Merge branch 'main' into explore-public-service-api

Author: Atheane

.github/workflows/tycho.yml

@@ -0,0 +1,105 @@
+name: Tycho
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+    types: [ opened, synchronize, reopened, edited ]
+    paths:
+      - "src/tycho/**"
+
+permissions:
+  contents: read
+
+jobs:
+  build-tycho:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./src/tycho
+    steps:
+      - uses: actions/checkout@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.7"
+          enable-cache: true
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version-file: "./src/tycho/.python-version"
+      - name: Install the project
+        run: uv sync --locked --all-extras --dev
+
+  build-docker-tycho:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Build tycho Docker image
+        run: bin/compose build tycho
+
+  lint-tycho:
+    needs: build-tycho
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./src/tycho
+    env:
+      TYCHO_SECRET_KEY: the_secret_key
+      TYCHO_DATABASE_URL: psql://tycho:pass@postgresql:5432/tycho
+    steps:
+      - uses: actions/checkout@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.7"
+          enable-cache: true
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version-file: "./src/tycho/.python-version"
+      - name: Lint with Ruff
+        run: uv run ruff check .
+      - name: Lint format with Ruff
+        run: uv run ruff format --check .
+      - name: Lint with MyPy
+        run: uv run mypy .
+
+  test-tycho:
+    needs: build-tycho
+    runs-on: ubuntu-latest
+    services:
+      postgresql:
+        image: postgres:16.10
+        env:
+          POSTGRES_DB: test-tycho
+          POSTGRES_USER: tycho
+          POSTGRES_PASSWORD: pass
+          TEST: true
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    defaults:
+      run:
+        working-directory: ./src/tycho
+    env:
+      TYCHO_SECRET_KEY: the_secret_key
+      TYCHO_DATABASE_URL: psql://tycho:pass@postgresql:5432/test-tycho
+    steps:
+      - uses: actions/checkout@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.7"
+          enable-cache: true
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version-file: "./src/tycho/.python-version"
+      - name: Test with pytest
+        run: uv run pytest .

.gitignore

@@ -29,7 +29,7 @@ share/python-wheels/
 *.egg
 MANIFEST
 
-# Installed pipenv packages
+# Installed packages
 .cache
 .local
 
@@ -63,3 +63,4 @@ scripts/*.csv
 # Data
 *.csv
 *.json
+.coverage

.pre-commit-config.yaml

@@ -9,15 +9,3 @@ repos:
       - id: trailing-whitespace
       - id: debug-statements
         files: ^src/.+\.py$
-
-  # Python linting and formatting with Make
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.13.2
-    hooks:
-      # Run the linter.
-      - id: ruff-check
-        args: [--config, dev/pyproject.toml]
-      # Run the formatter.
-      - id: ruff-format
-        args: [--config, dev/pyproject.toml]

Makefile

@@ -2,17 +2,21 @@
 SHELL := /bin/bash
 
 # -- Docker
-COMPOSE                    	 = bin/compose
-COMPOSE_UP                 	 = $(COMPOSE) up -d --remove-orphans
-COMPOSE_RUN                	 = $(COMPOSE) run --rm --no-deps
-COMPOSE_RUN_DEV_UV         	 = $(COMPOSE_RUN) dev uv run --project dev
+COMPOSE              = bin/compose
+COMPOSE_UP           = $(COMPOSE) up -d --remove-orphans
+COMPOSE_RUN          = $(COMPOSE) run --rm --no-deps
+COMPOSE_RUN_DEV_UV   = $(COMPOSE_RUN) dev uv run
+COMPOSE_RUN_TYCHO_UV = $(COMPOSE_RUN) tycho uv run
 
 default: help
 
 ## -- Files
 .pre-commit-cache:
 	mkdir .pre-commit-cache
 
+.git/hooks/_commons.inc.sh:
+	cp bin/_commons.inc.sh .git/hooks/_commons.inc.sh
+
 .git/hooks/pre-commit:
 	cp bin/git-pre-commit-hook .git/hooks/pre-commit
 
@@ -22,15 +26,18 @@ default: help
 ### BOOTSTRAP
 bootstrap: ## setup development environment (build dev service and install git hooks)
 bootstrap: \
-	build \
-	jupytext--to-ipynb
+  build \
+  migrate \
+  create-superuser \
+  jupytext--to-ipynb
 .PHONY: bootstrap
 
 git-hooks: ## install pre-commit hook
 git-hooks: \
-	.pre-commit-cache \
-	.git/hooks/pre-commit \
-	.git/hooks/commit-msg
+  .pre-commit-cache \
+  .git/hooks/_commons.inc.sh \
+  .git/hooks/pre-commit \
+  .git/hooks/commit-msg
 .PHONY: git-hooks
 
 ### BUILD
@@ -46,6 +53,10 @@ build-notebook: ## build custom jupyter notebook image
 	@$(COMPOSE) build notebook
 .PHONY: build-notebook
 
+build-tycho: ## build tycho image
+	@$(COMPOSE) build tycho
+.PHONY: build-tycho
+
 jupytext--to-md: ## convert local ipynb files into md
 	bin/jupytext --to md **/*.ipynb
 .PHONY: jupytext--to-md
@@ -63,6 +74,21 @@ logs-notebook: ## display notebook logs (follow mode)
 	@$(COMPOSE) logs -f notebook
 .PHONY: logs-notebook
 
+logs-tycho: ## display tycho logs (follow mode)
+	@$(COMPOSE) logs -f tycho
+.PHONY: logs-tycho
+
+### Setup
+migrate: ## migrate tycho database
+	@echo "Migrating tycho database…"
+	@bin/manage migrate
+.PHONY: migrate
+
+create-superuser: ## create tycho super user
+	@echo "Creating tycho super user…"
+	@bin/manage createsuperuser --noinput || true
+.PHONY: create-superuser
+
 ### RUN
 run-all: ## run the whole stack
 run-all: \
@@ -78,16 +104,22 @@ run-es: ## run the elasticsearch service
 	$(COMPOSE_UP) elasticsearch
 .PHONY: run-es
 
+run-tycho: ## run the tycho service
+	$(COMPOSE_UP) tycho
+.PHONY: run-tycho
+
 ## LINT
 # -- Global linting
 lint: ## lint all sources
 lint: \
-	lint-notebook
+  lint-notebook \
+  lint-tycho
 .PHONY: lint
 
 lint-fix: ## lint and fix all sources
 lint-fix: \
-	lint-notebook-fix
+  lint-notebook-fix \
+  lint-tycho-fix
 .PHONY: lint-fix
 
 # -- Per-service linting
@@ -103,7 +135,41 @@ lint-notebook-fix: ## lint and fix notebook python sources
 	$(COMPOSE_RUN_DEV_UV) ruff format src/notebook/
 .PHONY: lint-notebook-fix
 
-### MANAGE docker services
+lint-tycho: ## lint tycho python sources
+lint-tycho: \
+  lint-tycho-ruff \
+  lint-tycho-mypy
+.PHONY: lint-tycho
+
+lint-tycho-ruff: ## lint tycho python sources with ruff
+	@echo 'lint:tycho-ruff started…'
+	$(COMPOSE_RUN_TYCHO_UV) ruff check .
+	$(COMPOSE_RUN_TYCHO_UV) ruff format --check .
+.PHONY: lint-tycho-ruff
+
+lint-tycho-ruff-fix: ## lint and fix tycho python sources with ruff
+	@echo 'lint:tycho-ruff-fix started…'
+	$(COMPOSE_RUN_TYCHO_UV) ruff check --fix .
+	$(COMPOSE_RUN_TYCHO_UV) ruff format .
+.PHONY: lint-tycho-ruff-fix
+
+lint-tycho-mypy: ## lint tycho python sources with mypy
+	@echo 'lint:tycho-mypy started…'
+	$(COMPOSE_RUN_TYCHO_UV) mypy .
+.PHONY: lint-tycho-mypy
+
+## TEST
+test: ## test all services
+test: \
+  test-tycho
+.PHONY: test
+
+test-tycho: ## test tycho python sources
+	@echo 'test:tychostarted…'
+	$(COMPOSE_RUN_TYCHO_UV) pytest
+.PHONY: test-tycho
+
+## MANAGE docker services
 status: ## an alias for "docker compose ps"
 	@$(COMPOSE) ps
 .PHONY: status

