Fix covid-19 drdfm references in project (resolves #93)

.pre-commit-config.yaml

@@ -11,4 +11,4 @@ repos:
     rev: "22.8.0"
     hooks:
       - id: black
-        exclude: ^covid19-drDFM
+        exclude: ^DFMDash

CONTRIBUTING.rst

@@ -13,7 +13,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/jvivian/covid19-drDFM/issues
+Report bugs at https://github.com/jvivian/DFMDash/issues
 
 If you are reporting a bug, please include:
 
@@ -44,7 +44,7 @@ Submit Feedback
 ~~~~~~~~~~~~~~~
 
 The best way to send feedback is to file an issue at
-https://github.com/jvivian/covid19-drDFM/issues.
+https://github.com/jvivian/DFMDash/issues.
 
 If you are proposing a new feature:
 
@@ -56,25 +56,25 @@ If you are proposing a new feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `covid19-drDFM` for local
+Ready to contribute? Here's how to set up `DFMDash` for local
 development. Please note this documentation assumes you already have
 `poetry` and `Git` installed and ready to go.
 
-| 1. Fork the `covid19-drDFM` repo on GitHub.
+| 1. Fork the `DFMDash` repo on GitHub.
 
 | 2. Clone your fork locally:
 
    .. code-block:: bash
 
         cd <directory_in_which_repo_should_be_created>
-        git clone [email protected]:YOUR_NAME/covid19-drDFM.git
+        git clone [email protected]:YOUR_NAME/DFMDash.git
 
 
 | 3. Now we need to install the environment. Navigate into the directory
 
    .. code-block:: bash
 
-       cd covid19-drDFM
+       cd DFMDash
 
    If you are using ``pyenv``, select a version to use locally. (See installed versions with ``pyenv versions``)
 

README.html

@@ -79,13 +79,13 @@
 
 
 
-<section id="covid19-drdfm" class="level1">
-<h1>covid19-drDFM</h1>
-<p><a href="https://img.shields.io/github/v/release/jvivian/covid19-drDFM"><img src="https://img.shields.io/github/v/release/jvivian/covid19-drDFM.png" class="img-fluid" alt="Release"></a> <a href="https://github.com/jvivian/covid19-drDFM/actions/workflows/main.yml?query=branch%3Amain"><img src="https://img.shields.io/github/actions/workflow/status/jvivian/covid19-drDFM/main.yml?branch=main" class="img-fluid" alt="Build status"></a> <a href="https://codecov.io/gh/jvivian/covid19-drDFM"><img src="https://codecov.io/gh/jvivian/covid19-drDFM/branch/main/graph/badge.svg" class="img-fluid" alt="codecov"></a> <a href="https://img.shields.io/github/commit-activity/m/jvivian/covid19-drDFM"><img src="https://img.shields.io/github/commit-activity/m/jvivian/covid19-drDFM.png" class="img-fluid" alt="Commit activity"></a> <a href="https://img.shields.io/github/license/jvivian/covid19-drDFM"><img src="https://img.shields.io/github/license/jvivian/covid19-drDFM.png" class="img-fluid" alt="License"></a></p>
+<section id="DFMDash" class="level1">
+<h1>DFMDash</h1>
+<p><a href="https://img.shields.io/github/v/release/jvivian/DFMDash"><img src="https://img.shields.io/github/v/release/jvivian/DFMDash.png" class="img-fluid" alt="Release"></a> <a href="https://github.com/jvivian/DFMDash/actions/workflows/main.yml?query=branch%3Amain"><img src="https://img.shields.io/github/actions/workflow/status/jvivian/DFMDash/main.yml?branch=main" class="img-fluid" alt="Build status"></a> <a href="https://codecov.io/gh/jvivian/DFMDash"><img src="https://codecov.io/gh/jvivian/DFMDash/branch/main/graph/badge.svg" class="img-fluid" alt="codecov"></a> <a href="https://img.shields.io/github/commit-activity/m/jvivian/DFMDash"><img src="https://img.shields.io/github/commit-activity/m/jvivian/DFMDash.png" class="img-fluid" alt="Commit activity"></a> <a href="https://img.shields.io/github/license/jvivian/DFMDash"><img src="https://img.shields.io/github/license/jvivian/DFMDash.png" class="img-fluid" alt="License"></a></p>
