Merge pull request #109 from monarch-initiative/develop

adding sssom support

.github/workflows/documentation.yaml

@@ -0,0 +1,39 @@
+name: Build and Deploy Docs to GitHub Pages
+on:
+  push:
+    branches:
+      - main
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@main
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@main
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@main
+
+      - name: Install Dependencies
+        run: poetry install
+
+      - name: Build Documentation
+        run: make docs
+
+      - name: Deploy to gh-pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: site
+          target-folder: docs
+          clean: true
+

.github/workflows/test.yaml

@@ -0,0 +1,49 @@
+# Builds and runs pytest on ubuntu-latest
+# Tests python versions >=3.8
+name: Test Koza
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  # https://github.com/actions/setup-python
+  test-python3-ubuntu-latest:
+    name: test py${{ matrix.python-version }} on linux
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+    env:
+      PYTHON: ${{ matrix.python-version }}
+      OS: ubuntu
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      #----------------------------------------------
+      #          install & configure poetry
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      #----------------------------------------------
+      #    install your root project, if required
+      #----------------------------------------------
+      - name: Install library
+        run: poetry install --with dev --no-interaction
+
+      #----------------------------------------------
+      #              run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: poetry run pytest tests

.gitignore

@@ -1,6 +1,8 @@
-koza-env/
+# Default output / Generated / Unpacked data files
+output/
 tests/resources/source-files/string.tsv*
 
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -133,7 +135,3 @@ dmypy.json
 
 # IDE
 .idea
-
-# output directories
-output/
-test-output/

Makefile

@@ -1,4 +1,4 @@
-# Note that you should be in your virtual environment of choice before running make
+# Note that Poetry is required, see https://python-poetry.org/docs/#installation
 
 MAKEFLAGS += --warn-undefined-variables
 MAKEFLAGS += --no-builtin-rules
@@ -11,6 +11,7 @@ endif
 
 .DEFAULT_GOAL := all
 SHELL := bash
+RUN := poetry run
 
 .PHONY: all
 all: install test clean
@@ -24,12 +25,13 @@ build:
 	poetry build
 
 .PHONY: test
-test: install
-	poetry run python -m pytest
+test:
+	$(RUN) pytest tests
 
 .PHONY: docs
-docs: install
-	poetry run typer src/koza/main.py utils docs --name koza --output docs/Usage/CLI.md
+docs:
+	$(RUN) typer src/koza/main.py utils docs --name koza --output docs/Usage/CLI.md
+	$(RUN) mkdocs build
 
 .PHONY: clean
 clean:
@@ -41,17 +43,10 @@ clean:
 
 .PHONY: lint
 lint:
-	flake8 --exit-zero --max-line-length 120 koza/ tests/ examples/
-	black --check --diff koza tests
-	isort --check-only --diff koza tests
+	$(RUN) ruff check --diff --exit-zero src/ tests/ examples/
+	$(RUN) black --check --diff -l 120 src/ tests/ examples/
 
 .PHONY: format
 format:
-	autoflake \
-		--recursive \
-		--remove-all-unused-imports \
-		--remove-unused-variables \
-		--ignore-init-module-imports \
-		--in-place koza tests examples
-	isort koza tests examples
-	black koza tests examples
+	$(RUN) ruff check --fix --exit-zero src/ tests/ examples/
+	$(RUN) black -l 120 src/ tests/ examples/

README.md

@@ -8,23 +8,24 @@
 
 [**Documentation**](https://koza.monarchinitiative.org/  )
 
-_Disclaimer_: Koza is in beta; we are looking for beta testers
+_Disclaimer_: Koza is in beta - we are looking for testers!
 
-### Overview
+## Overview
   - Transform csv, json, yaml, jsonl, and xml and converting them to a target csv, json, or jsonl format based on your dataclass model.  
   - Koza also can output data in the [KGX format](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md#kgx-format-as-tsv)
   - Write data transforms in semi-declarative Python
   - Configure source files, expected columns/json properties and path filters, field filters, and metadata in yaml
   - Create or import mapping files to be used in ingests (eg id mapping, type mappings)
   - Create and use translation tables to map between source and target vocabularies
 
-### Installation
+## Installation
 Koza is available on PyPi and can be installed via pip/pipx:
 ```
 [pip|pipx] install koza
 ```
 
-### Usage
+## Usage
+
 
 **NOTE: As of version 0.2.0, there is a new method for getting your ingest's `KozaApp` instance. Please see the [updated documentation](https://koza.monarchinitiative.org/Usage/configuring_ingests/#transform-code) for details.**
 
@@ -61,8 +62,24 @@ koza validate \
 
 Run the example ingest, "string/protein-links-detailed"
 ```bash
-koza transform --source examples/string/protein-links-detailed.yaml --global-table examples/translation_table.yaml
+koza transform \
+  --source examples/string/protein-links-detailed.yaml \
+  --global-table examples/translation_table.yaml
 
-koza transform --source examples/string-declarative/protein-links-detailed.yaml --global-table examples/translation_table.yaml
+koza transform \
+  --source examples/string-declarative/protein-links-detailed.yaml \
+  --global-table examples/translation_table.yaml
 ```
-note: koza expects a directory structure as described in the above example (examples/ingest_name/ingest.yaml)
+
+**Note**: 
+  Koza expects a directory structure as described in the above example  
+  with the source config file and transform code in the same directory: 
+  ```
+  .
+  ├── ...
+  │   ├── your_source
+  │   │   ├── your_ingest.yaml
+  │   │   └── your_ingest.py
+  │   └── some_translation_table.yaml
+  └── ...
+  ```

docs/Usage/API.md

@@ -0,0 +1 @@
+::: src.koza.cli_runner