From 910688ee3295ebaf6f50e6f50dc04de4e7947cd7 Mon Sep 17 00:00:00 2001
From: Paul Campbell <pcampbell@kemitix.net>
Date: Thu, 20 Jun 2019 17:18:46 +0100
Subject: [PATCH] Add support for per directory configuration files (#71)

* [core] rename the config supplied from CLI as such

This distinguishes it as config supplied from the command line.

* [core] add ConfigOption

* [core] ConfigOption can update a Config

* [core] new validator for config

* [domain] Config doesn't validate source any more

* [cli] PrintLogger default to not print debug messages

* [cli] Use ConfigOptions and new ConfigValidator

* [sbt] Use common settings for project root

* [domain] RemoteKey can handle when prefix is empty

* [cli] remove banner

* [domain] Logger can create version of itself with debug flipped

* [core] Build and validate Config within core module

This means that the `thorp-lib` module can validate its input from a
list of `ConfigOption`s.

* [core] refactor ConfigurationBuilder

* [core] refactor ConfigurationBuilder

* [sbt] starting back from tagless-final by using IO where needed

* [core] Add ParseConfigFile

* [sbt] Make cats-effect available from the domain

* Roll back from tagless-final to just use cat-effect's IO

* [core] extract ParseConfigLines

* [core] ConfigurationBuilder rename apply as buildConfig

* [core] ParseConfig[Files,Lines] rename apply methods

* [core] refactor ParseConfigFile and add tests

* [core] Sync fix call to run

* [core] SyncSuite update tests to use ConfigOptions
---
 .../net/kemitix/thorp/aws/api/S3Client.scala  | 11 +--
 .../thorp/aws/lib/S3ClientBuilder.scala       |  7 +-
 .../thorp/aws/lib/S3ClientCopier.scala        | 13 ++--
 .../thorp/aws/lib/S3ClientDeleter.scala       | 17 ++---
 .../thorp/aws/lib/S3ClientLogging.scala       | 30 ++++----
 .../thorp/aws/lib/S3ClientObjectLister.scala  | 21 +++---
 .../kemitix/thorp/aws/lib/ThorpS3Client.scala | 22 +++---
 .../net/kemitix/thorp/aws/lib/Uploader.scala  | 15 ++--
 .../thorp/aws/lib/UploaderLogging.scala       | 10 +--
 .../kemitix/thorp/aws/lib/DummyLogger.scala   | 14 ++--
 .../kemitix/thorp/aws/lib/S3ClientSuite.scala |  5 +-
 .../thorp/aws/lib/ThorpS3ClientSuite.scala    |  7 +-
 .../kemitix/thorp/aws/lib/UploaderSuite.scala |  3 +-
 build.sbt                                     | 19 +----
 .../scala/net/kemitix/thorp/cli/Main.scala    | 12 +--
 .../net/kemitix/thorp/cli/ParseArgs.scala     | 33 ++++-----
 .../net/kemitix/thorp/cli/PrintLogger.scala   | 20 +++--
 .../scala/net/kemitix/thorp/cli/Program.scala | 28 ++++---
 .../net/kemitix/thorp/cli/ParseArgsTest.scala | 44 ++++-------
 .../kemitix/thorp/core/ActionSubmitter.scala  | 12 +--
 .../net/kemitix/thorp/core/ConfigOption.scala | 31 ++++++++
 .../kemitix/thorp/core/ConfigValidation.scala | 22 ++++++
 .../kemitix/thorp/core/ConfigValidator.scala  | 35 +++++++++
 .../thorp/core/ConfigurationBuilder.scala     | 47 ++++++++++++
 .../kemitix/thorp/core/LocalFileStream.scala  | 23 +++---
 .../kemitix/thorp/core/MD5HashGenerator.scala | 15 ++--
 .../kemitix/thorp/core/ParseConfigFile.scala  | 28 +++++++
 .../kemitix/thorp/core/ParseConfigLines.scala | 43 +++++++++++
 .../scala/net/kemitix/thorp/core/Sync.scala   | 54 +++++++++-----
 .../net/kemitix/thorp/core/SyncLogging.scala  | 17 ++---
 .../net/kemitix/thorp/core/empty-file         |  0
 .../net/kemitix/thorp/core/invalid-config     |  1 +
 .../net/kemitix/thorp/core/simple-config      |  2 +
 .../net/kemitix/thorp/core/DummyLogger.scala  | 14 ++--
 .../thorp/core/LocalFileStreamSuite.scala     |  8 +-
 .../thorp/core/MD5HashGeneratorTest.scala     |  7 +-
 .../thorp/core/ParseConfigFileTest.scala      | 37 ++++++++++
 .../thorp/core/ParseConfigLinesTest.scala     | 74 +++++++++++++++++++
 .../net/kemitix/thorp/core/SyncSuite.scala    | 46 +++++++-----
 .../net/kemitix/thorp/domain/Config.scala     |  1 -
 .../net/kemitix/thorp/domain/Logger.scala     | 17 +++--
 .../net/kemitix/thorp/domain/RemoteKey.scala  | 13 +++-
 42 files changed, 602 insertions(+), 276 deletions(-)
 create mode 100644 core/src/main/scala/net/kemitix/thorp/core/ConfigOption.scala
 create mode 100644 core/src/main/scala/net/kemitix/thorp/core/ConfigValidation.scala
 create mode 100644 core/src/main/scala/net/kemitix/thorp/core/ConfigValidator.scala
 create mode 100644 core/src/main/scala/net/kemitix/thorp/core/ConfigurationBuilder.scala
 create mode 100644 core/src/main/scala/net/kemitix/thorp/core/ParseConfigFile.scala
 create mode 100644 core/src/main/scala/net/kemitix/thorp/core/ParseConfigLines.scala
 create mode 100644 core/src/test/resources/net/kemitix/thorp/core/empty-file
 create mode 100644 core/src/test/resources/net/kemitix/thorp/core/invalid-config
 create mode 100644 core/src/test/resources/net/kemitix/thorp/core/simple-config
 create mode 100644 core/src/test/scala/net/kemitix/thorp/core/ParseConfigFileTest.scala
 create mode 100644 core/src/test/scala/net/kemitix/thorp/core/ParseConfigLinesTest.scala

diff --git a/aws-api/src/main/scala/net/kemitix/thorp/aws/api/S3Client.scala b/aws-api/src/main/scala/net/kemitix/thorp/aws/api/S3Client.scala
index c38e43c..497c93e 100644
--- a/aws-api/src/main/scala/net/kemitix/thorp/aws/api/S3Client.scala
+++ b/aws-api/src/main/scala/net/kemitix/thorp/aws/api/S3Client.scala
@@ -1,13 +1,14 @@
 package net.kemitix.thorp.aws.api
 
+import cats.effect.IO
 import net.kemitix.thorp.aws.api.S3Action.{CopyS3Action, DeleteS3Action}
 import net.kemitix.thorp.domain._
 
-trait S3Client[M[_]] {
+trait S3Client {
 
   def listObjects(bucket: Bucket,
                   prefix: RemoteKey
-                 )(implicit logger: Logger[M]): M[S3ObjectsData]
+                 )(implicit logger: Logger): IO[S3ObjectsData]
 
   def upload(localFile: LocalFile,
              bucket: Bucket,
@@ -15,16 +16,16 @@ trait S3Client[M[_]] {
              multiPartThreshold: Long,
              tryCount: Int,
              maxRetries: Int)
-            (implicit logger: Logger[M]): M[S3Action]
+            (implicit logger: Logger): IO[S3Action]
 
   def copy(bucket: Bucket,
            sourceKey: RemoteKey,
            hash: MD5Hash,
            targetKey: RemoteKey
-          )(implicit logger: Logger[M]): M[CopyS3Action]
+          )(implicit logger: Logger): IO[CopyS3Action]
 
   def delete(bucket: Bucket,
              remoteKey: RemoteKey
-            )(implicit logger: Logger[M]): M[DeleteS3Action]
+            )(implicit logger: Logger): IO[DeleteS3Action]
 
 }
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientBuilder.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientBuilder.scala
index ca75ef8..077776a 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientBuilder.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientBuilder.scala
@@ -1,17 +1,16 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
 import com.amazonaws.services.s3.transfer.{TransferManager, TransferManagerBuilder}
 import com.amazonaws.services.s3.{AmazonS3, AmazonS3ClientBuilder}
 import net.kemitix.thorp.aws.api.S3Client
 
 object S3ClientBuilder {
 
-  def createClient[M[_]: Monad](amazonS3Client: AmazonS3,
-                   amazonS3TransferManager: TransferManager): S3Client[M] =
+  def createClient(amazonS3Client: AmazonS3,
+                   amazonS3TransferManager: TransferManager): S3Client =
     new ThorpS3Client(amazonS3Client, amazonS3TransferManager)
 
-  def defaultClient[M[_]: Monad]: S3Client[M] =
+  def defaultClient: S3Client =
     createClient(AmazonS3ClientBuilder.defaultClient, TransferManagerBuilder.defaultTransferManager)
 
 }
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientCopier.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientCopier.scala
index b3662be..df8ab38 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientCopier.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientCopier.scala
@@ -1,24 +1,23 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.model.CopyObjectRequest
 import net.kemitix.thorp.aws.api.S3Action.CopyS3Action
 import net.kemitix.thorp.aws.lib.S3ClientLogging.{logCopyFinish, logCopyStart}
 import net.kemitix.thorp.domain.{Bucket, Logger, MD5Hash, RemoteKey}
 
-class S3ClientCopier[M[_]: Monad](amazonS3: AmazonS3) {
+class S3ClientCopier(amazonS3: AmazonS3) {
 
   def copy(bucket: Bucket,
            sourceKey: RemoteKey,
            hash: MD5Hash,
            targetKey: RemoteKey)
-          (implicit logger: Logger[M]): M[CopyS3Action] =
+          (implicit logger: Logger): IO[CopyS3Action] =
   for {
-    _ <- logCopyStart[M](bucket, sourceKey, targetKey)
+    _ <- logCopyStart(bucket, sourceKey, targetKey)
     _ <- copyObject(bucket, sourceKey, hash, targetKey)
-    _ <- logCopyFinish[M](bucket, sourceKey,targetKey)
+    _ <- logCopyFinish(bucket, sourceKey,targetKey)
   } yield CopyS3Action(targetKey)
 
   private def copyObject(bucket: Bucket,
@@ -28,7 +27,7 @@ class S3ClientCopier[M[_]: Monad](amazonS3: AmazonS3) {
     val request =
       new CopyObjectRequest(bucket.name, sourceKey.key, bucket.name, targetKey.key)
         .withMatchingETagConstraint(hash.hash)
-    Monad[M].pure(amazonS3.copyObject(request))
+    IO(amazonS3.copyObject(request))
   }
 
 }
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientDeleter.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientDeleter.scala
index 59c7877..68ed98b 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientDeleter.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientDeleter.scala
@@ -1,25 +1,24 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.model.DeleteObjectRequest
 import net.kemitix.thorp.aws.api.S3Action.DeleteS3Action
 import net.kemitix.thorp.aws.lib.S3ClientLogging.{logDeleteFinish, logDeleteStart}
 import net.kemitix.thorp.domain.{Bucket, Logger, RemoteKey}
 
-class S3ClientDeleter[M[_]: Monad](amazonS3: AmazonS3) {
+class S3ClientDeleter(amazonS3: AmazonS3) {
 
   def delete(bucket: Bucket,
              remoteKey: RemoteKey)
-            (implicit logger: Logger[M]): M[DeleteS3Action] =
+            (implicit logger: Logger): IO[DeleteS3Action] =
     for {
-      _ <- logDeleteStart[M](bucket, remoteKey)
+      _ <- logDeleteStart(bucket, remoteKey)
       _ <- deleteObject(bucket, remoteKey)
-      _ <- logDeleteFinish[M](bucket, remoteKey)
+      _ <- logDeleteFinish(bucket, remoteKey)
     } yield DeleteS3Action(remoteKey)
 
-  private def deleteObject(bucket: Bucket, remoteKey: RemoteKey) = Monad[M].pure {
-    amazonS3.deleteObject(new DeleteObjectRequest(bucket.name, remoteKey.key))
-  }
+  private def deleteObject(bucket: Bucket, remoteKey: RemoteKey) =
+    IO(amazonS3.deleteObject(new DeleteObjectRequest(bucket.name, remoteKey.key)))
+
 }
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientLogging.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientLogging.scala
index a7a9c63..7ada90e 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientLogging.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientLogging.scala
@@ -1,40 +1,40 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
+import cats.effect.IO
 import net.kemitix.thorp.domain.{Bucket, Logger, RemoteKey}
 
 object S3ClientLogging {
 
-  def logListObjectsStart[M[_]: Monad](bucket: Bucket,
+  def logListObjectsStart(bucket: Bucket,
                           prefix: RemoteKey)
-                         (implicit logger: Logger[M]): M[Unit] =
+                         (implicit logger: Logger): IO[Unit] =
     logger.info(s"Fetch S3 Summary: ${bucket.name}:${prefix.key}")
 
-  def logListObjectsFinish[M[_]: Monad](bucket: Bucket,
+  def logListObjectsFinish(bucket: Bucket,
                            prefix: RemoteKey)
-                          (implicit logger: Logger[M]): M[Unit] =
+                          (implicit logger: Logger): IO[Unit] =
     logger.info(s"Fetched S3 Summary: ${bucket.name}:${prefix.key}")
 
-  def logCopyStart[M[_]: Monad](bucket: Bucket,
-                                sourceKey: RemoteKey,
-                                targetKey: RemoteKey)
-                               (implicit logger: Logger[M]): M[Unit] =
+  def logCopyStart(bucket: Bucket,
+                   sourceKey: RemoteKey,
+                   targetKey: RemoteKey)
+                  (implicit logger: Logger): IO[Unit] =
     logger.info(s"Copy: ${bucket.name}:${sourceKey.key} => ${targetKey.key}")
 
-  def logCopyFinish[M[_]: Monad](bucket: Bucket,
+  def logCopyFinish(bucket: Bucket,
                     sourceKey: RemoteKey,
                     targetKey: RemoteKey)
-                   (implicit logger: Logger[M]): M[Unit] =
+                   (implicit logger: Logger): IO[Unit] =
     logger.info(s"Copied: ${bucket.name}:${sourceKey.key} => ${targetKey.key}")
 
-  def logDeleteStart[M[_]: Monad](bucket: Bucket,
+  def logDeleteStart(bucket: Bucket,
                      remoteKey: RemoteKey)
-                    (implicit logger: Logger[M]): M[Unit] =
+                    (implicit logger: Logger): IO[Unit] =
       logger.info(s"Delete: ${bucket.name}:${remoteKey.key}")
 
-  def logDeleteFinish[M[_]: Monad](bucket: Bucket,
+  def logDeleteFinish(bucket: Bucket,
                       remoteKey: RemoteKey)
-                     (implicit logger: Logger[M]): M[Unit] =
+                     (implicit logger: Logger): IO[Unit] =
       logger.info(s"Deleted: ${bucket.name}:${remoteKey.key}")
 
 }
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientObjectLister.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientObjectLister.scala
index c58a0cb..cc54677 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientObjectLister.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/S3ClientObjectLister.scala
@@ -1,7 +1,6 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.model.{ListObjectsV2Request, S3ObjectSummary}
 import net.kemitix.thorp.aws.lib.S3ClientLogging.{logListObjectsFinish, logListObjectsStart}
@@ -12,11 +11,11 @@ import net.kemitix.thorp.domain.{Bucket, Logger, RemoteKey, S3ObjectsData}
 
 import scala.collection.JavaConverters._
 
-class S3ClientObjectLister[M[_]: Monad](amazonS3: AmazonS3) {
+class S3ClientObjectLister(amazonS3: AmazonS3) {
 
   def listObjects(bucket: Bucket,
                   prefix: RemoteKey)
-                 (implicit logger: Logger[M]): M[S3ObjectsData] = {
+                 (implicit logger: Logger): IO[S3ObjectsData] = {
 
     type Token = String
     type Batch = (Stream[S3ObjectSummary], Option[Token])
@@ -26,8 +25,8 @@ class S3ClientObjectLister[M[_]: Monad](amazonS3: AmazonS3) {
       .withPrefix(prefix.key)
       .withContinuationToken(token)
 
-    def fetchBatch: ListObjectsV2Request => M[Batch] =
-      request => Monad[M].pure {
+    def fetchBatch: ListObjectsV2Request => IO[Batch] =
+      request => IO.pure {
         val result = amazonS3.listObjectsV2(request)
         val more: Option[Token] =
           if (result.isTruncated) Some(result.getNextContinuationToken)
@@ -35,14 +34,14 @@ class S3ClientObjectLister[M[_]: Monad](amazonS3: AmazonS3) {
         (result.getObjectSummaries.asScala.toStream, more)
       }
 
-    def fetchMore(more: Option[Token]): M[Stream[S3ObjectSummary]] = {
+    def fetchMore(more: Option[Token]): IO[Stream[S3ObjectSummary]] = {
       more match {
-        case None => Monad[M].pure(Stream.empty)
+        case None => IO.pure(Stream.empty)
         case Some(token) => fetch(requestMore(token))
       }
     }
 
-    def fetch: ListObjectsV2Request => M[Stream[S3ObjectSummary]] =
+    def fetch: ListObjectsV2Request => IO[Stream[S3ObjectSummary]] =
       request =>
           for {
             batch <- fetchBatch(request)
@@ -51,10 +50,10 @@ class S3ClientObjectLister[M[_]: Monad](amazonS3: AmazonS3) {
           } yield summaries ++ rest
 
     for {
-      _ <- logListObjectsStart[M](bucket, prefix)
+      _ <- logListObjectsStart(bucket, prefix)
       r = new ListObjectsV2Request().withBucketName(bucket.name).withPrefix(prefix.key)
       summaries <- fetch(r)
-      _ <- logListObjectsFinish[M](bucket, prefix)
+      _ <- logListObjectsFinish(bucket, prefix)
     } yield domain.S3ObjectsData(byHash(summaries), byKey(summaries))
   }
 
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/ThorpS3Client.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/ThorpS3Client.scala
index 7ceb671..7b721db 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/ThorpS3Client.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/ThorpS3Client.scala
@@ -1,31 +1,31 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
+import cats.effect.IO
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.transfer.TransferManager
 import net.kemitix.thorp.aws.api.S3Action.{CopyS3Action, DeleteS3Action}
 import net.kemitix.thorp.aws.api.{S3Action, S3Client, UploadProgressListener}
 import net.kemitix.thorp.domain._
 
-class ThorpS3Client[M[_]: Monad](amazonS3Client: => AmazonS3,
+class ThorpS3Client(amazonS3Client: => AmazonS3,
                     amazonS3TransferManager: => TransferManager)
-  extends S3Client[M] {
+  extends S3Client {
 
-  lazy val objectLister = new S3ClientObjectLister[M](amazonS3Client)
-  lazy val copier = new S3ClientCopier[M](amazonS3Client)
-  lazy val uploader = new Uploader[M](amazonS3TransferManager)
-  lazy val deleter = new S3ClientDeleter[M](amazonS3Client)
+  lazy val objectLister = new S3ClientObjectLister(amazonS3Client)
+  lazy val copier = new S3ClientCopier(amazonS3Client)
+  lazy val uploader = new Uploader(amazonS3TransferManager)
+  lazy val deleter = new S3ClientDeleter(amazonS3Client)
 
   override def listObjects(bucket: Bucket,
                            prefix: RemoteKey)
-                          (implicit logger: Logger[M]): M[S3ObjectsData] =
+                          (implicit logger: Logger): IO[S3ObjectsData] =
     objectLister.listObjects(bucket, prefix)
 
   override def copy(bucket: Bucket,
                     sourceKey: RemoteKey,
                     hash: MD5Hash,
                     targetKey: RemoteKey)
-                   (implicit logger: Logger[M]): M[CopyS3Action] =
+                   (implicit logger: Logger): IO[CopyS3Action] =
     copier.copy(bucket, sourceKey,hash, targetKey)
 
   override def upload(localFile: LocalFile,
@@ -34,12 +34,12 @@ class ThorpS3Client[M[_]: Monad](amazonS3Client: => AmazonS3,
                       multiPartThreshold: Long,
                       tryCount: Int,
                       maxRetries: Int)
-                     (implicit logger: Logger[M]): M[S3Action] =
+                     (implicit logger: Logger): IO[S3Action] =
     uploader.upload(localFile, bucket, progressListener, multiPartThreshold, 1, maxRetries)
 
   override def delete(bucket: Bucket,
                       remoteKey: RemoteKey)
-                     (implicit logger: Logger[M]): M[DeleteS3Action] =
+                     (implicit logger: Logger): IO[DeleteS3Action] =
     deleter.delete(bucket, remoteKey)
 
 }
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/Uploader.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/Uploader.scala
index 704ef8c..7699884 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/Uploader.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/Uploader.scala
@@ -1,7 +1,6 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import com.amazonaws.event.{ProgressEvent, ProgressEventType, ProgressListener}
 import com.amazonaws.services.s3.model.PutObjectRequest
 import com.amazonaws.services.s3.transfer.model.UploadResult
@@ -14,7 +13,7 @@ import net.kemitix.thorp.domain._
 
 import scala.util.Try
 
-class Uploader[M[_]: Monad](transferManager: => AmazonTransferManager) {
+class Uploader(transferManager: => AmazonTransferManager) {
 
   def accepts(localFile: LocalFile)
              (implicit multiPartThreshold: Long): Boolean =
@@ -26,11 +25,11 @@ class Uploader[M[_]: Monad](transferManager: => AmazonTransferManager) {
              multiPartThreshold: Long,
              tryCount: Int,
              maxRetries: Int)
-            (implicit logger: Logger[M]): M[S3Action] =
+            (implicit logger: Logger): IO[S3Action] =
     for {
-      _ <- logMultiPartUploadStart[M](localFile, tryCount)
+      _ <- logMultiPartUploadStart(localFile, tryCount)
       upload <- transfer(localFile, bucket, uploadProgressListener)
-      _ <- logMultiPartUploadFinished[M](localFile)
+      _ <- logMultiPartUploadFinished(localFile)
     } yield upload match {
       case Right(r) => UploadS3Action(RemoteKey(r.getKey), MD5Hash(r.getETag))
       case Left(e) => ErroredS3Action(localFile.remoteKey, e)
@@ -39,10 +38,10 @@ class Uploader[M[_]: Monad](transferManager: => AmazonTransferManager) {
   private def transfer(localFile: LocalFile,
                        bucket: Bucket,
                        uploadProgressListener: UploadProgressListener,
-                      ): M[Either[Throwable, UploadResult]] = {
+                      ): IO[Either[Throwable, UploadResult]] = {
     val listener: ProgressListener = progressListener(uploadProgressListener)
     val putObjectRequest = request(localFile, bucket, listener)
-    Monad[M].pure {
+    IO {
       Try(transferManager.upload(putObjectRequest))
         .map(_.waitForUploadResult)
         .toEither
diff --git a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/UploaderLogging.scala b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/UploaderLogging.scala
index 12c68e9..0324782 100644
--- a/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/UploaderLogging.scala
+++ b/aws-lib/src/main/scala/net/kemitix/thorp/aws/lib/UploaderLogging.scala
@@ -1,22 +1,22 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
+import cats.effect.IO
 import net.kemitix.thorp.domain.SizeTranslation.sizeInEnglish
 import net.kemitix.thorp.domain.Terminal.clearLine
 import net.kemitix.thorp.domain.{LocalFile, Logger}
 
 object UploaderLogging {
 
-  def logMultiPartUploadStart[M[_]: Monad](localFile: LocalFile,
+  def logMultiPartUploadStart(localFile: LocalFile,
                               tryCount: Int)
-                             (implicit logger: Logger[M]): M[Unit] = {
+                             (implicit logger: Logger): IO[Unit] = {
       val tryMessage = if (tryCount == 1) "" else s"try $tryCount"
       val size = sizeInEnglish(localFile.file.length)
       logger.info(s"${clearLine}upload:$tryMessage:$size:${localFile.remoteKey.key}")
     }
 
-  def logMultiPartUploadFinished[M[_]: Monad](localFile: LocalFile)
-                                (implicit logger: Logger[M]): M[Unit] =
+  def logMultiPartUploadFinished(localFile: LocalFile)
+                                (implicit logger: Logger): IO[Unit] =
     logger.debug(s"upload:finished: ${localFile.remoteKey.key}")
 
 }
diff --git a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/DummyLogger.scala b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/DummyLogger.scala
index 42b7507..236e704 100644
--- a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/DummyLogger.scala
+++ b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/DummyLogger.scala
@@ -1,16 +1,18 @@
 package net.kemitix.thorp.aws.lib
 
-import cats.Monad
+import cats.effect.IO
 import net.kemitix.thorp.domain.Logger
 
-class DummyLogger[M[_]: Monad] extends Logger[M] {
+class DummyLogger extends Logger {
 
-  override def debug(message: => String): M[Unit] = Monad[M].unit
+  override def debug(message: => String): IO[Unit] = IO.unit
 
-  override def info(message: =>String): M[Unit] = Monad[M].unit
+  override def info(message: =>String): IO[Unit] = IO.unit
 
-  override def warn(message: String): M[Unit] = Monad[M].unit
+  override def warn(message: String): IO[Unit] = IO.unit
 
-  override def error(message: String): M[Unit] = Monad[M].unit
+  override def error(message: String): IO[Unit] = IO.unit
+
+  override def withDebug(debug: Boolean): Logger = this
 
 }
diff --git a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/S3ClientSuite.scala b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/S3ClientSuite.scala
index 1e7d757..79ece93 100644
--- a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/S3ClientSuite.scala
+++ b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/S3ClientSuite.scala
@@ -2,7 +2,6 @@ package net.kemitix.thorp.aws.lib
 
 import java.time.Instant
 
-import cats.Id
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.model.PutObjectRequest
 import com.amazonaws.services.s3.transfer.model.UploadResult
@@ -23,7 +22,7 @@ class S3ClientSuite
 
   private val prefix = RemoteKey("prefix")
   implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
-  implicit private val implLogger: Logger[Id] = new DummyLogger[Id]
+  implicit private val implLogger: Logger = new DummyLogger
   private val fileToKey = KeyGenerator.generateKey(config.source, config.prefix) _
 
   describe("getS3Status") {
@@ -43,7 +42,7 @@ class S3ClientSuite
         keyotherkey.remoteKey -> HashModified(hash, lastModified),
         keydiffhash.remoteKey -> HashModified(diffhash, lastModified)))
 
-    def invoke(self: S3Client[Id], localFile: LocalFile) = {
+    def invoke(self: S3Client, localFile: LocalFile) = {
       S3MetaDataEnricher.getS3Status(localFile, s3ObjectsData)
     }
 
diff --git a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/ThorpS3ClientSuite.scala b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/ThorpS3ClientSuite.scala
index 8cb3507..b62f172 100644
--- a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/ThorpS3ClientSuite.scala
+++ b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/ThorpS3ClientSuite.scala
@@ -4,7 +4,6 @@ import java.time.Instant
 import java.time.temporal.ChronoUnit
 import java.util.Date
 
-import cats.Id
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.model.{ListObjectsV2Request, ListObjectsV2Result, S3ObjectSummary}
 import com.amazonaws.services.s3.transfer.TransferManager
@@ -21,7 +20,7 @@ class ThorpS3ClientSuite
     val source = Resource(this, "upload")
     val prefix = RemoteKey("prefix")
     implicit val config: Config = Config(Bucket("bucket"), prefix, source = source)
-    implicit val implLogger: Logger[Id] = new DummyLogger[Id]
+    implicit val implLogger: Logger = new DummyLogger
 
     val lm = LastModified(Instant.now.truncatedTo(ChronoUnit.MILLIS))
 
@@ -48,7 +47,7 @@ class ThorpS3ClientSuite
 
     val amazonS3 = stub[AmazonS3]
     val amazonS3TransferManager = stub[TransferManager]
-    val s3Client = new ThorpS3Client[Id](amazonS3, amazonS3TransferManager)
+    val s3Client = new ThorpS3Client(amazonS3, amazonS3TransferManager)
 
     val myFakeResponse = new ListObjectsV2Result()
     val summaries = myFakeResponse.getObjectSummaries
@@ -66,7 +65,7 @@ class ThorpS3ClientSuite
           k1a -> HashModified(h1, lm),
           k1b -> HashModified(h1, lm),
           k2 -> HashModified(h2, lm)))
-      val result = s3Client.listObjects(Bucket("bucket"), RemoteKey("prefix"))
+      val result = s3Client.listObjects(Bucket("bucket"), RemoteKey("prefix")).unsafeRunSync
       assertResult(expected.byHash.keys)(result.byHash.keys)
       assertResult(expected.byKey.keys)(result.byKey.keys)
       assertResult(expected)(result)
diff --git a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/UploaderSuite.scala b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/UploaderSuite.scala
index c9f04fe..1d501d1 100644
--- a/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/UploaderSuite.scala
+++ b/aws-lib/src/test/scala/net/kemitix/thorp/aws/lib/UploaderSuite.scala
@@ -2,7 +2,6 @@ package net.kemitix.thorp.aws.lib
 
 import java.time.Instant
 
-import cats.Id
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.s3.transfer._
 import net.kemitix.thorp.aws.api.S3Action.UploadS3Action
@@ -20,7 +19,7 @@ class UploaderSuite
   private val source = Resource(this, ".")
   private val prefix = RemoteKey("prefix")
   implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
-  implicit private val implLogger: Logger[Id] = new DummyLogger[Id]
+  implicit private val implLogger: Logger = new DummyLogger
   private val fileToKey = generateKey(config.source, config.prefix) _
   val lastModified = LastModified(Instant.now())
 
diff --git a/build.sbt b/build.sbt
index 94ef26e..86102ff 100644
--- a/build.sbt
+++ b/build.sbt
@@ -27,19 +27,6 @@ val awsSdkDependencies = Seq(
     "com.fasterxml.jackson.dataformat" % "jackson-dataformat-cbor" % "2.9.9"
   )
 )
-val catsSettings = Seq (
-  libraryDependencies ++=  Seq(
-    "org.typelevel" %% "cats-core" % "1.6.1"
-  ),
-  // recommended for cats-effects
-  scalacOptions ++= Seq(
-    "-feature",
-    "-deprecation",
-    "-unchecked",
-    "-language:postfixOps",
-    "-language:higherKinds",
-    "-Ypartial-unification")
-)
 val catsEffectsSettings = Seq(
   libraryDependencies ++=  Seq(
     "org.typelevel" %% "cats-effect" % "1.3.1"
@@ -56,11 +43,13 @@ val catsEffectsSettings = Seq(
 
 // cli -> thorp-lib -> aws-lib -> core -> aws-api -> domain
 
+lazy val root = (project in file("."))
+  .settings(commonSettings)
+
 lazy val cli = (project in file("cli"))
   .settings(commonSettings)
   .settings(mainClass in assembly := Some("net.kemitix.thorp.cli.Main"))
   .settings(applicationSettings)
-  .settings(catsEffectsSettings)
   .aggregate(`thorp-lib`, `aws-lib`, core, `aws-api`, domain)
   .settings(commandLineParsing)
   .settings(testDependencies)
@@ -87,10 +76,10 @@ lazy val core = (project in file("core"))
 lazy val `aws-api` = (project in file("aws-api"))
   .settings(commonSettings)
   .settings(assemblyJarName in assembly := "aws-api.jar")
-  .settings(catsSettings)
   .dependsOn(domain)
 
 lazy val domain = (project in file("domain"))
   .settings(commonSettings)
   .settings(assemblyJarName in assembly := "domain.jar")
+  .settings(catsEffectsSettings)
   .settings(testDependencies)
diff --git a/cli/src/main/scala/net/kemitix/thorp/cli/Main.scala b/cli/src/main/scala/net/kemitix/thorp/cli/Main.scala
index e9913ea..890512a 100644
--- a/cli/src/main/scala/net/kemitix/thorp/cli/Main.scala
+++ b/cli/src/main/scala/net/kemitix/thorp/cli/Main.scala
@@ -1,20 +1,14 @@
 package net.kemitix.thorp.cli
 
-import java.nio.file.Paths
-
 import cats.effect.ExitCase.{Canceled, Completed, Error}
 import cats.effect.{ExitCode, IO, IOApp}
-import net.kemitix.thorp.domain.Config
 
 object Main extends IOApp {
 
-  val defaultConfig: Config =
-    Config(source = Paths.get(".").toFile)
-
   override def run(args: List[String]): IO[ExitCode] = {
-    val exitCaseLogger = new PrintLogger[IO](false)
-    ParseArgs(args, defaultConfig)
-      .map(Program[IO])
+    val exitCaseLogger = new PrintLogger(false)
+    ParseArgs(args)
+      .map(Program(_))
       .getOrElse(IO(ExitCode.Error))
       .guaranteeCase {
           case Canceled => exitCaseLogger.warn("Interrupted")
diff --git a/cli/src/main/scala/net/kemitix/thorp/cli/ParseArgs.scala b/cli/src/main/scala/net/kemitix/thorp/cli/ParseArgs.scala
index 3c6133d..2b4aecf 100644
--- a/cli/src/main/scala/net/kemitix/thorp/cli/ParseArgs.scala
+++ b/cli/src/main/scala/net/kemitix/thorp/cli/ParseArgs.scala
@@ -1,47 +1,42 @@
 package net.kemitix.thorp.cli
 
-import java.io.File
 import java.nio.file.Paths
 
-import net.kemitix.thorp.domain.Filter.{Exclude, Include}
-import net.kemitix.thorp.domain.{Bucket, Config, RemoteKey}
+import net.kemitix.thorp.core.ConfigOption
 import scopt.OParser
 
 object ParseArgs {
 
-  val configParser: OParser[Unit, Config] = {
-    val parserBuilder = OParser.builder[Config]
+  val configParser: OParser[Unit, List[ConfigOption]] = {
+    val parserBuilder = OParser.builder[List[ConfigOption]]
     import parserBuilder._
     OParser.sequence(
       programName("thorp"),
       head("thorp"),
       opt[String]('s', "source")
-        .action((str, c) => c.copy(source = Paths.get(str).toFile))
-        .validate(s => if (new File(s).isDirectory) Right(()) else Left("Source is not a directory"))
-        .required()
-        .text("Source directory to sync to S3"),
+        .action((str, cos) => ConfigOption.Source(Paths.get(str)) :: cos)
+        .text("Source directory to sync to destination"),
       opt[String]('b', "bucket")
-        .action((str, c) => c.copy(bucket = Bucket(str)))
-        .required()
+        .action((str, cos) => ConfigOption.Bucket(str) :: cos)
         .text("S3 bucket name"),
       opt[String]('p', "prefix")
-        .action((str, c) => c.copy(prefix = RemoteKey(str)))
+        .action((str, cos) => ConfigOption.Prefix(str) :: cos)
         .text("Prefix within the S3 Bucket"),
-      opt[Seq[String]]('i', "include")
+      opt[String]('i', "include")
         .unbounded()
-        .action((str, c) => c.copy(filters = c.filters ++ str.map(Include)))
+        .action((str, cos) => ConfigOption.Include(str) :: cos)
         .text("Include only matching paths"),
-      opt[Seq[String]]('x', "exclude")
+      opt[String]('x', "exclude")
         .unbounded()
-        .action((str,c) => c.copy(filters = c.filters ++ str.map(Exclude)))
+        .action((str,cos) => ConfigOption.Exclude(str) :: cos)
         .text("Exclude matching paths"),
       opt[Unit]('d', "debug")
-        .action((_, c) => c.copy(debug = true))
+        .action((_, cos) => ConfigOption.Debug() :: cos)
         .text("Enable debug logging")
     )
   }
 
-  def apply(args: List[String], defaultConfig: Config): Option[Config] =
-    OParser.parse(configParser, args, defaultConfig)
+  def apply(args: List[String]): Option[List[ConfigOption]] =
+    OParser.parse(configParser, args, List())
 
 }
diff --git a/cli/src/main/scala/net/kemitix/thorp/cli/PrintLogger.scala b/cli/src/main/scala/net/kemitix/thorp/cli/PrintLogger.scala
index e37c15a..8b54d70 100644
--- a/cli/src/main/scala/net/kemitix/thorp/cli/PrintLogger.scala
+++ b/cli/src/main/scala/net/kemitix/thorp/cli/PrintLogger.scala
@@ -1,18 +1,22 @@
 package net.kemitix.thorp.cli
 
-import cats.Monad
+import cats.effect.IO
 import net.kemitix.thorp.domain.Logger
 
-class PrintLogger[M[_]: Monad](isDebug: Boolean) extends Logger[M] {
+class PrintLogger(isDebug: Boolean = false) extends Logger {
 
-  override def debug(message: => String): M[Unit] =
-    if (isDebug) Monad[M].pure(println(s"[ DEBUG] $message"))
-    else Monad[M].unit
+  override def debug(message: => String): IO[Unit] =
+    if (isDebug) IO(println(s"[ DEBUG] $message"))
+    else IO.unit
 
-  override def info(message: => String): M[Unit] = Monad[M].pure(println(s"[  INFO] $message"))
+  override def info(message: => String): IO[Unit] = IO(println(s"[  INFO] $message"))
 
-  override def warn(message: String): M[Unit] = Monad[M].pure(println(s"[  WARN] $message"))
+  override def warn(message: String): IO[Unit] = IO(println(s"[  WARN] $message"))
 
-  override def error(message: String): M[Unit] = Monad[M].pure(println(s"[ ERROR] $message"))
+  override def error(message: String): IO[Unit] = IO(println(s"[ ERROR] $message"))
+
+  override def withDebug(debug: Boolean): Logger =
+    if (isDebug == debug) this
+    else new PrintLogger(debug)
 
 }
diff --git a/cli/src/main/scala/net/kemitix/thorp/cli/Program.scala b/cli/src/main/scala/net/kemitix/thorp/cli/Program.scala
index 2395f13..22d6843 100644
--- a/cli/src/main/scala/net/kemitix/thorp/cli/Program.scala
+++ b/cli/src/main/scala/net/kemitix/thorp/cli/Program.scala
@@ -1,20 +1,24 @@
 package net.kemitix.thorp.cli
 
-import cats.Monad
-import cats.effect.ExitCode
-import cats.implicits._
+import cats.effect.{ExitCode, IO}
 import net.kemitix.thorp.aws.lib.S3ClientBuilder
-import net.kemitix.thorp.core.Sync
-import net.kemitix.thorp.domain.{Config, Logger}
+import net.kemitix.thorp.core.{ConfigOption, Sync}
+import net.kemitix.thorp.domain.Logger
 
-object Program {
+trait Program {
 
-  def apply[M[_]: Monad](config: Config): M[ExitCode] = {
-    implicit val logger: Logger[M] = new PrintLogger[M](config.debug)
-    for {
-      _ <- logger.info("Thorp - hashed sync for cloud storage")
-      _ <- Sync.run[M](config, S3ClientBuilder.defaultClient)
-    } yield ExitCode.Success
+  def apply(configOptions: Seq[ConfigOption]): IO[ExitCode] = {
+    implicit val logger: Logger = new PrintLogger()
+    Sync(S3ClientBuilder.defaultClient)(configOptions) flatMap {
+      case Left(errors) =>
+        for {
+          _ <- logger.error(s"There were errors:")
+          _ <- IO.pure(errors.map(error => logger.error(s" - $error")))
+        } yield ExitCode.Error
+      case Right(_) => IO.pure(ExitCode.Success)
+    }
   }
 
 }
+
+object Program extends Program
\ No newline at end of file
diff --git a/cli/src/test/scala/net/kemitix/thorp/cli/ParseArgsTest.scala b/cli/src/test/scala/net/kemitix/thorp/cli/ParseArgsTest.scala
index 2efbec1..74efca9 100644
--- a/cli/src/test/scala/net/kemitix/thorp/cli/ParseArgsTest.scala
+++ b/cli/src/test/scala/net/kemitix/thorp/cli/ParseArgsTest.scala
@@ -1,7 +1,7 @@
 package net.kemitix.thorp.cli
 
-import net.kemitix.thorp.core.Resource
-import net.kemitix.thorp.domain.Config
+import net.kemitix.thorp.core.ConfigOption.Debug
+import net.kemitix.thorp.core.{ConfigOption, Resource}
 import org.scalatest.FunSpec
 
 import scala.util.Try
@@ -9,11 +9,10 @@ import scala.util.Try
 class ParseArgsTest extends FunSpec {
 
   val source = Resource(this, "")
-  val defaultConfig: Config = Config(source = source)
 
   describe("parse - source") {
     def invokeWithSource(path: String) =
-      ParseArgs(List("--source", path, "--bucket", "bucket"), defaultConfig)
+      ParseArgs(List("--source", path, "--bucket", "bucket"))
 
     describe("when source is a directory") {
       val result = invokeWithSource(pathTo("."))
@@ -21,52 +20,35 @@ class ParseArgsTest extends FunSpec {
         assert(result.isDefined)
       }
     }
-    describe("when source is a file") {
-      val result = invokeWithSource(pathTo("ParseArgs.class"))
-      it("should fail") {
-        assert(result.isEmpty)
-      }
-    }
-    describe("when source is not found") {
-      val result = invokeWithSource(pathTo("not-found"))
-      it("should fail") {
-        assert(result.isEmpty)
-      }
-    }
     describe("when source is a relative path to a directory") {
       it("should succeed") {pending}
     }
-    describe("when source is a relative path to a file") {
-      it("should fail") {pending}
-    }
-    describe("when source is a relative path to a missing path") {
-      it("should fail") {pending}
-    }
   }
 
   describe("parse - debug") {
-    def invokeWithDebug(debug: String) = {
-      val strings = List("--source", pathTo("."), "--bucket", "bucket", debug)
+    def invokeWithArgument(arg: String): List[ConfigOption] = {
+      val strings = List("--source", pathTo("."), "--bucket", "bucket", arg)
           .filter(_ != "")
-      ParseArgs(strings, defaultConfig).map(_.debug)
+      val maybeOptions = ParseArgs(strings)
+      maybeOptions.getOrElse(List())
     }
 
