From dddac37ff08cb523fcfc0af968b4798a7a2a6b8c Mon Sep 17 00:00:00 2001 From: jaegglic Date: Fri, 25 Apr 2025 15:22:39 +0200 Subject: [PATCH] Changed docs and folder names --- .github/workflows/ci.yml | 4 +- CODE_OF_CONDUCT.md | 2 +- CONTRIBUTING.md | 16 +++---- LICENSE | 2 +- README.md | 40 +++++++++--------- citation.cff | 8 ++-- docs/_config.yml | 6 +-- docs/drugsafetycompare.md | 6 +-- docs/fraudcrawler.md | 2 +- docs/index.md | 25 +++-------- docs/spock.md | 10 ++--- docs/toxicologygan.md | 6 +-- pyproject.toml | 15 +++---- tests/tests-drugsafetycompare/test-compare.py | 6 +-- tests/tests-drugsafetycompare/test-germany.py | 4 +- .../test-switzerland.py | 4 +- tests/tests-lasa/unittests/test_src_units.py | 8 ++-- tests/tests-spock/unittests/test_src_base.py | 2 +- .../unittests/test_src_scraping.py | 2 +- {vianu => veanu}/__init__.py | 0 .../drugsafetycompare/__init__.py | 0 .../drugsafetycompare/launch_demo_app.py | 16 +++---- .../drugsafetycompare/launch_demo_pipeline.py | 2 +- .../drugsafetycompare/settings.py | 0 .../drugsafetycompare/src/__init__.py | 0 .../drugsafetycompare/src/compare.py | 0 .../drugsafetycompare/src/extract_germany.py | 0 .../src/extract_switzerland.py | 0 .../drugsafetycompare/src/gpt_pipeline.py | 0 .../src/transformer_pipeline.py | 0 {vianu => veanu}/fraudcrawler/.template_env | 0 {vianu => veanu}/fraudcrawler/__init__.py | 0 .../fraudcrawler/launch_demo_app.py | 6 +-- .../fraudcrawler/launch_demo_pipeline.py | 6 +-- {vianu => veanu}/fraudcrawler/settings.py | 0 {vianu => veanu}/fraudcrawler/src/__init__.py | 0 .../src/classify_suspicious_product.py | 2 +- {vianu => veanu}/fraudcrawler/src/client.py | 10 ++--- .../fraudcrawler/src/enrichment.py | 4 +- .../fraudcrawler/src/enrichment_utils.py | 0 .../fraudcrawler/src/processor.py | 0 {vianu => veanu}/fraudcrawler/src/serpapi.py | 0 {vianu => veanu}/fraudcrawler/src/zyteapi.py | 0 .../tests/test_keyword_enricher.py | 2 +- {vianu => veanu}/lasa/__init__.py | 0 {vianu => veanu}/lasa/__main__.py | 10 ++--- veanu/lasa/app/__init__.py | 3 ++ {vianu => veanu}/lasa/app/app.py | 10 ++--- {vianu => veanu}/lasa/assets/css/styles.css | 0 {vianu => veanu}/lasa/assets/images/bird.png | Bin .../lasa/assets/images/logo-circular.png | Bin {vianu => veanu}/lasa/assets/images/logo.png | Bin {vianu => veanu}/lasa/assets/images/logo.webp | Bin .../lasa/files/fda_products_20250121.csv | 0 .../lasa/files/swissmedic_20241231.xlsx | Bin {vianu => veanu}/lasa/launch_demo_app.py | 6 +-- {vianu => veanu}/lasa/launch_demo_pipeline.py | 2 +- {vianu => veanu}/lasa/requirements.txt | 0 {vianu => veanu}/lasa/settings.py | 0 {vianu => veanu}/lasa/src/__init__.py | 0 {vianu => veanu}/lasa/src/base.py | 0 {vianu => veanu}/lasa/src/cli.py | 2 +- {vianu => veanu}/lasa/src/units.py | 2 +- {vianu => veanu}/newsscraper/README.md | 0 {vianu => veanu}/newsscraper/envtemplate | 0 .../newsscraper/launch_demo_app.py | 4 +- .../newsscraper/src/db_manager.py | 0 {vianu => veanu}/newsscraper/src/db_setup.py | 0 .../newsscraper/src/entrypoint.sh | 0 .../newsscraper/src/requirements.txt | 0 .../newsscraper/src/run_scraper.py | 0 .../newsscraper/src/run_scraper.sh | 0 {vianu => veanu}/newsscraper/src/scrape.py | 2 +- {vianu => veanu}/newsscraper/src/scraper_cron | 0 {vianu => veanu}/spock/__init__.py | 0 {vianu => veanu}/spock/__main__.py | 12 +++--- veanu/spock/app/__init__.py | 3 ++ {vianu => veanu}/spock/app/app.py | 18 ++++---- {vianu => veanu}/spock/app/formatter.py | 4 +- {vianu => veanu}/spock/assets/css/styles.css | 0 .../spock/assets/head/scripts.html | 0 .../spock/assets/images/favicon.png | Bin .../spock/assets/images/spock_logo.png | Bin .../assets/images/spock_logo_circular.png | Bin {vianu => veanu}/spock/launch_demo_app.py | 6 +-- .../spock/launch_demo_pipeline.py | 6 +-- {vianu => veanu}/spock/requirements.txt | 0 {vianu => veanu}/spock/settings.py | 0 {vianu => veanu}/spock/src/__init__.py | 0 {vianu => veanu}/spock/src/base.py | 0 {vianu => veanu}/spock/src/cli.py | 6 +-- {vianu => veanu}/spock/src/ner.py | 4 +- {vianu => veanu}/spock/src/scraping.py | 6 +-- vianu/lasa/app/__init__.py | 3 -- vianu/spock/app/__init__.py | 3 -- 95 files changed, 157 insertions(+), 171 deletions(-) rename {vianu => veanu}/__init__.py (100%) rename {vianu => veanu}/drugsafetycompare/__init__.py (100%) rename {vianu => veanu}/drugsafetycompare/launch_demo_app.py (97%) rename {vianu => veanu}/drugsafetycompare/launch_demo_pipeline.py (94%) rename {vianu => veanu}/drugsafetycompare/settings.py (100%) rename {vianu => veanu}/drugsafetycompare/src/__init__.py (100%) rename {vianu => veanu}/drugsafetycompare/src/compare.py (100%) rename {vianu => veanu}/drugsafetycompare/src/extract_germany.py (100%) rename {vianu => veanu}/drugsafetycompare/src/extract_switzerland.py (100%) rename {vianu => veanu}/drugsafetycompare/src/gpt_pipeline.py (100%) rename {vianu => veanu}/drugsafetycompare/src/transformer_pipeline.py (100%) rename {vianu => veanu}/fraudcrawler/.template_env (100%) rename {vianu => veanu}/fraudcrawler/__init__.py (100%) rename {vianu => veanu}/fraudcrawler/launch_demo_app.py (98%) rename {vianu => veanu}/fraudcrawler/launch_demo_pipeline.py (82%) rename {vianu => veanu}/fraudcrawler/settings.py (100%) rename {vianu => veanu}/fraudcrawler/src/__init__.py (100%) rename {vianu => veanu}/fraudcrawler/src/classify_suspicious_product.py (98%) rename {vianu => veanu}/fraudcrawler/src/client.py (91%) rename {vianu => veanu}/fraudcrawler/src/enrichment.py (99%) rename {vianu => veanu}/fraudcrawler/src/enrichment_utils.py (100%) rename {vianu => veanu}/fraudcrawler/src/processor.py (100%) rename {vianu => veanu}/fraudcrawler/src/serpapi.py (100%) rename {vianu => veanu}/fraudcrawler/src/zyteapi.py (100%) rename {vianu => veanu}/fraudcrawler/tests/test_keyword_enricher.py (98%) rename {vianu => veanu}/lasa/__init__.py (100%) rename {vianu => veanu}/lasa/__main__.py (86%) create mode 100644 veanu/lasa/app/__init__.py rename {vianu => veanu}/lasa/app/app.py (97%) rename {vianu => veanu}/lasa/assets/css/styles.css (100%) rename {vianu => veanu}/lasa/assets/images/bird.png (100%) rename {vianu => veanu}/lasa/assets/images/logo-circular.png (100%) rename {vianu => veanu}/lasa/assets/images/logo.png (100%) rename {vianu => veanu}/lasa/assets/images/logo.webp (100%) rename {vianu => veanu}/lasa/files/fda_products_20250121.csv (100%) rename {vianu => veanu}/lasa/files/swissmedic_20241231.xlsx (100%) rename {vianu => veanu}/lasa/launch_demo_app.py (74%) rename {vianu => veanu}/lasa/launch_demo_pipeline.py (91%) rename {vianu => veanu}/lasa/requirements.txt (100%) rename {vianu => veanu}/lasa/settings.py (100%) rename {vianu => veanu}/lasa/src/__init__.py (100%) rename {vianu => veanu}/lasa/src/base.py (100%) rename {vianu => veanu}/lasa/src/cli.py (93%) rename {vianu => veanu}/lasa/src/units.py (98%) rename {vianu => veanu}/newsscraper/README.md (100%) rename {vianu => veanu}/newsscraper/envtemplate (100%) rename {vianu => veanu}/newsscraper/launch_demo_app.py (98%) rename {vianu => veanu}/newsscraper/src/db_manager.py (100%) rename {vianu => veanu}/newsscraper/src/db_setup.py (100%) rename {vianu => veanu}/newsscraper/src/entrypoint.sh (100%) rename {vianu => veanu}/newsscraper/src/requirements.txt (100%) rename {vianu => veanu}/newsscraper/src/run_scraper.py (100%) rename {vianu => veanu}/newsscraper/src/run_scraper.sh (100%) rename {vianu => veanu}/newsscraper/src/scrape.py (99%) rename {vianu => veanu}/newsscraper/src/scraper_cron (100%) rename {vianu => veanu}/spock/__init__.py (100%) rename {vianu => veanu}/spock/__main__.py (95%) create mode 100644 veanu/spock/app/__init__.py rename {vianu => veanu}/spock/app/app.py (98%) rename {vianu => veanu}/spock/app/formatter.py (96%) rename {vianu => veanu}/spock/assets/css/styles.css (100%) rename {vianu => veanu}/spock/assets/head/scripts.html (100%) rename {vianu => veanu}/spock/assets/images/favicon.png (100%) rename {vianu => veanu}/spock/assets/images/spock_logo.png (100%) rename {vianu => veanu}/spock/assets/images/spock_logo_circular.png (100%) rename {vianu => veanu}/spock/launch_demo_app.py (74%) rename {vianu => veanu}/spock/launch_demo_pipeline.py (68%) rename {vianu => veanu}/spock/requirements.txt (100%) rename {vianu => veanu}/spock/settings.py (100%) rename {vianu => veanu}/spock/src/__init__.py (100%) rename {vianu => veanu}/spock/src/base.py (100%) rename {vianu => veanu}/spock/src/cli.py (90%) rename {vianu => veanu}/spock/src/ner.py (99%) rename {vianu => veanu}/spock/src/scraping.py (99%) delete mode 100644 vianu/lasa/app/__init__.py delete mode 100644 vianu/spock/app/__init__.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4ee3cfc..50d762b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,7 +22,7 @@ jobs: - name: Python Vulnerability Check #bandit exits by defaul with status 1 if a vulerability was found. Status unequal to 0 lead to a github action failure run: | - poetry run bandit -r vianu + poetry run bandit -r veanu - name: Lint with Ruff run: | @@ -34,4 +34,4 @@ jobs: - name: Run Unit Tests run: | - poetry run pytest --cov=vianu --cov-report=html --cov-report=xml tests/tests-*/* -s \ No newline at end of file + poetry run pytest --cov=veanu --cov-report=html --cov-report=xml tests/tests-*/* -s \ No newline at end of file diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index e3fd0aa..020f66a 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -18,7 +18,7 @@ We are committed to creating a friendly and welcoming environment for everyone, ## Reporting Issues -If you experience or witness unacceptable behavior, please report it by contacting the project maintainers at [hello@vianu.org]. All reports will be handled confidentially. +If you experience or witness unacceptable behavior, please report it by contacting the project maintainers at [hello@veanu.ch]. All reports will be handled confidentially. ## Consequences diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8006d8b..c0ee123 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,19 +1,19 @@ -# Contributing to Vianu +# Contributing to open-veanu/veanu -First, let us thank you for considering contributing to Vianu! Your involvement is vital to the project's success. +First, let us thank you for considering contributing to open-veanu/veanu! Your involvement is vital to the project's success. ## How Can You Contribute? -- **Reporting Bugs**: If you encounter any issues, please [open an issue](https://github.com/smc40/vianu/issues) with detailed information. -- **Suggesting Enhancements**: Have an idea to improve Vianu? [Submit a feature request](https://github.com/smc40/vianu/issues) outlining your suggestion. +- **Reporting Bugs**: If you encounter any issues, please [open an issue](https://github.com/open-veanu/veanu/issues) with detailed information. +- **Suggesting Enhancements**: Have an idea to improve veanu? [Submit a feature request](https://github.com/open-veanu/veanu/issues) outlining your suggestion. - **Submitting Pull Requests**: Ready to code? Follow the steps below to submit your contributions. ## Getting Started -1. **Clone the Repository**: Clone the Vianu repository to your local machine: +1. **Clone the Repository**: Clone the veanu repository to your local machine: ```bash - git clone https://github.com/smc40/vianu.git - cd vianu + git clone https://github.com/open-veanu/veanu.git + cd veanu ``` 2. **Create a Branch**: Start by creating a new branch for your feature or bugfix: @@ -45,7 +45,7 @@ First, let us thank you for considering contributing to Vianu! Your involvement git push origin feature/your-feature-name ``` -8. **Open a Pull Request**: Go to the Vianu repository on GitHub and open a pull request from your branch. +8. **Open a Pull Request**: Go to the open-veanu/veanu repository on GitHub and open a pull request from your branch. ## Code Style diff --git a/LICENSE b/LICENSE index 4c40882..74e4f15 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2024 vianu +Copyright (c) 2025 veanu Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index c6da6e8..2e6f5f4 100644 --- a/README.md +++ b/README.md @@ -1,36 +1,36 @@

- vianu Logo -

vianu

+ veanu Logo +

veanu

Together we are building an Open Source Community for Life Sciences.

