pset1nik 0.1.4
pset1 test

# Pset 1

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## Objectives

In this problem set you will:

* Use [Pipenv](https://pipenv.pypa.io/en/latest/) to build and manage your
application

* Further explore CI/CD, pulling data from AWS S3 and performing an analysis

* Use decorators and context managers to implement an atomic write and pset
submission

* Dip your toes into hashing and parquet, which will be important in many of
our problem sets

<!-- START doctoc generated TOC please keep comment here to allow auto update -->
<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
**Table of Contents**  *generated with [DocToc](https://github.com/thlorenz/doctoc)*

- [Before you begin...](#before-you-begin)
  - [Document code and read documentation](#document-code-and-read-documentation)
  - [Docker shortcut](#docker-shortcut)
  - [Pipenv](#pipenv)
    - [Installation](#installation)
    - [Usage](#usage)
      - [Debugging pipenv installs](#debugging-pipenv-installs)
      - [Pipenv inside docker](#pipenv-inside-docker)
  - [Credentials and data](#credentials-and-data)
    - [Using `awscli`](#using-awscli)
      - [Installation (via pipenv)](#installation-via-pipenv)
    - [Configure `awscli` locally](#configure-awscli-locally)
      - [Make a .env (pronounced "dotenv") file](#make-a-env-pronounced-dotenv-file)
        - [Caveats](#caveats)
      - [Global config](#global-config)
    - [Copy the data locally](#copy-the-data-locally)
    - [Set the Travis environment variables](#set-the-travis-environment-variables)
- [Problems](#problems)
  - [Canvas helpers](#canvas-helpers)
  - [Hashed strings](#hashed-strings)
    - [Implement a standardized string hash](#implement-a-standardized-string-hash)
    - [Salt and Pepper](#salt-and-pepper)
  - [Atomic writes](#atomic-writes)
    - [Implement an atomic write](#implement-an-atomic-write)
  - [Parquet](#parquet)
  - [Your main script and submission context manager](#your-main-script-and-submission-context-manager)

<!-- END doctoc generated TOC please keep comment here to allow auto update -->

## Before you begin...

***Add your Build and Code Climate badges*** to the top of this README, using the
markdown template for your master branch.  If you  are not using Travis,
replace with a build badge for the appropriate service.

### Document code and read documentation

For some problems we have provided starter code. Please look carefully at the
doc strings and follow all input and output specifications.

For other problems, we might ask you to create new functions, please document
them using doc strings! Documentation factors into the "python quality" portion
of your grade.

### Docker shortcut

See [drun_app](./drun_app):

```bash
docker-compose build
./drun_app python # Equivalent to docker-compose run app python
```

### Pipenv

This pset will require dependencies.  Rather than using a requirements.txt, we
will use [pipenv](https://pipenv.readthedocs.io/en/latest/) to give us a pure,
repeatable, application environment.

#### Installation

If you are using the Docker environment, you should be good to go.  Mac/windows
users should [install
pipenv](https://pipenv.readthedocs.io/en/latest/#install-pipenv-today) into
their main python environment as instructed.  If you need a new python
environment, you can use a base
[conda](https://docs.conda.io/en/latest/miniconda.html) installation.  See
Canvas for instructions.

```bash
pipenv install --dev
pipenv run python some_python_file
```

If you get a TypeError, see [this
issue](https://github.com/pypa/pipenv/issues/3363)

#### Usage

Rather than `python some_file.py`, you should run `pipenv run python
some_file.py` or `pipenv shell` etc

***Never*** pip install something!  Instead you should `pipenv install pandas`
*or `pipenv install --dev pytest`.  Use `--dev` if your app only needs the
*dependency for development, not to actually do it's job.

You should ***avoid*** installing "IDE apps" like ipython or black into your
Pipenv environment - if you don't need it during CI or for the code to work, it
should not be an application dependency.

Pycharm [works great with
pipenv](https://www.jetbrains.com/help/pycharm/pipenv.html)

Be sure to commit any changes to your [Pipfile](./Pipfile) and
[Pipfile.lock](./Pipfile.lock)!

##### Debugging pipenv installs

If a pipenv install fails, it can be hard to see what the root cause is.  Try
these tips:

1. Ensure you don't have a bad package in your Pipfile (pipenv sometimes adds
them even if the install fails).  You can manually delete lines for packages you
don't want.

