From 3d1a7f3f8949b98fe5644989acc2509ec22623eb Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 18 Feb 2026 16:29:42 +0000 Subject: [PATCH 1/9] docs: Migrate from sphinx to mkdocs --- .readthedocs.yml | 20 +- docs/Makefile | 23 - docs/conf.py | 61 -- .../_static/screenshots-dashboards-alerts.png | Bin .../screenshots-dashboards-availability.png | Bin .../screenshots-dashboards-docker-metrics.png | Bin .../screenshots-dashboards-es-metrics.png | Bin .../screenshots-dashboards-vm-metrics.png | Bin docs/{ => docs/assets}/cogstack-logo.png | Bin docs/docs/index.md | 12 + docs/{ => docs}/overview/Data pipelines.md | 0 docs/{ => docs}/overview/Elasticsearch.md | 0 .../overview/Natural Language Processing.md | 0 .../09a8bb60-9864-41fa-be7b-cf9a9dc04498.png | Bin .../overview/attachments/architecture.png | Bin .../b5fc6b57-faf2-4747-9e77-eb9adf51d8b3.jpg | Bin .../df995677-ab49-4f74-ab65-a160882b23a6.jpg | Bin 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.../reference/concept-materials.md | 7 - .../reference/project-details.md | 9 - docs/platform/observability/setup/_index.md | 12 - docs/pyproject.toml | 19 + docs/requirements.txt | 6 - docs/uv.lock | 620 ++++++++++++++++++ 68 files changed, 827 insertions(+), 350 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/conf.py rename docs/{ => docs}/_static/screenshots-dashboards-alerts.png (100%) rename docs/{ => docs}/_static/screenshots-dashboards-availability.png (100%) rename docs/{ => docs}/_static/screenshots-dashboards-docker-metrics.png (100%) rename docs/{ => docs}/_static/screenshots-dashboards-es-metrics.png (100%) rename docs/{ => docs}/_static/screenshots-dashboards-vm-metrics.png (100%) rename docs/{ => docs/assets}/cogstack-logo.png (100%) create mode 100644 docs/docs/index.md rename docs/{ => docs}/overview/Data pipelines.md (100%) rename docs/{ => docs}/overview/Elasticsearch.md (100%) rename docs/{ => docs}/overview/Natural Language Processing.md (100%) 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--git a/.readthedocs.yml b/.readthedocs.yml index 0b2f93b..ae6db4d 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,14 +5,16 @@ version: 2 build: - os: ubuntu-20.04 + os: "ubuntu-24.04" tools: - python: "3.9" + python: "3.13" + jobs: + pre_create_environment: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + create_environment: + - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" + install: + - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs -sphinx: - configuration: docs/conf.py - fail_on_warning: false # Removed warnings to migrate existing docs - -python: - install: - - requirements: docs/requirements.txt \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index b7e8724..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,23 +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) - -build: - sphinx-autobuild . _build/ \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 0cf05c1..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,61 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# For the full list of built-in configuration values, see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html -import os -import sys -sys.path.insert(0, os.path.abspath("../observability/docs")) - -print("Hello") -# -- Project information ----------------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information - -project = 'CogStack Documentation' -copyright = '2025, CogStack Org' -author = 'CogStack Org' -release = 'latest' -html_title = "CogStack Documentation" - -# -- General configuration --------------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - -extensions = [ - 'sphinx_rtd_theme', - 'sphinx.ext.autodoc', - 'myst_parser', - 'sphinx.ext.inheritance_diagram', - 'sphinx.ext.intersphinx' -] - -templates_path = ['_templates'] -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - - -# -- Options for HTML output ------------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output - -html_theme = "furo" -html_static_path = ['_static'] -html_logo = "cogstack-logo.png" - -intersphinx_mapping = { - "sphinx": ("https://www.sphinx-doc.org/en/master/", None), -} -intersphinx_disabled_reftypes = ["*"] - -myst_enable_extensions = [ - "amsmath", - "attrs_inline", - "colon_fence", - "deflist", - "dollarmath", - "fieldlist", - "html_admonition", - "html_image", - # "linkify", - "replacements", - "smartquotes", - "strikethrough", - "substitution", - "tasklist", -] diff --git a/docs/_static/screenshots-dashboards-alerts.png b/docs/docs/_static/screenshots-dashboards-alerts.png similarity index 100% rename from docs/_static/screenshots-dashboards-alerts.png rename to docs/docs/_static/screenshots-dashboards-alerts.png diff --git a/docs/_static/screenshots-dashboards-availability.png b/docs/docs/_static/screenshots-dashboards-availability.png similarity index 100% rename from docs/_static/screenshots-dashboards-availability.png rename to docs/docs/_static/screenshots-dashboards-availability.png diff --git a/docs/_static/screenshots-dashboards-docker-metrics.png b/docs/docs/_static/screenshots-dashboards-docker-metrics.png similarity index 100% rename from docs/_static/screenshots-dashboards-docker-metrics.png rename to docs/docs/_static/screenshots-dashboards-docker-metrics.png diff --git a/docs/_static/screenshots-dashboards-es-metrics.png