Repo initial setup.

ogkdmr · Feb 26, 2024 · f8d353e · f8d353e
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diff --git a/.github/ISSUE_TEMPLATE/01_bug.yml b/.github/ISSUE_TEMPLATE/01_bug.yml
@@ -2,28 +2,28 @@ name: Bug Report
 description: Report errors or unexpected results.
 labels: ["bug"]
 assignees:
-  - foobar-bug-assign-dev
+  - ragamp-bug-assign-dev
 body:
   - type: textarea
     id: install
     attributes:
-      label: How did you install foobar?
+      label: How did you install RagAmp?
       description: >
         E.g., install via pip, install from source, etc. **Note:** this will
         be rendered as console text automatically.
       placeholder: |
-        $ pip install foobar
-        Collecting foobar
+        $ pip install ragamp
+        Collecting ragamp
         ...
-        Successfully installed foobar...
+        Successfully installed ragamp...
       render: console
     validations:
       required: true
 
   - type: input
     id: version
     attributes:
-      label: What version of foobar are you using?
+      label: What version of ragamp are you using?
       description: >
         Package version if installed via Pip or commit ID if installed
         from source.

diff --git a/.github/ISSUE_TEMPLATE/02_enhancement.yml b/.github/ISSUE_TEMPLATE/02_enhancement.yml
@@ -2,7 +2,7 @@ name: Enhancement Request
 description: Request a new feature or enhancement.
 labels: ["enhancement"]
 assignees:
-  - foobar-enh-assign-dev
+  - ragamp-enh-assign-dev
 body:
   - type: textarea
     id: request

diff --git a/.github/ISSUE_TEMPLATE/03_docs.yml b/.github/ISSUE_TEMPLATE/03_docs.yml
@@ -2,7 +2,7 @@ name: Documentation Improvements
 description: Suggest improvements to the documentation.
 labels: ["documentation"]
 assignees:
-  - foobar-doc-assignee-dev
+  - ragamp-doc-assignee-dev
 body:
   - type: textarea
     id: freeform

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,10 +1,10 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
 authors:
-  - family-names: Pauloski
-    given-names: Greg
-    orcid: https://orcid.org/0000-0002-6547-6902
+  - family-names: Gokdemir
+    given-names: Ozan
+    orcid: https://orcid.org/0000-0001-5299-1983
 license: MIT
-repository-code: https://github.com/foobar-author/foobar
-title: FooBar
-url: https://foobar.dev
+repository-code: https://github.com/ogkdmr/ragamp
+title: RagAmp
+url: https://ogkdmr.github.io/ragamp/
diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2023-Present FooBar Author
+Copyright (c) 2023-Present Ozan Gokdemir
 
 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
@@ -1,67 +1,8 @@
-# Python Package Template Repo
+# RagAmp: Retrieval Augmented Generation for Antimicrobial Peptide Generation
 
-[![docs](https://github.com/gpauloski/python-template/actions/workflows/docs.yml/badge.svg)](https://github.com/gpauloski/python-template/actions)
-[![tests](https://github.com/gpauloski/python-template/actions/workflows/tests.yml/badge.svg)](https://github.com/gpauloski/python-template/actions)
-[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/gpauloski/python-template/main.svg)](https://results.pre-commit.ci/latest/github/gpauloski/python-template/main)
-
-Python package template repo that provides:
-- Package, examples, and testing layout.
-- GitHub PR and Issue templates.
-- Example docs with MKDocs and GitHub Pages.
-- CI framework with `pre-commit` and `tox`.
-- GitHub actions for running tests and publishing packages.
-
-This package setup was based on [Anthony Sottile's project setup](https://www.youtube.com/watch?v=q8DkatMZvUs&list=PLWBKAf81pmOaP9naRiNAqug6EBnkPakvY) but deviates in some places (e.g., `pyproject.toml` and `ruff`).
-
-## Setup Instructions
-
-1. Click the "Use this template" button at the top right of this page.
-2. Delete and directories you will not be using (commonly `docs/` if you do not want to use MKDocs or `examples/` if you will not have example code).
-3. Follow the instructions to create the new repo then clone your repo locally.
-4. The template uses "foobar" to indicate things that need to be changed.
-   Start by searching for all instances (`git grep foobar`) and changing them accordingly.
-5. Configure pre-commit:
-    - Go to [https://pre-commit.ci/](https://pre-commit.ci/) and enable pre-commit on your repo.
-    - Update the pre-commit badge URL in this README with your new badge URL.
-6. Configure GitHub pages:
-    - Go to the "Pages" section of your repository settings.
-    - Select "Deploy from a branch" and use the "gh-pages" branch.
-7. Configure PyPI releases (if relevant):
-    - Create a new API token for [https://pypi.org/](https://pypi.org/).
-    - Add the token as a GitHub actions secret (see the instructions [here](https://github.com/pypa/gh-action-pypi-publish)).
-8. Delete this boilerplate stuff in the README.
-9. Commit and push changes.
-
-### GitHub Configuration
-
-I recommend making a few other changes to the repo's setting on GitHub.
-- In "General"
-  - Select/deselect features you need/don't need.
-  - Select "Automatically delete head branches
-- In "Branches": enable branch protection on `main`.
-  - Check "Require a pull request before merging"
-  - Check "Require status checks to pass before merging"
-    - Check "Require branches to be up to date before merging"
-    - Set required checks (e.g., pre-commit.ci, tests, etc.)
-  - Check "Do not allow bypassing the above settings"
-
-## Installation
-
-Install via pip:
-```
-$ pip install foobar
-```
-
-For local development:
-```
-$ tox --devenv venv -e py310
-$ pre-commit install
-```
-or
-```
-$ pip install -e .
-```
-
-## Additional README Sections
+[![docs](https://github.com/ogkdmr/ragamp/actions/workflows/docs.yml/badge.svg)](https://github.com/ogkdmr/ragamp/actions)
+[![tests](https://github.com/ogkdmr/ragamp/actions/workflows/tests.yml/badge.svg)](https://github.com/ogkdmr/ragamp/actions)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ogkdmr/ragamp/main.svg)](https://results.pre-commit.ci/latest/github/ogkdmr/ragamp/main)
 
+Documentation to follow
 ...
diff --git a/docs/_templates/python/material/module.html b/docs/_templates/python/material/module.html
@@ -48,7 +48,7 @@
   {% endif %}
 
   <p>
-      Source file: <a target="_blank" href="https://github.com/foobar-author/foobar/blob/main/{{ module.relative_package_filepath }}">{{ module.relative_package_filepath }}</a>
+      Source file: <a target="_blank" href="https://github.com/ogkdmr/ragamp/blob/main/{{ module.relative_package_filepath }}">{{ module.relative_package_filepath }}</a>
   </p>
 
   <div class="doc doc-contents {% if root %}first{% endif %}">

diff --git a/docs/contributing/index.md b/docs/contributing/index.md
@@ -3,11 +3,11 @@
 We recommend using [Tox](https://tox.wiki/en/latest/index.html){target=_blank}
 to setup the development environment. This will create a new virtual
 environment with all of the required packages installed
-and FooBar installed in editable mode with the necessary extras options.
+and RagAmp installed in editable mode with the necessary extras options.
 
 ```bash
-$ git clone https://github.com/foobar-author/foobar
-$ cd foobar
+$ git clone https://github.com/ogkdmr/ragamp.git
+$ cd ragamp
 $ tox --devenv venv -e py310
 $ . venv/bin/activate
 ```
@@ -21,16 +21,16 @@ $ . venv/bin/activate
 
 To install manually:
 ```bash
-$ git clone https://github.com/foobar-author/foobar
-$ cd foobar
+$ git clone https://github.com/ogkdmr/ragamp.git
+$ cd ragamp
 $ python -m venv venv
 $ . venv/bin/activate
 $ pip install -e .[dev,docs]
 ```
 
 ## Continuous Integration
 
-FooBar uses [pre-commit](https://pre-commit.com/){target=_blank} and
+RagAmp uses [pre-commit](https://pre-commit.com/){target=_blank} and
 [Tox](https://tox.wiki/en/latest/index.html){target=_blank} for continuous integration
 (test, linting, etc.).
 
@@ -49,8 +49,8 @@ The entire CI workflow can be run with `#!bash $ tox`.
 This will test against multiple versions of Python and can be slow.
 