2. Try verbose mode, with `pipenv install -v ...`.

3. Try manually installing with `pip install ...` or `pip install -v ...`. This
will often show you the 'real' error.  If it works, don't forget to `pipenv
install ...` to ensure the dep is tracked appropriately

##### Pipenv inside docker

Because of the way docker freezes the operating system, installing a new package
within docker is a two-step process:

```bash
docker-compose build

# Now i want a new thing
./drun_app pipenv install pandas # Updates pipfile, but does not rebuild image
# running ./drun_app python -c "import pandas" will fail!

# Rebuild
docker-compose build
./drun_app python -c "import pandas" # Now this works
```

### Credentials and data

Git should be for code, not data, so we've created an S3 bucket for problem set
file distribution.  For this problem set, we've uploaded a data set of your
answers to the "experience demographics" quiz that you should have completed in
the first week. In order to access the data in S3, we need to install and
configure `awscli` both for running the code locally and running our tests in
Travis.

You should have created an IAM key in your AWS account.  DO NOT SHARE THE SECRET
KEY WITH ANYONE. It gives anyone access to the S3 bucket.  It must not be
committed to your code.

For more reference on security, see [Travis Best
Practices](https://docs.travis-ci.com/user/best-practices-security/#recommendations-on-how-to-avoid-leaking-secrets-to-build-logs)
and [Removing Sensitive
Data](https://help.github.com/articles/removing-sensitive-data-from-a-repository/).

#### Using `awscli`

AWS provides a [CLI
tool](https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-welcome.html)
that helps interact with the many different services they offer.

##### Installation (via pipenv)

We have already installed `awscli` into your pipenv.  It is available within the
pipenv shell and the docker container via the same mechanism.

```bash
pipenv run aws --help
./drun_app aws --help
```

#### Configure `awscli` locally

Now
[configure](https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-configure.html)
`awscli` to access the S3 bucket.  You have a few options for how to do so:

1. Make a .env file for you pset
2. Globally configure your client (not recommended)
3. Manually manage environment variables

Note that, regardless of the option, ***your code does not change*** - the code
assumes it is running in a pre-configured environment.  In fact, your code will
likely be configured differently on your machine vs on Travis.

Personally, for local development, I find using [named
profiles](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-profiles.html)
(eg, `AWS_PROFILE=csci_student`) the easiest, since you can configure once on
your system and then just indicate the profile for each pset.  You will likely
need to provide the raw credentials in CI/CD.

##### Make a .env (pronounced "dotenv") file

Create a [.env](.env) file that looks something like this:

```
AWS_PROFILE=XXX
AWS_ACCESS_KEY_ID=XXXX
AWS_SECRET_ACCESS_KEY=XXX
OTHER_ENV_VAR=...
```

The `.env` file should be in your root project directory, the same directory as
this README.

***DO NOT*** commit this file to the repo (it's already in your
[.gitignore](.gitignore))

Both docker and pipenv will automatically inject these variables into your
environment!  Whenever you need new env variables, add them to a dotenv. You
***DO NOT*** need to install any additional modules (notably `python-dotenv`) in
order for this to work.

See env refs for
[docker](https://docs.docker.com/compose/environment-variables/) and
[pipenv](https://pipenv.readthedocs.io/en/latest/advanced/#automatic-loading-of-env)
for more details.

###### Caveats

Beware some small 'gotchas' with dotenv files:

* Pycharm does not load them directly, even if using a pipenv interpreter.  You
can install plugins to accomplish this, or manually add the env variables to
Pycharm's run configuration.  Try not to add them to the pytest run config!

* If using `pipenv shell` or a docker shell, changes to the dotenv will not be
loaded until you exit and restart the shell

##### Global config

According to the
[documentation](https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-configure.html)
the easiest way is:

```bash
aws configure
AWS Access Key ID [None]: ACCESS_KEY
AWS Secret Access Key [None]: SECRET_KEY
Default region name [None]:
Default output format [None]:
```

However, this is not generally recommended, if you want to use a special AWS key
just for this class.  It is more secure to create a dedicated IAM user/key with
no permissions except those needed for this course.

There are other, more complicated, configurations outlined in the documentation.
Feel free to use a solution using environment variables, a credentials file, a
profile, etc.

#### Copy the data locally

Read the [Makefile](Makefile) and [.travis.yml](./.travis.yml) to see how to
copy the data locally.

Note that we are using a [Requestor
Pays](https://docs.aws.amazon.com/AmazonS3/latest/dev/RequesterPaysBuckets.html)
bucket.  You are responsible for usage charges.