b/docs/docs/_static/screenshots-dashboards-es-metrics.png similarity index 100% rename from docs/_static/screenshots-dashboards-es-metrics.png rename to docs/docs/_static/screenshots-dashboards-es-metrics.png diff --git a/docs/_static/screenshots-dashboards-vm-metrics.png b/docs/docs/_static/screenshots-dashboards-vm-metrics.png similarity index 100% rename from docs/_static/screenshots-dashboards-vm-metrics.png rename to docs/docs/_static/screenshots-dashboards-vm-metrics.png diff --git a/docs/cogstack-logo.png b/docs/docs/assets/cogstack-logo.png similarity index 100% rename from docs/cogstack-logo.png rename to docs/docs/assets/cogstack-logo.png diff --git a/docs/docs/index.md b/docs/docs/index.md new file mode 100644 index 0000000..5f9b807 --- /dev/null +++ b/docs/docs/index.md @@ -0,0 +1,12 @@ +# Cogstack Documentation + +Welcome to the CogStack Documentation site. + +Get started by looking at the [Introduction](overview/introduction.md) + +Any broad questions then please do reach out in our community space [here](https://discourse.cogstack.org/) + +Further in development projects are [here](https://github.com/orgs/CogStack/repositories) + +![CogStack Architecture](./overview/attachments/architecture.png) + diff --git a/docs/overview/Data pipelines.md b/docs/docs/overview/Data pipelines.md similarity index 100% rename from docs/overview/Data pipelines.md rename to docs/docs/overview/Data pipelines.md diff --git a/docs/overview/Elasticsearch.md b/docs/docs/overview/Elasticsearch.md similarity index 100% rename from docs/overview/Elasticsearch.md rename to docs/docs/overview/Elasticsearch.md diff --git a/docs/overview/Natural Language Processing.md b/docs/docs/overview/Natural Language Processing.md similarity index 100% rename from docs/overview/Natural Language Processing.md rename to docs/docs/overview/Natural Language Processing.md diff --git a/docs/overview/attachments/09a8bb60-9864-41fa-be7b-cf9a9dc04498.png b/docs/docs/overview/attachments/09a8bb60-9864-41fa-be7b-cf9a9dc04498.png similarity index 100% rename from docs/overview/attachments/09a8bb60-9864-41fa-be7b-cf9a9dc04498.png rename to docs/docs/overview/attachments/09a8bb60-9864-41fa-be7b-cf9a9dc04498.png diff --git a/docs/overview/attachments/architecture.png b/docs/docs/overview/attachments/architecture.png similarity index 100% rename from docs/overview/attachments/architecture.png rename to docs/docs/overview/attachments/architecture.png diff --git a/docs/overview/attachments/b5fc6b57-faf2-4747-9e77-eb9adf51d8b3.jpg b/docs/docs/overview/attachments/b5fc6b57-faf2-4747-9e77-eb9adf51d8b3.jpg similarity index 100% rename from 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rename from docs/overview/attachments/f7a03376-ae0e-4980-929a-e3897da5d186.jpg rename to docs/docs/overview/attachments/f7a03376-ae0e-4980-929a-e3897da5d186.jpg diff --git a/docs/overview/cogstack-documentation.md b/docs/docs/overview/introduction.md similarity index 98% rename from docs/overview/cogstack-documentation.md rename to docs/docs/overview/introduction.md index f5539b8..7e1443f 100644 --- a/docs/overview/cogstack-documentation.md +++ b/docs/docs/overview/introduction.md @@ -1,4 +1,4 @@ -# CogStack Documentation +# Introduction ## What is CogStack? diff --git a/docs/platform/deployment/_index.md b/docs/docs/platform/deployment/_index.md similarity index 78% rename from docs/platform/deployment/_index.md rename to docs/docs/platform/deployment/_index.md index 91a51cd..e7d7187 100644 --- a/docs/platform/deployment/_index.md +++ b/docs/docs/platform/deployment/_index.md @@ -12,13 +12,13 @@ To setup a full deployment of CogStack including the data pipelines and infrastr ## Overview CogStack is a self-hosted platform made up of microservices and tools -If you want to get started quickly, check out the [Quickstart](./get-started/quickstart) guide to run CogStack locally in just a few simple steps. +If you want to get started quickly, check out the [Quickstart](./get-started/quickstart.md) guide to run CogStack locally in just a few simple steps. -Our recommended deployment method is on Kubernetes using Helm charts. This makes installing and managing CogStack easy and consistent. For a detailed walkthrough, see [Helm](./helm/_index) . +Our recommended deployment method is on Kubernetes using Helm charts. This makes installing and managing CogStack easy and consistent. For a detailed walkthrough, see [Helm](./helm/_index.md). -You can run Kubernetes anywhere — on your own hardware or through cloud providers like AWS (EKS) or Azure (AKS). To help with this, we provide basic examples using Terraform that will deploy the infrastructure, services, and perform tests using a few terraform commands. These are available in the [Examples](./examples/_index) folder. +You can run Kubernetes anywhere — on your own hardware or through cloud providers like AWS (EKS) or Azure (AKS). To help with this, we provide basic examples using Terraform that will deploy the infrastructure, services, and perform tests using a few terraform commands. These are available in the [Examples](./examples/_index.md) section. -Along with kubernetes, it is also possible to run CogStack through docker compose. See the [Reference](./reference/_index) folder for this. +Along with kubernetes, it is also possible to run CogStack through docker compose. See