Rewrite CLI (#71)

* Updates CLI functions

Author: Måns Magnusson

.gitignore

@@ -51,6 +51,7 @@ _DEVELOP/
 # Editors
 *.sublime-workspace
 .tm_properties
+.idea
 
 # project files should be version controlled, unless a significant
 # proportion of contributors will probably not be using SublimeText

.pre-commit-config.yaml

@@ -1,5 +1,6 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 20.8b1
     hooks:
       - id: black
+        args: [--line-length=100]

CHANGELOG.md

@@ -6,12 +6,9 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
 Please add a new candidate release at the top after changing the latest one. Feel free to copy paste from the "squash and commit" box that gets generated when creating PRs
 
-## [x.x.x]
-### Added
-
-### Fixed
-
+## [3.0]
 ### Changed
+- Reworks the CLI for complete API functionality
 
 ## [2.7.5]
 ### Added

DEPLOYMENT.md

@@ -1,26 +1,35 @@
-# Steps
-
-When all tests done and successful and PR is approved, follow these steps:
-
-1. Bump version:
-    1. Merge branch to master
-    1. In your local git version of this repo
-        1. Checkout master by: `git checkout master`
-        1. Update local branch by: `git pull origin master`
-        1. Bumpversion according to specifications, eg. `bumpversion <patch/minor/major>`
-        1. Push commit directly to master `git push`
-        1. Push commit directly to master `git push --tag`
-1. Deploy on the appropriate server(s):
-    1. Deploy on hasta:
-        1. Deploy master to stage
-            1. `ssh hasta`
-            1. `us`
-            1. Request stage environment `paxa` and follow instructions
-            1. `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-housekeeper-stage.sh master`
-            1. Make sure that installation was successful
-            1. `down`
-        1. Deploy master to production
-            1. `up`
-            1. `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-housekeeper-prod.sh`
-            1. Make sure that installation was successful
-1. Take a screenshot and post as a comment on the PR. Screenshot should include environment and that it succeeded
+# Deployment guide
+This includes instructions for deploying Houskeeper in the Clinical Genomics :hospital: setting. General instructions for deployment is in the [development guide][development-guide]
+
+## Branch model
+
+Housekeeper if following the [GitHub flow][gh-flow] branching model which means that every time a PR is merged to master a new release is created.
+
+## Requirements
+
+- `bumpversion`, install with `pip install bumpversion`
+
+## Steps
+
+1. Check in the PR if the change is a minor, mayor or patch: ![Version][pr-version]
+1. Make sure you are on `master` (`git checkout master`) and bump version according to step 1, example: `bumpversion minor`
+1. Push the commit: `git push`
+1. Push the tag: `git push --tags`
+1. First deploy on stage so log into hasta and run:
+    - `us`
+    - `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-housekeeper-stage.sh master`
+1. Deploy in productions by running the following commands:
+    - `down`
+    - `up`
+    - `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-housekeeper-prod.sh`
+1. Take a screen shot that includes the name of the environment and publish it as a comment on the PR: ![Deployed][confirm-deploy]
+1. Great job :whale2:
+
+
+
+
+
+[pr-version]: docs/img/version.png
+[confirm-deploy]: docs/img/confirm_deploy.png
+[development-guide]: http://www.clinicalgenomics.se/development/publish/prod/
+[gh-flow]: http://www.clinicalgenomics.se/development/dev/models/#rolling-release-github-flow

Pipfile

@@ -6,7 +6,7 @@ verify_ssl = true
 [dev-packages]
 pytest = "*"
 pytest-mock = "*"
-
+pre-commit = "*"
 
 [packages]
 alchy = "*"
@@ -16,6 +16,7 @@ marshmallow = "*"
 "ruamel.yaml" = "*"
 SQLAlchemy = "*"
 pytest-cov = "*"
+rich = "*"
 
 [requires]
 python_version = "3.7"