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Makefile
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.PHONY: clean data lint requirements sync_data_to_s3 sync_data_from_s3
#################################################################################
# GLOBALS #
#################################################################################
BUCKET = [OPTIONAL] your-bucket-for-syncing-data (do not include 's3://')
PROJECT_NAME = Synopsys Project 2016
PYTHON_INTERPRETER = python
TENSORBOARD = tensorboard
IS_ANACONDA=$(shell python -c "import sys;t=str('anaconda' in sys.version.lower() or 'continuum' in sys.version.lower());sys.stdout.write(t)")
MODELS = src/models
VISUALIZATION = src/visualization
LOGS_DIR = models/run_logs
MODEL_NAME = ${MODEL}
# MODEL_FUNC = ${MODEL_FUNC}
MODEL_ARGS_STR = ${MODEL_ARGS}
ADDITIONAL_ARGS = ${ARGS}
WEIGHTS_DIR = models/weights
JSON_DIR = models/json
YAML_DIR = models/yaml
CSV_DIR = models/csv
IMAGES_DIR = reports/figures
TENSORBOARD_DIR = models/run_logs/tensorboard
UNIT_TESTS = src/unit_tests/*.py
# Only writes to txt file if the argument "--test-only" is not set
PRINT_TO_TXT= if !(echo $(ADDITIONAL_ARGS) | grep -q "test-only"); then \
cat .tmp | col -b >> "$(LOGS_DIR)/$(MODEL_NAME).txt"; \
fi
#################################################################################
# COMMANDS #
#################################################################################
## Install Python Dependencies
requirements: test_environment
pip install -r requirements.txt
## Make Dataset
data: requirements
$(PYTHON_INTERPRETER) src/data/make_dataset.py
## Delete all compiled Python files
clean:
find . -name "*.pyc" -exec rm {} \;
## Lint using flake8
lint:
flake8 --exclude=lib/,bin/,docs/conf.py .
## Upload Data to S3
sync_data_to_s3:
aws s3 sync data/ s3://$(BUCKET)/data/
## Download Data from S3
sync_data_from_s3:
aws s3 sync s3://$(BUCKET)/data/ data/
## Set up python interpreter environment
create_environment:
ifeq (True,$(IS_ANACONDA))
@echo ">>> Detected Anaconda, creating conda environment."
ifeq (3,$(findstring 3,$(PYTHON_INTERPRETER)))
conda create --name $(PROJECT_NAME) python=3.5
else
conda create --name $(PROJECT_NAME) python=2.7
endif
@echo ">>> New conda env created. Activate with:\nsource activate $(PROJECT_NAME)"
else
@pip install -q virtualenv virtualenvwrapper
@echo ">>> Installing virtualenvwrapper if not already intalled.\nMake sure the following lines are in shell startup file\n\
export WORKON_HOME=$$HOME/.virtualenvs\nexport PROJECT_HOME=$$HOME/Devel\nsource /usr/local/bin/virtualenvwrapper.sh\n"
@bash -c "source `which virtualenvwrapper.sh`;mkvirtualenv $(PROJECT_NAME) --python=$(PYTHON_INTERPRETER)"
@echo ">>> New virtualenv created. Activate with:\nworkon $(PROJECT_NAME)"
endif
## Test python environment is setup correctly
test_environment:
$(PYTHON_INTERPRETER) test_environment.py
#################################################################################
# USER DEFINED ENVIRONMENTS #
#################################################################################
PYTHON2.7_ENV:
source activate python2.7
PYTHON3.5_ENV:
workon python3.5;
#################################################################################
# PROJECT RULES #
#################################################################################
# Interpret special characters like backspace (^H) with `col -b`
# and write (unbuffered) run output to a txt file with the specified model name
train:
@$(PYTHON_INTERPRETER) -u $(MODELS)/train_model.py \
$(MODEL_NAME) \
$(MODEL_FUNC) \
$(WEIGHTS_DIR)/$(MODEL_NAME).hdf5 \
$(JSON_DIR)/$(MODEL_NAME).json \
$(YAML_DIR)/$(MODEL_NAME).yaml \
$(CSV_DIR)/$(MODEL_NAME).csv \
$(TENSORBOARD_DIR) \
$(MODEL_ARGS_STR) \
$(ADDITIONAL_ARGS) | tee .tmp; \
$(PRINT_TO_TXT)
# TODO: Make testing and training be from the same file
test:
@$(PYTHON_INTERPRETER) -u $(MODELS)/test_model.py \
$(MODEL_NAME) \
${MODEL_FUNC} \
$(WEIGHTS_DIR)/$(MODEL_NAME).hdf5 \
$(JSON_DIR)/$(MODEL_NAME).json \
$(YAML_DIR)/$(MODEL_NAME).yaml \
$(CSV_DIR)/$(MODEL_NAME).csv \
$(TENSORBOARD_DIR) \
$(MODEL_ARGS_STR) \
$(ADDITIONAL_ARGS) | tee .tmp;
# train_conv_net:
# MODEL_FUNC="conv_net" \
# $(MAKE) train \
# $(MAKE) plot_train_valid
#
# train_danq:
# MODEL_FUNC="DanQ" \
# $(MAKE) train \
# $(MAKE) plot_train_valid
# Execute all the python unit tests
unit_tests:
@for f in $(UNIT_TESTS); do \
python $$f; \
done
# Reformat any badly formatted (but valid) JSON or YAML representations
# of a Keras model
resave_json_yaml:
@$(PYTHON_INTERPRETER) $(MODELS)/resave_json_yaml.py \
"$(JSON_DIR)/$(MODEL_NAME).json" \
"$(YAML_DIR)/$(MODEL_NAME).yaml"
# TODO: set up tox
# Plot the training and validation losses and accuracies
plot_train_valid:
@$(PYTHON_INTERPRETER) $(VISUALIZATION)/plot_train_valid.py \
"$(CSV_DIR)/$(MODEL_NAME).csv" \
"$(IMAGES_DIR)/losses/$(MODEL_NAME)_loss.png" \
"$(IMAGES_DIR)/accuracies/$(MODEL_NAME)_acc.png"
tensorboard:
$(TENSORBOARD) --logdir=$(LOGS_DIR)/tensorboard
#################################################################################
# Self Documenting Commands #
#################################################################################
.DEFAULT_GOAL := show-help
# Inspired by <http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html>
# sed script explained:
# /^##/:
# * save line in hold space
# * purge line
# * Loop:
# * append newline + line to hold space
# * go to next line
# * if line starts with doc comment, strip comment character off and loop
# * remove target prerequisites
# * append hold space (+ newline) to line
# * replace newline plus comments by `---`
# * print line
# Separate expressions are necessary because labels cannot be delimited by
# semicolon; see <http://stackoverflow.com/a/11799865/1968>
.PHONY: show-help
show-help:
@echo "$$(tput bold)Available rules:$$(tput sgr0)"
@echo
@sed -n -e "/^## / { \
h; \
s/.*//; \
:doc" \
-e "H; \
n; \
s/^## //; \
t doc" \
-e "s/:.*//; \
G; \
s/\\n## /---/; \
s/\\n/ /g; \
p; \
}" ${MAKEFILE_LIST} \
| LC_ALL='C' sort --ignore-case \
| awk -F '---' \
-v ncol=$$(tput cols) \
-v indent=19 \
-v col_on="$$(tput setaf 6)" \
-v col_off="$$(tput sgr0)" \
'{ \
printf "%s%*s%s ", col_on, -indent, $$1, col_off; \
n = split($$2, words, " "); \
line_length = ncol - indent; \
for (i = 1; i <= n; i++) { \
line_length -= length(words[i]) + 1; \
if (line_length <= 0) { \
line_length = ncol - indent - length(words[i]) - 1; \
printf "\n%*s ", -indent, " "; \
} \
printf "%s ", words[i]; \
} \
printf "\n"; \
}' \
| more $(shell test $(shell uname) == Darwin && echo '--no-init --raw-control-chars')