Merge pull request #278 from kipoi/add-singularity-tests

Add tests with singularity containers
kipoi · Nov 12, 2021 · e4787a1 · e4787a1
2 parents 7b14405 + 0f8a548
commit e4787a1
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Showing 2 changed files with 72 additions and 3 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -33,6 +33,11 @@ variables:
     run:
       name: Install hdf5 and pkgconfig
       command: conda install --yes -c conda-forge hdf5=1.10.6 pkgconfig
+  install_singularity: &install_singularity
+    run:
+      name: Install Singularity
+      command: |
+        conda install --yes -c conda-forge singularity
   restore_cache: &restore_cache
     restore_cache:
       keys:
@@ -71,6 +76,24 @@ jobs:
           command: kipoi test-source kipoi --git-range master HEAD --common_env
           no_output_timeout: 60m
       - *store_artifacts
+
+  # test only the newly added model with singularity
+  test_new_models_singularity:
+    <<: *defaults
+    steps:
+      - checkout
+      - *install_conda   
+      # - *install_sys_deps
+      - *install_gitlfs
+      - *install_additional_pkgs
+      - *install_singularity
+      # - *restore_cache
+      - *setup
+      - run:
+          name: run tests
+          command: kipoi test-source kipoi --git-range master HEAD --verbose --singularity
+          no_output_timeout: 60m
+      - *store_artifacts
 
   # test all models in the repo
   test_all_models:
@@ -95,6 +118,31 @@ jobs:
           command: kipoi test-source kipoi --all --num_of_shards << parameters.num_of_shards >> --shard_id << parameters.shard_id >>
       - *store_artifacts
 
+  # test all models in the repo
+  test_all_models_singularity:
+    parameters:
+      num_of_shards: 
+        type: integer
+      shard_id:
+        type: integer 
+    <<: *defaults
+    steps:
+      - checkout
+      - *install_conda   
+      # - *install_sys_deps
+      - *install_gitlfs
+      - *install_additional_pkgs
+      - *install_singularity
+      # - *restore_cache
+      - *setup
+      - run:
+          name: run tests
+          # Use  --clean_env to remove the environment of each model
+          no_output_timeout: 60m
+          command: kipoi test-source kipoi --all --num_of_shards << parameters.num_of_shards >> --shard_id << parameters.shard_id >> --singularity
+      - *store_artifacts
+
+
   test_all_models_common_env:
     <<: *defaults
     steps:
@@ -134,6 +182,12 @@ workflows:
                ignore:
                  - master
                  - test_all
+       - test_new_models_singularity:
+           filters:
+             branches:
+               ignore:
+                 - master
+                 - test_all
   test-all-branch:
      jobs:
        - test_all_models:
@@ -146,6 +200,16 @@ workflows:
                only:
                  - master
                  - test_all
+       - test_all_models_singularity:
+           matrix:
+             parameters:
+               num_of_shards: [4]
+               shard_id: [0, 1, 2, 3]
+           filters:
+             branches:
+               only:
+                 - master
+                 - test_all
        - test_all_models_common_env:
            filters:
              branches:
@@ -169,6 +233,11 @@ workflows:
             parameters:
               num_of_shards: [4]
               shard_id: [0, 1, 2, 3]
+       - test_all_models_singularity:
+          matrix:
+            parameters:
+              num_of_shards: [4]
+              shard_id: [0, 1, 2, 3]
        - test_all_models_common_env
 
 

diff --git a/shared/containers/model-to-singularity.json b/shared/containers/model-to-singularity.json
@@ -1,8 +1,8 @@
 {
     "DeepCpG_DNA": {
-        "url": "https://zenodo.org/record/5644007/files/kipoi-docker_sharedpy3keras2.sif?download=1",
-        "name": "kipoi-docker_sharedpy3keras2",
-        "md5": "0e5354145f54c2c8c7efc3bb265aebac"
+        "url": "https://zenodo.org/record/5644005/files/kipoi-docker_sharedpy3keras1.2.sif?download=1",
+        "name": "kipoi-docker_sharedpy3keras1.2",
+        "md5": "cd748bae471b6af0b2cdaecca1e1c6ac"
     },
     "CpGenie": {
         "url": "https://zenodo.org/record/5644005/files/kipoi-docker_sharedpy3keras1.2.sif?download=1",