- PyPI version + PyPI version

--- -Vianu is a Python package designed for developers working in the **life sciences and healthcare** sectors. It provides access to a variety of tools and workflows, allowing users to quickly build, validate, and deploy data-driven applications. +veanu is a Python package designed for developers working in the **life sciences and healthcare** sectors. It provides access to a variety of tools and workflows, allowing users to quickly build, validate, and deploy data-driven applications. ## Available Tools - **Lasa**: A tool for phonetic comparison of novel drug names with authorized ones from different locations. - **FraudCrawler**: A data ingestion and transformation pipeline for real-world healthcare data. - **SpoCK**: A tool to search public websites for spotting adverse drug reactions -- **DrugSafetyCompare**: A tool to search for published drug labels and compare their safety profiles. [See in action](https://huggingface.co/spaces/vianu/drugsafetycompare) +- **DrugSafetyCompare**: A tool to search for published drug labels and compare their safety profiles. [See in action](https://huggingface.co/spaces/veanu/drugsafetycompare) ## Installation -To install Vianu, use the following command: +To install veanu, use the following command: ```bash -pip install vianu +pip install veanu ``` -Alternatively, you can install vianu from source: +Alternatively, you can install veanu from source: ```bash -git clone https://github.com/smc40/vianu.git -cd vianu +git clone https://github.com/open-veanu/veanu.git +cd veanu poetry install poetry shell ``` @@ -44,10 +44,10 @@ TBD #### Launch a Demo Pipeline ```bash -cd vianu/lasa +cd veanu/lasa poetry install poetry shell -python -m vianu.tools.tici.launch_demo_pipeline +python -m veanu.tools.tici.launch_demo_pipeline ``` ### FraudCrawler @@ -55,13 +55,13 @@ python -m vianu.tools.tici.launch_demo_pipeline #### Launch a Demo App ```bash -python vianu/fraudcrawler/launch_demo_app.py +python veanu/fraudcrawler/launch_demo_app.py ``` #### Launch a Demo Pipeline ```bash -python -m vianu.fraudcrawler.launch_demo_pipeline +python -m veanu.fraudcrawler.launch_demo_pipeline ``` @@ -74,11 +74,11 @@ To lauch the demo app do the following: ```bash poetry install poetry shell -python vianu/tools/drugsafetycompare/launch_demo_app_count.py +python veanu/tools/drugsafetycompare/launch_demo_app_count.py ``` Or simply launch the starter-script: ```bash -vianu_drugsafetycompare_app +veanu_drugsafetycompare_app ``` @@ -87,7 +87,7 @@ vianu_drugsafetycompare_app ```bash poetry install poetry shell -python -m vianu.drugsafetycompare.launch_demo_pipeline +python -m veanu.drugsafetycompare.launch_demo_pipeline ``` @@ -96,13 +96,13 @@ python -m vianu.drugsafetycompare.launch_demo_pipeline #### Launch a Demo App ```bash -python vianu/spock/launch_demo_app.py +python veanu/spock/launch_demo_app.py ``` #### Launch a Demo Pipeline ```bash -python -m vianu.spock.launch_demo_pipeline +python -m veanu.spock.launch_demo_pipeline ``` @@ -129,7 +129,7 @@ This project is licensed under the MIT License. ## Feedback and Support -For any issues or feature requests, please use the [GitHub Issues](https://github.com/smc40/vianu/issues) page. +For any issues or feature requests, please use the [GitHub Issues](https://github.com/open-veanu/veanu/issues) page. ## Acknowledgments diff --git a/citation.cff b/citation.cff index 6c1b146..fff452c 100644 --- a/citation.cff +++ b/citation.cff @@ -1,5 +1,5 @@ cff-version: 1.2.0 -title: 'Vianu' +title: 'veanu' message: >- If you use this software, please cite it using the metadata from this file. @@ -9,12 +9,12 @@ authors: family-names: Perez Gonzalez - given-names: Alexander family-names: Horst -repository-code: 'https://github.com/smc40/vianu' -abstract: "Vianu enables developers to access tools applicable to life sciences and healthcare." +repository-code: 'https://github.com/open-veanu/veanu' +abstract: "veanu enables developers to access tools applicable to life sciences and healthcare." keywords: - healthcare - goverment - pytorch - tensorflow license: unclear -version: 0.0.0 \ No newline at end of file +version: 0.1.0 \ No newline at end of file diff --git a/docs/_config.yml b/docs/_config.yml index 1c47e4c..04b70dc 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -1,10 +1,10 @@ -title: vianu +title: veanu description: an open-source platform for the life sciences theme: just-the-docs -url: https://open-vianu.github.io/vianu +url: https://open-veanu.github.io/veanu -# These are individual configurations to vianu +# These are individual configurations to veanu logo: "/assets/images/pingu-logo.png" favicon_ico: "/assets/images/favicon-pingu.ico" search_enabled: true diff --git a/docs/drugsafetycompare.md b/docs/drugsafetycompare.md index 98ac137..ff4a47c 100644 --- a/docs/drugsafetycompare.md +++ b/docs/drugsafetycompare.md @@ -94,16 +94,16 @@ Before you begin, ensure you have the following installed: 1. **Download package** ```bash - pip install vianu + pip install veanu ``` 2. **Launch app** (with starterscript) ```bash - vianu_drugsafetycompare_app + veanu_drugsafetycompare_app ``` The application will launch and can be accessed via your web browser at `http://127.0.0.1:7860/?__theme=light`. 3. **Use Pipeline to Extract Drug Labels**: In Python you can use the following: ```python - from vianu.drugsafetycompare.src.germany import GermanDrugInfoExtractor + from veanu.drugsafetycompare.src.germany import GermanDrugInfoExtractor extractor = GermanDrugInfoExtractor() try: # Define the drug name diff --git a/docs/fraudcrawler.md b/docs/fraudcrawler.md index 1d00f1e..dfd3cc7 100644 --- a/docs/fraudcrawler.md +++ b/docs/fraudcrawler.md @@ -10,7 +10,7 @@ The `FraudCrawler` tool collects URLs suspicious of illegal activity based on me ## Usage ```python -from vianu.fraudcrawler.src.client import FraudcrawlerClient +from veanu.fraudcrawler.src.client import FraudcrawlerClient fc = FraudcrawlerClient() fc.serpapi_token = "your_serpapi_token" diff --git a/docs/index.md b/docs/index.md index a0a88ba..7668973 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,13 +4,13 @@ layout: home nav_order: 1 --- -# Welcome to VIANU! +# Welcome to open-veanu/veanu! -# Vianu is a package meant to provide support to devs in the life sciences +# veanu is a package meant to provide support to devs in the life sciences [Get Started](#getting-started){: .btn .btn-purple } -[Vianu] is a *Python package* designed for developers working in the life sciences and healthcare sectors. +[veanu] is a *Python package* designed for developers working in the life sciences and healthcare sectors. It provides access to a variety of tools and workflows, allowing users to quickly build, validate, and deploy data-driven applications. @@ -32,22 +32,9 @@ This is how you install all of our cool ninja moves ## Quick Installation ```bash -pip install vianu==0.1.2 +pip install veanu ``` -### Example usage +go ahead and `have fun` with this repository! -```python -from vianu.fraudcrawler.src.client import FraudcrawlerClient - -fc = FraudcrawlerClient() -fc.serpapi_token = "your_token" -fc.zyte_api_key = "your_key" - -df = fc.search("sildenafil", num_results=5, location="Switzerland") -print(df) -``` - -Other than that, go ahead and `have fun` with this repository! - -[Vianu]: https://github.com/open-vianu/vianu +[veanu]: https://github.com/open-veanu/veanu diff --git a/docs/spock.md b/docs/spock.md index bee8bd3..b7d9b99 100644 --- a/docs/spock.md +++ b/docs/spock.md @@ -39,8 +39,8 @@ docker exec -it ollama ollama pull