the [Docker Compose](./reference/docker-compose/_index.md) section for this. ## Deployment Recommendations @@ -28,15 +28,3 @@ Along with kubernetes, it is also possible to run CogStack through docker compos - Keep your Terraform code in your own Git repository and adopt GitOps practices -## Contents -```{toctree} -:maxdepth: 2 - -get-started/_index - -helm/_index - -examples/_index - -reference/_index -``` diff --git a/docs/platform/deployment/examples/_index.md b/docs/docs/platform/deployment/examples/_index.md similarity index 84% rename from docs/platform/deployment/examples/_index.md rename to docs/docs/platform/deployment/examples/_index.md index ed633c6..cdfd543 100644 --- a/docs/platform/deployment/examples/_index.md +++ b/docs/docs/platform/deployment/examples/_index.md @@ -8,10 +8,3 @@ Use them as a starting point or reference for your own deployments. Please note these examples are for demonstration and testing only. We do not advise using these with any real production data without review. Cloud infrastructure can be complex, and your IT department likely has guidelines or governance rules you’ll need to follow when moving beyond these basic setups. ::: -```{toctree} -:maxdepth: 2 -aws-kubernetes-eks -azure-kubernetes-aks -openstack-kubernetes-k3s -openstack-docker -``` diff --git a/docs/platform/deployment/examples/aws-kubernetes-eks.md b/docs/docs/platform/deployment/examples/aws-kubernetes-eks.md similarity index 100% rename from docs/platform/deployment/examples/aws-kubernetes-eks.md rename to docs/docs/platform/deployment/examples/aws-kubernetes-eks.md diff --git a/docs/platform/deployment/examples/azure-kubernetes-aks.md b/docs/docs/platform/deployment/examples/azure-kubernetes-aks.md similarity index 100% rename from docs/platform/deployment/examples/azure-kubernetes-aks.md rename to docs/docs/platform/deployment/examples/azure-kubernetes-aks.md diff --git a/docs/platform/deployment/examples/openstack-docker.md b/docs/docs/platform/deployment/examples/openstack-docker.md similarity index 100% rename from docs/platform/deployment/examples/openstack-docker.md rename to docs/docs/platform/deployment/examples/openstack-docker.md diff --git a/docs/platform/deployment/examples/openstack-kubernetes-k3s.md b/docs/docs/platform/deployment/examples/openstack-kubernetes-k3s.md similarity index 100% rename from docs/platform/deployment/examples/openstack-kubernetes-k3s.md rename to docs/docs/platform/deployment/examples/openstack-kubernetes-k3s.md diff --git a/docs/platform/deployment/get-started/_index.md b/docs/docs/platform/deployment/get-started/_index.md similarity index 96% rename from docs/platform/deployment/get-started/_index.md rename to docs/docs/platform/deployment/get-started/_index.md index f6fad99..fa2b8a5 100644 --- a/docs/platform/deployment/get-started/_index.md +++ b/docs/docs/platform/deployment/get-started/_index.md @@ -28,9 +28,3 @@ See the official documentation on these tools for the best documentation for ins If you plan to deploy on cloud providers like AWS, Azure, or OpenStack, ensure you have the appropriate accounts set up with necessary permissions. Refer to the respective provider’s documentation for guidance. -## Contents -```{toctree} -:maxdepth: 2 - -quickstart -``` diff --git a/docs/platform/deployment/get-started/quickstart.md b/docs/docs/platform/deployment/get-started/quickstart.md similarity index 100% rename from docs/platform/deployment/get-started/quickstart.md rename to docs/docs/platform/deployment/get-started/quickstart.md diff --git a/docs/platform/deployment/helm/_index.md b/docs/docs/platform/deployment/helm/_index.md similarity index 67% rename from docs/platform/deployment/helm/_index.md rename to docs/docs/platform/deployment/helm/_index.md index f2ae6e5..4b5a5ff 100644 --- a/docs/platform/deployment/helm/_index.md +++ b/docs/docs/platform/deployment/helm/_index.md @@ -5,16 +5,6 @@ Helm is our recommended way to deploy CogStack. It simplifies installing, upgrad For a detailed, step-by-step walkthrough on deploying CogStack with Helm, please see the [Tutorial](./tutorial.md). -To understand how the Helm charts are structured and how they work under the hood, check out the [architecture](./architecture) section. +To understand how the Helm charts are structured and how they work under the hood, check out the [Charts](./charts/_index.md) section. -## Contents - -```{toctree} -:maxdepth: 2 - -tutorial -cogstack-helm-module -charts/_index - -``` diff --git a/docs/platform/deployment/helm/charts/_index.md b/docs/docs/platform/deployment/helm/charts/_index.md similarity index 81% rename from docs/platform/deployment/helm/charts/_index.md rename to docs/docs/platform/deployment/helm/charts/_index.md index 84810a0..0de2123 100644 --- a/docs/platform/deployment/helm/charts/_index.md +++ b/docs/docs/platform/deployment/helm/charts/_index.md @@ -9,11 +9,8 @@ The Helm charts for CogStack are published to Docker Hub, which is an OCI-compli - **MedCAT Trainer:** https://hub.docker.com/r/cogstacksystems/medcat-trainer-helm -```{toctree} -:maxdepth: 1 -medcat-service-helm -medcat-trainer-helm -``` +- [MedCAT Service Helm](medcat-service-helm.md) +- [MedCAT Trainer Helm](medcat-trainer-helm.md) ## Chart Publishing diff --git a/docs/platform/deployment/helm/charts/medcat-service-helm.md