update pypi

ACED-IDP · Nov 1, 2024 · 95e32d5 · 95e32d5
1 parent 55a3dee
commit 95e32d5
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Showing 4 changed files with 63 additions and 20 deletions.
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
@@ -50,11 +50,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         id: setup-python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         id: install-dependencies
@@ -84,7 +84,8 @@ jobs:
           echo $CREDENTIALS > ~/.gen3/credentials.json
 
           gen3-client configure --profile=CALIPER --cred=~/.gen3/credentials.json --apiendpoint="${{ inputs.endpoint }}"
-          gen3-client auth --profile=CALIPER
+          export G3T_PROFILE=CALIPER
+          echo "G3T_PROFILE=CALIPER" >> $GITHUB_ENV
           g3t ping
 
       - name: Create Project
@@ -98,6 +99,7 @@ jobs:
           export PROJECT="${{ inputs.program }}-integration_test_$RANDOM"
           mkdir $PROJECT
           cd $PROJECT
+
           g3t init $PROJECT
           g3t collaborator approve --all
 
@@ -133,6 +135,7 @@ jobs:
 
           source ~/.bash_profile
           cd $PROJECT
+
           g3t push
 
           END=$(date +%s)
@@ -146,6 +149,7 @@ jobs:
           source ~/.bash_profile
           mkdir download-test
           cd download-test
+
           g3t clone $PROJECT
           cd $PROJECT
           g3t pull

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -5,36 +5,39 @@ on:
   workflow_dispatch: # Allow manual triggering of the workflow
 
 jobs:
+  cbds:
+    with:
+        environment: cbds
+        endpoint: "https://idp.cbds.ohsu.edu"
+        # Self-hosted runner to access https://idp.cbds.ohsu.edu
+        # https://github.com/ACED-IDP/gen3_util/settings/actions/runners/21
+        # https://docs.github.com/en/actions/hosting-your-own-runners/managing-self-hosted-runners/adding-self-hosted-runners#adding-a-self-hosted-runner-to-a-repository
+        runs-on: self-hosted
+        program: cbds
+    secrets:
+        CREDENTIALS: ${{ secrets.CREDENTIALS }}
+    uses: ./.github/workflows/integration.yaml
+
   production:
     with:
       environment: production
-      endpoint: https://aced-idp.org
+      endpoint: "https://aced-idp.org"
     secrets:
       CREDENTIALS: ${{ secrets.CREDENTIALS }}
     uses: ./.github/workflows/integration.yaml
 
   staging:
     with:
       environment: staging
-      endpoint: https://staging.aced-idp.org
+      endpoint: "https://staging.aced-idp.org"
     secrets:
       CREDENTIALS: ${{ secrets.CREDENTIALS }}
     uses: ./.github/workflows/integration.yaml
 
   development:
     with:
       environment: development
-      endpoint: https://development.aced-idp.org
-    secrets:
-      CREDENTIALS: ${{ secrets.CREDENTIALS }}
-    uses: ./.github/workflows/integration.yaml
-
-  cbds:
-    with:
-      environment: cbds
-      endpoint: https://idp.cbds.ohsu.edu
-      runs-on: self-hosted
-      program: cbds
+      endpoint: "https://development.aced-idp.org"
     secrets:
       CREDENTIALS: ${{ secrets.CREDENTIALS }}
     uses: ./.github/workflows/integration.yaml
diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
@@ -17,22 +17,58 @@ on:
 
 jobs:
   pytest:
-    runs-on: ubuntu-latest
+    # We're testing 'cbds' by default so we can use the self-hosted runner to access htps://idp.cbds.ohsu.edu
+    # https://github.com/ACED-IDP/gen3_util/settings/actions/runners/21
+    # https://docs.github.com/en/actions/hosting-your-own-runners/managing-self-hosted-runners/adding-self-hosted-runners#adding-a-self-hosted-runner-to-a-repository
+    environment: cbds
+    runs-on: self-hosted
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
+      - name: Install gen3-client
+        id: install-gen3-client
+        run: |
+          wget https://github.com/ACED-IDP/cdis-data-client/releases/latest/download/gen3-client-linux-amd64.zip
+          unzip gen3-client-linux-amd64.zip
+          mkdir -p ~/.gen3
+          mv gen3-client ~/.gen3/gen3-client
+          echo 'export PATH=$PATH:~/.gen3' >> ~/.bash_profile
+          source ~/.bash_profile
+          gen3-client
+        
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install -r requirements-dev.txt
           pip install -e .
 
+      - name: Configure gen3-client
+        id: configure-gen3-client
+        env:
+          CREDENTIALS: ${{ secrets.CREDENTIALS }}
+        run: |
+          source ~/.bash_profile
+          echo $CREDENTIALS > ~/.gen3/credentials.json
+
+          # Hardcoding the endpoint for now
+          # TODO: Should we make this configurable to run `pytest` against all Gen3 instances?
+          export ENDPOINT="https://idp.cbds.ohsu.edu"
+
+          gen3-client configure --profile=CALIPER --cred=~/.gen3/credentials.json --apiendpoint="$ENDPOINT"
+          export G3T_PROFILE=CALIPER
+          echo "G3T_PROFILE=CALIPER" >> $GITHUB_ENV
+          g3t ping
+
+          # A 'local' profile appears to be required for the `pytest` tests
+          # So we just "duplicate" the existing 'CALIPER' profile
+          gen3-client configure --profile=local --cred=~/.gen3/credentials.json --apiendpoint="$ENDPOINT"
+
       - name: Pytest
         run: |
           pytest tests/ --cov=gen3_util
diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setup(
     name='gen3_tracker',
-    version='0.0.5rc8',
+    version='0.0.6',
     description='A CLI for adding version control to Gen3 data submission projects.',
     long_description=long_description,
     long_description_content_type='text/markdown',