Make fetch_sequences.py easier to read, as part of #806.

Also reorder build steps to speed up test failures.
cfe-lab · Feb 7, 2022 · 16517be · 16517be
1 parent 4725d68
commit 16517be
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Showing 2 changed files with 28 additions and 27 deletions.
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
@@ -15,27 +15,6 @@ jobs:
       - uses: actions/setup-go@v2
         with:
           go-version: '^1.15.6'
-      - name: Install Singularity
-        run: |
-          sudo apt-get install -qq \
-              build-essential \
-              uuid-dev \
-              libgpgme-dev \
-              squashfs-tools \
-              libseccomp-dev \
-              wget \
-              pkg-config \
-              git \
-              cryptsetup-bin
-          git clone https://github.com/singularityware/singularity.git
-          cd singularity
-          git checkout -q tags/v3.7.1
-          ./mconfig && \
-              make -C ./builddir && \
-              sudo make -C ./builddir install
-          cd ..
-          rm -rf singularity
-          singularity --version
 
       - name: Install IVA assembler dependencies
         run: |
@@ -84,6 +63,28 @@ jobs:
 
       - name: Test with pytest
         run: coverage run --source=micall/core,micall/g2p,micall/resistance,micall/monitor -m pytest
+
+      - name: Install Singularity
+        run: |
+          sudo apt-get install -qq \
+              build-essential \
+              uuid-dev \
+              libgpgme-dev \
+              squashfs-tools \
+              libseccomp-dev \
+              wget \
+              pkg-config \
+              git \
+              cryptsetup-bin
+          git clone https://github.com/singularityware/singularity.git
+          cd singularity
+          git checkout -q tags/v3.7.1
+          ./mconfig && \
+              make -C ./builddir && \
+              sudo make -C ./builddir install
+          cd ..
+          rm -rf singularity
+          singularity --version
       - name: Singularity build
         run: sudo singularity build micall.simg Singularity
       - name: Upload Singularity Image

diff --git a/micall/utils/fetch_sequences.py b/micall/utils/fetch_sequences.py
@@ -98,14 +98,14 @@ def check_hiv_seeds(project_config, unchecked_ref_names: set):
 
 
 def check_hivgha_seeds(project_config, unchecked_ref_names: set):
-    print("HIVGHA project uses the same seeds as HIV, plus three chimeric seeds.")
-    ref_names = ["HIV1-CRF02_AG-GH-AB286855-seed",
-                 "HIV1-CRF06_CPX-GH-AB286851-seed"]
+    print("HIVGHA project uses the same seeds as HIV, plus two chimeric seeds.")
+    source_names = ["HIV1-CRF02_AG-GH-AB286855-seed",
+                    "HIV1-CRF06_CPX-GH-AB286851-seed"]
     source_sequences = {}
-    for ref_name in ref_names:
-        parts = ref_name.split('-')
+    for source_name in source_names:
+        parts = source_name.split('-')
         accession_number = parts[3]
-        source_sequences[ref_name] = fetch_by_accession(accession_number)
+        source_sequences[source_name] = fetch_by_accession(accession_number)
 
     ref_names = set(project_config.getProjectSeeds('HIVGHA'))
     ref_names -= set(project_config.getProjectSeeds('HIV'))