b/docs/docs/platform/deployment/helm/charts/medcat-service-helm.md similarity index 100% rename from docs/platform/deployment/helm/charts/medcat-service-helm.md rename to docs/docs/platform/deployment/helm/charts/medcat-service-helm.md diff --git a/docs/platform/deployment/helm/charts/medcat-trainer-helm.md b/docs/docs/platform/deployment/helm/charts/medcat-trainer-helm.md similarity index 100% rename from docs/platform/deployment/helm/charts/medcat-trainer-helm.md rename to docs/docs/platform/deployment/helm/charts/medcat-trainer-helm.md diff --git a/docs/platform/deployment/helm/cogstack-helm-module.md b/docs/docs/platform/deployment/helm/cogstack-helm-module.md similarity index 100% rename from docs/platform/deployment/helm/cogstack-helm-module.md rename to docs/docs/platform/deployment/helm/cogstack-helm-module.md diff --git a/docs/platform/deployment/helm/troubleshooting.md b/docs/docs/platform/deployment/helm/troubleshooting.md similarity index 100% rename from docs/platform/deployment/helm/troubleshooting.md rename to docs/docs/platform/deployment/helm/troubleshooting.md diff --git a/docs/platform/deployment/helm/tutorial.md b/docs/docs/platform/deployment/helm/tutorial.md similarity index 100% rename from docs/platform/deployment/helm/tutorial.md rename to docs/docs/platform/deployment/helm/tutorial.md diff --git a/docs/platform/deployment/reference/docker-compose/_index.md b/docs/docs/platform/deployment/reference/docker-compose/_index.md similarity index 100% rename from docs/platform/deployment/reference/docker-compose/_index.md rename to docs/docs/platform/deployment/reference/docker-compose/_index.md diff --git a/docs/docs/platform/observability/_index.md b/docs/docs/platform/observability/_index.md new file mode 100644 index 0000000..eb4fc76 --- /dev/null +++ b/docs/docs/platform/observability/_index.md @@ -0,0 +1,40 @@ +# Cogstack Observability + +This project provides observability of a cogstack deployment. + +It provides the following features: +- Dashboards for availability +- Telemetry of infrastructure such as host memory usage, and elasticsearch index size +- Alerting based on a defined Service Level Objective (SLO) and burn rates +- Blackbox Probing of services to find service level indicators of uptime and latency +- A working inventory of what is running where + + +See the [Quickstart](./get-started/quickstart.md) to see how to easily run this stack. + +## Getting Started + +- [Quickstart](./get-started/quickstart.md) +- [User Guide Tutorial](./get-started/userguide-tutorial.md) + +## Setup + +- [Production Setup](./setup/production-setup.md) +- [Probing](./setup/probing.md) +- [Telemetry](./setup/telemetry.md) +- [Alerting](./setup/alerting.md) + +## Customization + +- [Custom Dashboards](./customization/custom-dashboards.md) +- [Alerts Customization](./customization/alerts-customization.md) +- [Custom Prometheus Configs](./customization/custom-prometheus-configs.md) +- [Blackbox Exporter Config](./customization/blackbox-exporter-config.md) + +## Reference + +- [Project Details](./reference/project-details.md) +- [Concept Materials](./reference/concept-materials.md) +- [Quickstart Manual](./reference/quickstart-manual.md) +- [Understanding Metrics](./reference/understanding-metrics.md) + diff --git a/docs/docs/platform/observability/customization/_index.md b/docs/docs/platform/observability/customization/_index.md new file mode 100644 index 0000000..e663b50 --- /dev/null +++ b/docs/docs/platform/observability/customization/_index.md @@ -0,0 +1,5 @@ +# Customization + +## Grafana Customization + +## Prometheus Customization \ No newline at end of file diff --git a/docs/platform/observability/customization/alerts-customization.md b/docs/docs/platform/observability/customization/alerts-customization.md similarity index 100% rename from docs/platform/observability/customization/alerts-customization.md rename to docs/docs/platform/observability/customization/alerts-customization.md diff --git a/docs/platform/observability/customization/blackbox-exporter-config.md b/docs/docs/platform/observability/customization/blackbox-exporter-config.md similarity index 100% rename from docs/platform/observability/customization/blackbox-exporter-config.md rename to docs/docs/platform/observability/customization/blackbox-exporter-config.md diff --git a/docs/platform/observability/customization/custom-dashboards.md b/docs/docs/platform/observability/customization/custom-dashboards.md similarity index 100% rename from docs/platform/observability/customization/custom-dashboards.md rename to docs/docs/platform/observability/customization/custom-dashboards.md diff --git a/docs/platform/observability/customization/custom-prometheus-configs.md b/docs/docs/platform/observability/customization/custom-prometheus-configs.md similarity index 100% rename from docs/platform/observability/customization/custom-prometheus-configs.md rename to docs/docs/platform/observability/customization/custom-prometheus-configs.md diff --git a/docs/platform/observability/get-started/quickstart.md b/docs/docs/platform/observability/get-started/quickstart.md similarity index 100% rename from docs/platform/observability/get-started/quickstart.md rename to docs/docs/platform/observability/get-started/quickstart.md diff --git a/docs/platform/observability/get-started/userguide-tutorial.md