static/img/select-existing-project.png diff --git a/medcat-trainer/docs/_static/img/select-tasks.png b/medcat-trainer/docs/docs/_static/img/select-tasks.png similarity index 100% rename from medcat-trainer/docs/_static/img/select-tasks.png rename to medcat-trainer/docs/docs/_static/img/select-tasks.png diff --git a/medcat-trainer/docs/_static/img/summary-button.png b/medcat-trainer/docs/docs/_static/img/summary-button.png similarity index 100% rename from medcat-trainer/docs/_static/img/summary-button.png rename to medcat-trainer/docs/docs/_static/img/summary-button.png diff --git a/medcat-trainer/docs/_static/img/tick_mark.png b/medcat-trainer/docs/docs/_static/img/tick_mark.png similarity index 100% rename from medcat-trainer/docs/_static/img/tick_mark.png rename to medcat-trainer/docs/docs/_static/img/tick_mark.png diff --git a/medcat-trainer/docs/_static/img/users-select.png b/medcat-trainer/docs/docs/_static/img/users-select.png similarity index 100% rename from medcat-trainer/docs/_static/img/users-select.png rename to medcat-trainer/docs/docs/_static/img/users-select.png diff --git a/medcat-trainer/docs/admin_setup.md b/medcat-trainer/docs/docs/admin_setup.md similarity index 100% rename from medcat-trainer/docs/admin_setup.md rename to medcat-trainer/docs/docs/admin_setup.md diff --git a/medcat-trainer/docs/advanced_usage.md b/medcat-trainer/docs/docs/advanced_usage.md similarity index 100% rename from medcat-trainer/docs/advanced_usage.md rename to medcat-trainer/docs/docs/advanced_usage.md diff --git a/medcat-trainer/docs/annotator_guide.md b/medcat-trainer/docs/docs/annotator_guide.md similarity index 100% rename from medcat-trainer/docs/annotator_guide.md rename to medcat-trainer/docs/docs/annotator_guide.md diff --git a/medcat-trainer/docs/client.md b/medcat-trainer/docs/docs/client.md similarity index 100% rename from medcat-trainer/docs/client.md rename to medcat-trainer/docs/docs/client.md diff --git a/medcat-trainer/docs/demo_page.md b/medcat-trainer/docs/docs/demo_page.md similarity index 100% rename from medcat-trainer/docs/demo_page.md rename to medcat-trainer/docs/docs/demo_page.md diff --git a/medcat-trainer/docs/index.md b/medcat-trainer/docs/docs/index.md similarity index 100% rename from medcat-trainer/docs/index.md rename to medcat-trainer/docs/docs/index.md diff --git a/medcat-trainer/docs/installation.md b/medcat-trainer/docs/docs/installation.md similarity index 100% rename from medcat-trainer/docs/installation.md rename to medcat-trainer/docs/docs/installation.md diff --git a/medcat-trainer/docs/maintenance.md b/medcat-trainer/docs/docs/maintenance.md similarity index 100% rename from medcat-trainer/docs/maintenance.md rename to medcat-trainer/docs/docs/maintenance.md diff --git a/medcat-trainer/docs/meta_annotations.md b/medcat-trainer/docs/docs/meta_annotations.md similarity index 100% rename from medcat-trainer/docs/meta_annotations.md rename to medcat-trainer/docs/docs/meta_annotations.md diff --git a/medcat-trainer/docs/project_admin.md b/medcat-trainer/docs/docs/project_admin.md similarity index 100% rename from medcat-trainer/docs/project_admin.md rename to medcat-trainer/docs/docs/project_admin.md diff --git a/medcat-trainer/docs/project_group_admin.md b/medcat-trainer/docs/docs/project_group_admin.md similarity index 100% rename from medcat-trainer/docs/project_group_admin.md rename to medcat-trainer/docs/docs/project_group_admin.md diff --git a/medcat-trainer/mkdocs.yml b/medcat-trainer/docs/mkdocs.yml similarity index 100% rename from medcat-trainer/mkdocs.yml rename to medcat-trainer/docs/mkdocs.yml diff --git a/medcat-trainer/docs/requirements.txt b/medcat-trainer/docs/requirements.txt deleted file mode 100644 index 2cdd31719..000000000 --- a/medcat-trainer/docs/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -Sphinx==6.2.1 -sphinx-rtd-theme~=1.0 -myst-parser~=0.17 -sphinx-autoapi==3.0.0 \ No newline at end of file From 8387a80384e3f12550bbad2d71010832b6574dba Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:32:00 +0000 Subject: [PATCH 06/13] docs(medcat-trainer): Move all markdown files to docs folder --- medcat-trainer/.readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index e4f0e3a7e..5b08cd481 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -20,4 +20,4 @@ build: - cd medcat-trainer/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: - configuration: docs/mkdocs.yml \ No newline at end of file + configuration: medcat-trainer/docs/mkdocs.yml \ No newline at end of file From 0a33fa16063dc3ad6f4f5aca0407ac77ec9e4220 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:43:24 +0000 Subject: [PATCH 07/13] docs(medcat-trainer): Try undoing folder move --- medcat-trainer/.readthedocs.yaml | 2 +- .../docs/{docs => }/_static/css/overrides.css | 0 .../_static/img/add-annotation-concept-pick.png | Bin .../_static/img/add-annotation-concept.png | Bin .../{docs => }/_static/img/add-annotation-menu.png | Bin .../_static/img/add-annotation-select-concept.png | Bin .../{docs => }/_static/img/add-annotation-text.png | Bin .../{docs => }/_static/img/add-new-meta-task.png | Bin .../docs/{docs => }/_static/img/add-new-users.png | Bin .../_static/img/add_project_annotate_entities.png | Bin .../docs/{docs => }/_static/img/admin_page.png | Bin .../{docs => }/_static/img/available-projects.png | Bin .../docs/{docs => }/_static/img/cat-logo.png | Bin .../docs/{docs => }/_static/img/cat-logo.svg | 0 .../docs/{docs => }/_static/img/clone-projects.png | Bin .../_static/img/concepts-imported-status.png | Bin .../_static/img/delete-indexed-concepts.png | Bin .../docs/{docs => }/_static/img/demo_interface.png | Bin .../docs/{docs => }/_static/img/demo_tab.png | Bin .../docs/{docs => }/_static/img/download-annos.png | Bin .../docs/{docs => }/_static/img/help-button.png | Bin .../_static/img/home-screen-admin-options.png | Bin .../docs/{docs => }/_static/img/import-concepts.png | Bin .../docs/{docs => }/_static/img/login.png | Bin .../_static/img/main-annotation-interface.png | Bin .../docs/{docs => }/_static/img/meta-task-form.png | Bin .../{docs => }/_static/img/meta-tasks-interface.png | Bin .../docs/{docs => }/_static/img/new_projects.png | Bin .../_static/img/pick-alternative-concept.png | Bin .../_static/img/project-groups-view-available.png | Bin .../{docs => }/_static/img/project-groups-view.png | Bin .../_static/img/project_annotate_entities.png | Bin .../{docs => }/_static/img/projects-in-group.png | Bin .../{docs => }/_static/img/remove-default-user.png | Bin .../docs/{docs => }/_static/img/reset-button.png | Bin .../docs/{docs => }/_static/img/reset-projects.png | Bin .../docs/{docs => }/_static/img/save_cdb.png | Bin .../{docs => }/_static/img/select-concept-dbs.png | Bin .../_static/img/select-existing-project.png | Bin .../docs/{docs => }/_static/img/select-tasks.png | Bin .../docs/{docs => }/_static/img/summary-button.png | Bin .../docs/{docs => }/_static/img/tick_mark.png | Bin .../docs/{docs => }/_static/img/users-select.png | Bin medcat-trainer/docs/{docs => }/admin_setup.md | 0 medcat-trainer/docs/{docs => }/advanced_usage.md | 0 medcat-trainer/docs/{docs => }/annotator_guide.md | 0 medcat-trainer/docs/{docs => }/client.md | 0 medcat-trainer/docs/{docs => }/demo_page.md | 0 medcat-trainer/docs/{docs => }/index.md | 0 medcat-trainer/docs/{docs => }/installation.md | 0 medcat-trainer/docs/{docs => }/maintenance.md | 0 medcat-trainer/docs/{docs => }/meta_annotations.md | 0 medcat-trainer/docs/{docs => }/project_admin.md | 0 .../docs/{docs => }/project_group_admin.md | 0 medcat-trainer/{docs => }/mkdocs.yml | 0 55 files changed, 1 insertion(+), 1 deletion(-) rename medcat-trainer/docs/{docs => }/_static/css/overrides.css (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-annotation-concept-pick.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-annotation-concept.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-annotation-menu.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-annotation-select-concept.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-annotation-text.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-new-meta-task.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add-new-users.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/add_project_annotate_entities.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/admin_page.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/available-projects.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/cat-logo.