[feat] support conda platforms (#31)

* [feat] support conda platforms

Support specifying conda platforms (e.g. from conda-lock):

 For example
```
   - conda:
     channels:
       - conda-forge
       - bioconda
     requirements:
       - samtools
       - fgbio=1.1.0
     platforms:
       - linux-32
       - osx-arm64
       - win32
```

* Apply suggestions from code review

tools/src/com/github/condaincubator/condaenvbuilder/api/CondaStep.scala

@@ -1,16 +1,19 @@
 package com.github.condaincubator.condaenvbuilder.api
 
-import CondaStep.Channel
+import com.github.condaincubator.condaenvbuilder.api.CondaStep.Channel
+import com.github.condaincubator.condaenvbuilder.api.Platform.Platform
 import io.circe.Decoder.Result
 import io.circe.syntax._
 import io.circe.{Decoder, Encoder, HCursor, Json}
 
+import scala.collection.mutable.ArrayBuffer
+
 /** Specifies the conda channels and requirements for a conda environment.
   *
   * @param channels the conda channels, in priority order
   * @param requirements the package requirements.
   */
-case class CondaStep(channels: Seq[Channel]=Seq.empty, requirements: Seq[Requirement]=Seq.empty) extends StepWithDefaults {
+case class CondaStep(channels: Seq[Channel]=Seq.empty, requirements: Seq[Requirement]=IndexedSeq.empty, platforms: Seq[Platform]=IndexedSeq.empty) extends StepWithDefaults {
 
   /** Inherit (in-order) channels and requirements from the given step(s).
     *
@@ -23,6 +26,7 @@ case class CondaStep(channels: Seq[Channel]=Seq.empty, requirements: Seq[Require
     this.copy(
       channels     = (steps.flatMap(_.channels) ++ this.channels).distinct,
       requirements = Requirement.join(parent=steps.flatMap(_.requirements), child=requirements),
+      platforms    = (steps.flatMap(_.platforms) ++ this.platforms).distinct,
     )
   }
 
@@ -36,6 +40,7 @@ case class CondaStep(channels: Seq[Channel]=Seq.empty, requirements: Seq[Require
       this.copy(
         channels     = (this.channels ++ _defaults.channels).distinct,
         requirements = Requirement.withDefaults(requirements=this.requirements, defaults=_defaults.requirements),
+        platforms    = (this.platforms ++ _defaults.platforms).distinct,
       )
     case _ => this
   }
@@ -50,6 +55,10 @@ case class CondaStep(channels: Seq[Channel]=Seq.empty, requirements: Seq[Require
   *     requirements:
   *       - samtools
   *       - fgbio=1.1.0
+ *      platforms:
+ *        - linux-32
+ *        - osx-arm64
+ *        - win32
   * }}}
   *
   * Both `channels` and `requirements` are optional.
@@ -63,10 +72,13 @@ object CondaStep {
 
   /** Returns an YAML encoder for [[CondaStep]] */
   def encoder: Encoder[CondaStep] = new Encoder[CondaStep] {
-    final def apply(step: CondaStep): Json = Json.obj(
-      ("channels", Json.fromValues(step.channels.map(_.asJson))),
-      ("requirements", Json.fromValues(step.requirements.map(_.asJson)))
-    )
+    final def apply(step: CondaStep): Json = {
+      val fields = ArrayBuffer[(String, Json)]()
+      fields.append(("channels", Json.fromValues(step.channels.map(_.asJson))))
+      fields.append(("requirements", Json.fromValues(step.requirements.map(_.asJson))))
+      if (step.platforms.nonEmpty) fields.append(("platforms", Json.fromValues(step.platforms.map(_.asJson))))
+      Json.obj(fields.toSeq:_*)
+    }
   }
 
   /** Returns a YAML decoder for [[CondaStep]] */
@@ -86,11 +98,17 @@ object CondaStep {
         else Right(Seq.empty)
       }
 
+      val platformResults: Result[Seq[Platform]] = {
+        if (keys.contains("platforms")) c.downField("platforms").as[Seq[Platform]]
+        else Right(Seq.empty)
+      }
+
       for {
         channels <- channelsResults
         requirements <- requirementsResults
+        platforms <- platformResults
       } yield {
-        CondaStep(channels=channels, requirements=requirements)
+        CondaStep(channels=channels, requirements=requirements, platforms=platforms)
       }
     }
   }

tools/src/com/github/condaincubator/condaenvbuilder/api/Platform.scala

@@ -0,0 +1,6 @@
+package com.github.condaincubator.condaenvbuilder.api
+
+/** The name of the platform (e.g. linux-32, linux-armv7l, win-64, osx-arm64) */
+object Platform {
+  type Platform = String
+}