You should now have a new folder called `data` in your root directory with the
data we'll use for this problem set. You can find more details breaking down
this command at the [S3 Documentation
Site](https://docs.aws.amazon.com/cli/latest/reference/s3/cp.html).

#### Set the Travis environment variables

This is Advanced Python for Data Science, so of course we also want to automate
our tests and pset using CI/CD.  Unfortunately, we can't upload our .env or run
`aws configure` and interactively enter the credentials for the Travis builds,
so we have to configure Travis to use the access credentials without
compromising the credentials in our git repo.

We've provided a working `.travis.yml` configuration that only requires the AWS
credentials when running on the master branch, but you will still need to the
final step of adding the variables for your specific pset repository.

To add environment variables to your Travis environment, you can use of the
following options:

* Navigating to the settings, eg https://travis-ci.com/csci-e-29/YOUR_PSET_REPO/settings
* The [Travis CLI](https://github.com/travis-ci/travis.rb)
* encrypting into the `.travis.yml` as instructed [here](https://docs.travis-ci.com/user/environment-variables/#defining-encrypted-variables-in-travisyml).

Preferably, you should only make your 'prod' credentials available on your
master branch: [Travis
Settings](https://docs.travis-ci.com/user/environment-variables/#defining-variables-in-repository-settings)

You can chose the method you think is most appropriate.  Our only requirement is
that ***THE KEYS SHOULD NOT BE COMMITTED TO YOUR REPO IN PLAIN TEXT ANYWHERE***.

For more information, check out the [Travis Documentation on Environment
Variables](https://docs.travis-ci.com/user/environment-variables/)

__*IMPORTANT*__: If you find yourself getting stuck or running into issues,
please post on Piazza and ask for help.  We've provided most of the instructions
necessary for this step and do not want you spinning your wheels too long just
trying to download the data.

## Problems

### Canvas helpers

Note the module [pset_1/canvas.py](src/pset1/canvas.py).  As you complete this
problem set, think about anything you do which is a generalized utility for
Canvas (eg, you might want to reuse in your next psets).  Write those functions
in this module for now.

You should stick with using
[canvasapi](https://canvasapi.readthedocs.io/en/stable/) (unless you find
something better!).  Use the python code to help you understand the API!

Example functions you may want to write here:

* Get an active canvas course by name (`-> canvasapi.course.Course`).  Note the
many helper functions on the `Course` class.

* Get an assignment or quiz by name (`canvasapi.assignment.Assignment` and
`canvasapi.quiz.Quiz`).  Note that every quiz is also an assignment, with
`is_quiz=True` and `quiz_id` properties.

* Take a quiz or submit an assignment (at least the generalizable parts).

### Hashed strings

It can be extremely useful to
[hash](https://en.wikipedia.org/wiki/Cryptographic_hash_function) a string or
other data for various reasons - to distribute/partition it, to anonymize it, or
otherwise conceal the content.

#### Implement a standardized string hash

Use `sha256` as the backbone algorithm from
[hashlib](https://docs.python.org/3/library/hashlib.html). Hashlib is part of
the Python standard library, so you do not have to install it in order to import
it into your modules.

A `salt` is a prefix that may be added to increase the randomness or otherwise
change the outcome.  It may be a `str` or `bytes` string, or empty.

Implement it in [hash_str.py](src/pset1/hash_str.py), where the return value is the
`.digest()` of the hash, as a `bytes` array:

```python
def hash_str(some_val: Union[str, bytes], salt: Union[str, bytes] = "") -> bytes:
    """Converts strings to hash digest

    See: https://en.wikipedia.org/wiki/Salt_(cryptography)

    :param some_val: thing to hash, can be str or bytes
    :param salt: Add randomness to the hashing, can be str or bytes
    :return: sha256 hash digest of some_val with salt, type bytes
    """
```

Note you will need to
[encode](https://docs.python.org/3/library/stdtypes.html#str.encode) string
values into bytes (use `.encode()`!).

As an example, `hash_str('world!', salt='hello, ').hex()[:6] == '68e656'`

Note that if we ever ask you for a bytes value in Canvas, the expectation is the
hexadecimal representation as illustrated above.

#### Salt and Pepper

Note, however, that hashing isn't very secure without a secure salt.  We can
take raw `bytes` to get something with more entropy than standard text provides.

