Merge pull request #9 from quiltdata/add-makefile

Add makefile

Makefile

@@ -0,0 +1,40 @@
+sinclude .env
+TARGET = build/benchling_packager.yaml
+ACTIVATE = ./venv/bin/activate
+PKG_URL = "https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager"
+.PHONY: all clean install template upload 
+
+all: template upload
+
+clean:
+	rm -rf build
+	rm -rf venv
+	rm -f *requirements.txt
+
+template: $(TARGET) 
+
+$(TARGET): build venv install make.py lambdas/lambda.py
+	. $(ACTIVATE) && python3 make.py > $(TARGET)
+
+upload:
+	. $(ACTIVATE) && python3 upload.py
+	open $(PKG_URL)
+
+build:
+	mkdir -p build
+
+venv:
+	@python3.9 --version|| (echo "Python 3.9 required" && exit 1)
+	python3.9 -m venv venv
+
+venv/bin/pip-compile:
+	. $(ACTIVATE) && python3 -m pip install pip-tools
+
+venv/bin/pip-sync:
+	. $(ACTIVATE) && python3 -m pip install pip-tools
+
+install: venv/bin/pip-sync requirements.txt
+	. $(ACTIVATE) && pip-sync requirements.txt
+
+requirements.txt: venv/bin/pip-compile requirements.in
+	. $(ACTIVATE) && pip-compile requirements.in

README.md

@@ -5,25 +5,20 @@ This repository generates a CloudFormation template for processing
 (and link, if possible) a [Quilt](https://quiltdata.com/)
 package for every Benchling notebook.
 
-## Template generation
+## Template generation and upload
 
 Requires a recent version of Python 3.
 
-```shell
-python3 -m venv venv
-. ./venv/bin/activate
-python3 -m pip install -r requirements.txt
-python3 make.py > build/benchling_packager.yaml
+```bash
+make all
 ```
 
-## Template upload
+This will:
 
-Currently it's distributed as a Quilt [package](https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager)
-which is this way:
-
-```python
-quilt3.Package().set('README.md', 'Install.md').set('benchling_packager.yaml', 'build/benchling_packager.yaml').push('examples/benchling-packager', 's3://quilt-example')
-```
+- setup the Python environment
+- generate the template in the `build` directory
+- upload the template to a Quilt package (if you have appropriate permissions)
+- open the package URL: <https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager>
 
 ## Installation
 

requirements.in

@@ -1,2 +1,3 @@
 troposphere ~=4.1
+quilt3 ~=5.3
 cfn-lint

requirements.txt

@@ -2,43 +2,57 @@
 # This file is autogenerated by pip-compile with Python 3.9
 # by the following command:
 #
-#    pip-compile
+#    pip-compile requirements.in
 #
 attrs==23.1.0
     # via
     #   jschema-to-python
     #   jsonschema
     #   sarif-om
-aws-sam-translator==1.68.0
+aws-requests-auth==0.4.3
+    # via quilt3
+aws-sam-translator==1.73.0
     # via cfn-lint
-boto3==1.26.151
-    # via aws-sam-translator
-botocore==1.29.151
+boto3==1.28.27
+    # via
+    #   aws-sam-translator
+    #   quilt3
+botocore==1.31.27
     # via
+    #   -r requirements.in
     #   boto3
     #   s3transfer
+certifi==2023.7.22
+    # via requests
 cfn-flip==1.3.0
     # via troposphere
-cfn-lint==0.77.7
+cfn-lint==0.79.7
     # via -r requirements.in
-click==8.1.3
+charset-normalizer==3.2.0
+    # via requests
+click==8.1.6
     # via cfn-flip
+idna==3.4
+    # via requests
 jmespath==1.0.1
     # via
     #   boto3
     #   botocore
 jschema-to-python==1.2.3
     # via cfn-lint
-jsonpatch==1.32
+jsonlines==1.2.0
+    # via quilt3
+jsonpatch==1.33
     # via cfn-lint
-jsonpickle==3.0.1
+jsonpickle==3.0.2
     # via jschema-to-python
-jsonpointer==2.3
+jsonpointer==2.4
     # via jsonpatch
 jsonschema==4.17.3
     # via
     #   aws-sam-translator
     #   cfn-lint
+    #   quilt3
 junit-xml==1.9
     # via cfn-lint
 mpmath==1.3.0
@@ -49,34 +63,53 @@ pbr==5.11.1
     # via
     #   jschema-to-python
     #   sarif-om
-pydantic==1.10.9
+platformdirs==3.10.0
+    # via quilt3
+pydantic==1.10.12
     # via aws-sam-translator
 pyrsistent==0.19.3
     # via jsonschema
 python-dateutil==2.8.2
     # via botocore
-pyyaml==6.0
+pyyaml==6.0.1
     # via
     #   cfn-flip
     #   cfn-lint
-regex==2023.6.3
+    #   quilt3
+quilt3==5.3.1
+    # via -r requirements.in
+regex==2023.8.8
     # via cfn-lint
-s3transfer==0.6.1
+requests==2.31.0
+    # via
+    #   aws-requests-auth
+    #   quilt3
+    #   requests-futures
+requests-futures==1.0.0
+    # via quilt3
+s3transfer==0.6.2
     # via boto3
 sarif-om==1.0.4
     # via cfn-lint
 six==1.16.0
     # via
     #   cfn-flip
+    #   jsonlines
     #   junit-xml
     #   python-dateutil
 sympy==1.12
     # via cfn-lint
-troposphere==4.3.2
+tenacity==8.2.3
+    # via quilt3
+tqdm==4.66.1
+    # via quilt3
+troposphere==4.4.1
     # via -r requirements.in
-typing-extensions==4.6.3
+typing-extensions==4.7.1
     # via
     #   aws-sam-translator
     #   pydantic
 urllib3==1.26.16
-    # via botocore
+    # via
+    #   botocore
+    #   requests

upload.py

@@ -0,0 +1,15 @@
+import quilt3
+
+REGISTRY = "s3://quilt-example"
+PKG_NAME = "examples/benchling-packager"
+TEMPLATE = "benchling_packager.yaml"
+TARGET = f"build/{TEMPLATE}"
+
+def upload():
+    pkg = quilt3.Package()
+    pkg.set("README.md", "Install.md")
+    pkg.set(TEMPLATE, TARGET)
+    pkg.push(PKG_NAME, registry=REGISTRY)
+
+if __name__ == "__main__":
+    upload()