Merge pull request #603 from Aarhus-Psychiatry-Research/initialise_sp…

…ecs_from_primitives

feat: initialise specs from primitives

.devcontainer/post-start.sh

@@ -1,10 +1,3 @@
-# Setup lefthook
+#!/bin/bash
 git init
-lefthook install
-
-# Disable Graphite pager
-gt user pager --disable
-
-# Install dependencies
-pip install -e ".[dev, test]"
-
+uv sync --all-extras

.dockerignore

@@ -0,0 +1,170 @@
+# Byte-compiled / optimized / DLL files
+.git
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+*venv*/
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Testing
+pytest-coverage.txt
+
+# Mac
+.DS_Store
+
+#other
+*test_load_data.py
+wandb
+poetry.lock
+*.html
+
+# PyCharm
+/.idea/*
+**/tmp/
+**/.tmp/
+
+*nbconvert*
+.testmondata*
+.benchmark_cache/*

.github/actions/test/action.yml

@@ -11,19 +11,17 @@ runs:
     - name: Checkout (GitHub)
       uses: actions/checkout@v4
 
-    - name: Replace python version in Dockerfile
+    - name: Set up uv
       shell: bash
-      run: |
-        sed -i '/python:.*/c\FROM python:${{ inputs.python-version }}' Dockerfile
+      # Install a specific uv version using the installer
+      run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh
 
-    - name: Create github hosts file
+    - name: Set up Python
       shell: bash
-      run: | # If this file is not created, the dev container fails because of non-existent mount
-        mkdir -p ~/.config/gh
-        touch ~/.config/gh/hosts.yml
+      run: uv python install ${{ inputs.python-version }}
 
-    - name: Pre-build dev container image
-      uses: devcontainers/[email protected]
-      with:
-        runCmd: |
-          inv test --pytest-args "src/" --pytest-args --pytest-args "--cov=src" --pytest-args "--cov-report term-missing" --pytest-args="--color=yes" --pytest-args="-n auto"
+    # Installing
+    - name: Install dependencies
+      shell: bash
+      run: |
+        make test

.github/actions/test_tutorials/action.yml

@@ -8,27 +8,26 @@ runs:
   using: "composite"
   steps:
     ### Setup prerequisites
+    - name: Set up uv
+      shell: bash
+      # Install a specific uv version using the installer
+      run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh
+
     - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ inputs.python-version }}
+      shell: bash
+      run: uv python install
 
     # Installing
     - name: Install dependencies
       shell: bash
       run: |
-        pip install invoke
-        inv install
+        make install-tutorials
 
     ### Run tests
-    - name: Install jupyter
-      shell: bash
-      run: |
-        pip install jupyter
     - name: Compile notebooks and check for errors
       shell: bash
       run: |
-        inv test-tutorials
+        make test-tutorials
         for notebook in tutorials/*.ipynb; do
           if grep -q "\"cell_type\": \"error\"" $notebook; then
             echo "Error cell found in $notebook"

.github/workflows/documentation.yml

@@ -20,7 +20,7 @@ jobs:
         shell: bash
         run: |
           python -m pip install --upgrade pip
-          pip install -e ".[docs,tutorials,text]"
+          pip install -e ".[docs,tutorials]"
 
       - name: Build and Commit
         uses: sphinx-notes/[email protected]

.github/workflows/static_type_checks.yml

@@ -16,14 +16,15 @@ jobs:
     steps:
       - name: Checkout (GitHub)
         uses: actions/checkout@v4
+
+      - name: Set up uv
+        shell: bash
+        run: curl -LsSf https://astral.sh/uv/0.4.0/install.sh | sh
 
-      - name: Create github hosts file
-        run: | # If this file is not created, the dev container fails because of non-existent mount
-          mkdir -p ~/.config/gh
-          touch ~/.config/gh/hosts.yml
+      - name: Set up Python
+        shell: bash
+        run: uv python install
 
-      - name: Pre-build dev container image
-        uses: devcontainers/[email protected]
-        with:
-          runCmd: |
-            inv types
+      - name: Run static type checks
+        shell: bash
+        run: make types

.pre-commit-config.yaml

@@ -17,14 +17,4 @@ repos:
           ]
         types_or: [ python, pyi, jupyter ]
       - id: ruff-format
-        types_or: [ python, pyi, jupyter ]
-
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
-    hooks:
-      - id: check-yaml
-
-  - repo: https://github.com/repo-helper/pyproject-parser
-    rev: v0.7.0
-    hooks:
-      - id: check-pyproject
+        types_or: [ python, pyi, jupyter ]

.vscode/settings.json

@@ -6,4 +6,5 @@
     "python.testing.pytestEnabled": true,
     "python.analysis.typeCheckingMode": "standard",
     "python.analysis.diagnosticMode": "workspace",
+    "restructuredtext.pythonRecommendation.disabled": true,
 }

Dockerfile

@@ -1,8 +1,10 @@
 FROM python:3.9
+ENV UV_SYSTEM_PYTHON=true
+COPY --from=ghcr.io/astral-sh/uv:0.4.0 /uv /bin/uv
 
 RUN apt-get update && apt-get install -y curl
 
-# NVM and NPM are required for Graphite
+# NVM and NPM are required for pyright
 # Install nvm
 # Explicitly set HOME environment variable 
 ENV NVM_DIR=$HOME/.nvm
@@ -19,17 +21,10 @@ RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | b
 ENV NODE_PATH=$NVM_DIR/v$NODE_VERSION/lib/node_modules
 ENV PATH=$NVM_DIR/versions/node/v$NODE_VERSION/bin:$PATH
 
-
-# Install graphite (PR stacking), experimental, can be deleted without notice
-RUN npm install -g @withgraphite/graphite-cli@stable
-
-# Install lefthook (git hooks, e.g. pre-commit)
-RUN curl -1sLf 'https://dl.cloudsmith.io/public/evilmartians/lefthook/setup.deb.sh' | bash
-RUN apt install lefthook
-
 # Set the working directory to /app
 WORKDIR /app
 VOLUME psycop-common
 
 COPY . /app
-RUN --mount=type=cache,target=/root/.cache/pip pip install .
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync