docs: updating README, adding terraform docs

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020-2021, Manuel Holtgrewe
+Copyright (c) 2020-2023, Berlin Institute of Health, Manuel Holtgrewe
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -4,39 +4,35 @@
 
 # VarFish CLI
 
-Command line interface for [VarFishServer](https://github.com/bihealth/varfish-server).
+Command line interface for [bihealth/varfish-server](https://github.com/bihealth/varfish-server).
 
-## Getting Started
+> [!NOTE]
+> This repository focuses on the command line interface program `varfish-cli`.
+> If you are new to VarFish, you may want to start at the repository [bihealth/varfish-server](https://github.com/bihealth/varfish-server).
 
-- [VarFish Homepage](https://www.cubi.bihealth.org/software/varfish/)
-- [Manual](https://varfish-server.readthedocs.io/en/latest/)
-    - [Installation Instructions](https://varfish-server.readthedocs.io/en/latest/admin_install.html)
-- [Docker Compose Installer](https://github.com/bihealth/varfish-docker-compose#run-varfish-server-using-docker-compose)
+## Installation
 
-## VarFish Repositories
+You can install `varfish-cli` from [bioconda](https://bioconda.github.io/):
 
-- [varfish-server](https://github.com/bihealth/varfish-server) --
-  The VarFish Server is the web frontend used by the end users / data analysts.
-- [varfish-annotator](https://github.com/bihealth/varfish-annotator) --
-  The VarFish Annotator is a command line utility used for annotating VCF files and converting them to files that can be imported into VarFish Server.
-- [varfish-cli](https://github.com/bihealth/varfish-cli) --
-  The VarFish Command Line Interface allows to import data through the VarFish REST API.
-- [varfish-db-downloader](https://github.com/bihealth/varfish-db-downloader) --
-  The VarFish DB Downloader is a command line tool for downloading the background database.
-- [varfish-docker-compose](https://github.com/bihealth/varfish-docker-compose) --
-  Quickly get started running a VarFish server by using Docker Compose.
-  We provide a prebuilt data set with some already imported data.
+To create a new conda environment named `varfish-cli` with the package:
 
-## Installation
+```
+mamba create -y -n varfish-cli -c bioconda varfish-cli
+conda activate varfish-cli
+varfish-cli --help
+```
 
-### From Source
+To get help with individual sub commands:
+
+```
+varfish-cli importer
+# OR
+varfish-cli importer --help
+```
 
-```bash
-$ git clone [email protected]:bihealth/varfish-cli.git
-$ cd varfish-cli
-$ conda create -n varfish-cli python=3.7
-$ conda activate varfish-cli
-$ pip install -e .
+You will also need to create a configuration file in your home folder with the server address:
+
+```
 $ cat >~/.varfishrc.toml <<EOF
 [global]
 
@@ -47,14 +43,34 @@ varfish_api_token = "XXX"
 EOF
 ```
 
-### Using pip
+## Developer Information
+
+### Development Setup
+
+Preqrequisites:
+
+- Python >=3.10
+
+Clone the repository:
+
+```
+git clone [email protected]:bihealth/varfish-cli.git
+cd varfish-cli-ng
+```
+
+Now, create a virtualenv and install the software and its development requirements:
 
+```
+virtualenv venv
+source venv/bin/activate
+
+pip install -r requirements/develop.txt
+pip install -e .
+```
 
-`varfish-cli` is also available as a pip-Package.
-Preferably install into a separate venv.
+Finally, create the configuration file:
 
-```bash
-$ pip install varfish-cli
+```
 $ cat >~/.varfishrc.toml <<EOF
 [global]
 
@@ -64,3 +80,18 @@ varfish_server_url = "https://varfish.example.com/"
 varfish_api_token = "XXX"
 EOF
 ```
+
+### GitHub Project Management with Terraform
+
+```
+export GITHUB_OWNER=bihealth
+export GITHUB_TOKEN=ghp_<thetoken>
+
+cd utils/terraform
+terraform init
+terraform import github_repository.varfish-cli varfish-cli
+terraform validate
+terraform fmt
+terraform plan
+terraform apply
+```

codecov.yml

@@ -0,0 +1,27 @@
+# For more configuration details:
+# https://docs.codecov.io/docs/codecov-yaml
+
+# Check if this file is valid by running in bash:
+# curl -X POST --data-binary @.codecov.yml https://codecov.io/validate
+
+# Coverage configuration
+# ----------------------
+coverage:
+  status:
+    patch: false
+
+  range: 70..80     # First number represents red, and second represents green
+                    # (default is 70..100)
+  round: down       # up, down, or nearest
+  precision: 2      # Number of decimal places, between 0 and 5
+
+# Ignoring Paths
+# --------------
+# which folders/files to ignore
+
+# Pull request comments:
+# ----------------------
+# Diff is the Coverage Diff of the pull request.
+# Files are the files impacted by the pull request
+comment:
+  layout: diff, files  # accepted in any order: reach, diff, flags, and/or files

utils/terraform/.gitignore

@@ -0,0 +1,2 @@
+.terraform*
+terraform.tfstate*

utils/terraform/main.tf

@@ -0,0 +1,30 @@
+# Mangement of the GitHub project.
+
+resource "github_repository" "varfish-cli" {
+  name         = "varfish-cli"
+  description  = "VarFish REST API client (CLI + Python package)"
+  homepage_url = "https://github.com/bihealth/varfish-cli"
+  visibility   = "public"
+  topics = [
+    "bioinformatics",
+    "genetics",
+    "varfish",
+    "vcf",
+  ]
+
+  has_issues      = true
+  has_downloads   = true
+  has_discussions = false
+  has_projects    = false
+
+  allow_auto_merge   = true
+  allow_rebase_merge = false
+  allow_merge_commit = false
+
+  delete_branch_on_merge = true
+
+  vulnerability_alerts = true
+
+  squash_merge_commit_message = "BLANK"
+  squash_merge_commit_title   = "PR_TITLE"
+}

utils/terraform/provider.tf

@@ -0,0 +1,9 @@
+terraform {
+  required_providers {
+    github = {
+      source = "integrations/github"
+    }
+  }
+}
+
+provider "github" {}