 Module-level unit-test are located in the `tests/` directory and its
-structure is intended to match that of `foobar/`.
-E.g. the tests for `foobar/x/y.py` are located in
+structure is intended to match that of `ragamp/`.
+E.g. the tests for `ragamp/x/y.py` are located in
 `tests/x/y_test.py`; however, additional test files can be added
 as needed. Tests should be narrowly focused and target a single aspect of the
 code's functionality, tests should not test internal implementation details of

diff --git a/docs/contributing/issues-pull-requests.md b/docs/contributing/issues-pull-requests.md
@@ -1,6 +1,6 @@
 ## Issues
 
-[Issue Tracker](https://github.com/foobar-author/foobar/issues){target=_blank}
+[Issue Tracker](https://github.com/ogkdmr/ragamp/issues){target=_blank}
 
 We use GitHub issues to report problems, request and track changes, and discuss
 future ideas.

diff --git a/docs/contributing/releases.md b/docs/contributing/releases.md
@@ -1,7 +1,7 @@
 ## Release Timeline
 
 Releases are created on an as-needed basis.
-Milestones are the [Issue Tracker](https://github.com/foobar-author/foobar/issues){target=_blank} are used to track features to be included in upcoming releases.
+Milestones are the [Issue Tracker](https://github.com/ogkdmr/ragamp/issues){target=_blank} are used to track features to be included in upcoming releases.
 
 ## Creating Releases
 
@@ -15,13 +15,13 @@ Milestones are the [Issue Tracker](https://github.com/foobar-author/foobar/issue
 4. Tag the release commit and push (typically this is the commit updating the
    version numbers).
    ```bash
-   $ git tag -s v{VERSION} -m "FooBar v{VERSION}"
+   $ git tag -s v{VERSION} -m "RagAmp v{VERSION}"
    $ git push origin v{VERSION}
    ```
    Note the version number is prepended by "v" for the tags so we can
    distinguish release tags from non-release tags.
 5. Create a new release on GitHub using the tag. The title should be
-   `FooBar v{VERSION}`.
+   `RagAmp v{VERSION}`.
 6. **Official release:**
     1. Use the "Generate release notes" option and set the previous tag as the previous official release tag. E.g., for `v0.4.1`, the previous release tag should be `v0.4.0` and NOT `v0.4.1a1`.
     2. Add an "Upgrade Steps" section at the top (see previous releases for examples).

diff --git a/docs/examples.md b/docs/examples.md
diff --git a/docs/generate_api.py b/docs/generate_api.py
@@ -7,7 +7,7 @@
 
 nav = mkdocs_gen_files.Nav()
 
-PACKAGE_DIR = 'foobar/'
+PACKAGE_DIR = 'ragamp/'
 
 for path in sorted(Path(PACKAGE_DIR).rglob('**/*.py')):
     module_path = path.with_suffix('')

diff --git a/docs/get-started.md b/docs/get-started.md
@@ -1,19 +1,23 @@
 # Quick Start
 
-foobar brief description.
+RagAmp is a retrieval-augmented generation application for antimicrobial peptides.
 
 ## Overview
 
-foobar detailed overview.
+The tool is designed to encode unstructured text data (e.g., academic papers) about
+antimicrobial peptides and build vectorstores with their embeddings. It then uses
+this vectorstore to retrieve relevant documents to answer user queries. The queries
+can be arbitrary, but in our particular use case, they are engineered to investigate
+whether the model can propose novel hypotheses for AMP-microbe interactions such
+as suggesting novel potential targets that an AMP can be operating on based on its
+existing known targets.
 
 ## Installation
 
-```bash
-$ pip install foobar
-```
+TODO: TBD
 
 Documentation on installing for local development is provided in [Contributing](contributing/index.md).
 
 ## Usage
 
-foobar usage example.
+TODO: TBD
diff --git a/docs/installation.md b/docs/installation.md
diff --git a/docs/known-issues.md b/docs/known-issues.md
diff --git a/examples/README.md b/examples/README.md
@@ -1 +1 @@
-# foobar Examples
+# RagAmp Examples
diff --git a/examples/example.py b/examples/example.py
diff --git a/foobar/foo.py b/foobar/foo.py