[fix] Remove custom classes

.github/workflows/test.yml

@@ -0,0 +1,40 @@
+name: Test
+
+on:
+  push:
+    branches: [ main, develop, fix-*, feat-* ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install pytest pytest-cov pandas
+        
+    - name: Run unit tests
+      run: |
+        python -m pytest tests/ -v --tb=short --cov=cnb_tools --cov-report=term-missing
+    
+    - name: Test CLI basics
+      run: |
+        cnb-tools
+        cnb-tools --help
+        cnb-tools submission --help
+

README.md

@@ -12,7 +12,7 @@
   <a href="https://pypi.org/project/cnb-tools/" title="cnb-tools on PyPI">
     <img alt="PyPI version" src="https://img.shields.io/pypi/v/cnb-tools?style=flat-square&logo=pypi&logoColor=white&color=%23679EC1">
   </a>
-  <img alt="Supported Python versions" src="https://img.shields.io/badge/python-3.9 | 3.10 | 3.11 | 3.12-%23EB8231?style=flat-square&logo=python&logoColor=white">
+  <img alt="Supported Python versions" src="https://img.shields.io/badge/python-3.10 | 3.11 | 3.12 -%23EB8231?style=flat-square&logo=python&logoColor=white">
   <a href="https://github.com/Sage-Bionetworks-Challenges/cnb-tools/blob/main/LICENSE" title="License">
     <img alt="License" src="https://img.shields.io/github/license/Sage-Bionetworks-Challenges/cnb-tools?style=flat-square&logo=github&color=%236DB56D">
   </a>
@@ -33,23 +33,23 @@ but not limited to, [DREAM Challenges].
 
 ## Requirements
 
-- [Python 3.9+]
+- [Python 3.10+]
 - [Synapse account]
 
 To fully utilize **cnb-tools**, you must have a Synapse account and
-provide your credentials to the tool.  To do so, create a `.synapseConfig`
-file in your home directory and enter the following:
+provide your credentials to the tool. First, generate a Synapse
+[Personal Access Token (PAT)] with all token permissions enabled.
 
-```yaml
-[authentication]
-authtoken=<YOUR PAT>
-```
+Next, run the following command, then follow the prompts to enter
+your Synapse username and PAT:
 
-Generate a new Synapse [Personal Access Token (PAT)] with all token
-permissions enabled, then copy-paste it into `authtoken`. Save the file.
+```console
+synapse config
+```
 
-For security, we recommend updating its permissions so that other
-users on your machine do not have read access to your credentials, e.g.
+This will create a `.synapseConfig` file in your home directory. For
+security, we recommend updating its permissions so that other users
+on your machine do not have read access to your credentials, e.g.
 
 ```console
 chmod 600 ~/.synapseConfig
@@ -58,10 +58,9 @@ chmod 600 ~/.synapseConfig
 ## Installation
 
 For best practice, use a Python environment to install **cnb-tools**
-rather than directly into your base env.  In our docs, we will be
+rather than directly into your base env. In our docs, we will be
 using [miniconda], but you can use [miniforge], [venv], [pyenv], etc.
 
-<!-- termynal -->
 ```console
 # Create a new env and activate it
 conda create -n cnb-tools python=3.12 -y
@@ -114,7 +113,7 @@ docker run --rm \
 [https://sage-bionetworks-challenges.github.io/cnb-tools]: https://sage-bionetworks-challenges.github.io/cnb-tools
 [https://github.com/Sage-Bionetworks-Challenges/cnb-tools]: https://github.com/Sage-Bionetworks-Challenges/cnb-tools
 [DREAM Challenges]: https://dreamchallenges.org/
-[Python 3.9+]: https://www.python.org/downloads/
+[Python 3.10+]: https://www.python.org/downloads/
 [Synapse account]: https://www.synapse.org/#!LoginPlace:0
 [Personal Access Token (PAT)]: https://www.synapse.org/#!PersonalAccessTokens:
 [miniconda]: https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html