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/cat-logo.svg (100%) rename medcat-trainer/docs/{docs => }/_static/img/clone-projects.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/concepts-imported-status.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/delete-indexed-concepts.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/demo_interface.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/demo_tab.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/download-annos.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/help-button.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/home-screen-admin-options.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/import-concepts.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/login.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/main-annotation-interface.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/meta-task-form.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/meta-tasks-interface.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/new_projects.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/pick-alternative-concept.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/project-groups-view-available.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/project-groups-view.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/project_annotate_entities.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/projects-in-group.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/remove-default-user.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/reset-button.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/reset-projects.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/save_cdb.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/select-concept-dbs.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/select-existing-project.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/select-tasks.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/summary-button.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/tick_mark.png (100%) rename medcat-trainer/docs/{docs => }/_static/img/users-select.png (100%) rename medcat-trainer/docs/{docs => }/admin_setup.md (100%) rename medcat-trainer/docs/{docs => }/advanced_usage.md (100%) rename medcat-trainer/docs/{docs => }/annotator_guide.md (100%) rename medcat-trainer/docs/{docs => }/client.md (100%) rename medcat-trainer/docs/{docs => }/demo_page.md (100%) rename medcat-trainer/docs/{docs => }/index.md (100%) rename medcat-trainer/docs/{docs => }/installation.md (100%) rename medcat-trainer/docs/{docs => }/maintenance.md (100%) rename medcat-trainer/docs/{docs => }/meta_annotations.md (100%) rename medcat-trainer/docs/{docs => }/project_admin.md (100%) rename medcat-trainer/docs/{docs => }/project_group_admin.md (100%) rename medcat-trainer/{docs => }/mkdocs.yml (100%) diff --git a/medcat-trainer/.readthedocs.yaml b/medcat-trainer/.readthedocs.yaml index 5b08cd481..9880b16c9 100644 --- a/medcat-trainer/.readthedocs.yaml +++ b/medcat-trainer/.readthedocs.yaml @@ -20,4 +20,4 @@ build: - cd medcat-trainer/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: - configuration: medcat-trainer/docs/mkdocs.yml \ No newline at end of file + configuration: medcat-trainer/mkdocs.yml \ No newline at end of file diff --git a/medcat-trainer/docs/docs/_static/css/overrides.css b/medcat-trainer/docs/_static/css/overrides.css similarity index 100% rename from medcat-trainer/docs/docs/_static/css/overrides.css rename to medcat-trainer/docs/_static/css/overrides.css diff --git a/medcat-trainer/docs/docs/_static/img/add-annotation-concept-pick.png b/medcat-trainer/docs/_static/img/add-annotation-concept-pick.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-annotation-concept-pick.png rename to medcat-trainer/docs/_static/img/add-annotation-concept-pick.png diff --git a/medcat-trainer/docs/docs/_static/img/add-annotation-concept.png b/medcat-trainer/docs/_static/img/add-annotation-concept.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-annotation-concept.png rename to medcat-trainer/docs/_static/img/add-annotation-concept.png diff --git a/medcat-trainer/docs/docs/_static/img/add-annotation-menu.png b/medcat-trainer/docs/_static/img/add-annotation-menu.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-annotation-menu.png rename to medcat-trainer/docs/_static/img/add-annotation-menu.png diff --git a/medcat-trainer/docs/docs/_static/img/add-annotation-select-concept.png b/medcat-trainer/docs/_static/img/add-annotation-select-concept.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-annotation-select-concept.png rename to medcat-trainer/docs/_static/img/add-annotation-select-concept.png diff --git a/medcat-trainer/docs/docs/_static/img/add-annotation-text.png b/medcat-trainer/docs/_static/img/add-annotation-text.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-annotation-text.png rename to medcat-trainer/docs/_static/img/add-annotation-text.png diff --git a/medcat-trainer/docs/docs/_static/img/add-new-meta-task.png b/medcat-trainer/docs/_static/img/add-new-meta-task.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-new-meta-task.png rename to medcat-trainer/docs/_static/img/add-new-meta-task.png diff --git a/medcat-trainer/docs/docs/_static/img/add-new-users.png b/medcat-trainer/docs/_static/img/add-new-users.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add-new-users.png rename to medcat-trainer/docs/_static/img/add-new-users.png diff --git a/medcat-trainer/docs/docs/_static/img/add_project_annotate_entities.png b/medcat-trainer/docs/_static/img/add_project_annotate_entities.png similarity index 100% rename from medcat-trainer/docs/docs/_static/img/add_project_annotate_entities.png rename to 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b/medcat-trainer/docs/annotator_guide.md similarity index 100% rename from medcat-trainer/docs/docs/annotator_guide.md rename to medcat-trainer/docs/annotator_guide.md diff --git a/medcat-trainer/docs/docs/client.md b/medcat-trainer/docs/client.md similarity index 100% rename from medcat-trainer/docs/docs/client.md rename to medcat-trainer/docs/client.md diff --git a/medcat-trainer/docs/docs/demo_page.md b/medcat-trainer/docs/demo_page.md similarity index 100% rename from medcat-trainer/docs/docs/demo_page.md rename to medcat-trainer/docs/demo_page.md diff --git a/medcat-trainer/docs/docs/index.md b/medcat-trainer/docs/index.md similarity index 100% rename from medcat-trainer/docs/docs/index.md rename to medcat-trainer/docs/index.md diff --git a/medcat-trainer/docs/docs/installation.md b/medcat-trainer/docs/installation.md similarity index 100% rename from medcat-trainer/docs/docs/installation.md rename to medcat-trainer/docs/installation.md diff --git a/medcat-trainer/docs/docs/maintenance.md b/medcat-trainer/docs/maintenance.md similarity index 100% rename from medcat-trainer/docs/docs/maintenance.md rename to medcat-trainer/docs/maintenance.md diff --git a/medcat-trainer/docs/docs/meta_annotations.md b/medcat-trainer/docs/meta_annotations.md similarity index 100% rename from medcat-trainer/docs/docs/meta_annotations.md rename to medcat-trainer/docs/meta_annotations.md diff --git a/medcat-trainer/docs/docs/project_admin.md b/medcat-trainer/docs/project_admin.md similarity index 100% rename from medcat-trainer/docs/docs/project_admin.md rename to medcat-trainer/docs/project_admin.md diff --git a/medcat-trainer/docs/docs/project_group_admin.md b/medcat-trainer/docs/project_group_admin.md similarity index 100% rename from medcat-trainer/docs/docs/project_group_admin.md rename to medcat-trainer/docs/project_group_admin.md diff --git a/medcat-trainer/docs/mkdocs.yml b/medcat-trainer/mkdocs.yml similarity index 100% rename from medcat-trainer/docs/mkdocs.yml rename to medcat-trainer/mkdocs.yml From 54a20b8940883143d7cec30620082601d956ab1d Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:46:08 +0000 Subject: [PATCH 08/13] docs(medcat-trainer): Fix installation intro --- medcat-trainer/docs/installation.