Use CommonMark instead of GFM due to conflict with links

docs/templates/README-TEMPLATE.md

@@ -25,10 +25,22 @@ Context("Optional context name"){
 }
 ```
 
-* Get the loaded plugin instance via `context.request(SnarkHtml)`
+* Get the loaded plugin instance via `val snarkHtml = context.request(SnarkHtml)`
+
+* Use plugin like
+
+```kotlin
+val siteData = snarkHtml.readSiteData(context) {
+    directory(snark.io, Name.EMPTY, dataDirectory)
+}
+
+```
 
 ## SNARK-html
 
 SNARK-HTML module defines tools to work with HTML output format.
 
+### Postprocessing
+
+
 ${modules}

examples/document/build.gradle.kts

@@ -3,18 +3,13 @@ plugins {
     application
 }
 
-application {
-    mainClass.set("Mainkt")
-
-    val isDevelopment: Boolean = project.ext.has("development")
-    applicationDefaultJvmArgs = listOf("-Dio.ktor.development=$isDevelopment", "-Xmx200M")
-}
-
 val snarkVersion: String by extra
 val ktorVersion = space.kscience.gradle.KScienceVersions.ktorVersion
 
 kscience {
-    jvm()
+    jvm{
+        withJava()
+    }
     useContextReceivers()
 
     jvmMain {
@@ -30,4 +25,11 @@ kscience {
 
 kotlin {
     explicitApi = org.jetbrains.kotlin.gradle.dsl.ExplicitApiMode.Disabled
+}
+
+application {
+    mainClass.set("center.sciprog.snark.documents.Mainkt")
+
+    val isDevelopment: Boolean = project.ext.has("development")
+    applicationDefaultJvmArgs = listOf("-Dio.ktor.development=$isDevelopment", "-Xmx200M")
 }

examples/document/data/loremIpsum/chapter1.md

@@ -12,6 +12,12 @@ ${documentMeta.get('metaValue')}
 
 Curabitur hendrerit hendrerit rutrum. Nullam elementum libero a nisi viverra aliquet. Sed ut urna a sem bibendum dictum. Cras non elit sit amet ex ultrices iaculis. Fusce lobortis lacinia fermentum. Fusce in metus id massa mollis consequat. Quisque non dolor quis orci gravida vulputate. Vivamus sed pellentesque orci. Sed aliquet malesuada rhoncus. Mauris id aliquet lorem.
 
+Paragraph
+
+$$
+  \int_a^b {f(x)} = const
+$$
+
 ### Section ${section(2)}
 
 Maecenas at iaculis ipsum. Praesent maximus tristique magna eu faucibus. In tincidunt elementum pharetra. Nam scelerisque eros mattis, suscipit odio sit amet, efficitur mi. Etiam eleifend pulvinar erat a aliquet. Cras pellentesque tincidunt mi eget scelerisque. Proin eget ipsum a velit lobortis commodo. Nulla facilisi. Donec id pretium leo. Ut nec tortor sapien. Praesent vehicula dolor ut laoreet commodo. Pellentesque convallis, sapien et placerat luctus, tortor magna sodales sem, non tristique eros sem vel ipsum. Nulla vulputate accumsan nulla. Duis tempor, mi nec pharetra suscipit, sem odio sagittis mi, ut dignissim odio erat a dolor.

examples/document/src/jvmMain/kotlin/main.kt

@@ -1,3 +1,5 @@
+package center.sciprog.snark.documents
+
 import io.ktor.server.application.Application
 import io.ktor.server.cio.CIO
 import io.ktor.server.engine.embeddedServer
@@ -5,6 +7,7 @@ import kotlinx.html.ScriptCrossorigin
 import kotlinx.html.link
 import kotlinx.html.script
 import space.kscience.snark.html.document.allDocuments
+import space.kscience.snark.ktor.snarkApplication
 
 @Suppress("unused")
 fun Application.renderAllDocuments() = snarkApplication {
@@ -35,7 +38,5 @@ fun Application.renderAllDocuments() = snarkApplication {
 
 
 fun main() {
-    embeddedServer(CIO) {
+    embeddedServer(CIO, module = Application::renderAllDocuments).start(true)
-        renderAllDocuments()
-    }.start(true)
 }

examples/document/src/jvmMain/kotlin/snarkApplication.kt

@@ -1,49 +0,0 @@
-import io.ktor.server.application.Application
-import io.ktor.server.application.log
-import io.ktor.server.http.content.staticResources
-import io.ktor.server.routing.routing
-import space.kscience.dataforge.context.Context
-import space.kscience.dataforge.context.ContextBuilder
-import space.kscience.dataforge.context.request
-import space.kscience.dataforge.data.forEach
-import space.kscience.dataforge.names.Name
-import space.kscience.dataforge.workspace.FileData
-import space.kscience.dataforge.workspace.directory
-import space.kscience.snark.html.HtmlSite
-import space.kscience.snark.html.SnarkHtml
-import space.kscience.snark.html.readSiteData
-import space.kscience.snark.ktor.site
-import kotlin.io.path.Path
-import kotlin.io.path.exists
-
-
-fun Application.snarkApplication(contextBuilder: ContextBuilder.() -> Unit = {}, site: HtmlSite) {
-
-    val context = Context {
-        plugin(SnarkHtml)
-        contextBuilder()
-    }
-
-    val snark = context.request(SnarkHtml)
-
-    val dataDirectoryString = environment.config.propertyOrNull("snark.dataDirectory")?.getString() ?: "data"
-
-    val dataDirectory = Path(dataDirectoryString)
-
-    if (!dataDirectory.exists()) {
-        error("Data directory at $dataDirectory is not resolved")
-    }
-
-    val siteData = snark.readSiteData(context) {
-        directory(snark.io, Name.EMPTY, dataDirectory)
-    }
-
-    siteData.forEach { namedData ->