     describe("when no debug flag") {
-      val debugFlag = invokeWithDebug("")
+      val configOptions = invokeWithArgument("")
       it("debug should be false") {
-        assert(debugFlag.contains(false))
+        assertResult(false)(configOptions.contains(Debug()))
       }
     }
     describe("when long debug flag") {
-      val debugFlag = invokeWithDebug("--debug")
+      val configOptions = invokeWithArgument("--debug")
       it("debug should be true") {
-        assert(debugFlag.contains(true))
+        assert(configOptions.contains(Debug()))
       }
     }
     describe("when short debug flag") {
-      val debugFlag = invokeWithDebug("-d")
+      val configOptions = invokeWithArgument("-d")
       it("debug should be true") {
-        assert(debugFlag.contains(true))
+        assert(configOptions.contains(Debug()))
       }
     }
   }
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ActionSubmitter.scala b/core/src/main/scala/net/kemitix/thorp/core/ActionSubmitter.scala
index 2ba91dd..c743f1c 100644
--- a/core/src/main/scala/net/kemitix/thorp/core/ActionSubmitter.scala
+++ b/core/src/main/scala/net/kemitix/thorp/core/ActionSubmitter.scala
@@ -1,7 +1,6 @@
 package net.kemitix.thorp.core
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import net.kemitix.thorp.aws.api.S3Action.DoNothingS3Action
 import net.kemitix.thorp.aws.api.{S3Action, S3Client, UploadProgressListener}
 import net.kemitix.thorp.core.Action.{DoNothing, ToCopy, ToDelete, ToUpload}
@@ -9,9 +8,10 @@ import net.kemitix.thorp.domain.{Config, Logger}
 
 object ActionSubmitter {
 
-  def submitAction[M[_]: Monad](s3Client: S3Client[M], action: Action)
-                               (implicit c: Config,
-                                logger: Logger[M]): Stream[M[S3Action]] = {
+  def submitAction(s3Client: S3Client,
+                   action: Action)
+                  (implicit c: Config,
+                   logger: Logger): Stream[IO[S3Action]] = {
     Stream(
       action match {
         case ToUpload(bucket, localFile) =>
@@ -31,7 +31,7 @@ object ActionSubmitter {
             action <- s3Client.delete(bucket, remoteKey)
           } yield action
         case DoNothing(bucket, remoteKey) =>
-          Monad[M].pure(DoNothingS3Action(remoteKey))
+          IO.pure(DoNothingS3Action(remoteKey))
       })
   }
 }
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ConfigOption.scala b/core/src/main/scala/net/kemitix/thorp/core/ConfigOption.scala
new file mode 100644
index 0000000..85590d9
--- /dev/null
+++ b/core/src/main/scala/net/kemitix/thorp/core/ConfigOption.scala
@@ -0,0 +1,31 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.Path
+
+import net.kemitix.thorp.domain
+import net.kemitix.thorp.domain.{Config, RemoteKey}
+
+sealed trait ConfigOption {
+  def update(config: Config): Config
+}
+
+object ConfigOption {
+  case class Source(path: Path) extends ConfigOption {
+    override def update(config: Config): Config = config.copy(source = path.toFile)
+  }
+  case class Bucket(name: String) extends ConfigOption {
+    override def update(config: Config): Config = config.copy(bucket = domain.Bucket(name))
+  }
+  case class Prefix(path: String) extends ConfigOption {
+    override def update(config: Config): Config = config.copy(prefix = RemoteKey(path))
+  }
+  case class Include(pattern: String) extends ConfigOption {
+    override def update(config: Config): Config = config.copy(filters = domain.Filter.Include(pattern) :: config.filters)
+  }
+  case class Exclude(pattern: String) extends ConfigOption {
+    override def update(config: Config): Config = config.copy(filters = domain.Filter.Exclude(pattern) :: config.filters)
+  }
+  case class Debug() extends ConfigOption {
+    override def update(config: Config): Config = config.copy(debug = true)
+  }
+}
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ConfigValidation.scala b/core/src/main/scala/net/kemitix/thorp/core/ConfigValidation.scala
new file mode 100644
index 0000000..de9ad81
--- /dev/null
+++ b/core/src/main/scala/net/kemitix/thorp/core/ConfigValidation.scala
@@ -0,0 +1,22 @@
+package net.kemitix.thorp.core
+
+sealed trait ConfigValidation {
+
+  def errorMessage: String
+}
+
+object ConfigValidation {
+
+  case object SourceIsNotADirectory extends ConfigValidation {
+    override def errorMessage: String = "Source must be a directory"
+  }
+
+  case object SourceIsNotReadable extends ConfigValidation {
+    override def errorMessage: String = "Source must be readable"
+  }
+
+  case object BucketNameIsMissing extends ConfigValidation {
+    override def errorMessage: String = "Bucket name is missing"
+  }
+
+}
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ConfigValidator.scala b/core/src/main/scala/net/kemitix/thorp/core/ConfigValidator.scala
new file mode 100644
index 0000000..5a6a48f
--- /dev/null
+++ b/core/src/main/scala/net/kemitix/thorp/core/ConfigValidator.scala
@@ -0,0 +1,35 @@
+package net.kemitix.thorp.core
+
+import java.io.File
+
+import cats.data.{NonEmptyChain, Validated, ValidatedNec}
+import cats.implicits._
+import net.kemitix.thorp.domain.{Bucket, Config}
+
+sealed trait ConfigValidator {
+
+  type ValidationResult[A] = ValidatedNec[ConfigValidation, A]
+
+  def validateSourceIsDirectory(source: File): ValidationResult[File] =
+    if(source.isDirectory) source.validNec
+    else ConfigValidation.SourceIsNotADirectory.invalidNec
+
+  def validateSourceIsReadable(source: File): ValidationResult[File] =
+    if(source.canRead) source.validNec
+    else ConfigValidation.SourceIsNotReadable.invalidNec
+
+  def validateSource(source: File): ValidationResult[File] =
+    validateSourceIsDirectory(source).andThen(s => validateSourceIsReadable(s))
+
+  def validateBucket(bucket: Bucket): ValidationResult[Bucket] =
+    if (bucket.name.isEmpty) ConfigValidation.BucketNameIsMissing.invalidNec
+    else bucket.validNec
+
+  def validateConfig(config: Config): Validated[NonEmptyChain[ConfigValidation], Config] =
+    (
+      validateSource(config.source),
+      validateBucket(config.bucket)
+    ).mapN((_, _) => config)
+}
+
+object ConfigValidator extends ConfigValidator
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ConfigurationBuilder.scala b/core/src/main/scala/net/kemitix/thorp/core/ConfigurationBuilder.scala
new file mode 100644
index 0000000..4b48bd6
--- /dev/null
+++ b/core/src/main/scala/net/kemitix/thorp/core/ConfigurationBuilder.scala
@@ -0,0 +1,47 @@
+package net.kemitix.thorp.core
+
+import java.io.File
+import java.nio.file.Paths
+
+import cats.data.NonEmptyChain
+import cats.effect.IO
+import net.kemitix.thorp.core.ConfigValidator.validateConfig
+import net.kemitix.thorp.domain.Config
+import net.kemitix.thorp.core.ParseConfigFile.parseFile
+
+/**
+  * Builds a configuration from settings in a file within the
+  * `source` directory and from supplied configuration options.
+  */
+trait ConfigurationBuilder {
+
+  private val pwdFile: File = Paths.get(System.getenv("PWD")).toFile
+
+  private val defaultConfig: Config = Config(source = pwdFile)
+
+  def buildConfig(priorityOptions: Seq[ConfigOption]): IO[Either[NonEmptyChain[ConfigValidation], Config]] = {
+    val source = findSource(priorityOptions)
+    for {
+      options <- sourceOptions(source)
+      collected = priorityOptions ++ options
+      config = collateOptions(collected)
+    } yield validateConfig(config).toEither
+  }
+
+  private def findSource(priorityOptions: Seq[ConfigOption]): File =
+    priorityOptions.foldRight(pwdFile)((co, f) => co match {
+      case ConfigOption.Source(source) => source.toFile
+      case _ => f
+    })
+
+  private def sourceOptions(source: File): IO[Seq[ConfigOption]] =
+    readFile(source, ".thorp.conf")
+
+  private def readFile(source: File, filename: String): IO[Seq[ConfigOption]] =
+    parseFile(source.toPath.resolve(filename))
+
+  private def collateOptions(configOptions: Seq[ConfigOption]): Config =
+    configOptions.foldRight(defaultConfig)((co, c) => co.update(c))
+}
+
+object ConfigurationBuilder extends ConfigurationBuilder
diff --git a/core/src/main/scala/net/kemitix/thorp/core/LocalFileStream.scala b/core/src/main/scala/net/kemitix/thorp/core/LocalFileStream.scala
index 52ea218..5648dd9 100644
--- a/core/src/main/scala/net/kemitix/thorp/core/LocalFileStream.scala
+++ b/core/src/main/scala/net/kemitix/thorp/core/LocalFileStream.scala
@@ -3,25 +3,24 @@ package net.kemitix.thorp.core
 import java.io.File
 import java.nio.file.Path
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import net.kemitix.thorp.core.KeyGenerator.generateKey
 import net.kemitix.thorp.domain
 import net.kemitix.thorp.domain._
 
 object LocalFileStream {
 
-  def findFiles[M[_]: Monad](file: File,
-                             md5HashGenerator: File => M[MD5Hash])
-                            (implicit c: Config,
-                             logger: Logger[M]): M[Stream[LocalFile]] = {
+  def findFiles(file: File,
+                md5HashGenerator: File => IO[MD5Hash])
+               (implicit c: Config,
+                logger: Logger): IO[Stream[LocalFile]] = {
 
     val filters: Path => Boolean = Filter.isIncluded(c.filters)
 
-    def loop(file: File): M[Stream[LocalFile]] = {
+    def loop(file: File): IO[Stream[LocalFile]] = {
 
-      def dirPaths(file: File): M[Stream[File]] =
-        Monad[M].pure {
+      def dirPaths(file: File): IO[Stream[File]] =
+        IO.pure {
           Option(file.listFiles)
             .getOrElse(throw new IllegalArgumentException(s"Directory not found $file"))
         }
@@ -29,15 +28,15 @@ object LocalFileStream {
             Stream(fs: _*)
               .filter(f => filters(f.toPath)))
 
