Main clone

.github/workflows/test.yml

@@ -1,9 +1,9 @@
-name: Python package
+name: Run Tests
 
 on:
   push:
     branches:
-      - main
+      - '*'
   pull_request:
     branches:
       - main
@@ -13,23 +13,24 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Check out the code
+      # Checkout the repository
+      - name: Check out repository
         uses: actions/checkout@v3
 
-      - name: Set up Python
+      # Set up Python version
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: '3.9'  # You can change this to your desired Python version
-
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          python-version: "3.12"
 
+      # Install dependencies using requirements.txt
       - name: Install dependencies
         run: |
-          poetry install
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
 
-      - name: Run tests
+      # Run tests
+      - name: Run tests with pytest
         run: |
-          poetry run pytest  # Adjust this command based on your test framework
+          export PYTHONPATH=$(pwd)
+          pytest test/

.gitignore

@@ -8,5 +8,5 @@ htmlcov/
 env.yaml
 requirements.txt
 dist/
-.DS_Store
-walkthroughs/workflow-Copy1.ipynb
+*.DS_Store
+myvenv/

CONTRIBUTING.md

@@ -19,12 +19,15 @@ All types of contributions are encouraged and valued. See the [Table of Contents
 - [I Want To Contribute](#i-want-to-contribute)
   - [Reporting Bugs](#reporting-bugs)
   - [Suggesting Enhancements](#suggesting-enhancements)
-  - [Your First Code Contribution](#your-first-code-contribution)
-  - [Improving The Documentation](#improving-the-documentation)
-- [Styleguides](#styleguides)
+- [Styleguides](#style-guides)
+  - [Documentation](#documentation)
+  - [Dev Environments](#dev-environments)
+- [Code Quality](#code-quality)
+  - [Formatting](#formatting)
+  - [Linting](#linting)
+  - [Documentation Style Guide](#documentation-style-guide)
   - [Commit Messages](#commit-messages)
-- [Join The Project Team](#join-the-project-team)
-
+- [Attribution](#attribution)
 
 ## Code of Conduct
 
@@ -132,7 +135,102 @@ Enhancement suggestions are tracked as [GitHub issues](https://github.com/fanzha
 - **Explain why this enhancement would be useful** to most pyCellPhenoX users. You may also want to point out the other projects that solved it better and which could serve as inspiration.
 
 <!-- You might want to create an issue template for enhancement suggestions that can be used as a guide and that defines the structure of the information to be included. If you do so, reference it here in the description. -->
+## Your first code contribution
+
+We welcome contributions! Follow these steps to contribute:
+
+### 1. Fork, Clone, and Branch
+- Fork the repository and clone it to your local machine.
+
+```bash
+git clone https://github.com/fanzhanglab/pyCellPhenoX.git
+cd pyCellPhenoX
+```
+
+Please branch from the `main` branch given we have set up branch protections.
+``` bash 
+git checkout -b your-branch-name
+```
+
+### 2. Make Your Changes
+- Make sure your code follows the project standards.
+- Format your Python code with Black:
+
+``` bash
+black your_file.py
+```
+
+### 3. Commit and Push
+Commit your changes with a meaningful message:
+
+```bash
+git commit -m "Description of your changes"
+```
+
+Push your changes:
+
+``` bash
+git push origin your-branch-name
+```
+### 4. Submit a Pull Request
+Submit a pull request and explain the changes you've made. 
+
+
+## Style Guides 
+
+### Documentation
+
+We use [sphinx](https://www.sphinx-doc.org/en/master/index.html) for autodocumentation of docstrings, using the [napoleon extenstion](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html) to parse [NumPy style docstrings](https://numpydoc.readthedocs.io/en/latest/format.html), implemented with a [furo](https://pradyunsg.me/furo/) theme.
+We host our documentation on [readthedocs.org](https://readthedocs.org/) at [https://pyCellPhenoX.readthedocs.io/en/](https://pyCellPhenoX.readthedocs.io/en/).
+
+To build and test changes to the docs locally, run the following command:
+
+```bash
+sphinx-build -b html docs build
+```
+
+See [`docs/conf.py`](../conf.py) for full documentation configuration. 
+
+### Dev environments
+
+#### Local devcontainer
+
+Instructions for setting up a local development environment using VSCode DevContainers:
+
+1. Install [VSCode](https://code.visualstudio.com/download)
+2. Install the [Remote - Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) extension
+3. Open the repository in VSCode
+4. Click on the green "Reopen in Container" button in the lower left corner of the window
+5. Wait for the container to build and install the required dependencies
+
+## Code Quality
+
+Please follow the below quality guides to the best of your abilities.
+If you have configured your [dev environment](#dev-environments) as described above, the formatting and linting rules will also be enforced automatically using the installed [pre-commit](https://pre-commit.com/) hooks.
+
+### Formatting
+
+We use [black](https://black.readthedocs.io/en/stable/) for formatting Python code, and [prettier](https://prettier.io/) for formatting markdown, json and yaml files.
+We include `black` in the poetry dev dependencies so it can be run manually using `black format`
+Prettier (which is not python-based) is not included in the poetry dev dependencies, but can be installed and run manually.
+Alternately, both `black format` and `prettier` will be run automatically at commit time with the pre-commit hooks installed.
+
+### Linting
+
+For python code linting, we also use [black](https://black.readthedocs.io/en/stable/), which can perform same linting checks as Flake8.
+You can use the command `black --check your_file.py` or `black path/to/your/directory` to check for linting errors.
+We also include some commented-out rules in that section that we are working towards enabling in the future.
+All linting checks will also be run automatically at commit time with the pre-commit hooks as described above.
+
+### Documentation style guide
+
+We use the [numpy documentation style guide](https://numpydoc.readthedocs.io/en/latest/format.html).
+When writing markdown documentation, please also ensure that each sentence is on a new line.
+
+### Commit messages
 
