Merge pull request #13 from luabida/binary-build

refactor(episcanner): move binary build branch to updated main

.github/workflows/linux.yml

@@ -2,11 +2,6 @@ name: EpiScanner Build
 
 on: [pull_request]
 
-env:
-  HOST_GID: 1000
-  HOST_UID: 1000
-  ENV: prod
-
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -52,6 +47,6 @@ jobs:
         pre-commit install
         pre-commit run --all-files
 
-    # - name: Pytest
-    #   run: |
-    #     test-fetch-data
+    - name: Pytest
+      run: |
+        make tests

.github/workflows/release.yaml

@@ -41,6 +41,9 @@ jobs:
       with:
         node-version: 18
 
+    - name: Install dependencies
+      run: poetry install
+
     - name: Test release
       if: ${{ github.event_name != 'workflow_dispatch' }}
       env:

.releaserc.json

@@ -55,6 +55,12 @@
           "prepareCmd": "poetry build"
         }
       ],
+      [
+        "@semantic-release/github",
+        {
+          "assets": ["dist/*.whl", "dist/*.tar.gz"]
+        }
+      ],
       [
         "@semantic-release/git",
         {

Makefile

@@ -2,21 +2,15 @@
 ENV:=$(ENV)
 
 
-.PHONY: create-dotenv
-create-dotenv:
+.PHONY: dotenv
+dotenv:
 	export HOST_UID=$$(id -u) && \
 	export HOST_GID=$$(id -g) && \
 	envsubst < env.tpl > .env
 
-# Export data for all states and diseases to Parquet files in the default output directory
-.PHONY:fetch-data
-fetch-data:
-	python epi_scanner/downloader/export_data.py -s all -d dengue chikungunya
-
-#  Run pytest for all tests in epi_scanner/tests inside the container
-.PHONY:test-fetch-data
-test-fetch-data:
-	pytest -vv epi_scanner/tests
+.PHONY:tests
+tests:
+	pytest -vv src/tests
 
 .PHONY: clean
 clean: ## clean all artifacts

README.md

@@ -1,6 +1,6 @@
 # Episcanner Downloader
 
-Episcanner Downloader is a data downloader for the Episcanner application. It retrieves data related to diseases like dengue and chikungunya and saves it in a specified directory.
+Episcanner Downloader is a data downloader for the Episcanner application. It retrieves data related to diseases like dengue, zika and chikungunya and saves it in a specified directory with the formats csv, parquet or duckdb.
 
 ## Features
 
@@ -27,9 +27,9 @@ To install Episcanner Downloader, follow these steps:
 ```shell
    conda env create -f conda/env-base.yaml
 ``` 
-2. conda activate episcanner
+2. conda activate episcanner-downloader
 ```shell
-   conda activate episcanner
+   conda activate episcanner-downloader
 ``` 
 3. Install the dependencies using Poetry:
 ```shell
@@ -52,30 +52,24 @@ To install Episcanner Downloader, follow these steps:
 Before running Episcanner Downloader, make sure to set the required environment variables for connecting to the PSQL database. You can use the provided Makefile to create a .env file with the exported variables:
 1. Set the required environment variables for connecting to the PSQL database:
 ```shell
-   export PSQL_USER=<your_psql_user>
-   export PSQL_PASSWORD=<your_psql_password>
-   export PSQL_HOST=<your_psql_host>
-   export PSQL_PORT=<your_psql_port>
-   export PSQL_USER=<your_psql_database>
+   export EPISCANNER_PSQL_URI="postgresql://user:password@host:port/database"
 ```
 
 2. Create a .env file in the project root directory with the exported variables.
 ```shell
-   make create-dotenv
+   make dotenv
 ```
 ## Usage
 To use Episcanner Downloader, follow these steps:
 
-1. Activate the project's virtual environment:
+1. Execute the binary (examples for Linux):
 ```shell
-   source /path/to/episcanner-downloader/venv/bin/activate
+   cd dist/
+   ./episcanner -h
+   ./episcanner -y 2023 -s RJ -d dengue -o /tmp -f duckdb
+   ./episcanner -y 2021 2022 2023 --all -d zika -f csv parquet --verbose
 ``` 
-2. Run the Episcanner Downloader:
-```shell
-   mkdir data 
-   python epi_scanner/downloader/export_data.py -s <source> -d <diseases> -o data 
-``` 
-*Replace <source> with the desired source (e.g., 'MG', or 'all' to download all states) and <diseases> with the specific diseases you want to download (e.g., 'dengue chikungunya'). Specify the <output_directory> where the data should be saved.*
+*Replace <source> with the desired source (e.g., 'MG', or '--all' to download all states) and <diseases> with the specific diseases you want to download (e.g., 'dengue chikungunya'). Specify the <output_directory> where the data should be saved.*
 
 ## License
 Episcanner Downloader is licensed under the [MIT License](https://github.com/AlertaDengue/episcanner-downloader/blob/main/LICENSE). See the LICENSE file for more details.

env.tpl

@@ -1,10 +1 @@
-# Host
-HOST_GID=$HOST_GID
-HOST_UID=$HOST_UID
-
-# Used to fetch data from the database
-PSQL_DB=$PSQL_DB
-PSQL_HOST=$PSQL_HOST
-PSQL_PASSWORD=$PSQL_PASSWORD
-PSQL_PORT=$PSQL_PORT
-PSQL_USER=$PSQL_USER
+EPISCANNER_PSQL_URI=$EPISCANNER_PSQL_URI