llama3.2 #### Python environment ```bash -git clone https://github.com/open-vianu/vianu.git -cd vianu +git clone https://github.com/open-veanu/veanu.git +cd veanu poetry install poetry shell ``` @@ -54,17 +54,17 @@ or alternatively set the corresponding environment variable through the UI. ### Run demo pipeline ```bash -python vianu/spock/launch_demo_pipeline.py +python veanu/spock/launch_demo_pipeline.py ``` ### Run demo app ```bash -python vianu/spock/launch_demo_app.py +python veanu/spock/launch_demo_app.py ``` ### CLI ```bash -python -m vianu.spock --term dafalgan --model llama --data-path "/tmp/spock" --data-file "spock_data" --log-level DEBUG +python -m veanu.spock --term dafalgan --model llama --data-path "/tmp/spock" --data-file "spock_data" --log-level DEBUG ``` ### Disclaimer diff --git a/docs/toxicologygan.md b/docs/toxicologygan.md index 74756db..70182d2 100644 --- a/docs/toxicologygan.md +++ b/docs/toxicologygan.md @@ -6,7 +6,7 @@ nav_order: 3 # Welcome to ToxicologyGAN -**ToxicologyGAN** is an out-of-the-box tool within the vianu package to help users facilitate the training of a GAN +**ToxicologyGAN** is an out-of-the-box tool within the open-veanu/veanu package to help users facilitate the training of a GAN network in the context of simulating ... [Skip to Installation](#installation-guide){: .btn .btn-purple } @@ -22,7 +22,7 @@ to generate new data points. Based on the work of [Chen et al. (Nature Communications, 2023)](https://www.nature.com/articles/s41467-023-42933-9), we implemented a simpler version of the code to make it more accessible and easy to use. Once having the correct input -data, the training of the network is easily performed with the implementation in vianu. +data, the training of the network is easily performed with the implementation in veanu. ### Prerequisites @@ -35,7 +35,7 @@ data, the training of the network is easily performed with the implementation in 1. **Download package** ```bash - pip install vianu + pip install veanu ``` 2. **Use Pipeline to train GAN network and generate new data points**: In Python you can use the following: diff --git a/pyproject.toml b/pyproject.toml index bbaac5d..a46212b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,13 +1,13 @@ [tool.poetry] -name = "vianu" +name = "veanu" version = "0.1.3" -description = "Vianu enables developers to access tools applicable to life sciences and healthcare." +description = "veanu enables developers to access tools applicable to life sciences and healthcare." authors = [ - "Nicolas Perez Gonzalez ", - "Alexander Horst ", - "Chriguberto Jäggli " + "Domingo Bertus ", + "NicoBerto ", + "Penguin Berthold ", ] -repository = "https://github.com/smc40/vianu" +repository = "https://github.com/open-veanu/veanu" license = "MIT" keywords = ["healthcare", "government", "opensource", "data science"] readme = "README.md" @@ -45,8 +45,7 @@ pdfminer = "^20191125" google-search-results = "^2.4.2" [tool.poetry.scripts] -vianu_fraudcrawler_app = "vianu.fraudcrawler.launch_demo_app:main" -vianu_drugsafetycompare_app = "vianu.drugsafetycompare.launch_demo_app:main" +veanu_drugsafetycompare_app = "veanu.drugsafetycompare.launch_demo_app:main" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/tests/tests-drugsafetycompare/test-compare.py b/tests/tests-drugsafetycompare/test-compare.py index 624b626..a980e3d 100644 --- a/tests/tests-drugsafetycompare/test-compare.py +++ b/tests/tests-drugsafetycompare/test-compare.py @@ -1,10 +1,10 @@ # tests/tests-drugsafetycompare/test-compare.py from unittest.mock import patch, MagicMock -from vianu.drugsafetycompare.src.compare import compare_drugs_with_gpt +from veanu.drugsafetycompare.src.compare import compare_drugs_with_gpt -@patch("vianu.drugsafetycompare.src.compare.OpenAI") +@patch("veanu.drugsafetycompare.src.compare.OpenAI") def test_compare_drugs_with_gpt_success(mock_openai): # Mock OpenAI response mock_client_instance = MagicMock() @@ -44,7 +44,7 @@ def test_compare_drugs_with_gpt_success(mock_openai): mock_client_instance.chat.completions.create.assert_called_once() -@patch("vianu.drugsafetycompare.src.compare.OpenAI") +@patch("veanu.drugsafetycompare.src.compare.OpenAI") def test_compare_drugs_with_gpt_api_exception(mock_openai): # Mock OpenAI to raise an exception mock_client_instance = MagicMock() diff --git a/tests/tests-drugsafetycompare/test-germany.py b/tests/tests-drugsafetycompare/test-germany.py index dac09f7..ae5b28c 100644 --- a/tests/tests-drugsafetycompare/test-germany.py +++ b/tests/tests-drugsafetycompare/test-germany.py @@ -1,11 +1,11 @@ import pytest from unittest.mock import patch, MagicMock, PropertyMock -from vianu.drugsafetycompare.src.extract_germany import GermanDrugInfoExtractor +from veanu.drugsafetycompare.src.extract_germany import GermanDrugInfoExtractor @pytest.fixture def mock_webdriver(): - with patch("vianu.drugsafetycompare.src.extract_germany.webdriver.Chrome") as mock: + with patch("veanu.drugsafetycompare.src.extract_germany.webdriver.Chrome") as mock: yield mock diff --git a/tests/tests-drugsafetycompare/test-switzerland.py b/tests/tests-drugsafetycompare/test-switzerland.py index 2ee6ef3..75b518b 100644 --- a/tests/tests-drugsafetycompare/test-switzerland.py +++ b/tests/tests-drugsafetycompare/test-switzerland.py @@ -1,12 +1,12 @@ import pytest from unittest.mock import patch, MagicMock -from vianu.drugsafetycompare.src.extract_switzerland import SwissDrugInfoExtractor +from veanu.drugsafetycompare.src.extract_switzerland import SwissDrugInfoExtractor @pytest.fixture def mock_webdriver(): with patch( - "vianu.drugsafetycompare.src.extract_switzerland.webdriver.Chrome" + "veanu.drugsafetycompare.src.extract_switzerland.webdriver.Chrome" ) as mock: yield mock diff --git a/tests/tests-lasa/unittests/test_src_units.py b/tests/tests-lasa/unittests/test_src_units.py index 4c98210..6e3dfcb 100644 --- a/tests/tests-lasa/unittests/test_src_units.py +++ b/tests/tests-lasa/unittests/test_src_units.py @@ -1,14 +1,14 @@ import pytest -from vianu.lasa.src.units import ( +from veanu.lasa.src.units import ( Product, AuthorizationUnit, SwissmedicAuthorization, FDAAuthorization, ) -from vianu.lasa.src.units import AuthorizationFactory -from vianu.lasa.src.base import LASA, Match -from vianu.lasa.__main__ import process +from veanu.lasa.src.units import AuthorizationFactory +from veanu.lasa.src.base import LASA, Match +from veanu.lasa.__main__ import process _N_SMC_PRODUCTS = 5657 _N_FDA_PRODUCTS = 8075 diff --git a/tests/tests-spock/unittests/test_src_base.py b/tests/tests-spock/unittests/test_src_base.py index 38c0985..4a88a8f 100644 --- a/tests/tests-spock/unittests/test_src_base.py +++ b/tests/tests-spock/unittests/test_src_base.py @@ -3,7 +3,7 @@ import pytest -from vianu.spock.src import base +from veanu.spock.src import base @pytest.fixture diff --git a/tests/tests-spock/unittests/test_src_scraping.py b/tests/tests-spock/unittests/test_src_scraping.py index 1287779..f82977d 100644 --- a/tests/tests-spock/unittests/test_src_scraping.py +++ b/tests/tests-spock/unittests/test_src_scraping.py @@ -1,4 +1,4 @@ -from vianu.spock.src import scraping as scp +from veanu.spock.src import scraping as scp def test_split_text_into_chunks_zero_remaning(): diff --git a/vianu/__init__.py b/veanu/__init__.py similarity index 100% rename from vianu/__init__.py rename to veanu/__init__.py diff --git a/vianu/drugsafetycompare/__init__.py b/veanu/drugsafetycompare/__init__.py similarity index 100% rename from vianu/drugsafetycompare/__init__.py rename to veanu/drugsafetycompare/__init__.py diff --git a/vianu/drugsafetycompare/launch_demo_app.py b/veanu/drugsafetycompare/launch_demo_app.py similarity index 97% rename from vianu/drugsafetycompare/launch_demo_app.py rename to veanu/drugsafetycompare/launch_demo_app.py index b005fd6..f1e9bfe 100644 --- a/vianu/drugsafetycompare/launch_demo_app.py +++ b/veanu/drugsafetycompare/launch_demo_app.py @@ -14,10 +14,10 @@ All non-UI logic (data retrieval, classification, visualization) is handled in separate modules within `src/`. Modules used: -- `vianu.drugsafetycompare.src.transformer_pipeline` → Transformer-based classification and SHAP explainability. -- `vianu.drugsafetycompare.src.gpt_pipeline` → GPT-based adverse event extraction and visualization. -- `vianu.drugsafetycompare.src.extract_germany` → German drug information retrieval. -- `vianu.drugsafetycompare.src.extract_switzerland` → Swiss drug information retrieval. +- `veanu.drugsafetycompare.src.transformer_pipeline` → Transformer-based classification and SHAP explainability. +- `veanu.drugsafetycompare.src.gpt_pipeline` → GPT-based adverse event extraction and visualization. +- `veanu.drugsafetycompare.src.extract_germany` → German drug information retrieval. +- `veanu.drugsafetycompare.src.extract_switzerland` → Swiss drug information retrieval. """ # --------------------- Import Statements --------------------- @@ -33,12 +33,12 @@ from dotenv import load_dotenv # Import your two new pipeline classes -from vianu.drugsafetycompare.src.transformer_pipeline import TransformerPipeline -from vianu.drugsafetycompare.src.gpt_pipeline import GptPipeline +from veanu.drugsafetycompare.src.transformer_pipeline import TransformerPipeline +from veanu.drugsafetycompare.src.gpt_pipeline import GptPipeline # Import your drug extractors (assumed already existing in ./src) -from vianu.drugsafetycompare.src.extract_germany import GermanDrugInfoExtractor -from vianu.drugsafetycompare.src.extract_switzerland import SwissDrugInfoExtractor +from veanu.drugsafetycompare.src.extract_germany import GermanDrugInfoExtractor +from veanu.drugsafetycompare.src.extract_switzerland import SwissDrugInfoExtractor # --------------------- Configure Logging --------------------- diff --git a/vianu/drugsafetycompare/launch_demo_pipeline.py b/veanu/drugsafetycompare/launch_demo_pipeline.py similarity index 94% rename from vianu/drugsafetycompare/launch_demo_pipeline.py rename to veanu/drugsafetycompare/launch_demo_pipeline.py index cdb489a..cb71004 100644 --- a/vianu/drugsafetycompare/launch_demo_pipeline.py +++ b/veanu/drugsafetycompare/launch_demo_pipeline.py @@ -6,7 +6,7 @@ and print its undesired effects (Nebenwirkungen). """ -from vianu.drugsafetycompare.src.extract_germany import GermanDrugInfoExtractor +from veanu.drugsafetycompare.src.extract_germany import GermanDrugInfoExtractor import logging logger = logging.getLogger("drugsafetycompare_logger") diff --git a/vianu/drugsafetycompare/settings.py b/veanu/drugsafetycompare/settings.py similarity index 100% rename from vianu/drugsafetycompare/settings.py rename to veanu/drugsafetycompare/settings.py diff --git a/vianu/drugsafetycompare/src/__init__.py b/veanu/drugsafetycompare/src/__init__.py similarity index 100% rename from vianu/drugsafetycompare/src/__init__.py rename to veanu/drugsafetycompare/src/__init__.py diff --git a/vianu/drugsafetycompare/src/compare.py b/veanu/drugsafetycompare/src/compare.py similarity index 100% rename from vianu/drugsafetycompare/src/compare.py rename to veanu/drugsafetycompare/src/compare.py diff --git a/vianu/drugsafetycompare/src/extract_germany.py b/veanu/drugsafetycompare/src/extract_germany.py similarity index 100% rename from vianu/drugsafetycompare/src/extract_germany.py rename to veanu/drugsafetycompare/src/extract_germany.py diff --git a/vianu/drugsafetycompare/src/extract_switzerland.py b/veanu/drugsafetycompare/src/extract_switzerland.py similarity index 100% rename from vianu/drugsafetycompare/src/extract_switzerland.py rename to veanu/drugsafetycompare/src/extract_switzerland.py diff --git a/vianu/drugsafetycompare/src/gpt_pipeline.py b/veanu/drugsafetycompare/src/gpt_pipeline.py similarity index 100% rename from vianu/drugsafetycompare/src/gpt_pipeline.py rename to veanu/drugsafetycompare/src/gpt_pipeline.py diff --git a/vianu/drugsafetycompare/src/transformer_pipeline.py b/veanu/drugsafetycompare/src/transformer_pipeline.py similarity index 100% rename from vianu/drugsafetycompare/src/transformer_pipeline.py rename to veanu/drugsafetycompare/src/transformer_pipeline.py diff --git a/vianu/fraudcrawler/.template_env b/veanu/fraudcrawler/.template_env similarity index 100% rename from vianu/fraudcrawler/.template_env rename to veanu/fraudcrawler/.template_env diff --git a/vianu/fraudcrawler/__init__.py b/veanu/fraudcrawler/__init__.py similarity index 100% rename from vianu/fraudcrawler/__init__.py rename to veanu/fraudcrawler/__init__.py diff --git a/vianu/fraudcrawler/launch_demo_app.py b/veanu/fraudcrawler/launch_demo_app.py similarity index 98% rename from vianu/fraudcrawler/launch_demo_app.py rename to veanu/fraudcrawler/launch_demo_app.py index 642d4df..1fce873 100644 --- a/vianu/fraudcrawler/launch_demo_app.py +++ b/veanu/fraudcrawler/launch_demo_app.py @@ -1,5 +1,5 @@ import gradio as gr -from vianu.fraudcrawler.src.client import FraudCrawlerClient +from veanu.fraudcrawler.src.client import FraudCrawlerClient # Sample JSON data for three example drugs with valid image URLs iron_magic_milk_data = [ @@ -192,7 +192,7 @@ def handle_inputs(site_token, serp_token, search_term, selected_example): """ return html_content except Exception as e: - return f"

Error: {str(e)}, please check your credentials or reach out to us at hello@vianu.com.

" + return f"

Error: {str(e)}, please check your credentials or reach out to us at hello@veanu.ch.

" elif len(site_token) > 0 or len(serp_token) > 0 or len(search_term) > 0: return "

Please fill out all the required credentials (Zyte API, Serp API, and Search Term).

" else: @@ -234,7 +234,7 @@ def handle_inputs(site_token, serp_token, search_term, selected_example): - **Examples**: Choose from preloaded data to see how the results are displayed. - **Custom Search**: Input your search term along with a valid SERP API token and Site token. You can obtain these tokens for free by registering on their respective websites. - If you have any questions, feel free to reach out to us at hello@vianu.org. We're always happy to help! + If you have any questions, feel free to reach out to us at hello@veanu.ch. We're always happy to help! """) with gr.Row(): with gr.Column(scale=1): diff --git a/vianu/fraudcrawler/launch_demo_pipeline.py b/veanu/fraudcrawler/launch_demo_pipeline.py similarity index 82% rename from vianu/fraudcrawler/launch_demo_pipeline.py rename to veanu/fraudcrawler/launch_demo_pipeline.py index fb33641..cd27c3d 100644 --- a/vianu/fraudcrawler/launch_demo_pipeline.py +++ b/veanu/fraudcrawler/launch_demo_pipeline.py @@ -3,9 +3,9 @@ from dotenv import load_dotenv -from vianu import LOG_FMT -from vianu.fraudcrawler.settings import LOG_LEVEL -from vianu.fraudcrawler.src.client import FraudCrawlerClient +from veanu import LOG_FMT +from veanu.fraudcrawler.settings import LOG_LEVEL +from veanu.fraudcrawler.src.client import FraudCrawlerClient logging.basicConfig( level=LOG_LEVEL.upper(), format=LOG_FMT, datefmt="%Y-%m-%d %H:%M:%S" diff --git a/vianu/fraudcrawler/settings.py b/veanu/fraudcrawler/settings.py similarity index 100% rename from vianu/fraudcrawler/settings.py rename to veanu/fraudcrawler/settings.py diff --git