tools/test/src/com/github/condaincubator/condaenvbuilder/api/CondaStepTest.scala

@@ -15,19 +15,22 @@ object CondaStepTest extends UnitSpec {
         |  ]
         |}""".stripMargin
     }),
-    // one channel, one requirement
-    (api.CondaStep(channels=Seq("some channel"), requirements=Seq("a==1").reqs), {
+    // one channel, one requirement, one platform
+    (api.CondaStep(channels=Seq("some channel"), requirements=Seq("a==1").reqs, platforms=Seq("linux-32")), {
       """{
         |  "channels" : [
         |    "some channel"
         |  ],
         |  "requirements" : [
         |    "a==1"
+        |  ],
+        |  "platforms" : [
+        |    "linux-32"
         |  ]
         |}""".stripMargin
     }),
-    // multiple channels and requirements
-    (api.CondaStep(channels=Seq("channel 1", "channel 2"), requirements=Seq("a==1", "b==2").reqs), {
+    // multiple channels, requirements, and platforms
+    (api.CondaStep(channels=Seq("channel 1", "channel 2"), requirements=Seq("a==1", "b==2").reqs, platforms=Seq("linux-32", "win-32")), {
       """{
         |  "channels" : [
         |    "channel 1",
@@ -36,11 +39,15 @@ object CondaStepTest extends UnitSpec {
         |  "requirements" : [
         |    "a==1",
         |    "b==2"
+        |  ],
+        |  "platforms" : [
+        |    "linux-32",
+        |    "win-32"
         |  ]
         |}""".stripMargin
     }),
     // empty requirements, empty channels
-    (CondaStep(channels=Seq.empty, requirements=Seq.empty), {
+    (CondaStep(channels=Seq.empty, requirements=Seq.empty, platforms=Seq.empty), {
       """{
         |  "channels" : [
         |  ],

tools/test/src/com/github/condaincubator/condaenvbuilder/tools/ToolsTest.scala

@@ -24,6 +24,8 @@ class ToolsTest extends UnitSpec {
       |            - python=3.6.10
       |            - samtools=1.10
       |            - yaml=0.1.7
+      |          platforms:
+      |            - linux-32
       |      - pip:
       |          requirements:
       |            - defopt==5.1.0
@@ -81,6 +83,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - pybedtools=0.8.1
       |        - yaml=0.1.7
+      |        platforms:
+      |        - linux-32
       |    - pip:
       |        args: []
       |        requirements:
@@ -101,6 +105,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - samtools=1.9
       |        - hisat2=2.2.0
+      |        platforms:
+      |        - linux-32
       |  bwa:
       |    group: alignment
       |    steps:
@@ -111,6 +117,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - samtools=1.9
       |        - bwa=0.7.17
+      |        platforms:
+      |        - linux-32
       |  samtools:
       |    group: alignment
       |    steps:
@@ -119,7 +127,9 @@ class ToolsTest extends UnitSpec {
       |        - conda-forge
       |        - bioconda
       |        requirements:
-      |        - samtools=1.9""".stripMargin
+      |        - samtools=1.9
+      |        platforms:
+      |        - linux-32""".stripMargin
   }
 
   val tabulatedString: String = {
@@ -150,6 +160,8 @@ class ToolsTest extends UnitSpec {
       |        - bioconda
       |        requirements:
       |        - samtools=1.9
+      |        platforms:
+      |        - linux-32
       |  bwa:
       |    group: alignment
       |    steps:
@@ -160,6 +172,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - samtools=1.9
       |        - bwa=0.7.17
+      |        platforms:
+      |        - linux-32
       |  hisat2:
       |    group: alignment
       |    steps:
@@ -170,6 +184,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - samtools=1.9
       |        - hisat2=2.2.0
+      |        platforms:
+      |        - linux-32
       |  conda-env-builder:
       |    group: conda-env-builder
       |    steps:
@@ -181,6 +197,8 @@ class ToolsTest extends UnitSpec {
       |        - pybedtools=0.8.1
       |        - yaml=0.1.7
       |        - pip==default
+      |        platforms:
+      |        - linux-32
       |    - pip:
       |        args: []
       |        requirements:
@@ -206,6 +224,8 @@ class ToolsTest extends UnitSpec {
       |        - bioconda
       |        requirements:
       |        - samtools=1.9
+      |        platforms:
+      |        - linux-32
       |  bwa:
       |    group: alignment
       |    steps:
@@ -216,6 +236,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - samtools=1.9
       |        - bwa=0.7.17
+      |        platforms:
+      |        - linux-32
       |  hisat2:
       |    group: alignment
       |    steps:
@@ -226,6 +248,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - samtools=1.9
       |        - hisat2=2.2.0
+      |        platforms:
+      |        - linux-32
       |  conda-env-builder:
       |    group: conda-env-builder
       |    steps:
@@ -236,6 +260,8 @@ class ToolsTest extends UnitSpec {
       |        requirements:
       |        - pybedtools=0.8.1
       |        - yaml=0.1.7
+      |        platforms:
+      |        - linux-32
       |    - pip:
       |        args: []
       |        requirements: