Fix jupyter with tiny dataset and add tests (#9)

.circleci/config.yml

@@ -39,7 +39,7 @@ jobs:
           name: Install Dependencies, Configure Environment
           command: |
             pip install --user -r .circleci/requirements.txt
-            neuro config login-with-token $NEURO_TOKEN
+            neuro config login-with-token $NEURO_TOKEN $NEURO_URL
             neuro config show
 
       - run:
@@ -49,9 +49,10 @@ jobs:
             make setup __BAKE_SETUP=yes | tee
             export RUN_EXTRA="--tag=$JOBS_TAG"
 
-            make -f test.mk test_jupyter TRAINING_MACHINE_TYPE=cpu-small | tee
+            # note: with cpu-small, we get "Kernel died while waiting for execute reply"
+            make -f test.mk test_jupyter TRAINING_MACHINE_TYPE=cpu-large | tee
             make -f test.mk test_jupyter TRAINING_MACHINE_TYPE=gpu-small | tee
-            make -f test.mk test_jupyter_baked TRAINING_MACHINE_TYPE=cpu-small | tee
+            make -f test.mk test_jupyter_baked TRAINING_MACHINE_TYPE=cpu-large | tee
             make -f test.mk test_jupyter_baked TRAINING_MACHINE_TYPE=gpu-small | tee
 
       - run:
@@ -79,7 +80,7 @@ jobs:
 
       - docker/check
       - docker/push:
-          image: neuromation/ml-recipe-bone-age
+          image: $PROJECT_NAME
           tag: $CIRCLE_TAG,latest
 
 
@@ -88,14 +89,20 @@ workflows:
 
   main:
     jobs:
-      - build_and_test
+
+      - build_and_test:
+          filters:
+            tags:
+              only:
+                - /.*/
+
       - deploy:
           requires:
             - build_and_test
           filters:
             branches:
-              only:
-                - master
+              ignore:
+                - /.*/
             tags:
               only:
-                - /.*/
+                - /.*/

.circleci/requirements.txt

@@ -1 +1,2 @@
-neuromation>=20.4.6
+neuromation>=20.4.15
+certifi>=2020.4.5.1

.gitignore

@@ -127,3 +127,4 @@ dmypy.json
 
 # data/ folder
 # data/**/*
+wget-log

Makefile

@@ -6,13 +6,12 @@ CODE_DIR?=src
 NOTEBOOKS_DIR?=notebooks
 RESULTS_DIR?=results
 
-PROJECT_FILES=requirements.txt apt.txt setup.cfg
+PROJECT_FILES=requirements.txt apt.txt setup.cfg download_data.sh
 
 PROJECT_PATH_STORAGE?=storage:ml-recipe-bone-age
 
 PROJECT_PATH_ENV?=/ml-recipe-bone-age
 
-DATA_ROOT_STORAGE=storage:/neuromation/public/ml-recipe-bone-age
 DATA_ROOT_PATH_ENV=/data
 
 ##### JOB NAMES #####
@@ -129,12 +128,12 @@ training: upload-code  ### Run a training job
 	$(NEURO) run $(RUN_EXTRA) \
 		--name $(TRAINING_JOB) \
 		--preset $(TRAINING_MACHINE_TYPE) \
-		--volume $(DATA_ROOT_STORAGE):$(DATA_ROOT_PATH_ENV):ro \
 		--volume $(PROJECT_PATH_STORAGE)/$(CODE_DIR):$(PROJECT_PATH_ENV)/$(CODE_DIR):ro \
 		--volume $(PROJECT_PATH_STORAGE)/$(RESULTS_DIR):$(PROJECT_PATH_ENV)/$(RESULTS_DIR):rw \
 		--env EXPOSE_SSH=yes \
 		$(CUSTOM_ENV_NAME) \
 		bash -c 'cd $(PROJECT_PATH_ENV) && \
+		    sh download_data.sh bone-age-full.zip $(DATA_ROOT_PATH_ENV) && \
 		    python -u $(CODE_DIR)/train.py \
 		        --data_dir=$(DATA_ROOT_PATH_ENV)/data/train \
 		        --annotation_csv=$(DATA_ROOT_PATH_ENV)/data/train.csv'
@@ -155,7 +154,6 @@ jupyter: upload-code upload-notebooks ### Run a job with Jupyter Notebook and op
 		--http 8888 \
 		$(HTTP_AUTH) \
 		--browse \
-		--volume $(DATA_ROOT_STORAGE):$(DATA_ROOT_PATH_ENV):ro \
 		--volume $(PROJECT_PATH_STORAGE):$(PROJECT_PATH_ENV):rw \
 		$(CUSTOM_ENV_NAME) \
 		$(JUPYTER_CMD)
@@ -188,7 +186,6 @@ filebrowser:  ### Run a job with File Browser and open UI in the default browser
 		--http 80 \
 		$(HTTP_AUTH) \
 		--browse \
-		--volume $(DATA_ROOT_STORAGE):$(DATA_ROOT_PATH_ENV):ro \
 		--volume $(PROJECT_PATH_STORAGE):/srv:rw \
 		filebrowser/filebrowser \
 		--noauth

test.mk

@@ -13,25 +13,24 @@ CMD_NBCONVERT=\
   --to=asciidoc \
   --ExecutePreprocessor.timeout=1000 \
   --output=/tmp/out \
-  $(PROJECT_PATH_ENV)/$(NOTEBOOKS_DIR)/demo.ipynb && \
-  echo "Test succeeded: PROJECT_PATH_ENV=$(PROJECT_PATH_ENV) TRAINING_MACHINE_TYPE=$(TRAINING_MACHINE_TYPE)"
+  $(PROJECT_PATH_ENV)/$(NOTEBOOKS_DIR)/demo.ipynb
+
+SUCCESS_MSG="[+] Test succeeded: PROJECT_PATH_ENV=$(PROJECT_PATH_ENV) TRAINING_MACHINE_TYPE=$(TRAINING_MACHINE_TYPE)"
 
 
 .PHONY: test_jupyter
 test_jupyter: JUPYTER_CMD=bash -c '$(CMD_PREPARE) && $(CMD_NBCONVERT)'
 test_jupyter: jupyter
-	# kill job to set its SUCCEEDED status in platform-api
-	make kill-jupyter
+	@echo $(SUCCESS_MSG)
+
 
 .PHONY: test_jupyter_baked
 test_jupyter_baked: PROJECT_PATH_ENV=/project-local
-test_jupyter_baked: JOB_NAME=jupyter-baked-$(PROJECT_POSTFIX)
+test_jupyter_baked: JOB_NAME=$(JUPYTER_JOB)-baked
 test_jupyter_baked:
 	$(NEURO) run $(RUN_EXTRA) \
 	    --name $(JOB_NAME) \
 		--preset $(TRAINING_MACHINE_TYPE) \
-		--volume $(DATA_ROOT_STORAGE):$(DATA_ROOT_PATH_ENV):ro \
 		$(CUSTOM_ENV_NAME) \
 		bash -c '$(CMD_PREPARE) && $(CMD_NBCONVERT)'
-	# kill job to set its SUCCEEDED status in platform-api
-	$(NEURO) kill $(JOB_NAME) || :
+	@echo $(SUCCESS_MSG)