From f7fcbbcc014686ac597b783a8dcb38b43024b9d6 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 4 Aug 2023 09:28:29 +0300
Subject: Initialise the repository.

---
 .gitignore                     |  1 +
 .guix/modules/guix-package.scm | 71 ++++++++++++++++++++++++++++++++++++++++++
 README.md                      |  4 +++
 guix.scm                       |  1 +
 setup.cfg                      |  4 +++
 setup.py                       | 44 ++++++++++++++++++++++++++
 setup_commands/__init__.py     |  3 ++
 setup_commands/run_tests.py    | 40 ++++++++++++++++++++++++
 8 files changed, 168 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 .guix/modules/guix-package.scm
 create mode 100644 README.md
 create mode 120000 guix.scm
 create mode 100644 setup.cfg
 create mode 100644 setup.py
 create mode 100644 setup_commands/__init__.py
 create mode 100644 setup_commands/run_tests.py

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..565bfbc
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+/**/*~
\ No newline at end of file
diff --git a/.guix/modules/guix-package.scm b/.guix/modules/guix-package.scm
new file mode 100644
index 0000000..bda9204
--- /dev/null
+++ b/.guix/modules/guix-package.scm
@@ -0,0 +1,71 @@
+(define-module (genenetwork-auth)
+  #:use-module (guix)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system python)
+  #:use-module ((guix licenses) #:prefix license:)
+
+  #:use-module (git oid)
+  #:use-module (git bindings)
+  #:use-module (git reference)
+  #:use-module (git repository)
+
+
+  ;; Packages from guix
+  #:use-module (gnu packages check)
+
+  #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages python-crypto)
+
+  #:use-module (gnu packages databases)
+
+
+  ;; Packages from guix-bioinformatics
+  #:use-module (gn packages python-web))
+
+(define %source-dir (dirname (dirname (dirname (current-filename)))))
+
+(define (get-commit)
+  "Retrieve the commit if the source directory is a repository."
+  (if (git-predicate %source-dir)
+      (begin (let ((commit #f))
+	       (libgit2-init!)
+	       (set! commit (oid->string
+			     (reference-target
+			      (repository-head (repository-open %source-dir)))))
+	       (libgit2-shutdown!)
+	       commit))
+      "NOTAREPOSITORY"))
+
+(define (get-latest-version)
+  "Get latest version tag from repository."
+  ;; TODO: Implement
+  "v0.0.0")
+
+(define vcs-file?
+  (or (git-predicate %source-dir)
+      (const #t)))
+
+(package
+ (name "genenetwork-auth")
+ (version (string-append (get-latest-version)
+			 "-git-"
+			 (substring (get-commit) 0 9)))
+ (source (local-file %source-dir "genenetwork-auth-checkout"
+		     #:recursive? #t
+		     #:select? vcs-file?))
+ (build-system python-build-system)
+ ;; (inputs (list))
+ (native-inputs
+  (list python-pytest
+	python-pylint))
+ (propagated-inputs
+  (list python-flask
+	python-authlib
+	yoyo-migrations
+	python-argon2-cffi
+	python-email-validator))
+ (home-page "https://github.com/genenetwork/gn-auth")
+ (synopsis "Authentication and Authorisation server for GeneNetwork services.")
+ (description "Authentication and Authorisation server for GeneNetwork services.")
+ (license license:agpl3+))
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..7bf6f9c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,4 @@
+# GeneNetwork Auth
+
+This project is for the GeneNetwork Authentication/Authorisation server to be
+used across the entire suite of the GeneNetwork services.
diff --git a/guix.scm b/guix.scm
new file mode 120000
index 0000000..869bf3d
--- /dev/null
+++ b/guix.scm
@@ -0,0 +1 @@
+.guix/modules/guix-package.scm
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..41d118e
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,4 @@
+[aliases]
+run_unit_tests = run_tests --type=unit
+run_integration_tests = run_tests --type=integration
+run_performance_tests = run_tests --type=performance
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..52a928e
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+"""Setup script for GeneNetwork Auth package."""
+from setuptools import setup
+from setup_commands import RunTests
+
+long_description = """
+GeneNetwork-Auth project is the authentication/authorisation server to be used
+across all GeneNetwork services.
+"""
+
+setup(author="Frederick M. Muriithi",
+      author_email="fredmanglis@gmail.com",
+      description=(
+          "Authentication/Authorisation server for GeneNetwork Services."),
+      install_requires=[
+          "argon2-cffi>=20.1.0"
+          "click"
+          "Flask==1.1.2"
+          "mypy==0.790"
+          "mypy-extensions==0.4.3"
+          "mysqlclient==2.0.1"
+          "pylint==2.5.3"
+          "pymonad"
+          "redis==3.5.3"
+          "requests==2.25.1"
+          "flask-cors==3.0.9"
+          "xapian-bindings"
+      ],
+      scripts=[],
+      license="AGPLV3",
+      long_description=long_description,
+      long_description_content_type="text/markdown",
+      name="GeneNetwork-Auth",
+      packages=[
+          "gn_auth",
+          "gn_auth.auth",
+          "tests"
+      ],
+      url="https://github.com/genenetwork/gn-auth",
+      version="0.0.0",
+      tests_require=["pytest", "hypothesis"],
+      cmdclass={
+          "run_tests": RunTests ## testing
+      })
diff --git a/setup_commands/__init__.py b/setup_commands/__init__.py
new file mode 100644
index 0000000..967bb11
--- /dev/null
+++ b/setup_commands/__init__.py
@@ -0,0 +1,3 @@
+"""Module for custom setup commands."""
+
+from .run_tests import RunTests
diff --git a/setup_commands/run_tests.py b/setup_commands/run_tests.py
new file mode 100644
index 0000000..1bb5dab
--- /dev/null
+++ b/setup_commands/run_tests.py
@@ -0,0 +1,40 @@
+import os
+import sys
+from distutils.core import Command
+
+class RunTests(Command):
+    """
+    A custom command to run tests.
+    """
+    description = "Run the tests"
+    test_types = (
+        "all", "unit", "integration", "performance")
+    user_options = [
+        ("type=", None,
+         f"""Specify the type of tests to run.
+         Valid types are {tuple(test_types)}.
+         Default is `all`.""")]
+
+    def __init__(self, dist):
+        """Initialise the command."""
+        super().__init__(dist)
+        self.command = "pytest"
+
+    def initialize_options(self):
+        """Initialise the default values of all the options."""
+        self.type = "all"
+
+    def finalize_options(self):
+        """Set final value of all the options once they are processed."""
+        if self.type not in RunTests.test_types:
+            raise Exception(f"""
+            Invalid test type (self.type) requested!
+            Valid types are
+            {tuple(RunTests.test_types)}""")
+
+        if self.type != "all":
+            self.command = f"pytest -m {self.type}_test"
+    def run(self):
+        """Run the chosen tests"""
+        print(f"Running {self.type} tests")
+        os.system(self.command)
-- 
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