Candidate v2 (purple) release

Align production with staging (#555)

* Some changes to cset_upload.py to allow site observation short codes (#527)

* stashing

* fix: cset_upload.py updated to allow new-style site observation codes

NB! this probably still won't work! I suspect the file I was given is
broken and I cannot test it further

* stashing

* stashing

* Short code prefix and tooltip to backend

Target loader now reads short code prefix and tooltip from
meta_aligner.yaml. Tooltip is saved to Experiment model.

TODO: make tooltip available via API

* Prefix tooltip now serverd by api/site_observation

* stashing

* Site observation groups for shortcodes now by experiment

* feat: download structure fixed

TODO: add all the yamls

* All yaml files added to download

* New format to download zip (issue 1326) (#530)

* stashing

* stashing

* feat: download structure fixed

TODO: add all the yamls

* All yaml files added to download

* cset_upload.py: lhs_pdb renamed to ref_pdb

* Renamed canon- and conf site tags

* Adds support for key-based SSH connections (#534)

* Centralised environment variables (#529)

* refactor: Restructured settings.py

* docs: Minor tweaks

* refactor: Move security and infection config to settings

* refactor: b/e & f/e/ tags now in settings (also fixed f/e tag value)

* refactor: Move Neo4j config to settings

* refactor: More variables into settings

* refactor: Moved remaining config

* docs: Adds configuration guide as comments

* docs: Variable prefix now 'stack_' not 'stack_env_'

---------

Co-authored-by: Alan Christie <[email protected]>

* feat: Adds support for private keys on SSH tunnel

* fix: Fixes key-based logic

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Co-authored-by: Alan Christie <[email protected]>

* build(deps): bump cryptography from 42.0.0 to 42.0.2 (#533)

Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.0 to 42.0.2.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pyca/cryptography/compare/42.0.0...42.0.2)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* docs: Updates documentation (#536)

Co-authored-by: Alan Christie <[email protected]>

* build(deps): bump django from 3.2.20 to 3.2.24 (#535)

Bumps [django](https://github.com/django/django) from 3.2.20 to 3.2.24.
- [Commits](https://github.com/django/django/compare/3.2.20...3.2.24)

---
updated-dependencies:
- dependency-name: django
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* fix: reverting wrong changes

* fix: reverting wrong changes (#538)

* stashing

* add site observation's ligand sdf to aligned_files

* fix: custom pdb now downloadable

* fix: increased loglevel to error on unexpected exceptions block

* fix: Discourse service check now checks API key before creating a service (#544)

Co-authored-by: Alan Christie <[email protected]>

* build(deps): bump cryptography from 42.0.2 to 42.0.4 (#539)

Bumps [cryptography](https://github.com/pyca/cryptography) from 42.0.2 to 42.0.4.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pyca/cryptography/compare/42.0.2...42.0.4)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* metadata.csv populated

Started working on issue 1355 as well, it's too tightly coupled. Some
work remaining re that:
- when tag created in UI, make sure upload_name attribute is populated

* upload_name automatically pouplated when creating tags in UI

Only populated on creation, updates won't touch it

* changes to api/download_structures

- apo_file, bound_file, sdf_info and smiles_info merged into
all_aligned_structures
- added pdb_info field

NB! download_structures was requred to provide ligand_pdb as
well. This wasn't tracked previously, so I added field to
SiteObservation model. Meaning there's a migration and on stack
deployment data needs to be wiped and reuploaded

* don't download neighbourhoods.yaml unless trans_matrix_info is checked

* fixed error handling (errors.csv) and not returning combined sdf

* fix: Added parsing directives to DownloadStructuresserializer

* Consecutive numbering of observations under canon site

* SiteObservatdion.tag split to tag and tag_prefix (1361)

* fix: crystallographic_files folders in download now sans suffix (#550)

* fix: tag names underdand prefix in download's metadata.csv

* fix: return all proteins listed in api/download_structures

* fix: fixed 'All structures' option not working in download dialog

* Migrations for new file fields

* Issue 1326 - mol and smiles added to download bundle

NB! not prodction/staging ready, still contains a hack for testing
because XCA doesn't provide all the attributes.

* Target loader should handle empty code_prefix and tooltip

'Should' because haven't tested yet with real data

* Column 'Downloaded' to metadata.csv in downloads

* fix: restore 'upload_name' in site obvs tags to prefix-tag format

* Removed ligand_smiles workaround

All necessary files are now tracked by the database and returned in download.

* fix: Add force_error_display to connection functions (default False) (#559)

Co-authored-by: Alan Christie <[email protected]>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Kalev Takkis <[email protected]>
Co-authored-by: Warren Thompson <[email protected]>
Co-authored-by: Alan Christie <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Warren Thompson <[email protected]>