convert to cookiecutter template

.cruft.json

@@ -0,0 +1,25 @@
+{
+  "template": "https://github.com/monarch-initiative/cookiecutter-monarch-ingest.git",
+  "commit": "bd969c818d9380b12a43d0cc4a20765ea6aa12c8",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "github_org_name": "monarch-initiative",
+      "project_name": "NCBI Gene",
+      "project_description": "Ingest of genes from NCBI",
+      "__repo_name": "NCBI-Gene",
+      "__project_slug": "ncbi_gene",
+      "__project_url": "https://github.com/monarch-initiative/NCBI-Gene",
+      "ingest_source": "ncbi",
+      "ingest_type": "gene",
+      "__ingest_name": "ncbi_gene",
+      "min_python_version": "3.10",
+      "full_name": "Kevin Schaper",
+      "email": "[email protected]",
+      "__author": "Kevin Schaper <[email protected]>",
+      "license": "BSD-3",
+      "_template": "https://github.com/monarch-initiative/cookiecutter-monarch-ingest.git"
+    }
+  },
+  "directory": null
+}

.github/dependabot.yaml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/create-release.yaml

@@ -0,0 +1,53 @@
+### This workflow can be run manually from Actions tab in your repository by selecting the "Create Release" workflow.
+### When your project is ready for releases, you should:
+###   - Uncomment the `schedule` section to run this workflow automatically on a schedule.
+###     - As written, this workflow will run every Sunday at midnight UTC.
+###   - Remove the `draft: true` line from the `Create Release` step to publish the release immediately.
+# TODO: QC/Validation (ex. 0 rows)
+
+name: Create Release
+
+on:
+  workflow_dispatch:
+  # schedule:
+  #   - cron: '0 0 * * 0'
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Dependencies
+        run: poetry install --no-interaction
+
+      - name: Run Transform
+        run: |
+          make run
+          poetry run python scripts/generate-rdf.py
+
+      - name: Get Date for Release Tag
+        run: echo "DATE=$(date +%Y-%m-%d)" >> $GITHUB_ENV
+
+      # Further customization for this action is available. See:
+      # https://github.com/softprops/action-gh-release/?tab=readme-ov-file#-customizing
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ env.DATE }}
+          files: |
+            output/*
+          generate_release_notes: true
+          draft: true

.github/workflows/deploy-docs.yaml

@@ -0,0 +1,38 @@
+name: Auto-Deploy Documentation
+
+on:
+  push:
+    branches: [main]
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Dependencies
+        run: poetry install --with dev --no-interaction
+
+      - 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 +1,42 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test-backend:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        os: [ubuntu-latest]
+        #os: [ ubuntu-latest, windows-latest ]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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 --no-interaction
+
+      #----------------------------------------------
+      #              run pytest
+      #----------------------------------------------
+      - name: Run tests
+        run: poetry run pytest tests
+

.github/workflows/update-docs.yaml

@@ -0,0 +1,42 @@
+# This GitHub Action updates the documentation with information about the latest KG build/release.
+
+name: Update Documentation
+
+on:
+  workflow_run:
+    workflows: ["Create Release"]
+    types:
+      - completed
+
+jobs:
+  update-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Dependencies
+        run: |
+          poetry install --with dev --no-interaction
+
+      - name: Build Documentation
+        run: |
+          poetry run python scripts/get-latest-report.py
+          make docs
+
+      - name: Deploy to gh-pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: site
+          target-folder: docs
+          clean: true

.gitignore

@@ -1,4 +1,3 @@
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CONTRIBUTING.md

