Workflows

.github/workflows/autoformat.yml

@@ -0,0 +1,34 @@
+name: Auto-format Code
+
+on:
+  push:
+    branches: [main, develop]
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install formatters
+        run: pip install black isort
+
+      - name: Format with Black
+        run: black .
+
+      - name: Sort imports with isort
+        run: isort .
+
+      - name: Commit changes
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git diff --quiet || (git add -A && git commit -m "Auto-format code")
+          git push

.github/workflows/docs.yml

@@ -0,0 +1,35 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints
+          pip install -e .  # Install your package
+
+      - name: Build documentation
+        run: |
+          cd docs
+          make html
+
+      - name: Deploy to GitHub Pages
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html

.github/workflows/publish.yml

@@ -0,0 +1,70 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

README.md

@@ -1,4 +1,4 @@
-# pySEQ - Sequentially Nested Target Trial Emulation
+# pySEQTarget - Sequentially Nested Target Trial Emulation
 
 Implementation of sequential trial emulation for the analysis of
 observational databases. The ‘SEQTaRget’ software accommodates
@@ -9,13 +9,13 @@ intention-to-treat and per-protocol effects, and can adjust for
 potential selection bias.
 
 ## Installation
-You can install the development version of pySEQ from github with:
+You can install the development version of pySEQTarget from github with:
 ```shell
-pip install git+https://github.com/CausalInference/pySEQ
+pip install git+https://github.com/CausalInference/pySEQTarget
 ```
 Or from pypi iwth 
 ```shell
-pip install pySEQ
+pip install pySEQTarget
 ```
 
 ## Setting up your Analysis
@@ -25,7 +25,7 @@ From the user side, this amounts to creating a dataclass, `SEQopts`, and then fe
 
 ```python
 import polars as pl
-from pySEQ import SEQuential, SEQopts
+from pySEQTarget import SEQuential, SEQopts
 
 data = pl.from_pandas(SEQdata)
 options = SEQopts(km_curves = True)

pySEQ/docs/source/conf.py → docs/source/conf.py

@@ -6,10 +6,10 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'SEQuential'
-copyright = "2024, Ryan O'Dea, Alejandro Szmulewicz"
-author = "Ryan O'Dea, Alejandro Szmulewicz"
-release = '0.1.0'
+project = 'pySEQTarget'
+copyright = "2025, Ryan O'Dea, Alejandro Szmulewicz, Tom Palmer, Miguel Hernan"
+author = "Ryan O'Dea, Alejandro Szmulewicz, Tom Palmer, Miguel Hernan"
+release = '0.9.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/index.rst

@@ -0,0 +1,17 @@
+.. pySEQTarget documentation master file, created by
+   sphinx-quickstart on Mon Nov 24 20:43:34 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+pySEQTarget documentation
+=========================
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+