a/vianu/fraudcrawler/src/__init__.py b/veanu/fraudcrawler/src/__init__.py similarity index 100% rename from vianu/fraudcrawler/src/__init__.py rename to veanu/fraudcrawler/src/__init__.py diff --git a/vianu/fraudcrawler/src/classify_suspicious_product.py b/veanu/fraudcrawler/src/classify_suspicious_product.py similarity index 98% rename from vianu/fraudcrawler/src/classify_suspicious_product.py rename to veanu/fraudcrawler/src/classify_suspicious_product.py index 4d58fdb..7ed3e73 100644 --- a/vianu/fraudcrawler/src/classify_suspicious_product.py +++ b/veanu/fraudcrawler/src/classify_suspicious_product.py @@ -91,6 +91,6 @@ def handle_missing_fields(product: Dict[str, Any], field: str) -> Dict[str, Any] try: product_name = product["product"][field] # noqa: F841 except Exception as e: - product["product"][field] = "MISSING DATA, VIANU MODIFIED - it is a relevant product" + product["product"][field] = "MISSING DATA, VEANU MODIFIED - it is a relevant product" logger.error(f"PRODUCT DATA IN FIELD field does not exist. Error displayed: {e}") return product diff --git a/vianu/fraudcrawler/src/client.py b/veanu/fraudcrawler/src/client.py similarity index 91% rename from vianu/fraudcrawler/src/client.py rename to veanu/fraudcrawler/src/client.py index 08718d7..622fce6 100644 --- a/vianu/fraudcrawler/src/client.py +++ b/veanu/fraudcrawler/src/client.py @@ -1,11 +1,11 @@ import pandas as pd import logging -from vianu.fraudcrawler.src.serpapi import SerpApiClient -from vianu.fraudcrawler.src.zyteapi import ZyteAPIClient -from vianu.fraudcrawler.src.processor import Processor -from vianu.fraudcrawler.src.enrichment import KeywordEnricher -from vianu.fraudcrawler.src.classify_suspicious_product import ClassifySuspiciousProduct +from veanu.fraudcrawler.src.serpapi import SerpApiClient +from veanu.fraudcrawler.src.zyteapi import ZyteAPIClient +from veanu.fraudcrawler.src.processor import Processor +from veanu.fraudcrawler.src.enrichment import KeywordEnricher +from veanu.fraudcrawler.src.classify_suspicious_product import ClassifySuspiciousProduct logger = logging.getLogger(__name__) diff --git a/vianu/fraudcrawler/src/enrichment.py b/veanu/fraudcrawler/src/enrichment.py similarity index 99% rename from vianu/fraudcrawler/src/enrichment.py rename to veanu/fraudcrawler/src/enrichment.py index 9bef828..70ea9dc 100644 --- a/vianu/fraudcrawler/src/enrichment.py +++ b/veanu/fraudcrawler/src/enrichment.py @@ -1,11 +1,11 @@ -from vianu.fraudcrawler.src.serpapi import SerpApiClient +from veanu.fraudcrawler.src.serpapi import SerpApiClient from typing import Any, Dict, Callable, List import pandas as pd from json import dumps from json import loads from http.client import HTTPSConnection from base64 import b64encode -from vianu.fraudcrawler.src import enrichment_utils +from veanu.fraudcrawler.src import enrichment_utils import os import logging import hashlib diff --git a/vianu/fraudcrawler/src/enrichment_utils.py b/veanu/fraudcrawler/src/enrichment_utils.py similarity index 100% rename from vianu/fraudcrawler/src/enrichment_utils.py rename to veanu/fraudcrawler/src/enrichment_utils.py diff --git a/vianu/fraudcrawler/src/processor.py b/veanu/fraudcrawler/src/processor.py similarity index 100% rename from vianu/fraudcrawler/src/processor.py rename to veanu/fraudcrawler/src/processor.py diff --git a/vianu/fraudcrawler/src/serpapi.py b/veanu/fraudcrawler/src/serpapi.py similarity index 100% rename from vianu/fraudcrawler/src/serpapi.py rename to veanu/fraudcrawler/src/serpapi.py diff --git a/vianu/fraudcrawler/src/zyteapi.py b/veanu/fraudcrawler/src/zyteapi.py similarity index 100% rename from vianu/fraudcrawler/src/zyteapi.py rename to veanu/fraudcrawler/src/zyteapi.py diff --git a/vianu/fraudcrawler/tests/test_keyword_enricher.py b/veanu/fraudcrawler/tests/test_keyword_enricher.py similarity index 98% rename from vianu/fraudcrawler/tests/test_keyword_enricher.py rename to veanu/fraudcrawler/tests/test_keyword_enricher.py index f8cad69..d40f254 100644 --- a/vianu/fraudcrawler/tests/test_keyword_enricher.py +++ b/veanu/fraudcrawler/tests/test_keyword_enricher.py @@ -2,7 +2,7 @@ import pandas as pd from unittest.mock import patch -from vianu.fraudcrawler.src.enrichment import KeywordEnricher +from veanu.fraudcrawler.src.enrichment import KeywordEnricher class TestKeywordEnricher(unittest.TestCase): diff --git a/vianu/lasa/__init__.py b/veanu/lasa/__init__.py similarity index 100% rename from vianu/lasa/__init__.py rename to veanu/lasa/__init__.py diff --git a/vianu/lasa/__main__.py b/veanu/lasa/__main__.py similarity index 86% rename from vianu/lasa/__main__.py rename to veanu/lasa/__main__.py index c99ce0c..c23268a 100644 --- a/vianu/lasa/__main__.py +++ b/veanu/lasa/__main__.py @@ -5,11 +5,11 @@ from typing import Iterable, List -from vianu import LOG_FMT -from vianu.lasa.settings import LOG_LEVEL, PROCESSES, SOURCES -from vianu.lasa.src.base import LASA, Match -from vianu.lasa.src.units import AuthorizationFactory -from vianu.lasa.src.cli import parse_args +from veanu import LOG_FMT +from veanu.lasa.settings import LOG_LEVEL, PROCESSES, SOURCES +from veanu.lasa.src.base import LASA, Match +from veanu.lasa.src.units import AuthorizationFactory +from veanu.lasa.src.cli import parse_args logging.basicConfig(level=LOG_LEVEL.upper(), format=LOG_FMT) logger = logging.getLogger(__name__) diff --git a/veanu/lasa/app/__init__.py b/veanu/lasa/app/__init__.py new file mode 100644 index 0000000..e7bed15 --- /dev/null +++ b/veanu/lasa/app/__init__.py @@ -0,0 +1,3 @@ +from veanu.lasa.app.app import App + +__all__ = ["App"] diff --git a/vianu/lasa/app/app.py b/veanu/lasa/app/app.py similarity index 97% rename from vianu/lasa/app/app.py rename to veanu/lasa/app/app.py index f52963b..c453a48 100644 --- a/vianu/lasa/app/app.py +++ b/veanu/lasa/app/app.py @@ -6,15 +6,15 @@ import gradio as gr import pandas as pd -from vianu import BaseApp -from vianu.lasa.settings import LOG_LEVEL, PROCESSES -from vianu.lasa.settings import ( +from veanu import BaseApp +from veanu.lasa.settings import LOG_LEVEL, PROCESSES +from veanu.lasa.settings import ( GRADIO_APP_NAME, GRADIO_RESULTS_COLUMNS, GRADIO_RESULTS_COLUMNS_DEFAULT, ) -from vianu.lasa.settings import SOURCES, THRESHOLD -from vianu.lasa.__main__ import main +from veanu.lasa.settings import SOURCES, THRESHOLD +from veanu.lasa.__main__ import main logger = logging.getLogger(__name__) diff --git a/vianu/lasa/assets/css/styles.css b/veanu/lasa/assets/css/styles.css similarity index 100% rename from vianu/lasa/assets/css/styles.css rename to veanu/lasa/assets/css/styles.css diff --git a/vianu/lasa/assets/images/bird.png b/veanu/lasa/assets/images/bird.png similarity index 100% rename from vianu/lasa/assets/images/bird.png rename to veanu/lasa/assets/images/bird.png diff --git a/vianu/lasa/assets/images/logo-circular.png b/veanu/lasa/assets/images/logo-circular.png similarity index 100% rename from vianu/lasa/assets/images/logo-circular.png rename to veanu/lasa/assets/images/logo-circular.png diff --git a/vianu/lasa/assets/images/logo.png b/veanu/lasa/assets/images/logo.png similarity index 100% rename from vianu/lasa/assets/images/logo.png rename to veanu/lasa/assets/images/logo.png diff --git a/vianu/lasa/assets/images/logo.webp b/veanu/lasa/assets/images/logo.webp similarity index 100% rename from vianu/lasa/assets/images/logo.webp rename to veanu/lasa/assets/images/logo.webp diff --git a/vianu/lasa/files/fda_products_20250121.csv b/veanu/lasa/files/fda_products_20250121.csv similarity index 100% rename from vianu/lasa/files/fda_products_20250121.csv