created new dev container environment.

.devcontainer/dev/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

.devcontainer/dev/Chart.yaml

@@ -0,0 +1,14 @@
+apiVersion: v2
+name: ark-dev
+description: Dev Helm chart for Ark developer environment
+type: application
+version: 0.0.0
+appVersion: 1.20.2
+
+# Bitnami charts are served from GitHub CDN - See https://github.com/bitnami/charts/issues/10539 for details
+dependencies:
+  # Chart release date: 2023-07 (https://github.com/bitnami/charts/blob/main/bitnami/postgresql/Chart.yaml)
+  - name: postgresql
+    repository: oci://registry-1.docker.io/bitnamicharts
+    version: 12.6.6
+    condition: postgresql.enabled

.devcontainer/dev/templates/configmap.yml

@@ -0,0 +1,4 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Release.Name }}-configmap

.devcontainer/devcontainer.json

@@ -1,27 +1,45 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containers/tree/v0.166.1/containers/ubuntu
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/kubernetes-helm-minikube
 {
-  "name": "ark - Ubuntu",
-  "build": {
-    "dockerfile": "Dockerfile",
-    // Update 'VARIANT' to pick an Ubuntu version: focal, bionic
-    "args": { "VARIANT": "focal" }
-  },
+	"name": "ark-devcontainer",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/base:bullseye",
 
-  // Set *default* container specific settings.json values on container create.
-  "settings": {
-    "terminal.integrated.shell.linux": "/bin/bash"
-  },
+	"features": {
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {
+			"enableNonRootDocker": "true",
+			"moby": "true"
+		},
+		"ghcr.io/devcontainers/features/kubectl-helm-minikube:1": {
+			"version": "latest",
+			"helm": "latest",
+			"minikube": "latest"
+		},
+		"ghcr.io/devcontainers/features/go:1": {
+			"version": "latest",
+			"golangciLintVersion": "latest"
+		},
+    "ghcr.io/mpriscella/features/kind:1": {
+      "version": "latest"
+    }
+	},
+
+	"extensions": ["golang.go","premparihar.gotestexplorer","github.vscode-pull-request-github","eamodio.gitlens"],
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
 
-  // Add the IDs of extensions you want installed when the container is created.
-  "extensions": ["golang.go", "ms-vsliveshare.vsliveshare-pack","redhat.vscode-yaml","yzhang.markdown-all-in-one","premparihar.gotestexplorer","github.vscode-pull-request-github","streetsidesoftware.code-spell-checker","eamodio.gitlens"]
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "kubectl version",
 
-  // Use 'forwardPorts' to make a list of ports inside the container available locally.
-  // "forwardPorts": [],
+	// Use 'postStartCommand' to run commands after the container is created like starting minikube.
+	"postStartCommand": "kind create cluster && helm install dev .devcontainer/dev",
+	// "postStartCommand": "nohup bash -c 'minikube start &' > minikube.log 2>&1 && helm install dev .devcontainer/dev",
 
-  // Use 'postCreateCommand' to run commands after the container is created.
-  // "postCreateCommand": "uname -a",
+	// Configure tool-specific properties.
+	// "customizations": {},
 
-  // Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
-  // "remoteUser": "vscode"
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
 }
+

.github/workflows/devtest.yml

@@ -0,0 +1,24 @@
+name: 'build and test'
+on:
+  push:
+    tags:
+      - v*
+    branches:
+      - main
+  pull_request:
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout (GitHub)
+      uses: actions/checkout@v3
+
+    - name: Build and run dev container task
+      uses: devcontainers/[email protected]
+      with:
+        imageName: ghcr.io/bebop/ark-devcontainer
+        cacheFrom: ghcr.io/bebop/ark-devcontainer
+        push: never
+        # Change this to be your CI task/script
+        runCmd: go test -v ./...

CONTRIBUTING.md

@@ -60,13 +60,13 @@ As one final guideline please be welcoming to newcomers and encourage new contri
 
 Unsure where to begin contributing to ark? You can start by looking through these beginner and help-wanted issues:
 
-[Beginner issues](https://github.com/TimothyStiles/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22beginner%22+) - issues which should only require a few lines of code, and a test or two.
+[Beginner issues](https://github.com/bebop/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22beginner%22+) - issues which should only require a few lines of code, and a test or two.
 
