Release 1.4.2

.github/actions/docker-update/action.yml

@@ -25,9 +25,12 @@ inputs:
   image-tag:
     required: true
     description: Current workflow tag
-  env-secrets-b64:
+  env-secrets-b64-dev:
     required: true
-    description: Secret Environment variables (db hosts, password salt, etc)
+    description: Secret Dev Environment variables (db hosts, password salt, etc)
+  env-secrets-b64-prod:
+    required: true
+    description: Secret Prod Environment variables (db hosts, password salt, etc)
 
 runs:
   using: "composite"
@@ -76,7 +79,7 @@ runs:
       with:
         push: true
         file: ./src/casp/services/deploy/Dockerfile.pytorch
-        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64 }}
+        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64-dev }}
         tags: |
           ${{ inputs.pytorch-image-name-dev }}:${{ inputs.image-tag }}
           ${{ inputs.pytorch-image-name-dev }}:latest
@@ -88,7 +91,7 @@ runs:
       with:
         push: true
         file: ./src/casp/services/deploy/Dockerfile.pytorch
-        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64 }}
+        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64-prod }}
         tags: |
           ${{ inputs.pytorch-image-name-prod }}:${{ inputs.image-tag }}
           ${{ inputs.pytorch-image-name-prod }}:latest
@@ -100,7 +103,7 @@ runs:
       with:
         push: true
         file: ./src/casp/services/deploy/Dockerfile.pytorch_cuda
-        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64 }}
+        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64-dev }}
         tags: |
           ${{ inputs.pytorch-cuda-image-name-dev }}:${{ inputs.image-tag }}
           ${{ inputs.pytorch-cuda-image-name-dev }}:latest
@@ -112,7 +115,7 @@ runs:
       with:
         push: true
         file: ./src/casp/services/deploy/Dockerfile.pytorch_cuda
-        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64 }}
+        secrets: ENV_SECRETS=${{ inputs.env-secrets-b64-prod }}
         tags: |
           ${{ inputs.pytorch-cuda-image-name-prod }}:${{ inputs.image-tag }}
           ${{ inputs.pytorch-cuda-image-name-prod }}:latest

.github/workflows/main-workflow.yml

@@ -37,10 +37,11 @@ jobs:
         with:
           docker-registry-name: ${{ env.DOCKER_REGISTRY_NAME }}
           pytorch-image-name-dev: ${{ env.PYTORCH_IMAGE_NAME_DEV }}
-          pytorch-image-name-prod: ${{ env.PYTORCH_IMAGE_NAME_DEV }}
+          pytorch-image-name-prod: ${{ env.PYTORCH_IMAGE_NAME_PROD }}
           pytorch-cuda-image-name-dev: ${{ env.PYTORCH_CUDA_IMAGE_NAME_DEV }}
           pytorch-cuda-image-name-prod: ${{ env.PYTORCH_CUDA_IMAGE_NAME_PROD }}
           image-tag: ${{ env.TAG }}
           gcp-provider-id: ${{ secrets.GCP_PROVIDER_ID }}
           gcp-service-account-email: ${{ secrets.GCP_SERVICE_ACCOUNT_EMAIL }}
-          env-secrets-b64: ${{ secrets.CAS_SERVICES_ENV_b64 }}
+          env-secrets-b64-dev: ${{ secrets.CAS_SERVICES_ENV_B64_DEV }}
+          env-secrets-b64-prod: ${{ secrets.CAS_SERVICES_ENV_B64_PROD }}

.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  configuration: docs/source/conf.py

CHANGELOG.rst

@@ -0,0 +1,30 @@
+Changelog
+=========
+
+All notable changes to Cellarium Cloud will be documented in this file.
+
+The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_,
+and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
+
+
+
+
+
+1.4.2 - 2024-02-13
+----------------------
+
+Added
+~~~~~
+- Added Documentation in rst format for Sphinx build in `docs/` directory
+
+Changed
+~~~~~~~
+- ``src/casp/services/README.md`` is now ``casp/services/README.rst``
+- ``src/casp/services/admin/README.md`` is now ``casp/services/admin/README.rst``
+- ``src/casp/services/api/README.md`` is now ``casp/services/api/README.rst``
+- ``src/casp/services/model_inference/README.md`` is now ``casp/services/model_inference/README.rst``
+- ``src/casp/services/db/README.md`` is now ``casp/services/db/README.rst``
+- ``src/casp/services/wdl_workflows/README.md`` is now ``casp/services/wdl_workflows/README.rst``
+- ``docs/VERTEX_AI_MATCHING_ENGINE.md`` is now ``docs/vertex_ai_matching_engine.rst``
+- Requests to matching engine are now made in batches of 5 to avoid overloading Vertex API
+- Requests to matching engine are now made with retry logic to account for errors caused by rapid increases in traffic

MANIFEST.in

@@ -1,2 +1,2 @@
-include README.md
+include README.rst
 include requirements.txt

README.rst

@@ -0,0 +1,59 @@
+Cellarium Cloud
+===============
+
+**What's Cellarium Cloud?** Cellarium Cloud is the backend application that serves the Cellarium Cloud platform.
+This is a backend application that provides API for Cellarium Client tool. It is a mono-repository that contains all
+the services that are required to run the Cellarium Cloud platform.
+
+Repository Structure
+--------------------
+Each module of the repository contains its own `README.rst` file that explains the purpose of the module and how to run
+it. These files are united together in a documentation website that is available at
+`Cellarium Cloud Documentation <https://cellarium-cloud.readthedocs.io>`_.
+
+
+Prerequisites / Installation
+----------------------------
+
+ - Python 3.10+
+
+Developer Setup
+~~~~~~~~~~~~~~~
+
+To create a virtual python environment:
+
+.. code-block:: shell
+
+    python3 -mvenv python
+    source python/bin/activate
+    pip install --upgrade pip
+    pip install -r requirements.txt
+    pip install -r dev-requirements.txt
+    pip install -e .
+
+
+To run unit tests:
+
+.. code-block:: shell
+
+    tox -e unit
+
+To lint:
+
+.. code-block:: shell
+
+    tox -e lint
+
+To automatically fix formatting issues:
+
+.. code-block:: shell
+
+    tox -e format
+
+Repository Versioning
+---------------------
+The repository uses `Semantic Versioning <https://semver.org/>`_ for versioning. For the versions available, see the
+`tags on this repository <https://github.com/cellarium-ai/cellarium-cloud/tags>`_. Versioning is connected with the
+repository branches. The `main` branch is the main production branch and has stable versions. The `development` branch
+contains the latest development versions (such as release candidates (rc)). Other branches can be used for creating
+alpha or beta versions.

docs-requirements.txt

@@ -0,0 +1,5 @@
+Pillow~=9.5
+Sphinx~=7.2
+sphinx_gallery~=0.14
+sphinx_rtd_theme~=1.3
+setuptools-git-versioning==1.13.5

docs/Makefile

@@ -0,0 +1,20 @@
+# 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     = source
+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)