chore: allow a lesser selenium

Author: clintval

python/poetry.lock

@@ -36,7 +36,7 @@ google-api-python-client = "~2.151"
 google-auth-httplib2     = "~0.2"
 google-auth-oauthlib     = "~1.2.1"
 lxml                     = "~5.3"
-selenium                 = "~4.26"
+selenium                 = ">=3.141"
 types-beautifulsoup4     = "~4.12"
 
 [tool.poetry.group.dev.dependencies]

python/pyproject.toml

@@ -65,7 +65,7 @@ object SeshatMerge {
   val Delimiter: Char = '\t'
 
   /** Ignore these invariant fields in the annotation file, as they are copy-pasted from the source VCF. */
-  val FieldsToIgnore: Set[String] = {
+  private[seshat] val FieldsToIgnore: Set[String] = {
     Set("Sample", "CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT")
   }
 

scala/seshat/src/io/cvbio/seshat/SeshatMerge.scala

@@ -66,7 +66,7 @@ object SeshatRoundTrip {
   val SeshatInfix: String = ".seshat"
 
   /** Find a Seshat annotation file in a directory, by type. Annotation files have a date-time-stamp in their filename. */
-  def findAnnotations(dir: DirPath, kind: SeshatAnnotationType): Option[FilePath] = {
+  private[seshat] def findAnnotations(dir: DirPath, kind: SeshatAnnotationType): Option[FilePath] = {
     val pattern: Regex = s".*${kind.entryName}-\\d{8}_\\d{6}_\\d{6}\\.tsv".r
     Files.walk(dir, 1).iterator.find(path => pattern.matches(PathUtil.basename(path, trimExt = false)))
   }
@@ -78,7 +78,7 @@ object SeshatRoundTrip {
   object SeshatAnnotationType extends Enum[SeshatAnnotationType] {
 
     /** All values of this enumeration. */
-    val values = findValues
+    val values: IndexedSeq[SeshatAnnotationType] = findValues
 
     /** The short-form annotations. */
     case object Short extends SeshatAnnotationType

scala/seshat/src/io/cvbio/seshat/SeshatRoundTrip.scala

@@ -51,7 +51,7 @@ class SeshatUploadVcf(
     )
   }
 
-  /** The argument list for the [[SeshatUpload]] script. */
+  /** The argument list for the [[SeshatUploadVcf]] script. */
   private[seshat] def scriptArgs(input: PathToVcf): Seq[String] = {
     val buffer = new ListBuffer[String]()
     buffer.addAll(Seq("--input", input.toString))
@@ -112,7 +112,7 @@ object SeshatUploadVcf {
   object SeshatAssembly extends Enum[SeshatAssembly] {
 
     /** All values of this enumeration. */
-    val values = findValues
+    val values: IndexedSeq[SeshatAssembly] = findValues
 
     /** The assembly hg17. */
     case object Hg17 extends SeshatAssembly

…t/src/io/cvbio/seshat/SeshatUpload.scala …rc/io/cvbio/seshat/SeshatUploadVcf.scalascala/seshat/src/io/cvbio/seshat/SeshatUpload.scala renamed to scala/seshat/src/io/cvbio/seshat/SeshatUploadVcf.scala scala/seshat/src/io/cvbio/seshat/SeshatUpload.scala renamed to scala/seshat/src/io/cvbio/seshat/SeshatUploadVcf.scala

@@ -29,23 +29,23 @@ object VcfUtil {
   )
 
   /** Some characters have special meanings in VCF files.  When they appear in strings for use as an INFO/FORMAT key
-   * or value they must be encoded. These functions will perform this encoding/decoding for all characters as outlined
-   * in VCF 4.3 §1.2. This function is not to be used on a string representation of a list of INFO/FORMAT values.
-   * URL encoding is similar, but conflates Space (" ") and Plus ("+").
-   * Spaces are allowed in VCF v4.3, but this isn't yet supported by HTSJDK so they are also encoded.
-   *
-   * In the case of encoding a list of INFO/FORMAT values encoded as a string, you must first split the string on the
-   * comma-delimiter, encode, and then re-join the string:
-   *
-   * {{{
-   *     "1.0 2.0,3.0 4.0,5.0".split(',').map(VcfUtil.fieldEncode).mkString(",")
-   * }}}
-   *
-   * Which will return:
-   *
-   * {{{
-   *     "1.0%202.0,3.0%204.0,5.0"
-   * }}}
-   */
+    * or value they must be encoded. These functions will perform this encoding/decoding for all characters as outlined
+    * in VCF 4.3 §1.2. This function is not to be used on a string representation of a list of INFO/FORMAT values.
+    * URL encoding is similar, but conflates Space (" ") and Plus ("+").
+    * Spaces are allowed in VCF v4.3, but this isn't yet supported by HTSJDK so they are also encoded.
+    *
+    * In the case of encoding a list of INFO/FORMAT values encoded as a string, you must first split the string on the
+    * comma-delimiter, encode, and then re-join the string:
+    *
+    * {{{
+    *     "1.0 2.0,3.0 4.0,5.0".split(',').map(VcfUtil.fieldEncode).mkString(",")
+    * }}}
+    *
+    * Which will return:
+    *
+    * {{{
+    *     "1.0%202.0,3.0%204.0,5.0"
+    * }}}
+    */
   private[seshat] def fieldEncode(string: String): String = string.map(c => SpecialCharCodec.getOrElse(c, c.toString)).mkString
 }

scala/seshat/src/io/cvbio/seshat/VcfUtil.scala

@@ -8,8 +8,7 @@ import com.fulcrumgenomics.util.Io.makeTempFile
 import com.fulcrumgenomics.vcf.api.{AlleleSet, Genotype, Variant, VcfSource}
 import io.cvbio.UnitSpec
 import io.cvbio.seshat.SeshatMerge._
-import io.cvbio.seshat.VcfUtil
-import io.cvbio.seshat.VcfUtil.{VcfExtension, TextExtension}
+import io.cvbio.seshat.VcfUtil.{TextExtension, VcfExtension}
 
 import scala.util.Properties.lineSeparator