Merge pull request #934 from Sage-Bionetworks/develop

Release 22.9.1

Author: linglp

.dockerignore

@@ -0,0 +1,5 @@
+# ignore .git and .cache folders
+.git
+.cache
+.synapseConfig
+.env

.github/workflows/docker.yml

@@ -0,0 +1,58 @@
+# This workflow builds and pushes the docker image using docker's v2 action
+# which requires explicitly setting up buildx and logging in
+
+name: Build and publish container to Docker Hub
+
+on:
+  push:
+    tags: ['v[0-9]*', '[0-9]+.[0-9]+*']  # Match tags that resemble a version
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_ORG:  sagebionetworks
+      DOCKER_REPO: schematic
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: schematicbot
+          password: ${{ secrets.DOCKER_HUB_TOKEN }}
+      -
+        name: Compute short commit SHA ID
+        id: vars
+        run: echo "::set-output name=sha_short::$(git rev-parse --short HEAD)"
+      -
+        name: Build and push (tagged release)
+        uses: docker/build-push-action@v3
+        if: ${{ github.event_name == 'push' }}
+        with:
+          platforms: linux/amd64,linux/arm64
+          context: .
+          push: true
+          tags: |
+            ${{ env.DOCKER_ORG }}/${{ env.DOCKER_REPO }}:latest
+            ${{ env.DOCKER_ORG }}/${{ env.DOCKER_REPO }}:${{ github.ref_name }}
+            ${{ env.DOCKER_ORG }}/${{ env.DOCKER_REPO }}:commit-${{ steps.vars.outputs.sha_short }}
+      -
+        name: Build and push (manual release)
+        uses: docker/build-push-action@v3
+        if: ${{ github.event_name == 'workflow_dispatch' }}
+        with:
+          platforms: linux/amd64,linux/arm64
+          context: .
+          push: true
+          tags: |
+            ${{ env.DOCKER_ORG }}/${{ env.DOCKER_REPO }}:commit-${{ steps.vars.outputs.sha_short }}

.github/workflows/test.yml

@@ -5,15 +5,33 @@
 
 name: Test schematic
 
-on: [push, pull_request]
-
+on:
+  push:
+    branches: ['main']
+  pull_request: 
+    branches: ['*']
+  workflow_dispatch:  # Allow manually triggering the workflow
+concurrency:
+  # cancel the current running workflow from the same branch, PR when a new workflow is triggered 
+  # when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group
+  # {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows
+  # {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag 
+  # {{ github.event.pull_request.number}}: get PR number 
+  # {{ github.sha }}: full commit sha 
+  # credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
 jobs:
   test:
 
     runs-on: ubuntu-latest
+    env:
+      POETRY_VERSION:  1.2.0rc1
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
 
     steps:
 
@@ -32,10 +50,11 @@ jobs:
       #          install & configure poetry         
       #----------------------------------------------
       - name: Install Poetry
-        uses: snok/install-poetry@v1.1.1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
+        run: |
+          curl -sSL https://install.python-poetry.org \
+            | python3 - --version ${{ env.POETRY_VERSION }};
+          poetry config virtualenvs.create true; 
+          poetry config virtualenvs.in-project true; 
 
       #----------------------------------------------
       #       load cached venv if cache exists      

.gitignore

@@ -170,3 +170,6 @@ tests/data/example.MockComponent.schema.json
 tests/data/mock_manifests/Invalid_Test_Manifest_censored.csv
 tests/data/mock_manifests/valid_test_manifest_censored.csv
 tests/data/mock_manifests/Rule_Combo_Manifest_censored.csv
+
+# Pickle file
+tests/data/schema.gpickle

Dockerfile

@@ -0,0 +1,28 @@
+FROM python:3.10.6
+
+ENV PYTHONFAULTHANDLER=1 \
+  PYTHONUNBUFFERED=1 \
+  PYTHONHASHSEED=random \
+  PIP_NO_CACHE_DIR=off \
+  PIP_DISABLE_PIP_VERSION_CHECK=on \
+  PIP_DEFAULT_TIMEOUT=200 \
+  POETRY_VERSION=1.2.0rc1
+
+WORKDIR /usr/src/app
+
+RUN apt-get update -qqy \
+  && apt-get install -qqy \
+    libopenblas-dev \
+    gfortran
+
+RUN pip install --no-cache-dir "poetry==$POETRY_VERSION"
+
+COPY pyproject.toml poetry.lock ./
+
+RUN poetry config virtualenvs.create false
+
+RUN poetry install --no-interaction --no-ansi --no-root
+
+COPY . ./
+
+RUN poetry install --no-interaction --no-ansi --only-root

README.md

@@ -59,7 +59,8 @@ Please note we have a [code of conduct](CODE_OF_CONDUCT.md), please follow it in
 ```
 git clone https://github.com/Sage-Bionetworks/schematic.git
 ```
-2. Follow the [instructions](https://python-poetry.org/docs/) here to install `poetry`
+2. Install `poetry` (version 1.2 or later) using either the [official installer](https://python-poetry.org/docs/#installing-with-the-official-installer) or [pipx](https://python-poetry.org/docs/#installing-with-pipx). If you have an older installation of Poetry, we recommend uninstalling it first. 
+
 3. Start the virtual environment by doing: 
 ```
 poetry shell
@@ -68,7 +69,7 @@ poetry shell
 ```
 poetry install
 ```
-This command will install the dependencies based on what we specify in poetry.lock
+This command will install the dependencies based on what we specify in poetry.lock. If this step is taking a long time, try to go back to step 2 and check your version of poetry. Alternatively, you could also try deleting the lock file and regenerate it by doing `poetry install` (Please note this method should be used as a last resort because this would force other developers to change their development environment)
 
 5. Fill in credential files: 
 *Note*: If you won't interact with Synapse, please ignore this section.

api/__init__.py

@@ -13,9 +13,9 @@ def create_app():
     app = connexionapp.app
 
     # path to config.yml file saved as a Flask config variable
-    app.config["SCHEMATIC_CONFIG"] = os.path.abspath(
-        os.path.join(__file__, "../../config.yml")
-    )
+    default_config = os.path.abspath(os.path.join(__file__, "../../config.yml"))
+    schematic_config = os.environ.get("SCHEMATIC_CONFIG", default_config)
+    app.config["SCHEMATIC_CONFIG"] = schematic_config
 
     # Configure flask app
     # app.config[] = schematic[]