@@ -0,0 +1,31 @@
+# Contribution Guidelines
+
+When contributing to this repository, please first discuss the changes you wish to make via an issue, email, or any other method, with the owners of this repository before issuing a pull request.
+
+## How to contribute
+
+### Reporting bugs or making feature requests
+
+To report a bug or suggest a new feature, please go to the [monarch-initiative/NCBI-Gene issue tracker](https://github.com/monarch-initiative/NCBI-Gene/issues), as we consolidate issues there.
+
+Please supply enough details to the developers to enable them to verify and troubleshoot your issue:
+
+* Provide a clear and descriptive title as well as a concise summary of the issue to identify the problem.
+* Describe the exact steps which reproduce the problem in as many details as possible.
+* Describe the behavior you observed after following the steps and point out what exactly is the problem with that behavior.
+* Explain which behavior you expected to see instead and why.
+* Provide screenshots of the expected or actual behaviour where applicable.
+
+
+### The development lifecycle
+
+1. Create a bug fix or feature development branch, based off the `main` branch of the upstream repo, and not your fork. Name the branch appropriately, briefly summarizing the bug fix or feature request. If none come to mind, you can include the issue number in the branch name. Some examples of branch names are, `bugfix/breaking-pipfile-error` or `feature/add-click-cli-layer`, or `bugfix/issue-414`
+2. Make sure your development branch has all the latest commits from the `main` branch.
+3. After completing work and testing locally, push the code to the appropriate branch on your fork or origin repository.
+4. Create a pull request from the bug/feature branch of your fork to the `main` branch of the upstream repository.
+
+**NOTE**: All the development must be done on a separate branch, either in your fork or in the origin repository. The `main` branch of the upstream repository should never be used for development.
+
+**ALSO NOTE**: github.com lets you create a pull request from the main branch, automating the steps above.
+
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.

LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2024, Monarch Initiative
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of pytest-NCBI Gene nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Makefile

@@ -1,12 +1,101 @@
+ROOTDIR = $(shell pwd)
+RUN = poetry run
+VERSION = $(shell poetry -C src/ncbi_gene version -s)
+
+### Help ###
+
+define HELP
+╭───────────────────────────────────────────────────────────╮
+  Makefile for ncbi_gene			    
+│ ───────────────────────────────────────────────────────── │
+│ Usage:                                                    │
+│     make <target>                                         │
+│                                                           │
+│ Targets:                                                  │
+│     help                Print this help message           │
+│                                                           │
+│     all                 Install everything and test       │
+│     fresh               Clean and install everything      │
+│     clean               Clean up build artifacts          │
+│     clobber             Clean up generated files          │
+│                                                           │
+│     install             Poetry install package            │
+│     download            Download data                     │
+│     run                 Run the transform                 │
+│                                                           │
+│     docs                Generate documentation            │
+│                                                           │
+│     test                Run all tests                     │
+│                                                           │
+│     lint                Lint all code                     │
+│     format              Format all code                   │
+╰───────────────────────────────────────────────────────────╯
+endef
+export HELP
+
+.PHONY: help
+help:
+	@printf "$${HELP}"
+
+
+### Installation and Setup ###
+
+.PHONY: fresh
+fresh: clean clobber all
+
+.PHONY: all
+all: install test
+
+.PHONY: install
+install: 
+	poetry install --with dev
+
+
+### Documentation ###
+
+.PHONY: docs
+docs:
+	$(RUN) mkdocs build
+
+
+### Testing ###
+
+.PHONY: test
+test: download
+	$(RUN) pytest tests
+
+
+### Running ###
 
 .PHONY: download
 download:
-	downloader
+	$(RUN) ingest download
+
+.PHONY: run
+run: download
+	$(RUN) ingest transform
+	$(RUN) python scripts/generate-report.py
+
+
+### Linting, Formatting, and Cleaning ###
+
+.PHONY: clean
+clean:
+	rm -f `find . -type f -name '*.py[co]' `
+	rm -rf `find . -name __pycache__` \
+		.venv .ruff_cache .pytest_cache **/.ipynb_checkpoints
+
+.PHONY: clobber
+clobber:
+	# Add any files to remove here
+	@echo "Nothing to remove. Add files to remove to clobber target."
 
-.PHONY: transform
-transform:
-	koza transform --source ncbi_gene.yaml --target ncbi_gene.json
+.PHONY: lint
+lint: 
+	$(RUN) ruff check --diff --exit-zero
+	$(RUN) black -l 120 --check --diff src tests
 
-.PHONY: rdf
-rdf:
-	kgx transform -i tsv -f nt -d gz -o output/ncbi_gene_nodes.nt.gz output/ncbi_gene_nodes.tsv
+.PHONY: format
+format: 
+	$(RUN) ruff check --fix --exit-zero
+	$(RUN) black -l 120 src tests