add google auth to CI, fix np array in primer3 input

sanjaynagi · Sep 26, 2024 · 8699e1d · 8699e1d
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commit 8699e1d
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Showing 5 changed files with 32 additions and 8 deletions.
diff --git a/.github/workflows/github-action-AgamPrimer-funestus.yml b/.github/workflows/github-action-AgamPrimer-funestus.yml
@@ -37,6 +37,20 @@ jobs:
         poetry install
         poetry run python -m ipykernel install --user --name AnoPrimer
 
+    - id: 'auth'
+      name: 'Set up Google Cloud authentication'
+      uses: 'google-github-actions/auth@v2'
+      with:
+        credentials_json: '${{ secrets.GOOGLE_CREDENTIALS }}'
+
+    - name: 'Set up Google Cloud SDK'
+      uses: 'google-github-actions/setup-gcloud@v2'
+      with:
+        version: '>= 363.0.0'
+
+    - name: 'Check gcloud CLI'
+      run: 'gcloud info'
+
     - name: Run notebooks
       run: |
         poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params_fun.json

diff --git a/.github/workflows/github-action-AgamPrimer-gambiae.yml b/.github/workflows/github-action-AgamPrimer-gambiae.yml
@@ -37,6 +37,20 @@ jobs:
         poetry install
         poetry run python -m ipykernel install --user --name AnoPrimer
 
+    - id: 'auth'
+      name: 'Set up Google Cloud authentication'
+      uses: 'google-github-actions/auth@v2'
+      with:
+        credentials_json: '${{ secrets.GOOGLE_CREDENTIALS }}'
+
+    - name: 'Set up Google Cloud SDK'
+      uses: 'google-github-actions/setup-gcloud@v2'
+      with:
+        version: '>= 363.0.0'
+
+    - name: 'Check gcloud CLI'
+      run: 'gcloud info'
+
     - name: Run notebooks
       run: |
         poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params.json

diff --git a/AnoPrimer/design.py b/AnoPrimer/design.py
@@ -175,7 +175,7 @@ def prepare_gDNA_sequence(
         "SEQUENCE_TEMPLATE": target_sequence,
         "SEQUENCE_TARGET": target_loc_primer3,
         "GENOMIC_TARGET": target,
-        "GENOMIC_DNA_POSITIONS": gdna_pos,
+        "GENOMIC_DNA_POSITIONS": list(gdna_pos),
     }
 
     if "probe" in assay_type:
@@ -235,7 +235,7 @@ def prepare_cDNA_sequence(
         "SEQUENCE_ID": assay_name,
         "SEQUENCE_TEMPLATE": target_mRNA_seq,
         "GENOMIC_TARGET": transcript,
-        "GENOMIC_DNA_POSITIONS": gdna_pos,
+        "GENOMIC_DNA_POSITIONS": list(gdna_pos),
     }
 
     if cDNA_exon_junction:

diff --git a/AnoPrimer/evaluate.py b/AnoPrimer/evaluate.py
@@ -77,7 +77,7 @@ def __init__(
 
         # Extract additional attributes from seq_parameters
         self.target_sequence = seq_parameters.get("SEQUENCE_TEMPLATE")
-        self.gdna_pos = seq_parameters.get("GENOMIC_DNA_POSITIONS")
+        self.gdna_pos = np.array(seq_parameters.get("GENOMIC_DNA_POSITIONS"))
 
     def evaluate_primers(
         self,

diff --git a/notebooks/AnoPrimer-long.ipynb b/notebooks/AnoPrimer-long.ipynb
@@ -43,11 +43,7 @@
     "import malariagen_data\n",
     "import primer3\n",
     "import pandas as pd\n",
-    "import numpy as np\n",
-    "\n",
-    "import google.auth\n",
-    "\n",
-    "credentials, project = google.auth.default()"
+    "import numpy as np"
    ]
   },
   {