Let's designate an environment variable, `CSCI_SALT`, which will contain
[hex-encoded](https://en.wikipedia.org/wiki/Hexadecimal) bytes (be careful here
- `'68e656'.encode()` is not treating the input as hexadecimal!).

Implement the function `pset_1.hash_str.get_csci_salt`
which pulls and decodes an environment variable.  In Canvas, you will be given a
random salt taken from [random.org](http://random.org) for real security.

Additionally, we will add a per-course
[pepper](https://en.wikipedia.org/wiki/Pepper_(cryptography)), which we will
define as the UUID of the current canvas course.  You will fetch this from the
Canvas API.  Implement the function `get_csci_pepper`.  This will be added to
the salt to form the final 'salt' used for secure hashing.

(Note, the author is not a master cryptographer!  We may be abusing the terms
'salt' and 'pepper')

### Atomic writes

Use the module `pset_1.io`.  We will implement an atomic writer.

Atomic writes are used to ensure we never have an incomplete file output.
Basically, they perform the operations:

1. Create a temporary file which is unique (possibly involving a random file
   name)
2. Allow the code to take its sweet time writing to the file
3. Rename the file to the target destination name.

If the target and temporary file are on the same filesystem, the rename
operation is ***atomic*** - that is, it can only completely succeed or fail
entirely, and you can never be left with a bad file state.

See notes in
[Luigi](https://luigi.readthedocs.io/en/stable/luigi_patterns.html#atomic-writes-problem)
and the [Thanksgiving
Bug](https://www.arashrouhani.com/luigi-budapest-bi-oct-2015/#/21)

#### Implement an atomic write

Start with the following in [io.py](src/pset1/io.py):

```python
@contextmanager
def atomic_write(file: Union[str, os.PathLike], mode: str="w", as_file: bool=True, **kwargs) -> ContextManager:
    """Write a file atomically

    :param file: str or :class:`os.PathLike` target to write

    :param bool as_file:  if True, the yielded object is a :class:File.
        (eg, what you get with `open(...)`).  Otherwise, it will be the
        temporary file path string

    :param kwargs: anything else needed to open the file

    :raises: FileExistsError if target exists

    Example::

        with atomic_write("hello.txt") as f:
            f.write("world!")

    """
    ...
```

 Key considerations:

 * You can use [tempfile](https://docs.python.org/3.6/library/tempfile.html),
   write to the same directory as the target, or both.
   What are the tradeoffs? Add code comments for anything critical
 * Ensure the file does not already exist before you begin writing
 * Ensure the file is deleted if the writing code fails
 * Ensure the temporary file has the same extension(s) as the target.  This is
   important for any code that may infer something from the path (for example,
   extensions can have multiple periods such as `.tar.gz`).
 * If the writing code fails and you try again, the temp file should be new -
   you don't want the context to reopen the same temp file.
 * Others?

 Ensure these considerations are reflected in your unit tests!

***Every file written in this class must be written atomically, via this
function or otherwise.***

### Parquet

Excel is a very poor file format compared to modern column stores.
In [__main__.py](src/pset1/__main__.py) use
[Parquet via Pandas](https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#parquet)
to transform the provided excel file into a better format.

The user id is already hashed for you in this file.  However, you should set the
index to the user ID and sort by that value before writing.

The new file should keep the same name, but with the extension changed to
`.parquet`. The new file should otherwise keep the same path as the original
file.

Ensure you use your atomic write (consider using `as_file=False` with
`.to_parquet`).  If the file exists already, you do not need to write it out
again.

In [__main__.py](src/pset1/__main__.py) read back ***just the hashed id column***
and print it. ***DO NOT*** read the entire data set!

### Your main script and submission context manager

Implement top level execution in [pset_1/\__main__.py](src/pset1/__main__.py) to
show your work, answer the submission quiz, and submit the assignment to Canvas
via CI/CD.  It can be invoked with `python -m pset_1`.

Take a look at the `submit.py` from Pset 0.  You must submit the same metadata
along with your submission.  Copy over any relevant code into one or more
modules in this pset.  Think about how you can improve or generalize the code.

In addition to any other improvements you make, you should rewrite the
submission (`try...finally`) using a context manager.  Think about what args you
should pass to enter the context, and what context object you might want to
yield:

```python
with pset_submission(...) as ...:
    ...
```

Ensure the assignment is NOT submitted if the quiz submission fails!

We will use this construct for all future psets, so try to maximize the amount
of generic pset work that gets done in the context manager!