b/docs/docs/platform/observability/get-started/userguide-tutorial.md similarity index 100% rename from docs/platform/observability/get-started/userguide-tutorial.md rename to docs/docs/platform/observability/get-started/userguide-tutorial.md diff --git a/docs/docs/platform/observability/reference/concept-materials.md b/docs/docs/platform/observability/reference/concept-materials.md new file mode 100644 index 0000000..0d097e0 --- /dev/null +++ b/docs/docs/platform/observability/reference/concept-materials.md @@ -0,0 +1,4 @@ +# Concepts + +- [Understanding Metrics](understanding-metrics.md) + diff --git a/docs/docs/platform/observability/reference/project-details.md b/docs/docs/platform/observability/reference/project-details.md new file mode 100644 index 0000000..53eb772 --- /dev/null +++ b/docs/docs/platform/observability/reference/project-details.md @@ -0,0 +1,4 @@ +# Further Project Details + +- [Quickstart Manual](quickstart-manual.md) + diff --git a/docs/platform/observability/reference/quickstart-manual.md b/docs/docs/platform/observability/reference/quickstart-manual.md similarity index 73% rename from docs/platform/observability/reference/quickstart-manual.md rename to docs/docs/platform/observability/reference/quickstart-manual.md index 03ca2ea..9a6379c 100644 --- a/docs/platform/observability/reference/quickstart-manual.md +++ b/docs/docs/platform/observability/reference/quickstart-manual.md @@ -11,8 +11,8 @@ mkdir -p observability-simple/alloy/probers Download these two files, and place in the right folder -- [docker-compose.yml](../../../../observability/examples/simple/docker-compose.yml) in observability-simple/ -- [probe-observability.yml](../../../../observability/examples/simple/alloy/probers/probe-observability.yml) into observability-simple/alloy/probers +- [docker-compose.yml](../../../../../observability/examples/simple/docker-compose.yml) in observability-simple/ +- [probe-observability.yml](../../../../../observability/examples/simple/alloy/probers/probe-observability.yml) into observability-simple/alloy/probers ### Step 2: Start the stack diff --git a/docs/platform/observability/reference/understanding-metrics.md b/docs/docs/platform/observability/reference/understanding-metrics.md similarity index 100% rename from docs/platform/observability/reference/understanding-metrics.md rename to docs/docs/platform/observability/reference/understanding-metrics.md diff --git a/docs/platform/observability/setup/alerting.md b/docs/docs/platform/observability/setup/alerting.md similarity index 100% rename from docs/platform/observability/setup/alerting.md rename to docs/docs/platform/observability/setup/alerting.md diff --git a/docs/platform/observability/setup/probing.md b/docs/docs/platform/observability/setup/probing.md similarity index 100% rename from docs/platform/observability/setup/probing.md rename to docs/docs/platform/observability/setup/probing.md diff --git a/docs/platform/observability/setup/production-setup.md b/docs/docs/platform/observability/setup/production-setup.md similarity index 81% rename from docs/platform/observability/setup/production-setup.md rename to docs/docs/platform/observability/setup/production-setup.md index 4399f10..02b19e2 100644 --- a/docs/platform/observability/setup/production-setup.md +++ b/docs/docs/platform/observability/setup/production-setup.md @@ -26,15 +26,15 @@ This script will setup all the folder structure, and download all the relevant f The script automates making folders, and downloading these files: Downloads the example docker compose files: -- [docker-compose.yml](../../../../observability/examples/full/docker-compose.yml) -- [exporters.docker-compose.yml](../../../../observability/examples/full/exporters.docker-compose.yml) -- [exporters.elastic.docker-compose.yml](../../../../observability/examples/full/exporters.elastic.docker-compose.yml) +- [docker-compose.yml](../../../../../observability/examples/full/docker-compose.yml) +- [exporters.docker-compose.yml](../../../../../observability/examples/full/exporters.docker-compose.yml) +- [exporters.elastic.docker-compose.yml](../../../../../observability/examples/full/exporters.elastic.docker-compose.yml) Downloads the configurations: -- [alloy/probers/probe-external.yml](../../../../observability/examples/full/alloy/probers/probe-external.yml) -- [alloy/probers/probe-observability.yml ](../../../../observability/examples/full/alloy/probers/probe-observability.yml) -- [prometheus/scrape-configs/exporters/exporters.yml](../../../../observability/examples/full/prometheus/scrape-configs/exporters/exporters.yml) -- [prometheus/scrape-configs/recording-rules/slo.yml](../../../../observability/examples/full/prometheus/scrape-configs/recording-rules/slo.yml) +- [alloy/probers/probe-external.yml](../../../../../observability/examples/full/alloy/probers/probe-external.yml) +- [alloy/probers/probe-observability.yml ](../../../../../observability/examples/full/alloy/probers/probe-observability.yml) +- [prometheus/scrape-configs/exporters/exporters.yml](../../../../../observability/examples/full/prometheus/scrape-configs/exporters/exporters.yml) +- [prometheus/scrape-configs/recording-rules/slo.yml](../../../../../observability/examples/full/prometheus/scrape-configs/recording-rules/slo.yml) @@ -86,7 +86,7 @@ This is probably the hardest step: You will actually need to know what is runnin ## Step 5: Run Grafana Alloy on every VM The Grafana Alloy image needs to be run on each VM that you want to get information from. -Use the example docker compose file in [exporters.docker-compose.yml](../../../../observability/examples/full/exporters.docker-compose.yml) which will start up alloy and get metrics +Use the example docker compose file in [exporters.docker-compose.yml](../../../../../observability/examples/full/exporters.docker-compose.yml) which will start up alloy and get metrics ``` docker compose -f exporters.docker-compose.yml up -d diff --git a/docs/platform/observability/setup/telemetry.md b/docs/docs/platform/observability/setup/telemetry.md similarity index 83% rename from docs/platform/observability/setup/telemetry.md rename to docs/docs/platform/observability/setup/telemetry.md index 82d5512..c67881a 100644 --- a/docs/platform/observability/setup/telemetry.md +++ b/docs/docs/platform/observability/setup/telemetry.md @@ -16,7 +16,7 @@ We have to run Grafana Alloy on every single VM to get telemetry. Alloy is setup to push metrics to a central prometheus instance. -- Copy this docker compose file: [exporters.docker-compose.yml](../../../../observability/examples/full/exporters.docker-compose.yml) +- Copy this docker compose file: [exporters.docker-compose.yml](https://raw.githubusercontent.com/CogStack/cogstack-platform-toolkit/main/observability/examples/full/exporters.docker-compose.yml) - Edit the environment variables to point to your prometheus URL: ```yaml @@ -34,8 +34,8 @@ Now you have the setup, you will have to run this on every VM you want metrics f ### Elastic Search Metrics To get elasticsearch metrics we have to mount an alloy config file into the image. -- Copy this docker compose file: [exporters.elastic.docker-compose.yml](../../../../observability/examples/full/exporters.elastic.docker-compose.yml) -- Copy this configuration file [elasticsearch.alloy](../../../../observability/examples/full/alloy/elasticsearch.alloy) into `alloy/elasticsearch.alloy` +- Copy this docker compose file: [exporters.elastic.docker-compose.yml](https://raw.githubusercontent.com/CogStack/cogstack-platform-toolkit/main/observability/examples/full/exporters.elastic.docker-compose.yml) +- Copy this configuration file [elasticsearch.alloy](https://raw.githubusercontent.com/CogStack/cogstack-platform-toolkit/main/observability/examples/full/alloy/elasticsearch.alloy) into `alloy/elasticsearch.alloy` In the docker compose file, we can see there are two changes to the usual exporter: diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index 8e40e72..0000000 --- a/docs/index.md +++ /dev/null @@ -1,36 +0,0 @@ -# Cogstack Documentation - -Welcome to the CogStack Documentation site. - -Get started by looking at the [CogStack Overview](overview/cogstack-documentation.md) - -Any broad questions then please do reach out in our community space [here](https://discourse.cogstack.org/) - -Further in development projects are [here](https://github.com/orgs/CogStack/repositories) - -![](./overview/attachments/architecture.png){width=2000} - -```{toctree} -:hidden: -:maxdepth: 5 -overview/_index - -``` - -```{toctree} -:hidden: -:caption: CogStack NLP -MedCAT -MedCAT Trainer - -``` - -```{toctree} -:hidden: -:caption: CogStack Platform - -NiFi -platform/deployment/_index.md -platform/_index -``` - diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 8084272..0000000 --- a/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/docs/mkdocs.yml b/docs/mkdocs.yml new file mode 100644 index 0000000..7607978 --- /dev/null +++ b/docs/mkdocs.yml @@ -0,0 +1,91 @@ +site_name: Cogstack Documentation +site_url: http://localhost:8080/docs/ + +theme: + name: material + favicon: assets/cogstack-logo.png + logo: assets/cogstack-logo.png + icon: + logo: assets/cogstack-logo.png + palette: + primary: white + + features: + - navigation.tabs + - navigation.sections + - navigation.top + - navigation.expand + - navigation.indexes + - navigation.tracking + - header.autohide + - content.tooltips + - search.highlight + - search.share + - search.suggest + - toc.follow + +docs_dir: docs + +nav: + - Home: + - Home: index.md + - Overview: + - Introduction: overview/introduction.md + - Data pipelines: overview/Data pipelines.md + - Elasticsearch: overview/Elasticsearch.md + - Natural Language Processing: overview/Natural Language Processing.md + - MedCAT: https://docs.cogstack.org/projects/nlp + - MedCAT Trainer: https://docs.cogstack.org/projects/medcat-trainer/ + - NiFi: https://docs.cogstack.org/projects/nifi/ + - Platform: + - Deployment: + - Deployment Overview: platform/deployment/_index.md + - Getting Started: + - Getting Started: platform/deployment/get-started/_index.md + - Quickstart: platform/deployment/get-started/quickstart.md + - Helm: + - Helm Overview: platform/deployment/helm/_index.md + - Tutorial: platform/deployment/helm/tutorial.md + - CogStack Helm Module: platform/deployment/helm/cogstack-helm-module.md + - Troubleshooting: platform/deployment/helm/troubleshooting.md + - Charts: + - Charts Overview: platform/deployment/helm/charts/_index.md + - MedCAT Service Helm: platform/deployment/helm/charts/medcat-service-helm.md + - MedCAT Trainer Helm: platform/deployment/helm/charts/medcat-trainer-helm.md + - Examples: + - Examples Overview: platform/deployment/examples/_index.md + - AWS Kubernetes EKS: platform/deployment/examples/aws-kubernetes-eks.md + - Azure Kubernetes AKS: platform/deployment/examples/azure-kubernetes-aks.md + - OpenStack Kubernetes K3s: platform/deployment/examples/openstack-kubernetes-k3s.md + - OpenStack Docker: platform/deployment/examples/openstack-docker.md + - Docker Compose: platform/deployment/reference/docker-compose/_index.md + - Observability: + - Observability Overview: platform/observability/_index.md + - Getting Started: + - Quickstart: platform/observability/get-started/quickstart.md + - User Guide Tutorial: platform/observability/get-started/userguide-tutorial.md + - Setup: + - Production Setup: platform/observability/setup/production-setup.md + - Probing: platform/observability/setup/probing.md + - Telemetry: platform/observability/setup/telemetry.md + - Alerting: platform/observability/setup/alerting.md + - Customization: + - Customization Overview: platform/observability/customization/_index.md + - Custom Dashboards: platform/observability/customization/custom-dashboards.md + - Alerts Customization: platform/observability/customization/alerts-customization.md + - Custom Prometheus Configs: platform/observability/customization/custom-prometheus-configs.md + - Blackbox Exporter Config: platform/observability/customization/blackbox-exporter-config.md + - Reference: + - Project Details: platform/observability/reference/project-details.md + - Concept Materials: platform/observability/reference/concept-materials.md + - Quickstart Manual: platform/observability/reference/quickstart-manual.md + - Understanding Metrics: platform/observability/reference/understanding-metrics.md + +plugins: + - search + - termynal + +markdown_extensions: + - admonition + - pymdownx.details + - pymdownx.superfences diff --git a/docs/overview/_index.md b/docs/overview/_index.md deleted file mode 100644 index 48d7bcc..0000000 --- a/docs/overview/_index.md +++ /dev/null @@ -1,9 +0,0 @@ -# Overview - -```{toctree} -:maxdepth: 1 -cogstack-documentation -Data pipelines -Elasticsearch -Natural Language Processing -``` \ No newline at end of file diff --git a/docs/platform/_index.md b/docs/platform/_index.md deleted file mode 100644 index 6cb0d11..0000000 --- a/docs/platform/_index.md +++ /dev/null @@ -1,8 +0,0 @@ -# CogStack Tooling - -```{toctree} -:maxdepth: 2 - -observability/_index.md - -``` diff --git a/docs/platform/deployment/reference/_index.md b/docs/platform/deployment/reference/_index.md deleted file mode 100644 index 82f0220..0000000 --- a/docs/platform/deployment/reference/_index.md +++ /dev/null @@ -1,7 +0,0 @@ -# Reference - -```{toctree} -:maxdepth: 2 - -docker-compose/_index -``` diff --git a/docs/platform/observability/_index.md b/docs/platform/observability/_index.md deleted file mode 100644 index 00fb27f..0000000 --- a/docs/platform/observability/_index.md +++ /dev/null @@ -1,23 +0,0 @@ -# Cogstack Observability - -This project provides observability of a cogstack deployment. - -It provides the following features: -- Dashboards for availability -- Telemetry of infrastructure such as host memory usage, and elasticsearch index size -- Alerting based on a defined Service Level Objective (SLO) and burn rates -- Blackbox Probing of services to find service level indicators of uptime and latency -- A working inventory of what is running where - - -See the [Quickstart](./get-started/quickstart.md) to see how to easily run this stack. - -```{toctree} -:maxdepth: 2 - -get-started/_index -setup/_index -customization/_index -reference/_index - -``` diff --git a/docs/platform/observability/customization/_index.md b/docs/platform/observability/customization/_index.md deleted file mode 100644 index f0de41b..0000000 --- a/docs/platform/observability/customization/_index.md +++ /dev/null @@ -1,30 +0,0 @@ -# Customization - -## Grafana Customization -```{include} custom-dashboards.md -:heading-offset: 2 -``` - -```{include} alerts-customization.md -:heading-offset: 2 -``` - -## Prometheus Customization -```{include} custom-prometheus-configs.md -:heading-offset: 2 -``` -```{include} blackbox-exporter-config.md -:heading-offset: 2 -``` - - -```{toctree} -:titlesonly: -:hidden: - -custom-prometheus-configs -custom-dashboards -alerts-customization -blackbox-exporter-config - -``` \ No newline at end of file diff --git a/docs/platform/observability/get-started/_index.md b/docs/platform/observability/get-started/_index.md deleted file mode 100644 index 0dc7dff..0000000 --- a/docs/platform/observability/get-started/_index.md +++ /dev/null @@ -1,7 +0,0 @@ -# Getting Started - -```{toctree} -:maxdepth: 2 -quickstart -userguide-tutorial -``` diff --git a/docs/platform/observability/reference/_index.md b/docs/platform/observability/reference/_index.md deleted file mode 100644 index 10348bb..0000000 --- a/docs/platform/observability/reference/_index.md +++ /dev/null @@ -1,9 +0,0 @@ -# Reference - -```{toctree} -:maxdepth: 2 - -project-details.md -concept-materials.md - -``` diff --git a/docs/platform/observability/reference/concept-materials.md b/docs/platform/observability/reference/concept-materials.md deleted file mode 100644 index a65cd13..0000000 --- a/docs/platform/observability/reference/concept-materials.md +++ /dev/null @@ -1,7 +0,0 @@ -# Concepts -```{toctree} -:maxdepth: 2 -understanding-metrics.md - -``` - diff --git a/docs/platform/observability/reference/project-details.md b/docs/platform/observability/reference/project-details.md deleted file mode 100644 index e3b3041..0000000 --- a/docs/platform/observability/reference/project-details.md +++ /dev/null @@ -1,9 +0,0 @@ -# Further Project Details - - -```{toctree} -:maxdepth: 2 -quickstart-manual.md - -``` - diff --git a/docs/platform/observability/setup/_index.md b/docs/platform/observability/setup/_index.md deleted file mode 100644 index 3c77f3d..0000000 --- a/docs/platform/observability/setup/_index.md +++ /dev/null @@ -1,12 +0,0 @@ -# Setup - -```{toctree} -:maxdepth: 2 - -production-setup.md -probing.md -telemetry.md -alerting.md - - -``` diff --git a/docs/pyproject.toml b/docs/pyproject.toml new file mode 100644 index 0000000..9eb98e7 --- /dev/null +++ b/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/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index caa2a36..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -Sphinx==6.2.1 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UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs + - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen +mkdocs: + configuration: docs/mkdocs.yml \ No newline at end of file From 19db4064a27fb306800b6857783d2cf79bf4189b Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 18 Feb 2026 16:37:03 +0000 Subject: [PATCH 3/9] docs: Migrate from sphinx to mkdocs - build --- .github/workflows/doc-build.yml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml index cd098c3..0a08405 100644 --- a/.github/workflows/doc-build.yml +++ b/.github/workflows/doc-build.yml @@ -7,7 +7,7 @@ on: branches: - '**' tags: - - 'v*.*.*' + - 'docs-v*.*.*' release: types: [published] jobs: @@ -17,11 +17,15 @@ jobs: working-directory: ./docs steps: - uses: actions/checkout@v3 - - name: Check documentation build + - name: Install uv for Python 3.13 + uses: astral-sh/setup-uv@v6 + with: + python-version: 3.13 + enable-cache: true + cache-dependency-glob: "docs/uv.lock" + - name: Install the project run: | - cd docs - pip3 install -r requirements.txt - make clean - # Fail buiild on any docs warning - # make html O=-W # Removed whilst migrating existing docs - make html \ No newline at end of file + uv sync --all-extras + - name: Build documentation + run: | + uv run mkdocs build From 640f5aa06f3a6323197595cd481b03100c31554c Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 18 Feb 2026 16:39:07 +0000 Subject: [PATCH 4/9] docs: Migrate from sphinx to mkdocs - build --- .github/workflows/doc-build.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml index 0a08405..ef27239 100644 --- a/.github/workflows/doc-build.yml +++ b/.github/workflows/doc-build.yml @@ -10,11 +10,13 @@ on: - 'docs-v*.*.*' release: types: [published] + +defaults: + run: + working-directory: ./docs jobs: build: runs-on: ubuntu-latest - env: - working-directory: ./docs steps: - uses: actions/checkout@v3 - name: Install uv for Python 3.13 From b31688fa11ae68af51fb5404adf30e488aa56de5 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 18 Feb 2026 16:41:15 +0000 Subject: [PATCH 5/9] docs: Migrate from sphinx to mkdocs - readthedocs --- .readthedocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.readthedocs.yml b/.readthedocs.yml index 3573006..247b085 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -17,6 +17,7 @@ build: create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: + - cd docs - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: From 82cc773408ec9b1992558b738222828f8e89332f Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 18 Feb 2026 16:42:24 +0000 Subject: [PATCH 6/9] docs: Migrate from sphinx to mkdocs - readthedocs --- .readthedocs.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 247b085..8bc102d 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -17,8 +17,7 @@ build: create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: - - cd docs - - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen + - cd docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: configuration: docs/mkdocs.yml \ No newline at end of file From f69a3284713ae655b738a483dd241bd801aa81bc Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 18 Feb 2026 16:46:14 +0000 Subject: [PATCH 7/9] docs: Migrate from sphinx to mkdocs - fix nifi link --- docs/docs/overview/Data pipelines.md | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/docs/docs/overview/Data pipelines.md b/docs/docs/overview/Data pipelines.md index 79f3d5e..01d08ab 100644 --- a/docs/docs/overview/Data pipelines.md +++ b/docs/docs/overview/Data pipelines.md @@ -7,7 +7,19 @@ This page covers the data pipelines used in CogStack ecosystem. ## CogStack-NiFi ### Overview -CogStack-NiFi is the re-architected version of CogStack-Pipeline that replaces the fixed Spring Batch-based pipeline engine with [Apache NiFi](https://nifi.apache.org/). It focuses on fully configurable and scalable data flows with the data processing engine that is easy to use, deploy and tailor to any site-specific data flow requirements. Apache NiFi also comes in with build-in monitoring, data provenance and security features that puts the operations in better control and reliability.
**CogStack-NiFi useful links:**

**Apache NiFi resources:**