Bugzoo

Bug Fixes

* Updated `clear` of `ContainerManager` to properly delete all running
containers.
* Fixed `coverage` method in server-side `BugManager` to no longer use
removed `CoverageManager`.

Features

* Added `__contains__` to client- and server-side `BugManager`.
* Added `__delitem__` to client- and server-side `BugManager`.
* Added `head` method to client API interface.
* Added `has_image` method to client-side Docker manager.

Features

* Added `ip_address` method to client-side container manager.
* Added `mktemp` method to client-side container manager.
* Added `resolve` method to client-side file manager for resolving relative
paths to absolute paths.

Changes

* Updated RESTful API for accessing files to rely on absolute file paths.

Bug Fixes

* Updated `copy_to` to ensure that files copied to the container are owned by
the user inside the container.
* Updated `extract` function to fix a reference before assignment error.

Bug Fixes

* Fixed infinite loop in `BuildInstructions.file` by removing the method and
replacing all `.file` accesses with equivalent `.filename` accesses. Also
renamed `file_abs` to `filename_abs`.
* Fixed bug in blueprint construction that caused source name and dependent
image names to be swapped with one another.
* Fixed use-before-defined in `gcov` coverage extractor.

Features

* Added `write` method to client-side and server-side file manager.
* Individual log files for each CLI session are now saved to `.bugzoo/logs`.
* Added better error reporting to CLI, which now reports the location of the
relevant log file to the user.


Changes

* Switched implementation of command-line interface from `argparse` to
`cement`.
* Replaced `bug uninstall` command with `bug rm` and `bug remove` commands.
* Replaced `tool uninstall` command with `tool rm` and `tool remove`
commands.
* Refactored core data structures using `attrs`.
* Updated patch command to use `patch` rather than `git apply` to avoid
errors when using containers that do not have an appropriate version of
Git installed.


Bug Fixes

* Resolved permissions issue when instrumenting source files by using the
file manager's read/write API to apply coverage.