-      def recurseIntoSubDirectories(file: File)(implicit c: Config): M[Stream[LocalFile]] =
+      def recurseIntoSubDirectories(file: File)(implicit c: Config): IO[Stream[LocalFile]] =
         file match {
           case f if f.isDirectory => loop(file)
           case _ => for(hash <- md5HashGenerator(file))
             yield Stream(domain.LocalFile(file, c.source, hash, generateKey(c.source, c.prefix)))
         }
 
-      def recurse(fs: Stream[File]): M[Stream[LocalFile]] =
-        fs.foldLeft(Monad[M].pure(Stream.empty[LocalFile]))((acc, f) =>
+      def recurse(fs: Stream[File]): IO[Stream[LocalFile]] =
+        fs.foldLeft(IO.pure(Stream.empty[LocalFile]))((acc, f) =>
           recurseIntoSubDirectories(f)
             .flatMap(lfs => acc.map(s => s ++ lfs)))
 
diff --git a/core/src/main/scala/net/kemitix/thorp/core/MD5HashGenerator.scala b/core/src/main/scala/net/kemitix/thorp/core/MD5HashGenerator.scala
index 321ec46..7cdc7b7 100644
--- a/core/src/main/scala/net/kemitix/thorp/core/MD5HashGenerator.scala
+++ b/core/src/main/scala/net/kemitix/thorp/core/MD5HashGenerator.scala
@@ -3,21 +3,20 @@ package net.kemitix.thorp.core
 import java.io.{File, FileInputStream}
 import java.security.MessageDigest
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import net.kemitix.thorp.domain.{Logger, MD5Hash}
 
 import scala.collection.immutable.NumericRange
 
 object MD5HashGenerator {
 
-  def md5File[M[_]: Monad](file: File)
-                          (implicit logger: Logger[M]): M[MD5Hash] = {
+  def md5File(file: File)
+             (implicit logger: Logger): IO[MD5Hash] = {
 
     val maxBufferSize = 8048
     val defaultBuffer = new Array[Byte](maxBufferSize)
-    def openFile = Monad[M].pure(new FileInputStream(file))
-    def closeFile = {fis: FileInputStream => Monad[M].pure(fis.close())}
+    def openFile = IO.pure(new FileInputStream(file))
+    def closeFile = {fis: FileInputStream => IO(fis.close())}
 
     def nextChunkSize(currentOffset: Long) = {
       // a value between 1 and maxBufferSize
@@ -36,7 +35,7 @@ object MD5HashGenerator {
     }
 
     def digestFile(fis: FileInputStream) =
-      Monad[M].pure {
+      IO {
         val md5 = MessageDigest getInstance "MD5"
         NumericRange(0, file.length, maxBufferSize)
           .foreach { currentOffset => {
@@ -46,7 +45,7 @@ object MD5HashGenerator {
         (md5.digest map ("%02x" format _)).mkString
       }
 
-    def readFile: M[String] =
+    def readFile: IO[String] =
       for {
         fis <- openFile
         md5 <- digestFile(fis)
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ParseConfigFile.scala b/core/src/main/scala/net/kemitix/thorp/core/ParseConfigFile.scala
new file mode 100644
index 0000000..935065a
--- /dev/null
+++ b/core/src/main/scala/net/kemitix/thorp/core/ParseConfigFile.scala
@@ -0,0 +1,28 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.{Files, Path}
+
+import cats.effect.IO
+
+import scala.collection.JavaConverters._
+
+trait ParseConfigFile {
+
+  def parseFile(filename: Path): IO[Seq[ConfigOption]] =
+    readFile(filename).map(ParseConfigLines.parseLines)
+
+  private def readFile(filename: Path) = {
+    if (Files.exists(filename)) readFileThatExists(filename)
+    else IO.pure(List())
+  }
+
+  private def readFileThatExists(filename: Path) =
+    for {
+      lines <- IO(Files.lines(filename))
+      list = lines.iterator.asScala.toList
+      _ <- IO(lines.close())
+    } yield list
+
+}
+
+object ParseConfigFile extends ParseConfigFile
\ No newline at end of file
diff --git a/core/src/main/scala/net/kemitix/thorp/core/ParseConfigLines.scala b/core/src/main/scala/net/kemitix/thorp/core/ParseConfigLines.scala
new file mode 100644
index 0000000..7e273bb
--- /dev/null
+++ b/core/src/main/scala/net/kemitix/thorp/core/ParseConfigLines.scala
@@ -0,0 +1,43 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.Paths
+import java.util.regex.Pattern
+
+import net.kemitix.thorp.core.ConfigOption.{Bucket, Debug, Exclude, Include, Prefix, Source}
+
+trait ParseConfigLines {
+
+  def parseLines(lines: List[String]): List[ConfigOption] =
+    lines.flatMap(parseLine)
+
+  private val pattern = "^\\s*(?<key>\\S*)\\s*=\\s*(?<value>\\S*)\\s*$"
+  private val format = Pattern.compile(pattern)
+
+  private def parseLine(str: String) =
+    format.matcher(str) match {
+      case m if m.matches => parseKeyValue(m.group("key"), m.group("value"))
+      case _ =>None
+    }
+
+  def truthy(value: String): Boolean =
+    value.toLowerCase match {
+      case "true" => true
+      case "yes" => true
+      case "enabled" => true
+      case _ => false
+    }
+
+  private def parseKeyValue(key: String, value: String): Option[ConfigOption] =
+    key.toLowerCase match {
+      case "source" => Some(Source(Paths.get(value)))
+      case "bucket" => Some(Bucket(value))
+      case "prefix" => Some(Prefix(value))
+      case "include" => Some(Include(value))
+      case "exclude" => Some(Exclude(value))
+      case "debug" => if (truthy(value)) Some(Debug()) else None
+      case _ => None
+    }
+
+}
+
+object ParseConfigLines extends ParseConfigLines
diff --git a/core/src/main/scala/net/kemitix/thorp/core/Sync.scala b/core/src/main/scala/net/kemitix/thorp/core/Sync.scala
index 41cd855..bfc3bf7 100644
--- a/core/src/main/scala/net/kemitix/thorp/core/Sync.scala
+++ b/core/src/main/scala/net/kemitix/thorp/core/Sync.scala
@@ -1,36 +1,55 @@
 package net.kemitix.thorp.core
 
-import cats.Monad
+import cats.effect.IO
 import cats.implicits._
 import net.kemitix.thorp.aws.api.{S3Action, S3Client}
 import net.kemitix.thorp.core.Action.ToDelete
 import net.kemitix.thorp.core.ActionGenerator.createActions
 import net.kemitix.thorp.core.ActionSubmitter.submitAction
+import net.kemitix.thorp.core.ConfigurationBuilder.buildConfig
 import net.kemitix.thorp.core.LocalFileStream.findFiles
 import net.kemitix.thorp.core.S3MetaDataEnricher.getMetadata
 import net.kemitix.thorp.core.SyncLogging.{logFileScan, logRunFinished, logRunStart}
 import net.kemitix.thorp.domain._
 
-object Sync {
+trait Sync {
 
-  def run[M[_]: Monad](config: Config,
-                       s3Client: S3Client[M])
-                      (implicit logger: Logger[M]): M[Unit] = {
+  def errorMessages(errors: List[ConfigValidation]): List[String] = {
+    for {
+      errorMessages <- errors.map(cv => cv.errorMessage)
+    } yield errorMessages
+  }
 
-    implicit val c: Config = config
+  def apply(s3Client: S3Client)
+           (configOptions: Seq[ConfigOption])
+           (implicit defaultLogger: Logger): IO[Either[List[String], Unit]] =
+    buildConfig(configOptions).flatMap {
+      case Left(errors) => IO.pure(Left(errorMessages(errors.toList)))
+      case Right(config) =>
+        for {
+          _ <- run(config, s3Client, defaultLogger.withDebug(config.debug))
+        } yield Right(())
+    }
+
+  private def run(cliConfig: Config,
+                  s3Client: S3Client,
+                  logger: Logger): IO[Unit] = {
+
+    implicit val c: Config = cliConfig
+    implicit val l: Logger = logger
 
     def metaData(s3Data: S3ObjectsData, sFiles: Stream[LocalFile]) =
-      Monad[M].pure(sFiles.map(file => getMetadata(file, s3Data)))
+      IO.pure(sFiles.map(file => getMetadata(file, s3Data)))
 
     def actions(sData: Stream[S3MetaData]) =
-      Monad[M].pure(sData.flatMap(s3MetaData => createActions(s3MetaData)))
+      IO.pure(sData.flatMap(s3MetaData => createActions(s3MetaData)))
 
     def submit(sActions: Stream[Action]) =
-      Monad[M].pure(sActions.flatMap(action => submitAction[M](s3Client, action)))
+      IO(sActions.flatMap(action => submitAction(s3Client, action)))
 
-    def copyUploadActions(s3Data: S3ObjectsData): M[Stream[S3Action]] =
+    def copyUploadActions(s3Data: S3ObjectsData): IO[Stream[S3Action]] =
       (for {
-        files <- findFiles(c.source, MD5HashGenerator.md5File[M](_))
+        files <- findFiles(c.source, MD5HashGenerator.md5File(_))
         metaData <- metaData(s3Data, files)
         actions <- actions(metaData)
         s3Actions <- submit(actions)
@@ -38,23 +57,24 @@ object Sync {
         .flatten
         .map(streamS3Actions => streamS3Actions.sorted)
 
-    def deleteActions(s3ObjectsData: S3ObjectsData): M[Stream[S3Action]] =
+    def deleteActions(s3ObjectsData: S3ObjectsData): IO[Stream[S3Action]] =
       (for {
         key <- s3ObjectsData.byKey.keys
         if key.isMissingLocally(c.source, c.prefix)
-        ioDelAction <- submitAction[M](s3Client, ToDelete(c.bucket, key))
+        ioDelAction <- submitAction(s3Client, ToDelete(c.bucket, key))
       } yield ioDelAction)
         .toStream
         .sequence
 
     for {
-      _ <- logRunStart[M]
+      _ <- logRunStart
       s3data <- s3Client.listObjects(c.bucket, c.prefix)
-      _ <- logFileScan[M]
+      _ <- logFileScan
       copyUploadActions <- copyUploadActions(s3data)
       deleteActions <- deleteActions(s3data)
-      _ <- logRunFinished[M](copyUploadActions ++ deleteActions)
+      _ <- logRunFinished(copyUploadActions ++ deleteActions)
     } yield ()
   }
-
 }
+
+object Sync extends Sync
diff --git a/core/src/main/scala/net/kemitix/thorp/core/SyncLogging.scala b/core/src/main/scala/net/kemitix/thorp/core/SyncLogging.scala
index 3c077bb..80e940b 100644
--- a/core/src/main/scala/net/kemitix/thorp/core/SyncLogging.scala
+++ b/core/src/main/scala/net/kemitix/thorp/core/SyncLogging.scala
@@ -1,7 +1,6 @@
 package net.kemitix.thorp.core
 
-import cats.Monad
-import cats.implicits._
+import cats.effect.IO
 import net.kemitix.thorp.aws.api.S3Action
 import net.kemitix.thorp.aws.api.S3Action.{CopyS3Action, DeleteS3Action, ErroredS3Action, UploadS3Action}
 import net.kemitix.thorp.domain.{Config, Logger}
@@ -9,17 +8,17 @@ import net.kemitix.thorp.domain.{Config, Logger}
 // Logging for the Sync class
 object SyncLogging {
 
-  def logRunStart[M[_]: Monad](implicit c: Config,
-                               logger: Logger[M]): M[Unit] =
+  def logRunStart(implicit c: Config,
+                  logger: Logger): IO[Unit] =
     logger.info(s"Bucket: ${c.bucket.name}, Prefix: ${c.prefix.key}, Source: ${c.source}, ")
 
-  def logFileScan[M[_]: Monad](implicit c: Config,
-                               logger: Logger[M]): M[Unit] =
+  def logFileScan(implicit c: Config,
+                  logger: Logger): IO[Unit] =
     logger.info(s"Scanning local files: ${c.source}...")
 
-  def logRunFinished[M[_]: Monad](actions: Stream[S3Action])
-                                 (implicit c: Config,
-                                  logger: Logger[M]): M[Unit] = {
+  def logRunFinished(actions: Stream[S3Action])
+                    (implicit c: Config,
+                     logger: Logger): IO[Unit] = {
     val counters = actions.foldLeft(Counters())(countActivities)
     for {
       _ <- logger.info(s"Uploaded ${counters.uploaded} files")
diff --git a/core/src/test/resources/net/kemitix/thorp/core/empty-file b/core/src/test/resources/net/kemitix/thorp/core/empty-file
new file mode 100644
index 0000000..e69de29
diff --git a/core/src/test/resources/net/kemitix/thorp/core/invalid-config b/core/src/test/resources/net/kemitix/thorp/core/invalid-config
new file mode 100644
index 0000000..7d5b540
--- /dev/null
+++ b/core/src/test/resources/net/kemitix/thorp/core/invalid-config
@@ -0,0 +1 @@
+no valid = config items
diff --git a/core/src/test/resources/net/kemitix/thorp/core/simple-config b/core/src/test/resources/net/kemitix/thorp/core/simple-config
new file mode 100644
index 0000000..fcac950
--- /dev/null
+++ b/core/src/test/resources/net/kemitix/thorp/core/simple-config
@@ -0,0 +1,2 @@
+source = /path/to/source
+bucket = bucket-name
diff --git a/core/src/test/scala/net/kemitix/thorp/core/DummyLogger.scala b/core/src/test/scala/net/kemitix/thorp/core/DummyLogger.scala
index de2449e..4825a31 100644
--- a/core/src/test/scala/net/kemitix/thorp/core/DummyLogger.scala
+++ b/core/src/test/scala/net/kemitix/thorp/core/DummyLogger.scala
@@ -1,16 +1,18 @@
 package net.kemitix.thorp.core
 
-import cats.Monad
+import cats.effect.IO
 import net.kemitix.thorp.domain.Logger
 
-class DummyLogger[M[_]: Monad] extends Logger[M] {
+class DummyLogger extends Logger {
 
-  override def debug(message: => String): M[Unit] = Monad[M].unit
+  override def debug(message: => String): IO[Unit] = IO.unit
 
-  override def info(message: =>String): M[Unit] = Monad[M].unit
+  override def info(message: =>String): IO[Unit] = IO.unit
 
-  override def warn(message: String): M[Unit] = Monad[M].unit
+  override def warn(message: String): IO[Unit] = IO.unit
 
-  override def error(message: String): M[Unit] = Monad[M].unit
+  override def error(message: String): IO[Unit] = IO.unit
+
+  override def withDebug(debug: Boolean): Logger = this
 
 }
diff --git a/core/src/test/scala/net/kemitix/thorp/core/LocalFileStreamSuite.scala b/core/src/test/scala/net/kemitix/thorp/core/LocalFileStreamSuite.scala
index beddece..f5485b7 100644
--- a/core/src/test/scala/net/kemitix/thorp/core/LocalFileStreamSuite.scala
+++ b/core/src/test/scala/net/kemitix/thorp/core/LocalFileStreamSuite.scala
@@ -2,7 +2,7 @@ package net.kemitix.thorp.core
 
 import java.io.File
 
-import cats.Id
+import cats.effect.IO
 import net.kemitix.thorp.domain.{Config, LocalFile, Logger, MD5Hash}
 import org.scalatest.FunSpec
 
@@ -10,13 +10,13 @@ class LocalFileStreamSuite extends FunSpec {
 
   val uploadResource = Resource(this, "upload")
   implicit val config: Config = Config(source = uploadResource)
-  implicit private val logger: Logger[Id] = new DummyLogger[Id]
-  val md5HashGenerator: File => Id[MD5Hash] = file => MD5HashGenerator.md5File[Id](file)
+  implicit private val logger: Logger = new DummyLogger
+  val md5HashGenerator: File => IO[MD5Hash] = file => MD5HashGenerator.md5File(file)
 
   describe("findFiles") {
     it("should find all files") {
       val result: Set[String] =
-        LocalFileStream.findFiles[Id](uploadResource, md5HashGenerator).toSet
+        LocalFileStream.findFiles(uploadResource, md5HashGenerator).unsafeRunSync.toSet
           .map { x: LocalFile => x.relative.toString }
       assertResult(Set("subdir/leaf-file", "root-file"))(result)
     }
diff --git a/core/src/test/scala/net/kemitix/thorp/core/MD5HashGeneratorTest.scala b/core/src/test/scala/net/kemitix/thorp/core/MD5HashGeneratorTest.scala
index 4bbc8ec..607a3d1 100644
--- a/core/src/test/scala/net/kemitix/thorp/core/MD5HashGeneratorTest.scala
+++ b/core/src/test/scala/net/kemitix/thorp/core/MD5HashGeneratorTest.scala
@@ -1,6 +1,5 @@
 package net.kemitix.thorp.core
 
-import cats.Id
 import net.kemitix.thorp.core.MD5HashData.rootHash
 import net.kemitix.thorp.domain._
 import org.scalatest.FunSpec
@@ -10,12 +9,12 @@ class MD5HashGeneratorTest extends FunSpec {
   private val source = Resource(this, "upload")
   private val prefix = RemoteKey("prefix")
   implicit private val config: Config = Config(Bucket("bucket"), prefix, source = source)
-  implicit private val logger: Logger[Id] = new DummyLogger[Id]
+  implicit private val logger: Logger = new DummyLogger
 
     describe("read a small file (smaller than buffer)") {
       val file = Resource(this, "upload/root-file")
       it("should generate the correct hash") {
-        val result = MD5HashGenerator.md5File[Id](file)
+        val result = MD5HashGenerator.md5File(file).unsafeRunSync
         assertResult(rootHash)(result)
       }
     }
@@ -23,7 +22,7 @@ class MD5HashGeneratorTest extends FunSpec {
       val file = Resource(this, "big-file")
       it("should generate the correct hash") {
         val expected = MD5Hash("b1ab1f7680138e6db7309200584e35d8")
-        val result = MD5HashGenerator.md5File[Id](file)
+        val result = MD5HashGenerator.md5File(file).unsafeRunSync
         assertResult(expected)(result)
       }
     }
diff --git a/core/src/test/scala/net/kemitix/thorp/core/ParseConfigFileTest.scala b/core/src/test/scala/net/kemitix/thorp/core/ParseConfigFileTest.scala
new file mode 100644
index 0000000..7a11de4
--- /dev/null
+++ b/core/src/test/scala/net/kemitix/thorp/core/ParseConfigFileTest.scala
@@ -0,0 +1,37 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.{Path, Paths}
+
+import org.scalatest.FunSpec
+
+class ParseConfigFileTest extends FunSpec {
+
+  private def invoke(filename: Path) = ParseConfigFile.parseFile(filename).unsafeRunSync
+  private val empty = List()
+
+  describe("parse a missing file") {
+    val filename = Paths.get("/path/to/missing/file")
+    it("should return no options") {
+      assertResult(empty)(invoke(filename))
+    }
+  }
+  describe("parse an empty file") {
+    val filename = Resource(this, "empty-file").toPath
+    it("should return no options") {
+      assertResult(empty)(invoke(filename))
+    }
+  }
+  describe("parse a file with no valid entries") {
+    val filename = Resource(this, "invalid-config").toPath
+    it("should return no options") {
+      assertResult(empty)(invoke(filename))
+    }
+  }
+  describe("parse a file with properties") {
+    val filename = Resource(this, "simple-config").toPath
+    val expected = List(ConfigOption.Source(Paths.get("/path/to/source")), ConfigOption.Bucket("bucket-name"))
+    it("should return some options") {
+      assertResult(expected)(invoke(filename))
+    }
+  }
+}
diff --git a/core/src/test/scala/net/kemitix/thorp/core/ParseConfigLinesTest.scala b/core/src/test/scala/net/kemitix/thorp/core/ParseConfigLinesTest.scala
new file mode 100644
index 0000000..525a858
--- /dev/null
+++ b/core/src/test/scala/net/kemitix/thorp/core/ParseConfigLinesTest.scala
@@ -0,0 +1,74 @@
+package net.kemitix.thorp.core
+
+import java.nio.file.Paths
+
+import org.scalatest.FunSpec
+
+class ParseConfigLinesTest extends FunSpec {
+
+  describe("parse single lines") {
+    describe("source") {
+      it("should parse") {
+        val expected = List(ConfigOption.Source(Paths.get("/path/to/source")))
+        val result = ParseConfigLines.parseLines(List("source = /path/to/source"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("bucket") {
+      it("should parse") {
+        val expected = List(ConfigOption.Bucket("bucket-name"))
+        val result = ParseConfigLines.parseLines(List("bucket = bucket-name"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("prefix") {
+      it("should parse") {
+        val expected = List(ConfigOption.Prefix("prefix/to/files"))
+        val result = ParseConfigLines.parseLines(List("prefix = prefix/to/files"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("include") {
+      it("should parse") {
+        val expected = List(ConfigOption.Include("path/to/include"))
+        val result = ParseConfigLines.parseLines(List("include = path/to/include"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("exclude") {
+      it("should parse") {
+        val expected = List(ConfigOption.Exclude("path/to/exclude"))
+        val result = ParseConfigLines.parseLines(List("exclude = path/to/exclude"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("debug - true") {
+      it("should parse") {
+        val expected = List(ConfigOption.Debug())
+        val result = ParseConfigLines.parseLines(List("debug = true"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("debug - false") {
+      it("should parse") {
+        val expected = List()
+        val result = ParseConfigLines.parseLines(List("debug = false"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("comment line") {
+      it("should be ignored") {
+        val expected = List()
+        val result = ParseConfigLines.parseLines(List("# ignore me"))
+        assertResult(expected)(result)
+      }
+    }
+    describe("unrecognised option") {
+      it("should be ignored") {
+        val expected = List()
+        val result = ParseConfigLines.parseLines(List("unsupported = option"))
+        assertResult(expected)(result)
+      }
+    }
+  }
+}
diff --git a/core/src/test/scala/net/kemitix/thorp/core/SyncSuite.scala b/core/src/test/scala/net/kemitix/thorp/core/SyncSuite.scala
index bc28da7..dcf789e 100644
--- a/core/src/test/scala/net/kemitix/thorp/core/SyncSuite.scala
+++ b/core/src/test/scala/net/kemitix/thorp/core/SyncSuite.scala
@@ -3,7 +3,7 @@ package net.kemitix.thorp.core
 import java.io.File
 import java.time.Instant
 