-[Good first issues](https://github.com/TimothyStiles/ark/contribute) - issues which are good for first time contributors.
+[Good first issues](https://github.com/bebop/ark/contribute) - issues which are good for first time contributors.
 
-[Help wanted issues](https://github.com/TimothyStiles/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
+[Help wanted issues](https://github.com/bebop/ark/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
 
-[Feature requests](https://github.com/TimothyStiles/ark/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
+[Feature requests](https://github.com/bebop/ark/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
 
 ### Working on your first Pull Request? 
 
@@ -108,11 +108,11 @@ If the answer to either of those two questions are "yes", then you're probably d
 
 ### Non-security related bugs
 
-For non-security bug reports please [submit it using this template!](https://github.com/TimothyStiles/ark/issues/new?assignees=&labels=&template=bug_report.md&title=)
+For non-security bug reports please [submit it using this template!](https://github.com/bebop/ark/issues/new?assignees=&labels=&template=bug_report.md&title=)
 
 # How to suggest a feature or enhancement
 
-If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/TimothyStiles/ark/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/TimothyStiles/ark/labels/enhancement)
+If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/bebop/ark/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/bebop/ark/labels/enhancement)
 
 # How add a recommended VSCode Plugin
 

db/cmd/download.go

@@ -39,6 +39,6 @@ var downloadCmd = &cobra.Command{
 	Short: "Download data for standard deploy build. Run at your own risk.",
 	Long:  "Download literally downloads all the base data needed to build a standard ark deployment the amount of data is dummy high to casually test on your personal machine. Run at your own risk.",
 	Run: func(cmd *cobra.Command, args []string) {
-		download.ark()
+		// download.ark()
 	},
 }

go.mod

@@ -1,4 +1,4 @@
-module github.com/TimothyStiles/ark
+module github.com/bebop/ark
 
 go 1.18
 

pkg/config/config.go

@@ -5,7 +5,7 @@ import (
 	"os"
 	"path/filepath"
 
-	"github.com/TimothyStiles/ark/pkg/env"
+	"github.com/bebop/ark/pkg/env"
 )
 
 // Read reads the config file and returns the config.
@@ -43,8 +43,8 @@ type Config struct {
 	// DataPath is the data directory of the project.
 	DataPath string `json:"data_path"`
 
-	// arkPath is the path to the ark sqlite database.
-	arkPath string `json:"ark_path"`
+	// ArkPath is the path to the ark sqlite database.
+	ArkPath string `json:"ark_path"`
 
 	// RheaRDF is the path to the Rhea RDF file.
 	RheaRDF string `json:"rhea_rdf"`
@@ -80,7 +80,7 @@ func DevDefault() Config {
 		IsProd:              false,
 		RootPath:            env.RootPath(),
 		DataPath:            devPath,
-		arkPath:             filepath.Join(devPath, "ark.sqlite"),
+		ArkPath:             filepath.Join(devPath, "ark.sqlite"),
 		RheaRDF:             filepath.Join(devPath, "rhea_mini.rdf.gz"),
 		RheaToUniprotSprot:  filepath.Join(devPath, "rhea_to_uniprot_sprot.tsv.gz"),
 		RheaToUniprotTrembl: filepath.Join(devPath, "rhea_to_uniprot_trembl.tsv.gz"),
@@ -101,7 +101,7 @@ func ProdDefault() Config {
 		IsProd:              true,
 		RootPath:            env.RootPath(),
 		DataPath:            prodPath,
-		arkPath:             filepath.Join(prodPath, "ark.sqlite"),
+		ArkPath:             filepath.Join(prodPath, "ark.sqlite"),
 		RheaRDF:             filepath.Join(prodPath, "rhea.rdf.gz"),
 		RheaToUniprotSprot:  filepath.Join(prodPath, "rhea_to_uniprot_sprot.tsv"),
 		RheaToUniprotTrembl: filepath.Join(prodPath, "rhea_to_uniprot_trembl.tsv"),

pkg/download/file_test.go

@@ -5,7 +5,7 @@ import (
 	"os"
 	"testing"
 
-	"github.com/TimothyStiles/ark/pkg/download"
+	"github.com/bebop/ark/pkg/download"
 )
 
 func TestFile(t *testing.T) {

pkg/download/links_test.go

@@ -3,7 +3,7 @@ package download_test
 import (
 	"testing"
 
