Merge pull request #323 from metrumresearchgroup/gh-actions

ci: switch to GitHub Actions

.github/workflows/lint.yml

@@ -0,0 +1,33 @@
+name: lint
+on:
+  push:
+    branches:
+      - main
+      - 'scratch/**'
+  pull_request:
+
+# Note: this avoids golangci/golangci-lint-action to work around an
+# error triggered by us pinning to a golangci-lint version built with
+# an older Go.  Revisit when moving from golangci-lint v1.47.2.
+#
+# https://github.com/golangci/golangci-lint-action/issues/442#issuecomment-1203786890
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-go@v5
+        with:
+          go-version-file: go.mod
+      - name: Install golangci-lint
+        shell: bash
+        run: |
+          bin=$(mktemp -d)
+          curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | \
+            sh -s -- -b "$bin" v1.47.2
+          echo "$bin" >>$GITHUB_PATH
+      - name: Run golangci-lint
+        shell: bash
+        run: |
+          command -v golangci-lint
+          golangci-lint run --out-format=github-actions

.github/workflows/main.yaml

@@ -0,0 +1,67 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+      - 'scratch/**'
+    tags:
+      - 'v*'
+  pull_request:
+
+jobs:
+  check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.go }})
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - os: ubuntu-20.04
+            go: 1.21.x
+          - os: ubuntu-latest
+            go: stable
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-go@v5
+        with:
+          go-version: ${{ matrix.config.go }}
+      - name: Unit tests
+        shell: bash
+        run: go list ./... | grep -v integration | xargs go test
+      - name: Build bbi
+        shell: bash
+        run: |
+          version=$(git rev-parse 'HEAD^{tree}')
+          bin=$(mktemp -d)
+          go build -o "$bin/bbi" \
+            -ldflags "-X github.com/metrumresearchgroup/bbi/cmd.VERSION=$version" \
+            cmd/bbi/main.go
+          echo "$bin" >>$GITHUB_PATH
+      - name: Integration tests (postrun)
+        shell: bash
+        run: |
+          bbi version
+          go test ./integration/postrun
+  release:
+    if: github.ref_type == 'tag'
+    name: Make release
+    needs: check
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-go@v5
+        with:
+          go-version: stable
+      - name: Run GoReleaser
+        uses: goreleaser/goreleaser-action@v6
+        with:
+          distribution: goreleaser
+          version: '~> v2'
+          args: release --clean
+          workdir: cmd/bbi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

cmd/nonmem.go

@@ -18,7 +18,6 @@ import (
 	"bytes"
 	"errors"
 	"fmt"
-	"io/ioutil"
 	"os"
 	"path"
 	"path/filepath"
@@ -301,12 +300,12 @@ func copyFileToDestination(l *NonMemModel, modifyPath bool) error {
 		}
 	} else {
 		var input []byte
-		input, err = ioutil.ReadFile(l.Path)
+		input, err = os.ReadFile(l.Path)
 		if err != nil {
 			return fmt.Errorf("unable to read %s: %w", l.Path, err)
 		}
 
-		err = ioutil.WriteFile(path.Join(l.OutputDir, filename), input, stats.Mode())
+		err = os.WriteFile(path.Join(l.OutputDir, filename), input, stats.Mode())
 		if err != nil {
 			return fmt.Errorf("unable to write contents %s: %w", l.Path, err)
 		}

cmd/run.go

@@ -3,7 +3,6 @@ package cmd
 import (
 	"bytes"
 	"errors"
-	"io/ioutil"
 	"os"
 	"os/exec"
 	"path/filepath"
@@ -281,7 +280,7 @@ func ExecutePostWorkDirectivesWithEnvironment(worker PostWorkExecutor) (string,
 	}).Debug("Writing contents to file in output directory")
 
 	// TODO: use more secure permission of 0600 or less
-	err = ioutil.WriteFile(filepath.Join(worker.GetWorkingPath(), "post_processing.sh"), processedBytes, 0755) // nolint:gosec
+	err = os.WriteFile(filepath.Join(worker.GetWorkingPath(), "post_processing.sh"), processedBytes, 0755) // nolint:gosec
 
 	if err != nil {
 		return "", err

go.mod

@@ -1,6 +1,6 @@
 module github.com/metrumresearchgroup/bbi
 
-go 1.15
+go 1.16
 
 require (
 	github.com/clbanning/mxj v1.8.4

integration/execute.go

@@ -1,4 +1,4 @@
-package bbitest
+package integration
 
 import (
 	"context"
@@ -10,7 +10,7 @@ import (
 	log "github.com/sirupsen/logrus"
 )
 
-func executeCommand(ctx context.Context, command string, args ...string) (string, error) {
+func ExecuteCommand(ctx context.Context, command string, args ...string) (string, error) {
 	//Find it in path
 	binary, _ := exec.LookPath(command)
 	cmd := exec.CommandContext(ctx, binary, args...)
@@ -40,7 +40,7 @@ func executeCommand(ctx context.Context, command string, args ...string) (string
 }
 
 // nolint:unparam
-func executeCommandNoErrorCheck(ctx context.Context, command string, args ...string) (string, error) {
+func ExecuteCommandNoErrorCheck(ctx context.Context, command string, args ...string) (string, error) {
 	binary, _ := exec.LookPath(command)
 	cmd := exec.CommandContext(ctx, binary, args...)
 	cmd.Env = os.Environ()

integration/nonmem/README.md

@@ -0,0 +1 @@
+This directory contains integration tests that rely on having NONMEM installed.

integration/bbi_expansion_test.go → integration/nonmem/bbi_expansion_test.go

@@ -1,4 +1,4 @@
-package bbitest
+package nonmem
 
 import (
 	"context"
@@ -8,6 +8,7 @@ import (
 	"strings"
 	"testing"
 
+	. "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/bbi/utils"
 
 	"github.com/metrumresearchgroup/wrapt"
@@ -38,7 +39,7 @@ func TestBBIExpandsWithoutPrefix(tt *testing.T) {
 			filepath.Join(scenario.Workpath, "model", targets),
 		}
 
-		output, err := executeCommand(context.Background(), "bbi", commandAndArgs...)
+		output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 		t.R.NoError(err)
 		t.R.NotEmpty(output)
@@ -107,7 +108,7 @@ func TestBBIExpandsWithPrefix(tt *testing.T) {
 			filepath.Join(scenario.Workpath, "model", targets),
 		}
 
-		output, err := executeCommand(context.Background(), "bbi", commandAndArgs...)
+		output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 		t.R.NoError(err)
 		t.R.NotEmpty(output)
@@ -177,7 +178,7 @@ func TestBBIExpandsWithPrefixToPartialMatch(tt *testing.T) {
 				filepath.Join(scenario.Workpath, "model", targets),
 			}
 
-			output, err := executeCommand(context.Background(), "bbi", commandAndArgs...)
+			output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 			t.R.NoError(err)
 			t.R.NotEmpty(output)