+pyCellPhenoX uses [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/) standard for commit messages to aid in automatic changelog generation.
+We prepare commit messages that follow this standard using [commitizen](https://commitizen-tools.github.io/commitizen/), which comes with the poetry dev dependencies.
 
 ## Attribution
 This guide is based on the **contributing-gen**. [Make your own](https://github.com/bttger/contributing-gen)!

Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

README.md

@@ -1,3 +1,4 @@
+# pyCellPhenoX
 
 <p>
    <img height="270" align="centre" src="https://github.com/fanzhanglab/pyCellPhenoX/blob/main/logo/cellphenoX_logo_banner.png">
@@ -38,7 +39,7 @@ conda install -c conda-forge pyCellPhenoX
 git clone [email protected]:fanzhanglab/pyCellPhenoX.git
 ```
 
-### Dependencies/ Requirements
+### Dependencies / Requirements
 When using pyCellPhenoX please ensure you are using the following dependency versions or requirements
 ``` python 
 python = "^3.9"
@@ -51,60 +52,6 @@ scikit-learn = "^1.5.2"
 matplotlib = "^3.9.2"
 statsmodels = "^0.14.3"
 ```
-To check if you have the right depenencies please run the following:
-#### Check Python Version
-``` bash
-python --version
-```
-
-#### Check individual package versions
-``` bash 
-pip show {package} | grep Version
-```
-> Replace {package} with the name of the package you want to check (e.g., pandas, numpy, etc.). This will display the installed version of the package.
-
-### Virtual Environment
-
-If any of the versions are not compatible with your working environment, please set up a virtual environment using one of the following methods: **conda/mamba**, **pip**, or **poetry**.
-
-#### Conda and Mamba
-
-To create a virtual environment using **conda** or **mamba**, follow these steps:
-
-1. **Create the environment:**
-   ```bash
-   conda create --name {name_the_environment} 
-    ```
-2. **Activate the environment:**
-   ```bash
-   conda activate {name_the_environment} 
-    ```
-3. **Install the requirements.txt:**
-   ```bash
-   conda install -f requirements.txt
-    ```
-
-#### PIP
-To create a virtual environment using **PIP** follow these steps:
-
-1. **Create the environment:**
-   ```bash
-   python -m venv {name_the_environment} 
-    ```
-2. **Activate the environment:**
-- on Windows
-   ```bash
-   {name_the_environment}\Scripts\activate
-    ```
-- on macOS
-   ```bash
-   source {name_the_environment}\bin\activate
-    ```
-3. **Install the requirements.txt:**
-   ```bash
-   pip install -r requirements.txt
-    ```
-
 
 ## Tutorials
 Please see the [Command-line Reference] for details. Additonally, please see [Walkthroughs] on the documentation page. 
@@ -125,16 +72,16 @@ Additional major functions associated with pyCellPhenoX are:
 Each function has uniqure arguments, see our [documentation] for more information
 
 ## Usage
-- TODO
+For more information please see [Walkthrough](walkthroughs/workflow.ipynb) or [Workflow Documentation]
 
 ## License
 Distributed under the terms of the [MIT license][license],
 _pyCellPhenoX_ is free and open source software.
 
-## Code of Conduct
+### Code of Conduct
 For more information please see [Code of Conduct](CODE_OF_CONDUCT.md) or [Code of Conduct Documentation]
 
-## Contributing
+### Contributing
 For more information please see [Contributing](CONTRIBUTING.md) or [Contributing Documentation]
 
 ## Issues
@@ -167,8 +114,8 @@ or
 ```
 
 ## Contact
-Please contact [[email protected]]([email protected]) for
-further questions or protential collaborative opportunities!
+Please contact [[email protected]](mailto:[email protected]) for
+further questions or potential collaborative opportunities!
 
 <!-- github-only -->
 
@@ -182,3 +129,4 @@ further questions or protential collaborative opportunities!
 [documentation]: https://pyCellPhenoXreadthedocs.io/
 [Code of Conduct Documentation]: https://pyCellPhenoXreadthedocs.io/code_of_conduct
 [Contributing Documentation]: https://pyCellPhenoXreadthedocs.io/contributing
+[Workflow Documentation]: https://pyCellPhenoXreadthedocs.io/walkthroughs/workflows

build/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 752896d6acf2089b607d9cda8b02be6b
+tags: 645f666f9bcd5a90fca523b33c5a78b7

build/.buildinfo.bak

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 15f57f3ca10b6230b4abc06d59abc2dc
+tags: 645f666f9bcd5a90fca523b33c5a78b7