bin/_commons.inc.sh

@@ -0,0 +1,66 @@
+#
+# Bash library for utility scripts
+#
+# shellcheck shell=bash
+
+declare DOCKER_USER
+declare -i DOCKER_UID
+declare -i DOCKER_GID
+
+DOCKER_UID="$(id -u)"
+DOCKER_GID="$(id -g)"
+# Use a higher GID for MacOS users to prevent permission issues with the default
+# GID=20
+if [[ "${OSTYPE}" =~ "darwin" ]]; then
+  DOCKER_GID=1000
+fi
+DOCKER_USER="${DOCKER_UID}:${DOCKER_GID}"
+
+export DOCKER_UID
+export DOCKER_GID
+export DOCKER_USER
+
+
+function compose(){
+
+  docker compose "$@"
+}
+
+
+function compose_run(){
+
+  if [[ -z "${2}" ]]; then
+    echo "usage: compose_run [--no-deps] SERVICE COMMAND"
+    exit 1
+  fi
+
+  # Arguments
+  declare -i no_deps
+  if [[ "$1" == "--no-deps" ]]; then
+    no_deps=1
+    shift
+  fi
+
+  declare service="${1}"
+  shift
+
+  declare user="${DOCKER_USER}"
+  declare volume="./src/${service}:/app"
+  declare -a args=(--rm --user "${user}" --volume "${volume}")
+
+  # Prevent 'the input device is not a TTY' error from `docker compose run`
+  # by disabling TTY when standard output is not a TTY
+  if [[ "$(tty 2>/dev/null)" == "not a tty" ]]; then
+    args+=(--no-TTY)
+  fi
+
+  # Do not run related services
+  if [[ no_deps -eq 1 ]]; then
+    args+=(--no-deps)
+  fi
+
+  compose run \
+    "${args[@]}" \
+    "${service}" \
+    "$@"
+}

bin/compose

@@ -2,28 +2,14 @@
 
 set -eo pipefail
 
-declare DOCKER_USER
-DOCKER_UID="$(id -u)"
-DOCKER_GID="$(id -g)"
+declare cmd
 
+source "$(dirname "$(readlink -f "$0")")/_commons.inc.sh"
 
-DOCKER_USER="${DOCKER_UID}:${DOCKER_GID}"
-
-extra_args=()
-# Prevent 'the input device is not a TTY' error from `docker compose run`
-# by disabling TTY when standard output is not a TTY
-if [[ "$1" == run && "$(tty 2>/dev/null)" == "not a tty" ]]; then
-  extra_args=(run --no-TTY)
+cmd="compose"
+if [[ "$1" == run ]]; then
+  cmd="compose_run"
   shift
 fi
 
-# On macOS, GID 20 is reserved for the "staff" group which may cause permission issues
-if [[ "$OSTYPE" == "darwin"* ]] && [[ "$DOCKER_GID" -le "20" ]]; then
-    DOCKER_GID="1000"
-fi
-
-
-DOCKER_USER=${DOCKER_USER} \
-  DOCKER_UID=${DOCKER_UID} \
-  DOCKER_GID=${DOCKER_GID} \
-  docker compose "${extra_args[@]}" "$@"
+eval $cmd "$@"

bin/cz

@@ -1,3 +1,5 @@
 #!/usr/bin/env bash
 
+set -eo pipefail
+
 cz --config dev/pyproject.toml "$@"