Deprecate repository DataBiosphere/azul#2897 (#526)

Remove dss-prod from testing (#522)
Update hca/dss/util/__init__.py
remove EACCES, improve explanatory comments
remove link to documentation
fall back to copying when os.link raises error
Close file handlers after use
Add specific version of gitdb2 dependency (#514)

pin docutils in requirements.txt (#511)

Remove references to query service (#504)

Allow user-specified bundle uuid for upload(). (#499)
Add `httpie` as dev requirement (#495)
Fix some progress bar tests failing silently

Move and refactor broken hardlink tests

Add TestCase that creates and uses a temp dir
Set maxDiff for client tests
Fix duplicate downloads (#450)
Fix parallel download test to reveal linking bug
Consolidate test code
DSS Subscriptions: Callback Url (#492)
Remove optional args from super calls
Work around link limit for manifest download (#427)
Refactor mocked call in test methods
Rename test case
Use proper configurations for csv reading/writing (#427)
Remove outdated comment
Prettify the contents of bundle.json (#444)
Add API/CLI tutorial pages to Sphinx documentation (#472)
Fix dss download docstring to use correct flags (#486)
Fix documentation - remove extra periods between paragraphs (#460)
Refresh session token when the jwt expires. (#446)
update version number to revert #476 (#484)
Fix import dependencies (#483)
Reposition import. (#482)
Fix version numbering (#476)
change flags starting with - to start with -- (#480)
Fix sub-command description indentation in sphinx docs (#479)
auto pagination (#465)
update required python version to 3.5+ (#459)
Add Fusillade API client (#417)

- Improvements to package dependency lists (#463)

- Unpin cryptography dependency and set min version to 2.6.1 (#462)

- PaginatingClientMethodFactory: Use configurable paginated content keys (#457)

- Swagger client parser fixes (#451)

- Adding header values into request when values are present in req_args (#447)

- Add progress bar to `hca dss upload` (closes #117)

- Deprecate python2.7 (remove python2.7 testing). (#430)

- Modify how HCA cache is cleared (#431)

- Fix pagination bug in download-collection

- Add query service to documentation (#421)

- Remove POST /search retry logic (reverts b2a87f) (#429)

- Rename path builder to make dirs

- Refactor download (#406)

- Autodocs: call all SwaggerClient constructors (#416)

- added delete for login_logout (#408)

Make filters more intuitive for manifest download (#338)

Make file filters more intuitive for bundle download (#207)
Fix get collection iteration bug. (#407)
Clarify how bundle manifest can be a DSSFile
Correct bundle.json format from dict to array (#398)
Fix timestamp in bundle.json download log
Rename metadata to manifest for bundle.json download
Clarity improvement to download-collection
Update CLI integration tests for brevity
Skip download-collections tests on Windows
[easy] Help menu formatting. (#395)
Add basic support for downloading collections (closes #339)
Download bundle metadata into bundle.json (#231)

- Begin DCP Query Service CLI (#359)

Read whole file for checksumming instead of part of file.

CLI is using a blocksize that is different than upload. Changing to m…

…atch.

Update manifest structure docs (#354)