 <p>Repository for Covid-19 Dynamic Factor Model</p>
 <ul>
-<li><strong>Github repository</strong>: <a href="https://github.com/jvivian/covid19-drDFM/" class="uri">https://github.com/jvivian/covid19-drDFM/</a></li>
-<li><strong>Documentation</strong> <a href="https://jvivian.github.io/covid19-drDFM/" class="uri">https://jvivian.github.io/covid19-drDFM/</a></li>
+<li><strong>Github repository</strong>: <a href="https://github.com/jvivian/DFMDash/" class="uri">https://github.com/jvivian/DFMDash/</a></li>
+<li><strong>Documentation</strong> <a href="https://jvivian.github.io/DFMDash/" class="uri">https://jvivian.github.io/DFMDash/</a></li>
 </ul>
 </section>
 <section id="quickstart" class="level1">

README.md

@@ -1,15 +1,15 @@
-# covid19-drDFM
+# DFMDash
 
-[![Release](https://img.shields.io/github/v/release/jvivian/covid19-drDFM)](https://img.shields.io/github/v/release/jvivian/covid19-drDFM)
-[![Build status](https://img.shields.io/github/actions/workflow/status/jvivian/covid19-drDFM/main.yml?branch=main)](https://github.com/jvivian/covid19-drDFM/actions/workflows/main.yml?query=branch%3Amain)
-[![codecov](https://codecov.io/gh/jvivian/covid19-drDFM/graph/badge.svg?token=RVT01PK8TT)](https://codecov.io/gh/jvivian/covid19-drDFM)
-[![Commit activity](https://img.shields.io/github/commit-activity/m/jvivian/covid19-drDFM)](https://img.shields.io/github/commit-activity/m/jvivian/covid19-drDFM)
-[![License](https://img.shields.io/github/license/jvivian/covid19-drDFM)](https://img.shields.io/github/license/jvivian/covid19-drDFM)
+[![Release](https://img.shields.io/github/v/release/jvivian/DFMDash)](https://img.shields.io/github/v/release/jvivian/DFMDash)
+[![Build status](https://img.shields.io/github/actions/workflow/status/jvivian/DFMDash/main.yml?branch=main)](https://github.com/jvivian/DFMDash/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/jvivian/DFMDash/graph/badge.svg?token=RVT01PK8TT)](https://codecov.io/gh/jvivian/DFMDash)
+[![Commit activity](https://img.shields.io/github/commit-activity/m/jvivian/DFMDash)](https://img.shields.io/github/commit-activity/m/jvivian/DFMDash)
+[![License](https://img.shields.io/github/license/jvivian/DFMDash)](https://img.shields.io/github/license/jvivian/DFMDash)
 
 Repository for Covid-19 Dynamic Factor Model
 
-- **Github repository**: <https://github.com/jvivian/covid19-drDFM/>
-- **Documentation** <https://jvivian.github.io/covid19-drDFM/>
+- **Github repository**: <https://github.com/jvivian/DFMDash/>
+- **Documentation** <https://jvivian.github.io/DFMDash/>
 
 # Quickstart
 > Tested on Ubuntu, Windows WSL2: Ubuntu, and Mac OSX (M1)
@@ -18,8 +18,8 @@ Repository for Covid-19 Dynamic Factor Model
 - Download and install [Anaconda]() to your PATH and run:
 
 ```bash
-git clone https://github.com/jvivian/covid19-drDFM/ # Get source code
-cd covid19-drDFM
+git clone https://github.com/jvivian/DFMDash/ # Get source code
+cd DFMDash
 conda env update -f environment.yml  # Create python env for project
 conda activate py3.10  # Activate env
 poetry install  # Install dependencies and package
@@ -33,8 +33,8 @@ c19dfm --help  # Run tool's help message
 or to build locally
 
 ```bash
-git clone https://github.com/jvivian/covid19-drDFM/ # Get source code
-cd covid19-drDFM
+git clone https://github.com/jvivian/DFMDash/ # Get source code
+cd DFMDash
 docker build -t covid19-dfm .
 docker run covid19-dfm
 ```

dfmdash/io.py

@@ -10,7 +10,7 @@
 @dataclass
 class DataLoader:
     """
-    A class for loading and manipulating data for the covid19-drDFM project.
+    A class for loading and manipulating data for the DFMDash project.
 