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/medcat-trainer/docs/installation.md b/medcat-trainer/docs/installation.md index 89b91396d..50488432d 100644 --- a/medcat-trainer/docs/installation.md +++ b/medcat-trainer/docs/installation.md @@ -1,11 +1,12 @@ # Installation The steps to setup Medcat trainer are as follows: + 1. Run MedCAT Trainer with Docker or Helm 2. Setup the Administrator user with [Administrator Setup](admin_setup.md) 3. Configure annotations Projects -This page details the initial running of the application. +This page details the initial running of the application with Docker MedCATtrainer is packaged as a Docker Compose deployment with three core services: From 3f4316398564bc7a8d91869b24fffbcfaa6e8ce1 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:50:50 +0000 Subject: [PATCH 09/13] docs(medcat-trainer): Fix markdown bullet list items needing 4 spaces not 2 --- medcat-trainer/docs/demo_page.md | 4 ++-- medcat-trainer/docs/index.md | 14 +++++++------- medcat-trainer/docs/maintenance.md | 4 ++-- medcat-trainer/docs/meta_annotations.md | 10 +++++----- medcat-trainer/docs/project_admin.md | 10 +++++----- 5 files changed, 21 insertions(+), 21 deletions(-) diff --git a/medcat-trainer/docs/demo_page.md b/medcat-trainer/docs/demo_page.md index 3fd397c22..7571d40bb 100644 --- a/medcat-trainer/docs/demo_page.md +++ b/medcat-trainer/docs/demo_page.md @@ -17,8 +17,8 @@ It does **not** persist annotation decisions like a project workflow does. 1. Select a **Model Pack**. 2. Optionally add CUI filters: - - pick concepts from the concept picker, or - - paste a comma-separated CUI list. + - pick concepts from the concept picker, or + - paste a comma-separated CUI list. 3. Optionally enable **Include sub-concepts**. 4. Enter or paste free text. diff --git a/medcat-trainer/docs/index.md b/medcat-trainer/docs/index.md index 1f9a8a07d..3e0f9a54c 100644 --- a/medcat-trainer/docs/index.md +++ b/medcat-trainer/docs/index.md @@ -10,15 +10,15 @@ review-only workflows (collect annotations without changing the model). - Build annotation projects from CSV/XLSX datasets. - Use either: - - a **Model Pack** (recommended), or - - a **Concept DB + Vocabulary** pair. + - a **Model Pack** (recommended), or + - a **Concept DB + Vocabulary** pair. - Optionally use a **remote MedCAT model service** for document preparation. - Collect concept-level labels: - - Correct - - Incorrect - - Alternative concept - - Terminate - - Irrelevant + - Correct + - Incorrect + - Alternative concept + - Terminate + - Irrelevant - Collect optional **meta annotations** and **relation annotations**. - Use **Project Groups** for multi-annotator setups. - Run **metrics reports** across one or more compatible projects. diff --git a/medcat-trainer/docs/maintenance.md b/medcat-trainer/docs/maintenance.md index 6b25dcf4e..ee2290cc0 100644 --- a/medcat-trainer/docs/maintenance.md +++ b/medcat-trainer/docs/maintenance.md @@ -36,8 +36,8 @@ The backup scripts are SQLite-focused (`DB_ENGINE=sqlite3`). - A backup is taken on startup before migrations. - A scheduled backup job also runs regularly. - Backup location is controlled by: - - `DB_PATH` - - `DB_BACKUP_DIR` + - `DB_PATH` + - `DB_BACKUP_DIR` ### Restore process diff --git a/medcat-trainer/docs/meta_annotations.md b/medcat-trainer/docs/meta_annotations.md index 069c6512b..be9671aab 100644 --- a/medcat-trainer/docs/meta_annotations.md +++ b/medcat-trainer/docs/meta_annotations.md @@ -16,11 +16,11 @@ Create and manage tasks in Django admin (`/admin`): 1. Create **Meta Task Values** (the allowed label options). 2. Create a **Meta Task**: - - name - - values - - default value (optional) - - description - - ordering + - name + - values + - default value (optional) + - description + - ordering 3. Attach selected tasks to your project (`Project annotate entities`). ## Model-pack predictions vs manual labels diff --git a/medcat-trainer/docs/project_admin.md b/medcat-trainer/docs/project_admin.md index 7ce879bb5..2d3c87cc2 100644 --- a/medcat-trainer/docs/project_admin.md +++ b/medcat-trainer/docs/project_admin.md @@ -10,11 +10,11 @@ MedCATtrainer supports two management surfaces: 1. Open `/project-admin`. 2. Go to the **Projects** tab and select **Create New Project**. 3. Fill in: - - **Basic information** (name, dataset, description, guideline link) - - **Model configuration** - - **Annotation settings** - - **Concept filter (optional)** - - **Members** + - **Basic information** (name, dataset, description, guideline link) + - **Model configuration** + - **Annotation settings** + - **Concept filter (optional)** + - **Members** 4. Save. ### Model configuration options From a9421a42223802da1b8dcae1e770a22231f892ac Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:52:00 +0000 Subject: [PATCH 10/13] docs(medcat-trainer): Fix installation next steps missing from contents --- medcat-trainer/docs/installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/docs/installation.md b/medcat-trainer/docs/installation.md index 50488432d..47fbed688 100644 --- a/medcat-trainer/docs/installation.md +++ b/medcat-trainer/docs/installation.md @@ -139,5 +139,5 @@ An example compose file is available at - **Concept picker empty**: confirm Solr is running and concepts were imported for the selected CDB. -# Next Steps +## Next Steps Now that medcat trainer is installed and running, proceed to [Administrator Setup](admin_setup.md) to create the Admin user. \ No newline at end of file From 38763ec6d47a496dff4359485f24ad2be151408f Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Thu, 26 Feb 2026 17:53:31 +0000 Subject: [PATCH 11/13] docs(medcat-trainer): Fix installation next steps missing from contents --- medcat-trainer/docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-trainer/docs/index.md b/medcat-trainer/docs/index.md index 3e0f9a54c..685cd513c 100644 --- a/medcat-trainer/docs/index.md +++ b/medcat-trainer/docs/index.md @@ -1,4 +1,4 @@ -# Medical MedCAToncept Annotation Tool Trainer +# Medical Concept Annotation Tool Trainer MedCATtrainer is a web application for creating, validating, and improving MedCAT concept annotation models on biomedical or clinical text. From c864fdf6399ef32d723b0f40829fcca626a92575 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Fri, 27 Feb 2026 10:50:06 +0000 Subject: [PATCH 12/13] docs(medcat-trainer): Fix pyproject.toml values --- medcat-trainer/docs/pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat-trainer/docs/pyproject.toml b/medcat-trainer/docs/pyproject.toml index 9eb98e729..6e5c4bac6 100644 --- a/medcat-trainer/docs/pyproject.toml +++ b/medcat-trainer/docs/pyproject.toml @@ -1,7 +1,7 @@ [project] -name = "cogstack-documentation" +name = "medcat-trainer-documentation" version = "0.1.0" -description = "CogStack Documentation" +description = "MedCAT Trainer Documentation" readme = "README.md" requires-python = ">=3.10" dependencies = [ From 75b52f2349c0dded592b4f5ec360a730d8ca25f3 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Fri, 27 Feb 2026 10:51:19 +0000 Subject: [PATCH 13/13] docs(medcat-trainer): Fix pyproject.toml values --- medcat-trainer/docs/uv.lock | 44 ++++++++++++++++++------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/medcat-trainer/docs/uv.lock b/medcat-trainer/docs/uv.lock index 4feaaa650..d696abf40 100644 --- a/medcat-trainer/docs/uv.lock +++ b/medcat-trainer/docs/uv.lock @@ -135,28 +135,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/98/78/01c019cdb5d6498122777c1a43056ebb3ebfeef2076d9d026bfe15583b2b/click-8.3.1-py3-none-any.whl", hash = "sha256:981153a64e25f12d547d3426c367a4857371575ee7ad18df2a6183ab0545b2a6", size = 108274, upload-time = "2025-11-15T20:45:41.139Z" }, ] -[[package]] -name = "cogstack-documentation" -version = "0.1.0" -source = { virtual = "." } -dependencies = [ - { name = "mkdocs-material" }, - { name = "termynal" }, -] - -[package.optional-dependencies] -dev = [ - { name = "ruff" }, -] - -[package.metadata] -requires-dist = [ - { name = "mkdocs-material", specifier = ">=9.7.0" }, - { name = "ruff", marker = "extra == 'dev'", specifier = ">=0.12.11" }, - { name = "termynal", specifier = ">=0.13.1" }, -] -provides-extras = ["dev"] - [[package]] name = "colorama" version = "0.4.6" @@ -293,6 +271,28 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/70/bc/6f1c2f612465f5fa89b95bead1f44dcb607670fd42891d8fdcd5d039f4f4/markupsafe-3.0.3-cp314-cp314t-win_arm64.whl", hash = "sha256:32001d6a8fc98c8cb5c947787c5d08b0a50663d139f1305bac5885d98d9b40fa", size = 14146, upload-time = "2025-09-27T18:37:28.327Z" }, ] +[[package]] +name = "medcat-trainer-documentation" +version = "0.1.0" +source = { virtual = "." } +dependencies = [ + { name = "mkdocs-material" }, + { name = "termynal" }, +] + +[package.optional-dependencies] +dev = [ + { name = "ruff" }, +] + +[package.metadata] +requires-dist = [ + { name = "mkdocs-material", specifier = ">=9.7.0" }, + { name = "ruff", marker = "extra == 'dev'", specifier = ">=0.12.11" }, + { name = "termynal", specifier = ">=0.13.1" }, +] +provides-extras = ["dev"] + [[package]] name = "mergedeep" version = "1.3.4"