fix(docker): simplify docker instalation & some fixes

.github/workflows/python-package.yml

@@ -7,10 +7,6 @@ jobs:
     runs-on: ${{ matrix.os }}
     timeout-minutes: ${{ (matrix.os == 'windows-latest' && 30) || 15 }}
 
-    defaults:
-      run:
-        shell: bash -l {0}
-
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
@@ -33,6 +29,7 @@ jobs:
         conda-solver: libmamba
 
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
         pip install poetry poetry-plugin-export
         poetry config virtualenvs.create false
@@ -46,15 +43,54 @@ jobs:
 
     - name: Linting
       if: matrix.os == 'ubuntu-latest'
+      shell: bash -l {0}
       run: pre-commit run --files pysus/**/*
 
-    - name: Tests
+    - name: Tests (Linux)
+      if: matrix.os != 'windows-latest'
+      shell: bash -l {0}
       run: |
         poetry run pytest -vv pysus/tests/ --retries 3 --retry-delay 15 --cov=pysus --cov-report=xml:coverage.xml --cov-report=term-missing
 
+    - name: Tests (Windows)
+      if: matrix.os == 'windows-latest'
+      shell: bash -l {0}
+      run: |
+        export DUCKDB_NO_THREADS=1
+        poetry run pytest -vv pysus/tests/ --retries 3 --retry-delay 15 --timeout=480 -p no:cacheprovider -p no:asyncio
+
     - name: Upload coverage to Codecov
       if: matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v5
       with:
         files: ./coverage.xml
         fail_ci_if_error: false
+
+  docker-tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    defaults:
+      run:
+        shell: bash
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build Docker image
+      run: docker compose -f docker/docker-compose.yaml build
+
+    - name: Start container
+      run: docker compose -f docker/docker-compose.yaml up -d
+
+    - name: Wait for Jupyter
+      run: |
+        for i in $(seq 1 10); do
+          curl -s -o /dev/null http://127.0.0.1:8888 && break
+          sleep 2
+        done
+
+    - name: Run tests inside container
+      run: docker compose -f docker/docker-compose.yaml exec -T -w /usr/src jupyter python3 -m pytest -vv pysus/tests/ --retries 3 --retry-delay 15 -x -o cache_dir=/tmp/.pytest_cache
+
+    - name: Cleanup
+      if: always()
+      run: docker compose -f docker/docker-compose.yaml down -v

.github/workflows/release.yaml

@@ -2,23 +2,27 @@ name: release
 
 on:
   workflow_dispatch:
+    inputs:
+      version:
+        description: "Version tag for Docker image (e.g., 9.9.9-test)"
+        required: false
+        type: string
   push:
-    branches: [ main ]
+    branches: [main]
+    tags:
+      - "[0-9]*"
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 concurrency:
-  group: ci-${{ github.ref }}
-  cancel-in-progress: true
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
 jobs:
   build:
+    if: ${{ !startsWith(github.ref, 'refs/tags/') }}
     runs-on: ubuntu-latest
 
-    defaults:
-      run:
-        shell: bash -l {0}
-
     steps:
     - uses: actions/checkout@v4
 
@@ -44,7 +48,40 @@ jobs:
         poetry config pypi-token.pypi ${PYPI_TOKEN}
         make release
 
+  docker-push:
+    if: startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: alertadengue
+        password: ${{ secrets.DOCKER_TOKEN }}
+
+    - name: Extract version
+      id: version
+      run: |
+        if [ -n "${{ inputs.version }}" ]; then
+          echo "tag=${{ inputs.version }}" >> "$GITHUB_OUTPUT"
+        else
+          echo "tag=${GITHUB_REF_NAME#v}" >> "$GITHUB_OUTPUT"
+        fi
+
+    - name: Build and push
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        file: docker/Dockerfile
+        push: true
+        tags: |
+          alertadengue/pysus:latest
+          alertadengue/pysus:${{ steps.version.outputs.tag }}
+
   docs:
+    if: ${{ !startsWith(github.ref, 'refs/tags/') }}
     runs-on: ubuntu-latest
 
     defaults:

README.md

@@ -32,6 +32,29 @@ For the terminal user interface (TUI):
 pip install pysus[tui]
 ```
 
+### Docker
+
+A pre-built JupyterLab image is available on Docker Hub:
+
+```bash
+docker pull alertadengue/pysus
+docker run -p 8888:8888 alertadengue/pysus
+```
+
+Or build locally and start the container:
+
+```bash
+docker compose -f docker/docker-compose.yaml up --build
+```
+
+Then open [http://127.0.0.1:8888/lab](http://127.0.0.1:8888/lab) in your browser.
+
+Stop the container:
+
+```bash
+docker compose -f docker/docker-compose.yaml down
+```
+
 ## Quick Start
 
 ### Simplified Database Functions (New in 2.0)
@@ -41,7 +64,7 @@ The easiest way to get data as a pandas DataFrame:
 ```python
 from pysus import sinan, sinasc, sim, sih, sia, pni, ibge, cnes, ciha
 
-# Download SINAN Dengue data for 2024
+# Download SINAN Dengue data for 2000
 df = sinan(disease="deng", year=2000)
 
 # Multiple years
@@ -238,6 +261,12 @@ Run tests:
 pytest tests/
 ```
 
+Run tests inside the Docker container:
+
+```bash
+docker compose -f docker/docker-compose.yaml exec -T -w /usr/src jupyter python3 -m pytest pysus/tests/
+```
+
 ## License
 
 GPL

docker/Dockerfile

@@ -1,52 +1,39 @@
-FROM condaforge/mambaforge
+FROM python:3.12-slim
 
-LABEL maintainer="es.loch@gmail.com"
-
-USER root
+LABEL maintainer="luabidaa@gmail.com"
+LABEL org.opencontainers.image.source="https://github.com/AlertaDengue/PySUS"
+LABEL org.opencontainers.image.description="PySUS - Data extraction from Brazilian public health systems"
 
 ENV DEBIAN_FRONTEND=noninteractive
-
 ENV HOME "/home/pysus"
 ENV PATH "$PATH:/home/pysus/.local/bin"
-ENV ENV_NAME pysus
-ENV PATH "/opt/conda/envs/$ENV_NAME/bin:$PATH"
-ENV PATH "/opt/poetry/bin:$PATH"
 
 RUN apt-get -qq update --yes \
   && apt-get -qq install --yes --no-install-recommends \
+  libffi-dev \
   build-essential \
-  firefox \
   ca-certificates \
   sudo \
   curl \
   && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash pysus \
   && echo "pysus ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/pysus \
-  && chmod 0440 /etc/sudoers.d/ \
-  && echo 'source /opt/conda/bin/activate "$ENV_NAME" && exec "$@"' > /activate.sh \
-  && echo 'source activate "$ENV_NAME"' >  /home/pysus/.bashrc \
-  && chmod +x /activate.sh \
-  && chmod -R a+rwx /opt/conda /tmp \
-  && sudo chown -R pysus:pysus /usr/src
-
-USER pysus
+  && chmod 0440 /etc/sudoers.d/pysus \
+  && mkdir -p /home/pysus/Notebooks \
+  && chown -R pysus:pysus /home/pysus
 
-RUN mkdir -p /home/pysus/Notebooks/
+COPY pyproject.toml poetry.lock LICENSE README.md /usr/src/
+COPY pysus /usr/src/pysus
+COPY docker/scripts/entrypoint.sh /entrypoint.sh
+COPY docker/notebooks/ /home/pysus/Notebooks/
 
-COPY --chown=pysus:pysus conda/dev.yaml /tmp/dev.yaml
-COPY --chown=pysus:pysus docker/scripts/entrypoint.sh /entrypoint.sh
-COPY --chown=pysus:pysus docker/scripts/poetry-install.sh /tmp/poetry-install.sh
-COPY --chown=pysus:pysus pyproject.toml poetry.lock LICENSE README.md /usr/src/
-COPY --chown=pysus:pysus pysus /usr/src/pysus
-COPY --chown=pysus:pysus docs/source/**/*.ipynb /home/pysus/Notebooks/
-COPY --chown=pysus:pysus docs/source/data /home/pysus/Notebooks/
-
-RUN mamba env create -n $ENV_NAME --file /tmp/dev.yaml \
-  && mamba clean -afy
-
-RUN cd /usr/src/ && bash /tmp/poetry-install.sh
+RUN pip install poetry \
+  && cd /usr/src && poetry config virtualenvs.create false && poetry install --with docs --extras dbc \
+  && pip install 'httpx<0.28' \
+  && chown -R pysus:pysus /home/pysus
 
+USER pysus
 WORKDIR /home/pysus/Notebooks
 
-ENTRYPOINT ["bash", "/activate.sh", "jupyter", "notebook", "--port=8888", "--ip=0.0.0.0"]
+ENTRYPOINT ["/entrypoint.sh"]

docker/docker-compose.yaml

@@ -1,16 +1,16 @@
-version: '3.3'
 services:
   jupyter:
     build:
       context: ".."
       dockerfile: docker/Dockerfile
     hostname: pysus-jupyter
     container_name: pysus-jupyter
+    ports:
+      - "8888:8888"
     privileged: true
     environment:
       - DISPLAY=:0
       - CI=${CI:-0}
     volumes:
       - /tmp/.X11-unix:/tmp/.X11-unix
     entrypoint: ["/entrypoint.sh"]
-    command: ["/usr/bin/firefox"]

docker/notebooks/Welcome.ipynb

@@ -0,0 +1,89 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Welcome to PySUS\n",
+    "\n",
+    "PySUS provides tools for dealing with Brazil's public health data (SINAN, SINASC, SIM, SIH, SIA, PNI, IBGE, CNES, CIHA).\n",
+    "\n",
+    "## Quick start\n",
+    "\n",
+    "List available datasets and files:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pysus\n",
+    "\n",
+    "pysus.list_files()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Fetch SINAN data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pysus import sinan\n",
+    "\n",
+    "df = sinan(\"deng\", year=2023)\n",
+    "df.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Fetch SINASC data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pysus import sinasc\n",
+    "\n",
+    "df = sinasc(state=\"RJ\", year=2023)\n",
+    "df.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Documentation\n",
+    "\n",
+    "- [PySUS GitHub](https://github.com/InfoDengue/PySUS)\n",
+    "- [PySUS Docs](https://pysus.readthedocs.io/)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.12.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}