Feature/logging, read-only, python style, documentation

[hexylena]

Just wanted to share the changes I've made while getting ready to run this in freiburg.

Still work-in-progress, will fix the title whenever I'm happy. I may rewrite the history before being done. Feel free to comment though!

• many python style changes
  • I've made everything flake8 compliant (minus line length since)
  • python/denbi/ was moved up to just be denbi/ which is more to my experience
  • Scripts are moved into denbi/scripts
  • setup.py is modified to be aware of the scripts, when pip installing this module, those will now be placed on the user's path for their convenience.
  • more complete .gitignore from gitignore.io
• fixes #2 adds logging whenever a modifying or destruction keystone call is made
• fixes #16 adds a --read-only flag (could be renamed, meh.) to the perun_propagation file-based script.
• documentation fixes, how to run with gunicorn if flasks's warning gives you concern.
• Makefile which has lint and test targets and serves as documentation of how to do both of those things (running tests was not otherwise documented.)
• Adds a Dockerfile
• Adds a docker-compose.yml in case you want to run a pKA/keystone locally.
• Adds sphinx based documentation
• fixes https://github.com/deNBI/perunKeystoneAdapter/issues/18

[pbelmann]

:+1: Thanks for your help improving this tool! I think we can also remove/rename the bielefeld folder since the functionality is independend of the location. @jkrue please correct me if you have different opinion. I would be happy to review your PR together with @jkrue once you are done.

[hexylena]

Added a docker file (and improved docker-compose.yml). Can now test with

curl -T perun.tgz http://127.0.0.1:5000/upload --verbose

and see something like

adapter_1   | Processing data uploaded by Perun: /tmp/perun_uploadf5bk9mz_.tar.gz
adapter_1   | INFO:denbi.bielefeld.perun.endpoint:Importing data mode=denbi_portal_compute_center users_path=/tmp/tmpllhsvmns/users.scim groups_path=/tmp/tmpllhsvmns/groups.scim
adapter_1   | INFO:denbi.bielefeld.perun.endpoint:Updating user <redacted> elixir_id=<redacted>@elixir-europe.org email=None enabled=True
adapter_1   | INFO:denbi.bielefeld.perun.endpoint:Updating user <redacted> elixir_id=<redacted>@elixir-europe.org email=None enabled=True
adapter_1   | INFO:denbi.bielefeld.perun.endpoint:Updating user <redacted> elixir_id=<redacted>@elixir-europe.org email=None enabled=True
adapter_1   | Finished processing /tmp/perun_uploadf5bk9mz_.tar.gz

in the docker-compose logs

[hexylena]

Done @pbelmann @jkrue. I've cleaned up the history and added auto-generated documentation. (Could be posted with read-the-docs or github pages, depending on preferences.)

[pbelmann]

Done @pbelmann @jkrue. I've cleaned up the history and added auto-generated documentation. (Could be posted with read-the-docs or github pages, depending on preferences.)

Nice! I will enable github pages after merge!

[hexylena]

Dunno what's wrong with the testing, some specific container variable I'm forgetting, so I've disabled it for now and we're just linting. Will re-enable (in this PR or another) whenever I get that sorted out.

[pbelmann]

@erasche can you squash and merge it? I can then create the release and register github pages.