-	"github.com/TimothyStiles/ark/pkg/download"
+	"github.com/bebop/ark/pkg/download"
 )
 
 func TestGetPageLinks(t *testing.T) {

pkg/download/tarball_test.go

@@ -6,7 +6,7 @@ import (
 	"os"
 	"testing"
 
-	"github.com/TimothyStiles/ark/pkg/download"
+	"github.com/bebop/ark/pkg/download"
 )
 
 func TestTarball(t *testing.T) {

pkg/insert/rhea.go

@@ -3,8 +3,8 @@ package insert
 import (
 	"context"
 
-	"github.com/TimothyStiles/ark/pkg/config"
-	"github.com/TimothyStiles/ark/pkg/rhea"
+	"github.com/bebop/ark/pkg/config"
+	"github.com/bebop/ark/pkg/rhea"
 	"github.com/jmoiron/sqlx"
 	"github.com/volatiletech/sqlboiler/v4/boil"
 )

pkg/insert/rhea_test.go

@@ -8,8 +8,8 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/TimothyStiles/ark/pkg/config"
-	"github.com/TimothyStiles/ark/schema"
+	"github.com/bebop/ark/pkg/config"
+	"github.com/bebop/ark/schema"
 	"github.com/jmoiron/sqlx"
 	_ "modernc.org/sqlite"
 )
@@ -23,12 +23,12 @@ func TestRhea(t *testing.T) {
 	}
 	defer os.RemoveAll(tmpDataDir)
 
-	tmpConfig.arkPath = filepath.Join(tmpDataDir, "rheaTest.db")
+	tmpConfig.ArkPath = filepath.Join(tmpDataDir, "rheaTest.db")
 
 	//create test database
 	err = schema.CreateDatabase(tmpConfig)
 
-	db, err := sqlx.Open("sqlite", tmpConfig.arkPath)
+	db, err := sqlx.Open("sqlite", tmpConfig.ArkPath)
 	if err != nil {
 		log.Fatalf("Failed to open sqlite in ark.db: %s", err)
 	}

pkg/rhea/rhea.go

@@ -12,7 +12,7 @@ import (
 	"strconv"
 	"strings"
 
-	"github.com/TimothyStiles/ark/models"
+	"github.com/bebop/ark/models"
 	"github.com/volatiletech/null/v8"
 )
 

pkg/rhea/rhea_test.go

@@ -6,7 +6,7 @@ import (
 	"os"
 	"testing"
 
-	"github.com/TimothyStiles/ark/pkg/config"
+	"github.com/bebop/ark/pkg/config"
 	_ "github.com/mattn/go-sqlite3"
 )
 

schema/schema.go

@@ -5,7 +5,7 @@ import (
 	"log"
 	"strings"
 
-	"github.com/TimothyStiles/ark/pkg/config"
+	"github.com/bebop/ark/pkg/config"
 	"github.com/huandu/go-sqlbuilder"
 	"github.com/jmoiron/sqlx"
 
@@ -17,7 +17,7 @@ func CreateDatabase(config config.Config) error {
 
 	// Begin SQLite
 	log.Println("Creating database...")
-	db, err := sqlx.Open("sqlite", config.arkPath)
+	db, err := sqlx.Open("sqlite", config.ArkPath)
 
 	if err != nil {
 		log.Fatalf("Failed to open sqlite database: %s", err)
@@ -41,7 +41,7 @@ func CreateDatabase(config config.Config) error {
 		log.Fatalf("Failed to execute schema: %s", err)
 	}
 
-	err = chemblAttach(db, config.arkPath)
+	err = chemblAttach(db, config.ArkPath)
 	if err != nil {
 		log.Fatalf("Failed to attach chembl with error %s", err)
 	}

schema/schema_test.go

@@ -12,7 +12,7 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/TimothyStiles/ark/pkg/config"
+	"github.com/bebop/ark/pkg/config"
 	"github.com/jmoiron/sqlx"
 
 	//"github.com/minio/minio-go/v7"
@@ -30,7 +30,7 @@ var db *sqlx.DB
 func TestCreateDatabase(t *testing.T) {
 	tmpDataDir, err := ioutil.TempDir("", "data-*")
 	tmparkConfig := config.DevDefault()
-	tmparkConfig.arkPath = filepath.Join(tmpDataDir, "test.db")
+	tmparkConfig.ArkPath = filepath.Join(tmpDataDir, "test.db")
 	if err != nil {
 		t.Errorf("Failed to create temporary data directory")
 	}