Modernization: uv, SQLAlchemy 2.0, psycopg3, pytest-postgresql

.bumpversion.cfg

@@ -0,0 +1,12 @@
+[bumpversion]
+current_version = 5.5.3
+commit = True
+tag = True
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:src/triage/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'

.dockerignore

@@ -10,7 +10,6 @@ develop
 .pytest_cache
 tox.ini
 .travis.yml
-tutorial.sh
 .pyup.yml
 .python-version
 .python-version.current

.env.example

@@ -0,0 +1,27 @@
+# Triage Database Configuration
+# Copy this file to .env and fill in your values
+
+# PostgreSQL Connection (Option 1: Standard PostgreSQL variables)
+# Official PostgreSQL environment variables
+PGHOST=localhost
+PGPORT=5432
+PGUSER=postgres
+PGPASSWORD=your_password_here
+PGDATABASE=triage
+
+# PostgreSQL Connection (Option 2: DATABASE_URL)
+# Full connection string format
+# DATABASE_URL=postgresql://user:password@host:port/database
+
+# Notes:
+# - Triage checks for database configuration in this order:
+#   1. --dbfile CLI argument
+#   2. database.yaml in current directory
+#   3. DATABASE_URL environment variable
+#   4. PGHOST, PGUSER, PGDATABASE, PGPASSWORD, PGPORT (PostgreSQL standard)
+#   5. .env file (loaded automatically)
+#
+# - You can use direnv to automatically load these variables:
+#   echo "dotenv" > .envrc && direnv allow
+#
+# - For production, consider using a secrets manager instead of .env files

.github/workflows/build-mkdocs.yaml

@@ -6,7 +6,7 @@ on:
       - master
     paths:
       - 'docs/**'
-  
+
 jobs:
   docs:
     name: Build Docs and Serve to Github Pages
@@ -16,17 +16,19 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
         with:
-          python-version: 3.9
-
+          version: "latest"
+
+      - name: Set up Python 3.12
+        run: uv python install 3.12
+
       - name: Install dependencies
         run: |
-          pip install --upgrade pip && pip install -r requirement/dev.txt
-          pip install git+https://github.com/dssg/triage.git@master
+          uv sync --extra docs
           git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com'
-      
+
       - name: Publish docs
-        run: mkdocs gh-deploy -f "$(pwd)/docs/mkdocs.yml"
+        run: uv run mkdocs gh-deploy -f "$(pwd)/docs/mkdocs.yml"

.github/workflows/publish-to-pypi.yml

@@ -11,40 +11,36 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: 3.9
-    - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
+        version: "latest"
+    - name: Set up Python
+      run: uv python install 3.12
     - name: Build a binary wheel and a source tarball
-      run: python -m build
+      run: uv build
     - name: Store the distribution packages
       uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
+
   publish-to-pypi:
     name: Publish python distribution to PyPI
     if: startsWith(github.ref, 'refs/tags/')
-    needs: 
+    needs:
     - build
     runs-on: ubuntu-latest
     environment:
       name: pypi
       url: https://pypi.org/p/triage
+    permissions:
+      id-token: write
     steps:
       - name: Download all the dists
         uses: actions/download-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
-      - name: Publish distribution to PyPI 
+      - name: Publish distribution to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-

.github/workflows/test.yaml

@@ -2,33 +2,42 @@ name: Python package
 
 on:
   push:
-    tags:
-     - '*'
-
+    branches:
+      - master
+      - 'tooling-migration'
+  pull_request:
+    branches:
+      - master
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10']
+        python-version: ['3.12']
+
+    # Note: pytest-postgresql creates its own temporary PostgreSQL instances
+    # using system PostgreSQL binaries, so no Docker service is needed
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        version: "latest"
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
     - name: Install system dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran
+        sudo apt-get install -y libblas-dev liblapack-dev libatlas-base-dev gfortran postgresql postgresql-contrib
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        pip install -r requirement/include/build.txt
-        pip install -r requirement/include/test-management.txt
-    - name: Test with tox
+        uv sync --extra dev
+    - name: Run linter
+      run: |
+        uv run ruff check src/
+    - name: Run tests
       run: |
-        tox
+        uv run pytest src/tests/ -v --tb=short --timeout=300 -x
+      timeout-minutes: 30

.gitignore

@@ -18,6 +18,9 @@ venv/
 my_db_config.yaml
 database.yaml
 database*.yaml
+.env
+.envrc
+triage_tui.log
 dirtyduck/triage/**
 
 *~
@@ -28,4 +31,26 @@ dirtyduck/triage/**
 src/triage/component/postmodeling/postmodeling_tmp.ipynb
 src/triage/component/postmodeling/model_class_testing.py
 src/triage/component/postmodeling/model_class_testing.ipynb
-src/triage/component/postmodeling/model_groups_testing.ipynb
+src/triage/component/postmodeling/model_groups_testing.ipynb
+
+# Personal/local files
+.secrets
+TODO.org
+TRIAGE_ICON.md
+channels-lock.scm
+manifest.scm
+
+# Session handoff files (local-only)
+docs/triage-session-summary.org
+docs/triage-session-summary.md
+working-outline.md
+CLAUDE.md
+AGENTS.md
+GEMINI.md
+GIT_REMOTE
+.project
+handoff-trace.log
+README.org
+COMPACT.md
+COMPACT-archive-*.md
+.claude

.travis.yml

@@ -13,7 +13,10 @@ before_install:
 - sudo apt-get update
 - sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran
 install:
-- pip install -r requirement/include/build.txt -r requirement/include/test-management.txt
+- python -m pip install --upgrade pip
+- curl -LsSf https://astral.sh/uv/install.sh | sh
+- export PATH="$HOME/.local/bin:$PATH"
+- uv pip install --system 'tox>=4.14,<5' codecov
 env:
   matrix:
     - BOTO_CONFIG=/tmp/nowhere