-import cats.Id
+import cats.effect.IO
 import net.kemitix.thorp.aws.api.S3Action.{CopyS3Action, DeleteS3Action, UploadS3Action}
 import net.kemitix.thorp.aws.api.{S3Client, UploadProgressListener}
 import net.kemitix.thorp.core.MD5HashData.{leafHash, rootHash}
@@ -16,23 +16,32 @@ class SyncSuite
 
   private val source = Resource(this, "upload")
   private val prefix = RemoteKey("prefix")
-  val config = Config(Bucket("bucket"), prefix, source = source)
-  implicit private val logger: Logger[Id] = new DummyLogger[Id]
+  private val configOptions = List(
+    ConfigOption.Source(source.toPath),
+    ConfigOption.Bucket("bucket"),
+    ConfigOption.Prefix("prefix")
+  )
+  implicit private val logger: Logger = new DummyLogger
   private val lastModified = LastModified(Instant.now)
 
   def putObjectRequest(bucket: Bucket, remoteKey: RemoteKey, localFile: LocalFile): (String, String, File) =
     (bucket.name, remoteKey.key, localFile.file)
 
-  describe("run") {
+  describe("Sync.apply") {
     val testBucket = Bucket("bucket")
     // source contains the files root-file and subdir/leaf-file
     val rootRemoteKey = RemoteKey("prefix/root-file")
     val leafRemoteKey = RemoteKey("prefix/subdir/leaf-file")
+
+    def invokeSubject(s3Client: RecordingClient, configOptions: List[ConfigOption]) = {
+      Sync(s3Client)(configOptions).unsafeRunSync
+    }
+
     describe("when all files should be uploaded") {
       val s3Client = new RecordingClient(testBucket, S3ObjectsData(
         byHash = Map(),
         byKey = Map()))
-      Sync.run(config, s3Client)
+      invokeSubject(s3Client, configOptions)
       it("uploads all files") {
         val expectedUploads = Map(
           "subdir/leaf-file" -> leafRemoteKey,
@@ -58,7 +67,7 @@ class SyncSuite
           RemoteKey("prefix/root-file") -> HashModified(rootHash, lastModified),
           RemoteKey("prefix/subdir/leaf-file") -> HashModified(leafHash, lastModified)))
       val s3Client = new RecordingClient(testBucket, s3ObjectsData)
-      Sync.run(config, s3Client)
+      invokeSubject(s3Client, configOptions)
       it("uploads nothing") {
         val expectedUploads = Map()
         assertResult(expectedUploads)(s3Client.uploadsRecord)
@@ -82,7 +91,7 @@ class SyncSuite
           RemoteKey("prefix/root-file-old") -> HashModified(rootHash, lastModified),
           RemoteKey("prefix/subdir/leaf-file") -> HashModified(leafHash, lastModified)))
       val s3Client = new RecordingClient(testBucket, s3ObjectsData)
-      Sync.run(config, s3Client)
+      invokeSubject(s3Client, configOptions)
       it("uploads nothing") {
         val expectedUploads = Map()
         assertResult(expectedUploads)(s3Client.uploadsRecord)
@@ -110,17 +119,16 @@ class SyncSuite
         byKey = Map(
           deletedKey -> HashModified(deletedHash, lastModified)))
       val s3Client = new RecordingClient(testBucket, s3ObjectsData)
-      Sync.run(config, s3Client)
+      invokeSubject(s3Client, configOptions)
       it("deleted key") {
         val expectedDeletions = Set(deletedKey)
         assertResult(expectedDeletions)(s3Client.deletionsRecord)
       }
     }
     describe("when a file is excluded") {
-      val config: Config = Config(Bucket("bucket"), prefix, source = source, filters = List(Exclude("leaf")))
       val s3ObjectsData = S3ObjectsData(Map(), Map())
       val s3Client = new RecordingClient(testBucket, s3ObjectsData)
-      Sync.run(config, s3Client)
+      invokeSubject(s3Client, ConfigOption.Exclude("leaf") :: configOptions)
       it("is not uploaded") {
         val expectedUploads = Map(
           "root-file" -> rootRemoteKey
@@ -132,7 +140,7 @@ class SyncSuite
 
   class RecordingClient(testBucket: Bucket,
                         s3ObjectsData: S3ObjectsData)
-    extends S3Client[Id] {
+    extends S3Client {
 
     var uploadsRecord: Map[String, RemoteKey] = Map()
     var copiesRecord: Map[RemoteKey, RemoteKey] = Map()
@@ -140,8 +148,8 @@ class SyncSuite
 
     override def listObjects(bucket: Bucket,
                              prefix: RemoteKey)
-                            (implicit logger: Logger[Id]): S3ObjectsData =
-      s3ObjectsData
+                            (implicit logger: Logger): IO[S3ObjectsData] =
+      IO.pure(s3ObjectsData)
 
     override def upload(localFile: LocalFile,
                         bucket: Bucket,
@@ -149,28 +157,28 @@ class SyncSuite
                         multiPartThreshold: Long,
                         tryCount: Int,
                         maxRetries: Int)
-                       (implicit logger: Logger[Id]): UploadS3Action = {
+                       (implicit logger: Logger): IO[UploadS3Action] = {
       if (bucket == testBucket)
         uploadsRecord += (localFile.relative.toString -> localFile.remoteKey)
-      UploadS3Action(localFile.remoteKey, MD5Hash("some hash value"))
+      IO.pure(UploadS3Action(localFile.remoteKey, MD5Hash("some hash value")))
     }
 
     override def copy(bucket: Bucket,
                       sourceKey: RemoteKey,
                       hash: MD5Hash,
                       targetKey: RemoteKey
-                     )(implicit logger: Logger[Id]): CopyS3Action = {
+                     )(implicit logger: Logger): IO[CopyS3Action] = {
       if (bucket == testBucket)
         copiesRecord += (sourceKey -> targetKey)
-      CopyS3Action(targetKey)
+      IO.pure(CopyS3Action(targetKey))
     }
 
     override def delete(bucket: Bucket,
                         remoteKey: RemoteKey
-                       )(implicit logger: Logger[Id]): DeleteS3Action = {
+                       )(implicit logger: Logger): IO[DeleteS3Action] = {
       if (bucket == testBucket)
         deletionsRecord += remoteKey
-      DeleteS3Action(remoteKey)
+      IO.pure(DeleteS3Action(remoteKey))
     }
   }
 }
diff --git a/domain/src/main/scala/net/kemitix/thorp/domain/Config.scala b/domain/src/main/scala/net/kemitix/thorp/domain/Config.scala
index 072ae70..282c7b3 100644
--- a/domain/src/main/scala/net/kemitix/thorp/domain/Config.scala
+++ b/domain/src/main/scala/net/kemitix/thorp/domain/Config.scala
@@ -11,6 +11,5 @@ final case class Config(
                          debug: Boolean = false,
                          source: File
 ) {
-  require(source.isDirectory, s"Source must be a directory: $source")
   require(multiPartThreshold >= 1024 * 1024 * 5, s"Threshold for multi-part upload is 5Mb: '$multiPartThreshold'")
 }
diff --git a/domain/src/main/scala/net/kemitix/thorp/domain/Logger.scala b/domain/src/main/scala/net/kemitix/thorp/domain/Logger.scala
index d3196c1..6e13b78 100644
--- a/domain/src/main/scala/net/kemitix/thorp/domain/Logger.scala
+++ b/domain/src/main/scala/net/kemitix/thorp/domain/Logger.scala
@@ -1,10 +1,17 @@
 package net.kemitix.thorp.domain
 
-trait Logger[M[_]] {
+import cats.effect.IO
 
-  def debug(message: => String): M[Unit]
-  def info(message: => String): M[Unit]
-  def warn(message: String): M[Unit]
-  def error(message: String): M[Unit]
+trait Logger {
+
+  // returns an instance of Logger with debug set as indicated
+  // where the current Logger already matches this state, then
+  // it returns itself, unmodified
+  def withDebug(debug: Boolean): Logger
+
+  def debug(message: => String): IO[Unit]
+  def info(message: => String): IO[Unit]
+  def warn(message: String): IO[Unit]
+  def error(message: String): IO[Unit]
 
 }
diff --git a/domain/src/main/scala/net/kemitix/thorp/domain/RemoteKey.scala b/domain/src/main/scala/net/kemitix/thorp/domain/RemoteKey.scala
index 599b6fe..f75cb8c 100644
--- a/domain/src/main/scala/net/kemitix/thorp/domain/RemoteKey.scala
+++ b/domain/src/main/scala/net/kemitix/thorp/domain/RemoteKey.scala
@@ -4,10 +4,21 @@ import java.io.File
 import java.nio.file.Paths
 
 final case class RemoteKey(key: String) {
+
   def asFile(source: File, prefix: RemoteKey): File =
-    source.toPath.resolve(Paths.get(prefix.key).relativize(Paths.get(key))).toFile
+    source.toPath.resolve(relativeTo(prefix)).toFile
+
+  private def relativeTo(prefix: RemoteKey) = {
+    prefix match {
+      case RemoteKey("") => Paths.get(prefix.key)
+      case _ => Paths.get(prefix.key).relativize(Paths.get(key))
+    }
+  }
+
   def isMissingLocally(source: File, prefix: RemoteKey): Boolean =
     ! asFile(source, prefix).exists
+
   def resolve(path: String): RemoteKey =
     RemoteKey(key + "/" + path)
+
 }