diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000000000000000000000000000000000..23e4b92b69dbf611c2bd82ba9b374a0856baeeb1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +data/** filter=lfs diff=lfs merge=lfs -text +trained_models/** filter=lfs diff=lfs merge=lfs -text diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc --- /dev/null +++ b/LICENSE @@ -0,0 +1 @@ + diff --git a/Makefile b/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..b9e6ea6df9ec70ef7a109e26f8c93ed5e545c537 --- /dev/null +++ b/Makefile @@ -0,0 +1,144 @@ +.PHONY: clean data lint requirements sync_data_to_s3 sync_data_from_s3 + +################################################################################# +# GLOBALS # +################################################################################# + +PROJECT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST)))) +BUCKET = [OPTIONAL] your-bucket-for-syncing-data (do not include 's3://') +PROFILE = default +PROJECT_NAME = decoder-code-summarization +PYTHON_INTERPRETER = python + +ifeq (,$(shell which conda)) +HAS_CONDA=False +else +HAS_CONDA=True +endif + +################################################################################# +# COMMANDS # +################################################################################# + +## Install Python Dependencies +requirements: test_environment + $(PYTHON_INTERPRETER) -m pip install -U pip setuptools wheel + $(PYTHON_INTERPRETER) -m pip install -r requirements.txt + +## Make Dataset +data: requirements + $(PYTHON_INTERPRETER) src/data/make_dataset.py data/raw data/processed + +## Delete all compiled Python files +clean: + find . -type f -name "*.py[co]" -delete + find . -type d -name "__pycache__" -delete + +## Lint using flake8 +lint: + flake8 src + +## Upload Data to S3 +sync_data_to_s3: +ifeq (default,$(PROFILE)) + aws s3 sync data/ s3://$(BUCKET)/data/ +else + aws s3 sync data/ s3://$(BUCKET)/data/ --profile $(PROFILE) +endif + +## Download Data from S3 +sync_data_from_s3: +ifeq (default,$(PROFILE)) + aws s3 sync s3://$(BUCKET)/data/ data/ +else + aws s3 sync s3://$(BUCKET)/data/ data/ --profile $(PROFILE) +endif + +## Set up python interpreter environment +create_environment: +ifeq (True,$(HAS_CONDA)) + @echo ">>> Detected conda, creating conda environment." +ifeq (3,$(findstring 3,$(PYTHON_INTERPRETER))) + conda create --name $(PROJECT_NAME) python=3 +else + conda create --name $(PROJECT_NAME) python=2.7 +endif + @echo ">>> New conda env created. Activate with:\nsource activate $(PROJECT_NAME)" +else + $(PYTHON_INTERPRETER) -m pip install -q virtualenv virtualenvwrapper + @echo ">>> Installing virtualenvwrapper if not already installed.\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 + +################################################################################# +# PROJECT RULES # +################################################################################# + + + +################################################################################# +# Self Documenting Commands # +################################################################################# + +.DEFAULT_GOAL := help + +# Inspired by +# 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 +.PHONY: help +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') diff --git a/README.md b/README.md index a2b0a2c7f7beec4ab4a636a03b42ce27bbde9bb9..262f8014fcfd2bb39385cc445fd30d326f7c3fc3 100644 --- a/README.md +++ b/README.md @@ -1 +1,54 @@ -# DECODER CODE SUMMARIZATION TOOL \ No newline at end of file +# decoder-code-summarization-development-environment + +This is a generic development environment for the development of software components and machine learning models for code summarization. + +## First steps + +The docker environment comes without pre-install packages, the basic environment is created with the following command than only needs to be executed the first time the environment is setup: + +```bash +conda env create -f environment.yml +``` + +Once the environment is created, it is preserved in between environment restarts, it can be activated as: + +```bash +conda activate tensorflow-gpu +``` + +## Train model + +In order to train the model with `hyperopt`: + +```bash +python3 src/transformers/RUN_hyperopt.py +``` + +## Model inference + +For inference: + +```bash +python3 src/transformers/RUN_inference.py +``` + +### Arguments meaning + +`Programming language` can be: +1. Java +2. C + +`Dataset mode` can be: +1. augmented: For training with data augmentation +2. use_case: With no data augmentation + +`Optimization iterations` can be: +Integer for hyperopt optimizations + +### Git LFS data + +Be careful that the LFS files tracked are downloaded when you run the scripts. If they are not downloaded, you can download all with: +```bash +git lfs pull +``` +from the root directory of this repo \ No newline at end of file diff --git a/README_cloud.md b/README_cloud.md new file mode 100644 index 0000000000000000000000000000000000000000..be50a0b81088e69ec11e18ccc4fb3d5f3ef1b3d5 --- /dev/null +++ b/README_cloud.md @@ -0,0 +1,193 @@ +decoder-code-summarization +============================== + +Machine Learning Model. Extraction of information from source code and the automatic generation of summaries to describe the goal of the different methods. + +Project Organization +------------ + + ├── LICENSE + ├── Makefile <- Makefile with commands like `make data` or `make train` + ├── README.md <- The top-level README for developers using this project. + ├── data + │   ├── external <- Data from third party sources. + │   ├── interim <- Intermediate data that has been transformed. + │   ├── processed <- The final, canonical data sets for modeling. + │   └── raw <- The original, immutable data dump. + │ + ├── docs <- A default Sphinx project; see sphinx-doc.org for details + │ + ├── models <- Trained and serialized models, model predictions, or model summaries + │ + ├── notebooks <- Jupyter notebooks. Naming convention is a number (for ordering), + │ the creator's initials, and a short `-` delimited description, e.g. + │ `1.0-jqp-initial-data-exploration`. + │ + ├── references <- Data dictionaries, manuals, and all other explanatory materials. + │ + ├── reports <- Generated analysis as HTML, PDF, LaTeX, etc. + │   └── figures <- Generated graphics and figures to be used in reporting + │ + ├── requirements.txt <- The requirements file for reproducing the analysis environment, e.g. + │ generated with `pip freeze > requirements.txt` + │ + ├── setup.py <- makes project pip installable (pip install -e .) so src can be imported + ├── src <- Source code for use in this project. + │   ├── __init__.py <- Makes src a Python module + │ │ + │   ├── data <- Scripts to download or generate data + │   │   └── make_dataset.py + │ │ + │   ├── features <- Scripts to turn raw data into features for modeling + │   │   └── build_features.py + │ │ + │   ├── models <- Scripts to train models and then use trained models to make + │ │ │ predictions + │   │   ├── predict_model.py + │   │   └── train_model.py + │ │ + │   └── visualization <- Scripts to create exploratory and results oriented visualizations + │   └── visualize.py + │ + └── tox.ini <- tox file with settings for running tox; see tox.readthedocs.io + + +-------- + +# HOW-TOs + +## How to run in local from source code + +0. Prerequisites: +- DECODER source code. +- Docker: https://docs.docker.com/engine/install/. +- Access to the internet to download data and dependencies. + +1. Navigate to decoder-code-summarization/ folder and generate DECODER Docker images: +``` +sudo docker build -f ./docker/Dockerfile -t decoder/transformer_training:latest . +``` + +2. Train the model: +``` +sudo docker run -it --rm decoder/transformer_training:latest c use_case 2 +``` +Where: + * First parameter (c) represents the use case data to use. Possible options are c and java. + * Second parameter (use_case) represents the amount of data to use. Posible options are use_case (use data coming only from use cases) or augmented (use also augmented datasets). + * Third parameter (2) represents the number of optimization iterations to use. Any integer greater than 0 is valid. + + +## Training in Amazon EC2 + +### Infrastructure setup +To train the transformers using the cloud the following Amazon services are needed: +1. Amazon Elastic Container Registry (ECR): Container registry in which to upload the Docker images that will be executed. + * Name: code_summarization_transformers + * URI: 670194352001.dkr.ecr.eu-west-3.amazonaws.com/code_summarization_transformers + +2. Amazon Simple Storage Service (S3): Service to store the output of the execution, in this case the vocabulary dictionaries of the transformers, the best model and its hyperparameters. + * Name of the bucket: decoder-transformer-training + +3. Amazon Elastic Compute Cloud (EC2): Server in which the training will take place: + * Instance type: g4dn.2xlarge (single GPU virtual machine with 32 GB of memory and 225 GB storage). + * AMI + * Public DNS: ec2-13-36-168-21.eu-west-3.compute.amazonaws.com + * The machine has already been configured to install Docker client and AWCLI with the following commands (after connecting via ssh): + * sudo apt update + * sudo apt install apt-transport-https ca-certificates curl software-properties-common + * curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - + * sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu focal stable" + * sudo apt update + * sudo apt install docker-ce + * sudo apt install awscli + + +### How to build images for uploading to Amazon ECR +**Important**: all commands below should be run from project root folder on the local machine (/decoder_code_summarization, branch amazon). +``` +sudo docker build -f ./docker/Dockerfile -t 670194352001.dkr.ecr.eu-west-3.amazonaws.com/code_summarization_transformers:latest . +``` + +### How to push and pull images to/from ECR +**Important**: First you need to authenticate aws and docker clients. + +0. Prerequisites: + - Install aws client: $ sudo apt install awscli + - Install Docker client: $ sudo apt install docker.io + - Generate AWS access KEY ID and secret Access KEY: https://console.aws.amazon.com/iam/home#/security_credentials (these are already in the folder resources/amazon from the root of the repo). + +1. Set Amazon credentials to aws client (this step should be done only once): +``` +aws configure +``` + +It will ask for: + - Access key ID + - Secret access key + - region: set to "eu-west-3" + +2. Login Docker client: +``` +sudo $(aws ecr get-login --registry-ids 670194352001 --no-include-email) +``` + +You should get a "Login Succeeded" message. + +3. Push existing image to ECR: +``` +sudo docker push 670194352001.dkr.ecr.eu-west-3.amazonaws.com/code_summarization_transformers:latest +``` + +4. Once an image is pushed to the registry it can be pulled from any machine with the following command: +``` +sudo docker pull 670194352001.dkr.ecr.eu-west-3.amazonaws.com/code_summarization_transformers:latest +``` +This has to be done once connected via ssh to the EC2 instance in order to run the docker image (see section below). + + +### How to connect to the EC2 instance via ssh and run the image +Go to the resources/amazon from the root of the repo and type: +``` +ssh -i "decoder.pem" ubuntu@ec2-13-36-168-21.eu-west-3.compute.amazonaws.com +``` + +Please note pem file permissions must be changed in order to use the file: +``` +sudo chmod 400 decoder.pem +``` + +These are the steps to follow: +1. Set Amazon credentials to aws client (you can skip this step if it has already been done before): +``` +aws configure +``` + +It will ask for: + - Access key ID + - Secret access key + - region: set to "eu-west-3" + +2. 2. Login Docker client: +``` +sudo $(aws ecr get-login --registry-ids 670194352001 --no-include-email) +``` + +3. Pull the image from the ECR registry: +``` +sudo docker pull 670194352001.dkr.ecr.eu-west-3.amazonaws.com/code_summarization_transformers:latest +``` + +4. Run the execution: +``` +sudo docker run -it --name=decoder --rm 670194352001.dkr.ecr.eu-west-3.amazonaws.com/code_summarization_transformers:latest c use_case 50 +``` + +Where: + * c represents the use case, options are: c or java + * use_case represents the data to load, options are: use_case (for only use case related data) or augmented (for training with use case data plus the augmented datasets) + * 50 represents the number of iterations for bayesian optimization. In this case 50 models will be trained and the best one will be retained. + +5. To see the logs if you want to close the local terminal: + * Connect to the EC2 instance via ssh as described in section above. + * Execute 'sudo docker logs decoder' diff --git a/data/cleaned_C_Cpp_dataset.csv b/data/cleaned_C_Cpp_dataset.csv new file mode 100644 index 0000000000000000000000000000000000000000..c8562012edb6521df5d7b61f5ee034467cf08e6a --- /dev/null +++ b/data/cleaned_C_Cpp_dataset.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0f3dc8bcecc329fdef52c376ee38f14ef4a62175f493a7b77a2d8cf30cd4b564 +size 616527434 diff --git a/data/cleaned_DeepCom_dataset.csv b/data/cleaned_DeepCom_dataset.csv new file mode 100644 index 0000000000000000000000000000000000000000..dda4aa59002ca600a2f97a4c7a5d5143fee9b336 --- /dev/null +++ b/data/cleaned_DeepCom_dataset.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ff25bc5aa2d0317cff3e6bd4a817f03ef18829d5cb3c4aeced0f9810a510892b +size 521870505 diff --git 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