     Attributes:
         ad (Optional[AnnData]): An optional AnnData object representing the loaded data.

docs/index.md

@@ -1,8 +1,8 @@
-# covid19-drDFM
+# DFMDash
 
-[![Release](https://img.shields.io/github/v/release/jvivian/covid19-drDFM)](https://img.shields.io/github/v/release/jvivian/covid19-drDFM)
-[![Build status](https://img.shields.io/github/actions/workflow/status/jvivian/covid19-drDFM/main.yml?branch=main)](https://github.com/jvivian/covid19-drDFM/actions/workflows/main.yml?query=branch%3Amain)
-[![Commit activity](https://img.shields.io/github/commit-activity/m/jvivian/covid19-drDFM)](https://img.shields.io/github/commit-activity/m/jvivian/covid19-drDFM)
-[![License](https://img.shields.io/github/license/jvivian/covid19-drDFM)](https://img.shields.io/github/license/jvivian/covid19-drDFM)
+[![Release](https://img.shields.io/github/v/release/jvivian/DFMDash)](https://img.shields.io/github/v/release/jvivian/DFMDash)
+[![Build status](https://img.shields.io/github/actions/workflow/status/jvivian/DFMDash/main.yml?branch=main)](https://github.com/jvivian/DFMDash/actions/workflows/main.yml?query=branch%3Amain)
+[![Commit activity](https://img.shields.io/github/commit-activity/m/jvivian/DFMDash)](https://img.shields.io/github/commit-activity/m/jvivian/DFMDash)
+[![License](https://img.shields.io/github/license/jvivian/DFMDash)](https://img.shields.io/github/license/jvivian/DFMDash)
 
 Repository for Covid-19 Dynamic Factor Model

mkdocs.yml

@@ -1,10 +1,10 @@
-site_name: covid19-drDFM
-repo_url: https://github.com/jvivian/covid19-drDFM
-site_url: https://jvivian.github.io/covid19-drDFM
+site_name: DFMDash
+repo_url: https://github.com/jvivian/DFMDash
+site_url: https://jvivian.github.io/DFMDash
 site_description: Repository for Covid-19 Dynamic Factor Model
 site_author: J. Vivian, A. Cooke, J. Fitz
 edit_uri: edit/main/docs/
-repo_name: jvivian/covid19-drDFM
+repo_name: jvivian/DFMDash
 copyright: Maintained by <a href="https://jvivian.github.io/">jvivian</a>.
 
 nav:
@@ -48,9 +48,9 @@ theme:
 extra:
   social:
     - icon: fontawesome/brands/github
-      link: https://github.com/jvivian/covid19-drDFM
+      link: https://github.com/jvivian/DFMDash
     - icon: fontawesome/brands/python
-      link: https://pypi.org/project/covid19-drDFM
+      link: https://pypi.org/project/DFMDash
 
 markdown_extensions:
   - toc:

pyproject.toml

@@ -3,8 +3,8 @@ name = "dfmdash"
 version = "0.0.1"
 description = "Repository for Covid-19 Dynamic Factor Model"
 authors = ["J. Vivian, A. Cooke, J. Fitz <[email protected]>"]
-repository = "https://github.com/jvivian/covid19-drDFM"
-documentation = "https://jvivian.github.io/covid19-drDFM/"
+repository = "https://github.com/jvivian/DFMDash"
+documentation = "https://jvivian.github.io/DFMDash/"
 readme = "README.md"
 packages = [
   {include = "dfmdash"}