Merge pull request #7 from WrightonLabCSU/develop

0.1.0 Release

.github/workflows/ci.yaml

@@ -0,0 +1,49 @@
+name: tests
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - "*"
+  schedule:
+    - cron: "0 19 * * SUN"
+
+
+jobs:
+  ci:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        # This is the version of the action for setting up Python, not the Python version.
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+      # You can test your matrix by printing the current Python version
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install  -e '.[dev]'
+
+      - name: Install pre-commit hooks
+        run: pre-commit install
+
+      - name: Run pre-commit hooks for linting and other checks
+        run: pre-commit run --all-files
+
+      - name: Run tests
+        run: pytest tests --doctest-modules --cov=dram2_viz --cov-report=xml --cov-report=html
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-xml-coverage-path: ./coverage.xml

.gitignore

@@ -1,6 +1,7 @@
 # Visualization Output Files
 product.html
 product.tsv
+output/
 
 # docs build
 docs/_build

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+# This is the configuration for pre-commit, a local framework for managing pre-commit hooks
+#   Check out the docs at: https://pre-commit.com/
+
+default_stages: [commit]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-json
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.5
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: ['--select', 'I', '--fix']
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

README.md

@@ -1,6 +1,6 @@
 # DRAM2 Visualization Library
 
-This directory contains the visualization code for DRAM2. The visualization code is written in Python and uses the [Bokeh](https://bokeh.org) and [Panel](https://panel.holoviz.org) libraries. The visualization code is used to generate the figures 
+This directory contains the visualization code for DRAM2. The visualization code is written in Python and uses the [Bokeh](https://bokeh.org) and [Panel](https://panel.holoviz.org) libraries. The visualization code is used to generate the figures
 and dashboards for the [DRAM2 gene annotation tool](https://github.com/WrightonLabCSU/DRAM2).
 
 ## Nextflow Integration
@@ -29,14 +29,30 @@ The DRAM2 Visualization Library can also be used as a standalone Python package
 pip install git+https://github.com/WrightonLabCSU/dram2_viz.git
 ```
 
-This will install the DRAM2 Visualization Library and all of its dependencies from the main branch of the GitHub repository. To install the DRAM2 Visualization Library as a development package, clone the repository, cd into the repository, create your environment, and run:
+This will install the DRAM2 Visualization Library and all of its dependencies from the main branch of the GitHub repository.
+
+#### Development Installation
+
+To install the DRAM2 Visualization Library as a development package, clone the repository, cd into the repository, create your environment, and run:
 
 ```bash
-pip install -e .[dev]
+pip install -e '.[dev]'
 ```
 
 This will install the DRAM2 Visualization Library and all of its dependencies from the main branch of the GitHub repository, as well as the development dependencies.
 
+We use [pre-commit](https://pre-commit.com) to manage our pre-commit hooks (e.g., linting, formatting that run commit to keep code formatting in check). To install the pre-commit hooks, run:
+
+```bash
+pre-commit install
+```
+
+now pre-commit will run automatically on git commit, but you can run it manually by running:
+
+```bash
+pre-commit run --all-files
+```
+
 ### Usage
 
 To generate a figure like the one shown above [TODO: insert figure], run the following command:
@@ -55,7 +71,7 @@ This should open your default web browser and display the dashboard. If the dash
 ### SSH Tunneling
 
 If you are using the DRAM2 Visualization Library as a standalone Python package, you can run the dashboard on a remote server and use SSH tunneling to view the dashboard on your local machine. This will allow you to avoid downloading large data files to your local machine. To do this, first launch the dashboard on the remote server by ssh'ing into the server, navigating to the DRAM2 visualization directory, and running the above dashboard command. Then, on your local machine, run the following command:
-    
+
 ```bash
 ssh -NfL localhost:5006:localhost:5006 <username>@<remote-server>
 ```

dram2_viz/__init__.py

@@ -0,0 +1,10 @@
+try:
+    from dram2_viz._version import __version__
+
+except ImportError:
+    # package not installed
+    __version__ = "0.0.0"
+
+
+__authors__ = ["Madeline Scyphers", "Rory Flynn"]
+__copyright__ = "Copyright 2024, Wrighton Lab"

dram2_viz/__main__.py

@@ -1,5 +1,4 @@
 from dram2_viz.make_product import main
 
-
 if __name__ == "__main__":
     main()