CONTRIBUTING.md

@@ -26,15 +26,21 @@ Triage could always use more documentation, whether as part of the
 official Triage docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
-The [documentation site](https://dssg.github.io/triage) runs on [mkdocs](https://www.mkdocs.org) and is controlled by the [docs/sources](docs/sources) directory. We recommend building the docs locally to preview any documentation pages. The python dependencies for this are handled by [requirement/dev.txt](requirement/dev.txt):
+The [documentation site](https://dssg.github.io/triage) runs on [mkdocs](https://www.mkdocs.org) and is controlled by the [docs/sources](docs/sources) directory. We recommend building the docs locally to preview any documentation pages. Install the documentation dependencies with [uv](https://docs.astral.sh/uv/) using the `docs` extra:
 
 ```
-pip install -r requirement/dev.txt
+curl -LsSf https://astral.sh/uv/install.sh | sh
+uv sync --extra docs
 ```
 
 Once this is done, you can modify any of the pages under the documentation root directory, and change general doc site configuration in [docs/mkdocs.yml](docs/mkdocs.yml). While modifying a documentation page, you can preview your changes by running the mkdocs dev server:
 ```
-manage docs
+just docs
+```
+
+Or directly:
+```
+cd docs && uv run mkdocs serve
 ```
 
 ### Submit Feedback
@@ -76,10 +82,10 @@ Triage always has a backlog of issues. Want to help out? Here's how to set up tr
 5.  When you're done making changes, check that your changes pass flake8
     and the tests, including testing other Python versions with tox:
 
-        $ pip install -r requirement/test.txt
-        $ flake8 triage tests
-        $ python setup.py test or py.test
-        $ tox
+        $ uv sync --extra test
+        $ uv run flake8 triage src/tests
+        $ uv run pytest
+        $ uv run tox -e py3
 
 6.  Commit your changes and push your branch to GitHub. If you've made multiple commits, squash them into one. Each pull request should be one commit (unless there are multiple logical places to split up the code, for instance a big reformatting commit followed by a smaller commit that actually changes behavior). To make the pull request easier to create, the last commit on the branch should be formatted like the following.
 
@@ -114,44 +120,29 @@ This section describes the initial setup of a Triage development environment tha
 
         $ git clone git@github.com:your_name_here/triage.git
 
-3.  Set up your local environment.
-
-    You can control your development environment any way you'd like (virtualenv, pyenv, _etc._).
-
-    To quickly bootstrap an environment, invoke the executable `develop` script – found in the triage repo root – from your system shell:
+3.  Install development tools (optional but recommended):
 
-        $ ./develop
+        $ curl --proto '=https' --tlsv1.2 -sSf https://just.systems/install.sh | bash -s -- --to ~/.local/bin
 
-    The script will launch a "wizard," which will suggest set-up steps and optionally execute these, for example:
+    The `just` command runner provides convenient shortcuts for common development tasks. If you prefer not to install it, you can run the commands directly (see the justfile for the full commands).
 
-        (install) begin
+4.  Set up your local environment.
 
-        (pyenv) installed ✓
-
-        (python-3.6.2) installed ✓
-
-        (virtualenv) installed ✓
-
-        (activation) installed ✓
-
-        (libs) install?
-        1) yes, install {pip install -r requirement/main.txt -r requirement/test.txt -r requirement/dev.txt}
-        2) no, ignore
-        #? 1
+    You can control your development environment any way you'd like (virtualenv, pyenv, _etc._).
 
-    Alternatively, you might manage your environment via `virtualenvwrapper`:
+    To quickly bootstrap an environment, install uv with the official script and sync the project with the development extras:
 
-        $ mkvirtualenv triage
-        $ cd triage/
-        $ python setup.py develop
+        $ curl -LsSf https://astral.sh/uv/install.sh | sh
+        $ uv sync --extra dev
 
-    Or simply via the `venv` module:
+    This creates a local `.venv` that uv will reuse. You can either activate it manually (`source .venv/bin/activate`) or invoke tools through uv (for example, `uv run pytest`).
 
-        $ cd triage/
-        $ python -m venv --prompt triage venv
-        $ python setup.py develop
+    If you prefer to manage virtual environments manually, create one however you like and install the project in editable mode with the development extras:
 
-    Regardless of your Python environment, we do recommend installing `triage` in development mode, via `python setup.py develop` or `pip install -e .` (The `develop` script handles this for you.)
+        $ python -m venv .venv
+        $ source .venv/bin/activate
+        $ pip install --upgrade pip
+        $ uv pip install --system --editable .[dev]
 
 
 Small Changes
@@ -166,10 +157,10 @@ Triage has an extensive test suite that is run with every commit by travis-ci. A
 - [Wikipedia Page](https://en.wikipedia.org/wiki/Test-driven_development)
 - [Test Driven Development: what it is, and what it is not](https://medium.freecodecamp.org/test-driven-development-what-it-is-and-what-it-is-not-41fa6bca02a2)
 
-In addition to any requirements needed by the main library (which should be installed when you ran `python setup.py develop` to gain access to Triage itself), you can ensure all testing requirements are installed with:
+In addition to the project dependencies installed via `uv sync --extra dev`, you can refresh testing requirements explicitly with:
 
 ```
-pip install -r requirement/test.txt
+uv sync --extra test
 ```
 
 This is mentioned in the main setup section, but you may have to rerun it over time as test requirements change.