rename to veanu/lasa/files/fda_products_20250121.csv diff --git a/vianu/lasa/files/swissmedic_20241231.xlsx b/veanu/lasa/files/swissmedic_20241231.xlsx similarity index 100% rename from vianu/lasa/files/swissmedic_20241231.xlsx rename to veanu/lasa/files/swissmedic_20241231.xlsx diff --git a/vianu/lasa/launch_demo_app.py b/veanu/lasa/launch_demo_app.py similarity index 74% rename from vianu/lasa/launch_demo_app.py rename to veanu/lasa/launch_demo_app.py index 42fff34..c7458fc 100644 --- a/vianu/lasa/launch_demo_app.py +++ b/veanu/lasa/launch_demo_app.py @@ -1,9 +1,9 @@ import logging import os -from vianu import LOG_FMT -from vianu.lasa.settings import LOG_LEVEL, GRADIO_SERVER_PORT -from vianu.lasa.app import App +from veanu import LOG_FMT +from veanu.lasa.settings import LOG_LEVEL, GRADIO_SERVER_PORT +from veanu.lasa.app import App logging.basicConfig(level=LOG_LEVEL.upper(), format=LOG_FMT) os.environ["GRADIO_SERVER_PORT"] = str(GRADIO_SERVER_PORT) diff --git a/vianu/lasa/launch_demo_pipeline.py b/veanu/lasa/launch_demo_pipeline.py similarity index 91% rename from vianu/lasa/launch_demo_pipeline.py rename to veanu/lasa/launch_demo_pipeline.py index 4c5de79..0a6bf63 100644 --- a/vianu/lasa/launch_demo_pipeline.py +++ b/veanu/lasa/launch_demo_pipeline.py @@ -1,6 +1,6 @@ from argparse import Namespace -from vianu.lasa.__main__ import main +from veanu.lasa.__main__ import main _ARGS = { "search": "CABAZITAXEL", diff --git a/vianu/lasa/requirements.txt b/veanu/lasa/requirements.txt similarity index 100% rename from vianu/lasa/requirements.txt rename to veanu/lasa/requirements.txt diff --git a/vianu/lasa/settings.py b/veanu/lasa/settings.py similarity index 100% rename from vianu/lasa/settings.py rename to veanu/lasa/settings.py diff --git a/vianu/lasa/src/__init__.py b/veanu/lasa/src/__init__.py similarity index 100% rename from vianu/lasa/src/__init__.py rename to veanu/lasa/src/__init__.py diff --git a/vianu/lasa/src/base.py b/veanu/lasa/src/base.py similarity index 100% rename from vianu/lasa/src/base.py rename to veanu/lasa/src/base.py diff --git a/vianu/lasa/src/cli.py b/veanu/lasa/src/cli.py similarity index 93% rename from vianu/lasa/src/cli.py rename to veanu/lasa/src/cli.py index 1889a3a..8098f78 100644 --- a/vianu/lasa/src/cli.py +++ b/veanu/lasa/src/cli.py @@ -3,7 +3,7 @@ import argparse from typing import Sequence -from vianu.lasa.settings import LOG_LEVEL, SOURCES +from veanu.lasa.settings import LOG_LEVEL, SOURCES def parse_args(args_: Sequence) -> argparse.Namespace: diff --git a/vianu/lasa/src/units.py b/veanu/lasa/src/units.py similarity index 98% rename from vianu/lasa/src/units.py rename to veanu/lasa/src/units.py index 5c3c96a..76f0402 100644 --- a/vianu/lasa/src/units.py +++ b/veanu/lasa/src/units.py @@ -8,7 +8,7 @@ import pandas as pd -from vianu.lasa.settings import SMC_NON_DRUGS, SOURCES, SMC_FILENAME, FDA_FILENAME +from veanu.lasa.settings import SMC_NON_DRUGS, SOURCES, SMC_FILENAME, FDA_FILENAME logger = logging.getLogger(__name__) diff --git a/vianu/newsscraper/README.md b/veanu/newsscraper/README.md similarity index 100% rename from vianu/newsscraper/README.md rename to veanu/newsscraper/README.md diff --git a/vianu/newsscraper/envtemplate b/veanu/newsscraper/envtemplate similarity index 100% rename from vianu/newsscraper/envtemplate rename to veanu/newsscraper/envtemplate diff --git a/vianu/newsscraper/launch_demo_app.py b/veanu/newsscraper/launch_demo_app.py similarity index 98% rename from vianu/newsscraper/launch_demo_app.py rename to veanu/newsscraper/launch_demo_app.py index 475ea64..c895519 100644 --- a/vianu/newsscraper/launch_demo_app.py +++ b/veanu/newsscraper/launch_demo_app.py @@ -3,8 +3,8 @@ import os import gradio as gr import logging -from vianu.newsscraper.src.db_manager import DatabaseManager -from vianu.newsscraper.src.scrape import start_scraper +from veanu.newsscraper.src.db_manager import DatabaseManager +from veanu.newsscraper.src.scrape import start_scraper import plotly.graph_objects as go # Import Plotly for charting logging.basicConfig( diff --git a/vianu/newsscraper/src/db_manager.py b/veanu/newsscraper/src/db_manager.py similarity index 100% rename from vianu/newsscraper/src/db_manager.py rename to veanu/newsscraper/src/db_manager.py diff --git a/vianu/newsscraper/src/db_setup.py b/veanu/newsscraper/src/db_setup.py similarity index 100% rename from vianu/newsscraper/src/db_setup.py rename to veanu/newsscraper/src/db_setup.py diff --git a/vianu/newsscraper/src/entrypoint.sh b/veanu/newsscraper/src/entrypoint.sh similarity index 100% rename from vianu/newsscraper/src/entrypoint.sh rename to veanu/newsscraper/src/entrypoint.sh diff --git a/vianu/newsscraper/src/requirements.txt b/veanu/newsscraper/src/requirements.txt similarity index 100% rename from vianu/newsscraper/src/requirements.txt rename to veanu/newsscraper/src/requirements.txt diff --git a/vianu/newsscraper/src/run_scraper.py b/veanu/newsscraper/src/run_scraper.py similarity index 100% rename from vianu/newsscraper/src/run_scraper.py rename to veanu/newsscraper/src/run_scraper.py diff --git a/vianu/newsscraper/src/run_scraper.sh b/veanu/newsscraper/src/run_scraper.sh similarity index 100% rename from vianu/newsscraper/src/run_scraper.sh rename to veanu/newsscraper/src/run_scraper.sh diff --git a/vianu/newsscraper/src/scrape.py b/veanu/newsscraper/src/scrape.py similarity index 99% rename from vianu/newsscraper/src/scrape.py rename to veanu/newsscraper/src/scrape.py index 4b715f3..cdabe08 100644 --- a/vianu/newsscraper/src/scrape.py +++ b/veanu/newsscraper/src/scrape.py @@ -25,7 +25,7 @@ from pdfminer.layout import LAParams from pdfminer.pdfpage import PDFPage -from vianu.newsscraper.src.db_manager import DatabaseManager +from veanu.newsscraper.src.db_manager import DatabaseManager # Configure logging logging.basicConfig( diff --git a/vianu/newsscraper/src/scraper_cron b/veanu/newsscraper/src/scraper_cron similarity index 100% rename from vianu/newsscraper/src/scraper_cron rename to veanu/newsscraper/src/scraper_cron diff --git a/vianu/spock/__init__.py b/veanu/spock/__init__.py similarity index 100% rename from vianu/spock/__init__.py rename to veanu/spock/__init__.py diff --git a/vianu/spock/__main__.py b/veanu/spock/__main__.py similarity index 95% rename from vianu/spock/__main__.py rename to veanu/spock/__main__.py index e13adc0..72d7911 100644 --- a/vianu/spock/__main__.py +++ b/veanu/spock/__main__.py @@ -8,12 +8,12 @@ from dotenv import load_dotenv -from vianu import LOG_FMT -from vianu.spock.settings import SCRAPING_SOURCES, LOG_LEVEL, MODEL_TEST_QUESTION -from vianu.spock.src.cli import parse_args -from vianu.spock.src.base import Setup, Document, SpoCK, FileHandler -from vianu.spock.src import scraping as scp -from vianu.spock.src import ner +from veanu import LOG_FMT +from veanu.spock.settings import SCRAPING_SOURCES, LOG_LEVEL, MODEL_TEST_QUESTION +from veanu.spock.src.cli import parse_args +from veanu.spock.src.base import Setup, Document, SpoCK, FileHandler +from veanu.spock.src import scraping as scp +from veanu.spock.src import ner logging.basicConfig(format=LOG_FMT, level=LOG_LEVEL) logger = logging.getLogger(__name__) diff --git a/veanu/spock/app/__init__.py b/veanu/spock/app/__init__.py new file mode 100644 index 0000000..82003ee --- /dev/null +++ b/veanu/spock/app/__init__.py @@ -0,0 +1,3 @@ +from veanu.spock.app.app import App + +__all__ = ["App"] diff --git a/vianu/spock/app/app.py b/veanu/spock/app/app.py similarity index 98% rename from vianu/spock/app/app.py rename to veanu/spock/app/app.py index 708138c..41bb39a 100644 --- a/vianu/spock/app/app.py +++ b/veanu/spock/app/app.py @@ -9,24 +9,24 @@ from dotenv import load_dotenv import gradio as gr -from vianu.spock.settings import LOG_LEVEL, N_SCP_TASKS, N_NER_TASKS -from vianu.spock.settings import ( +from veanu.spock.settings import LOG_LEVEL, N_SCP_TASKS, N_NER_TASKS +from veanu.spock.settings import ( LARGE_LANGUAGE_MODELS, SCRAPING_SOURCES, MAX_DOCS_SRC, MODEL_TEST_QUESTION, ) -from vianu.spock.settings import ( +from veanu.spock.settings import ( GRADIO_APP_NAME, GRADIO_SERVER_PORT, GRADIO_MAX_JOBS, GRADIO_UPDATE_INTERVAL, ) -from vianu.spock.src.base import Setup, SpoCK, SpoCKList, QueueItem # noqa: F401 -from vianu import BaseApp -from vianu.spock.