-        log.debug("Loading data {} from {}", namedData.name, namedData.meta[FileData.FILE_PATH_KEY])
-    }
-
-    routing {
-        staticResources("/css","css")
-        site(context, siteData, content = site)
-    }
-}

snark-core/src/commonMain/kotlin/space/kscience/snark/Snark.kt

@@ -46,8 +46,8 @@ public class Snark : WorkspacePlugin() {
 
         override fun build(context: Context, meta: Meta): Snark = Snark()
 
-        private val byteArrayIOReader = IOReader {
+        private val byteArrayIOReader: IOReader<ByteArray> = IOReader { source ->
-            readByteArray()
+            source.readByteArray()
         }
 
         internal val byteArraySnarkParser = SnarkReader(byteArrayIOReader)

snark-html/src/jvmMain/kotlin/space/kscience/snark/html/MarkdownReader.kt

@@ -7,6 +7,7 @@ import org.intellij.markdown.MarkdownElementTypes
 import org.intellij.markdown.ast.ASTNode
 import org.intellij.markdown.ast.findChildOfType
 import org.intellij.markdown.ast.getTextInNode
+import org.intellij.markdown.flavours.commonmark.CommonMarkFlavourDescriptor
 import org.intellij.markdown.flavours.gfm.GFMFlavourDescriptor
 import org.intellij.markdown.flavours.space.SFMFlavourDescriptor
 import org.intellij.markdown.html.*
@@ -60,7 +61,7 @@ private class SnarkImageGeneratingProvider(
     }
 }
 
-public object SnarkFlavorDescriptor : GFMFlavourDescriptor(false) {
+public object SnarkFlavorDescriptor : CommonMarkFlavourDescriptor(false) {
     override fun createHtmlGeneratingProviders(linkMap: LinkMap, baseURI: URI?): Map<IElementType, GeneratingProvider> =
         super.createHtmlGeneratingProviders(linkMap, baseURI) + mapOf(
             MarkdownElementTypes.INLINE_LINK to SnarkInlineLinkGeneratingProvider(baseURI, absolutizeAnchorLinks)

snark-html/src/jvmMain/kotlin/space/kscience/snark/html/SnarkHtml.kt

@@ -134,8 +134,8 @@ public class SnarkHtml : WorkspacePlugin() {
 
         override fun build(context: Context, meta: Meta): SnarkHtml = SnarkHtml()
 
-        private val byteArrayIOReader = IOReader {
+        private val byteArrayIOReader = IOReader { source->
-            readByteArray()
+            source.readByteArray()
         }
 
         internal val byteArraySnarkParser = SnarkReader(byteArrayIOReader)
@@ -158,5 +158,6 @@ public fun SnarkHtml.readSiteData(
 public fun SnarkHtml.readSiteData(
     coroutineScope: CoroutineScope,
     meta: Meta = Meta.EMPTY,
+    //TODO add IO plugin as a context parameter
     builder: DataSink<Binary>.() -> Unit,
 ): DataTree<Any> = readSiteData(ObservableDataTree(coroutineScope) { builder() }, meta)

snark-ktor/src/jvmMain/kotlin/space/kscience/snark/ktor/snarkApplication.kt

@@ -0,0 +1,74 @@
+package space.kscience.snark.ktor
+
+import io.ktor.server.application.Application
+import io.ktor.server.application.log
+import io.ktor.server.http.content.staticResources
+import io.ktor.server.routing.Route
+import io.ktor.server.routing.application
+import io.ktor.server.routing.routing
+import space.kscience.dataforge.context.Context
+import space.kscience.dataforge.context.ContextBuilder
+import space.kscience.dataforge.context.request
+import space.kscience.dataforge.data.forEach
+import space.kscience.dataforge.names.Name
+import space.kscience.dataforge.workspace.FileData
+import space.kscience.dataforge.workspace.directory
+import space.kscience.snark.html.HtmlSite
+import space.kscience.snark.html.SnarkHtml
+import space.kscience.snark.html.readSiteData
+import kotlin.io.path.Path
+import kotlin.io.path.exists
+
+private fun Application.defaultDataPath() = environment.config
+    .propertyOrNull("snark.dataDirectory")?.getString() ?: "data"
+
+/**
+ * Create a snark site at a given route. Uses [dataPath] as a path to data directory.
+ *
+ * The default [dataPath] is taken from "snark.dataDirectory" property.
+ * If not defined, use "data" directory in current work directory.
+ */
+public fun Route.site(
+    contextBuilder: ContextBuilder.() -> Unit = {},
+    dataPath: String = application.defaultDataPath(),
+    site: HtmlSite,
+) {
+
+    val context = Context {
+        plugin(SnarkHtml)
+        contextBuilder()
+    }
+
+    val snark = context.request(SnarkHtml)
+
+    val dataDirectory = Path(dataPath)
+
+    if (!dataDirectory.exists()) {
+        error("Data directory at $dataDirectory is not resolved")
+    }
+
+    val siteData = snark.readSiteData(context) {
+        directory(snark.io, Name.EMPTY, dataDirectory)
+    }
+
+    siteData.forEach { namedData ->
+        application.log.debug("Loading data {} from {}", namedData.name, namedData.meta[FileData.FILE_PATH_KEY])
+    }
+
+    staticResources("/css", "css")
+    site(context, siteData, content = site)
+
+}
+
+/**
+ * A Ktor module for snark application builder
+ */
+public fun Application.snarkApplication(
+    contextBuilder: ContextBuilder.() -> Unit = {},
+    dataPath: String = defaultDataPath(),
+    site: HtmlSite,
+) {
+    routing {
+        site(contextBuilder, dataPath, site)
+    }
+}