Merge pull request #20 from databio/dev

Release 0.1.0

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - uses: psf/black@stable

.github/workflows/python-publish.yml

@@ -0,0 +1,30 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      run: |
+        python setup.py sdist bdist_wheel
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-pytest.yml

@@ -0,0 +1,33 @@
+## we can't run test, but lets just install all dependencies and package
+name: Installation test
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [master, dev]
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.12"]
+        os: [ubuntu-latest]
+
+    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 dev dependencies
+      run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
+
+    - name: Install package
+      run: python -m pip install .
+
+    - name: Run pytest tests
+      run: pytest tests -x -vv

README.md

@@ -1,28 +1,37 @@
-# bedmess
+# BEDMS
 
-bedmess is a tool used to standardize genomics/epigenomics metadata based on a schema chosen by the user ( eg. ENCODE, FAIRTRACKS).
+BEDMS (BED Metadata Standardizer) is a tool used to standardize genomics/epigenomics metadata based on a schema chosen by the user ( eg. ENCODE, FAIRTRACKS, BEDBASE).
 
 
-To install `attribute-standardizer` , you need to clone this repository first. Follow the steps given below to install:
+## Installation
 
+To install `bedms` use this command: 
 ```
-git clone https://github.com/databio/bedmess.git
-
-cd bedmess
-
-pip install .
-
+pip install bedms
+```
+or install the latest version from the GitHub repository:
+```
+pip install git+https://github.com/databio/bedms.git
 ```
 
 ## Usage
 
-Using Python, this is how you can run `attribute_standardizer` :
+```python
+from bedms import AttrStandardizer
 
+model = AttrStandardizer("ENCODE")
+results = model.standardize(pep="geo/gse228634:default")
 
+assert results
 ```
-from attribute_standardizer.attribute_standardizer import attr_standardizer
 
-attr_standardizer(pep=/path/to/pep, schema="ENCODE")
+
+To see the available schemas, you can run:
 ```
+from bedms.constants import AVAILABLE_SCHEMAS
+print(AVAILABLE_SCHEMAS)
 
-You can use the format provided in the `trial.py` script in this repository as a reference. 
+# >> ['ENCODE', 'FAIRTRACKS', 'BEDBASE'] 
+
+```
+AVAILABLE_SCHEMAS is a list of available schemas that you can use to standardize your metadata.