__main__ import get_model_config, setup_asyncio_framework -import vianu.spock.app.formatter as fmt -from vianu.spock.src.ner import NERFactory +from veanu.spock.src.base import Setup, SpoCK, SpoCKList, QueueItem # noqa: F401 +from veanu import BaseApp +from veanu.spock.__main__ import get_model_config, setup_asyncio_framework +import veanu.spock.app.formatter as fmt +from veanu.spock.src.ner import NERFactory logger = logging.getLogger(__name__) load_dotenv() @@ -752,7 +752,7 @@ def register_events(self): if __name__ == "__main__": - from vianu.spock.app import App + from veanu.spock.app import App app = App() demo = app.make() diff --git a/vianu/spock/app/formatter.py b/veanu/spock/app/formatter.py similarity index 96% rename from vianu/spock/app/formatter.py rename to veanu/spock/app/formatter.py index 092a253..f2c9744 100644 --- a/vianu/spock/app/formatter.py +++ b/veanu/spock/app/formatter.py @@ -1,8 +1,8 @@ import logging from typing import List -from vianu.spock.src.base import Document, SpoCK -from vianu.spock.settings import DATE_FORMAT +from veanu.spock.src.base import Document, SpoCK +from veanu.spock.settings import DATE_FORMAT logger = logging.getLogger(__name__) diff --git a/vianu/spock/assets/css/styles.css b/veanu/spock/assets/css/styles.css similarity index 100% rename from vianu/spock/assets/css/styles.css rename to veanu/spock/assets/css/styles.css diff --git a/vianu/spock/assets/head/scripts.html b/veanu/spock/assets/head/scripts.html similarity index 100% rename from vianu/spock/assets/head/scripts.html rename to veanu/spock/assets/head/scripts.html diff --git a/vianu/spock/assets/images/favicon.png b/veanu/spock/assets/images/favicon.png similarity index 100% rename from vianu/spock/assets/images/favicon.png rename to veanu/spock/assets/images/favicon.png diff --git a/vianu/spock/assets/images/spock_logo.png b/veanu/spock/assets/images/spock_logo.png similarity index 100% rename from vianu/spock/assets/images/spock_logo.png rename to veanu/spock/assets/images/spock_logo.png diff --git a/vianu/spock/assets/images/spock_logo_circular.png b/veanu/spock/assets/images/spock_logo_circular.png similarity index 100% rename from vianu/spock/assets/images/spock_logo_circular.png rename to veanu/spock/assets/images/spock_logo_circular.png diff --git a/vianu/spock/launch_demo_app.py b/veanu/spock/launch_demo_app.py similarity index 74% rename from vianu/spock/launch_demo_app.py rename to veanu/spock/launch_demo_app.py index 7fa911e..c9e177c 100644 --- a/vianu/spock/launch_demo_app.py +++ b/veanu/spock/launch_demo_app.py @@ -1,9 +1,9 @@ import logging import os -from vianu import LOG_FMT -from vianu.spock.settings import LOG_LEVEL, GRADIO_SERVER_PORT -from vianu.spock.app import App +from veanu import LOG_FMT +from veanu.spock.settings import LOG_LEVEL, GRADIO_SERVER_PORT +from veanu.spock.app import App logging.basicConfig(level=LOG_LEVEL.upper(), format=LOG_FMT) os.environ["GRADIO_SERVER_PORT"] = str(GRADIO_SERVER_PORT) diff --git a/vianu/spock/launch_demo_pipeline.py b/veanu/spock/launch_demo_pipeline.py similarity index 68% rename from vianu/spock/launch_demo_pipeline.py rename to veanu/spock/launch_demo_pipeline.py index 260e959..c425c2d 100644 --- a/vianu/spock/launch_demo_pipeline.py +++ b/veanu/spock/launch_demo_pipeline.py @@ -1,9 +1,9 @@ from argparse import Namespace import asyncio -from vianu.spock.__main__ import main -from vianu.spock.settings import SCRAPING_SOURCES, MAX_DOCS_SRC -from vianu.spock.settings import N_SCP_TASKS, N_NER_TASKS +from veanu.spock.__main__ import main +from veanu.spock.settings import SCRAPING_SOURCES, MAX_DOCS_SRC +from veanu.spock.settings import N_SCP_TASKS, N_NER_TASKS _ARGS = { diff --git a/vianu/spock/requirements.txt b/veanu/spock/requirements.txt similarity index 100% rename from vianu/spock/requirements.txt rename to veanu/spock/requirements.txt diff --git a/vianu/spock/settings.py b/veanu/spock/settings.py similarity index 100% rename from vianu/spock/settings.py rename to veanu/spock/settings.py diff --git a/vianu/spock/src/__init__.py b/veanu/spock/src/__init__.py similarity index 100% rename from vianu/spock/src/__init__.py rename to veanu/spock/src/__init__.py diff --git a/vianu/spock/src/base.py b/veanu/spock/src/base.py similarity index 100% rename from vianu/spock/src/base.py rename to veanu/spock/src/base.py diff --git a/vianu/spock/src/cli.py b/veanu/spock/src/cli.py similarity index 90% rename from vianu/spock/src/cli.py rename to veanu/spock/src/cli.py index 7b759a2..64cb9b8 100644 --- a/vianu/spock/src/cli.py +++ b/veanu/spock/src/cli.py @@ -3,9 +3,9 @@ import argparse from typing import Sequence -from vianu.spock.settings import LOG_LEVEL, FILE_NAME, FILE_PATH, MAX_DOCS_SRC -from vianu.spock.settings import SCRAPING_SOURCES, N_SCP_TASKS -from vianu.spock.settings import N_NER_TASKS, LARGE_LANGUAGE_MODELS +from veanu.spock.settings import LOG_LEVEL, FILE_NAME, FILE_PATH, MAX_DOCS_SRC +from veanu.spock.settings import SCRAPING_SOURCES, N_SCP_TASKS +from veanu.spock.settings import N_NER_TASKS, LARGE_LANGUAGE_MODELS def parse_args(args_: Sequence) -> argparse.Namespace: diff --git a/vianu/spock/src/ner.py b/veanu/spock/src/ner.py similarity index 99% rename from vianu/spock/src/ner.py rename to veanu/spock/src/ner.py index 11306cc..86bb709 100644 --- a/vianu/spock/src/ner.py +++ b/veanu/spock/src/ner.py @@ -9,8 +9,8 @@ from openai import AsyncOpenAI -from vianu.spock.src.base import NamedEntity, QueueItem # noqa: F401 -from vianu.spock.settings import ( +from veanu.spock.src.base import NamedEntity, QueueItem # noqa: F401 +from veanu.spock.settings import ( N_CHAR_DOC_ID, LLAMA_MODEL, OPENAI_MODEL, diff --git a/vianu/spock/src/scraping.py b/veanu/spock/src/scraping.py similarity index 99% rename from vianu/spock/src/scraping.py rename to veanu/spock/src/scraping.py index f543890..076f3b3 100644 --- a/vianu/spock/src/scraping.py +++ b/veanu/spock/src/scraping.py @@ -25,9 +25,9 @@ import numpy as np import pymupdf -from vianu.spock.src.base import Document, QueueItem # noqa: F401 -from vianu.spock.settings import MAX_CHUNK_SIZE, SCRAPING_SOURCES -from vianu.spock.settings import ( +from veanu.spock.src.base import Document, QueueItem # noqa: F401 +from veanu.spock.settings import MAX_CHUNK_SIZE, SCRAPING_SOURCES +from veanu.spock.settings import ( PUBMED_ESEARCH_URL, PUBMED_DB, PUBMED_EFETCH_URL, diff --git a/vianu/lasa/app/__init__.py b/vianu/lasa/app/__init__.py deleted file mode 100644 index 899a23c..0000000 --- a/vianu/lasa/app/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from vianu.lasa.app.app import App - -__all__ = ["App"] diff --git a/vianu/spock/app/__init__.py b/vianu/spock/app/__init__.py deleted file mode 100644 index 235b6bf..0000000 --- a/vianu/spock/app/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from vianu.spock.app.app import App - -__all__ = ["App"]