Bdbag

* Added a monkeypatch for `hashlib.algorithms_guaranteed` prior to the
import of any `bagit` code so that `bagit-1.7.0` (which assumes
`algorithms_guaranteed` is present, but in reality only _consistently_
exists on Python 2.7.9 or greater) can still be used by `bdbag` on
systems that only have Python 2.7.0 to 2.7.8 installed.
Lifted the strict pin on Python>=2.7.9. Note that this won't make
standalone `bagit` installations work on these systems, but it will
allow `bdbag` to successfully import and use `bagit` as a library.
Additional notes
[here](https://github.com/fair-research/bdbag/commit/86517b9ba89524c3e1328eea7f4537552f0af82e#commitcomment-31548879).

* Added code to properly url encode whitespace and other illegal
characters in the `filename` field of `fetch.txt`, per the `bagit` spec.
This will automatically be encoded when `bdbag` generates a bag from a
`remote-file-manifest`, and will automatically decoded when attempting
to resolve files via fetch. Added a corresponding unit test.
* Added a new CLI validate option: `--completeness`. This is in parity
with `bagit` CLI options and is useful primarily for determining which
files in `fetch.txt` have not yet been retrieved. Added a corresponding
unit test.
* Added code in the CLIs to print stack traces in when `--debug` is
specified.

* Fixed bug with `bdbagit.save()` and "strict mode" version check logic
that prohibited mixing of checksum types for payload files when the
`bagit` specification version of the bag being updated was < `1.0`.
Added a unit test that would have caught it.

__Milestone feature release__

* Added `materialize` CLI and API function. The materialize function is
basically a bag bootstrapper. When invoked, it will attempt to fully
_reconstitute_ a bag by performing multiple actions depending on the
context of the input `path` parameter. If `path` is a URL or a URI of a
resolvable identifier scheme, the file referenced by this value will
first be downloaded to the current directory. Next, if the `path` value
(or previously downloaded file) is a local path to a supported archive
format, the archive will be extracted to the current directory. Then,
if the `path` value (or previously extracted file) is a valid bag
directory, any remote file references contained within the bag's
`fetch.txt` file will attempt to be resolved. Finally, full validation
will be run on the materialized bag. If any one of these steps fail,
an error is raised.

* Refactored identifier resolution into a modular plug-in system. Added
support for DOI and DataGUID identifier schemes in addition to existing
ARK/Minid schemes. Additional schemes can be supported by creating a
compliant "plug-in" resolver class and configuring it via the
`bdbag.json` configuration file.

* Bagit specification version compliance is now configurable. The
default specification version used is `0.97` which permits heterogeneous
mixing of checksums in bag payload manifests. Addresses
[27](https://github.com/fair-research/bdbag/issues/27) and reverts the
restriction introduced in release `1.3.0`.

* Implement cloud storage fetch transports for access to secured Amazon
S3 and Google Cloud Store via `boto3` library. GCS bucket and object
access via `boto3` is only supported when the target GCS bucket is set
to "interoperability mode". The `boto3` library is an optional runtime
dependency and need only be installed if support for automatic download
of `S3` or `GS` URLs from `fetch.txt` entries is desired. Various
parameters relating to the operation of this fetch handler are exposed
via the `bdbag.json` configuration file and can be tuned accordingly.
Addresses [25](https://github.com/fair-research/bdbag/issues/25).

* Numerous improvements to HTTP fetch handler:

* Support for "Authorization" header based authentication via
the `keychain.json` configuration file. This authentication mode
allows for Bearer Token authentication scenarios such as those
used in OAuth 2.0 authorization flows.
* Improved handling for cookie-based authentication. Added a
configurable mechanism that scans for multiple
Mozilla/Netscape/CURL/WGET compatible cookie files, merges them, and
automatically uses them in outbound HTTP fetch requests.
* Exposed some of the `requests` module's session parameters in the
`bdbag.json` configuration file. This allows for tuning such values
as connect/read retry count, backoff factor, and the status code
retry forcelist, along with the option of disabling automatic
redirect following.

* Refactored `bdbag.json` configuration file processing into a separate
module and significantly increased the scope of the configuration file.
Added a basic mechanism for versioning the configuration file and
upgrading existing config files to newer versions while preserving
backward-compatible configuration settings, when possible.

* Improved unit test coverage.

* Updated documentation.

* Fix bug when no expr passed to filter_dict(), missed from code refactor.

* Add partial (selective) fetch functionality to API and CLI per
[20](https://github.com/fair-research/bdbag/issues/20).
* Add an API and CLI function to automatically generate a basic RO
manifest via bag introspection.
* Add 'Bagging-Time' as a default bag-info metadata element.
* Allow 'url' field in remote file manifest to be an array as well as a
string, but only read array[0] when generating fetch.txt.
* Add logic to allow an RO manifest object to be "updated" without
generating new unique URNs for existing nodes.
* Fixed some issues with keychain handling and HTTP fetch handler.
* Changed `globus-sdk` to a run-time dependency.
* Numerous functional changes to bdbag-utils. New create-rfm-from-file
function that can create an RFM by parsing a CSV file.
Added documentation [here](https://github.com/fair-research/bdbag/blob/master/doc/utils.md).
* Added additional unit tests
(copied over from https://github.com/LibraryOfCongress/bagit-python/blob/master/test.py,
with modifications) for additional coverage of bdbagit.py.
* Improved unit test coverage.
* Update docs.

* Enhanced RO/JSON-LD tagfile metadata support. Additions to the CLI and
API now support the creation of the RO tagfile metadata directory and
any associated JSON-LD files from a single JSON "meta-manifest".
Coupling this with `remote-file-manifest`-based bag creation allows for
entirely remote payloads but with local RO/JSON-LD metadata using only
two metadata input files.
* Refactored the overridden manifest saving functions in `bdbagit.py` to
be more inline with the current `bagit` approach and upcoming `bagit`
1.0 spec changes.

IMPORTANT NOTES:
* Due to this change, it will no longer be possible to create/update
bags using multiple checksum manifests unless _every_ file in the
payload is listed in _every_ payload manifest. In other words, it
now is an error condition to specify more than one checksum
algorithm (e.g., both `md5` and `sha256`) and not be able to
calculate or provide all specified checksum types for each payload
file, including those listed in `fetch.txt`.
* The primary impact of this change is the creation of bags via
`remote-file-manifest`, since the checksums for these files must be
known _a priori_ and therefore _all_ remote file references must
provide the same checksum algorithm type(s) uniformly across the
entire set of payload files.

* Allow the `bag-info.txt` metadata value `Contact-Orcid` to be
specified when using the CLI via the argument `--contact-orcid`.
* Fixed an issue with the handling of the `metadata` and `metadata_file`
arguments of `make_bag` that allowed for arbitrarily complex JSON
content as `bag-info.txt` lines. Per the `bagit` spec, only string
values are supported.
* Ensure URL escaping (of whitespace only) in generated `fetch.txt`
URLs, per `bagit` spec.
* Build universal (Python 2 and 3 compat.) wheels by default.
Fixes [19](https://github.com/fair-research/bdbag/issues/19)