align seqspec version and upgrade paths

Author: sbooeshaghi

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "seqspec"
-version = "0.1.0"
+version = "0.4.0"
 edition = "2021"
 license = "MIT"
 repository = "https://github.com/pachterlab/seqspec"
@@ -27,4 +27,3 @@ flate2 = "1"
 [features]
 default = []
 python-binding = ["pyo3"]          # enable PyO3 only when building Python wheels
-

seqspec/seqspec_upgrade.py

@@ -52,8 +52,8 @@ def run_upgrade(parser: ArgumentParser, args: Namespace) -> None:
     """Run the upgrade command."""
     validate_upgrade_args(parser, args)
 
-    spec = load_spec(args.yaml)
-    version = spec.seqspec_version
+    spec = load_spec(args.yaml, strict=False)
+    version = spec.seqspec_version or "0.0.0"
     upgraded_spec = seqspec_upgrade(spec, version)
 
     if args.output:
@@ -65,11 +65,12 @@ def run_upgrade(parser: ArgumentParser, args: Namespace) -> None:
 def seqspec_upgrade(spec: Assay, version: str) -> Assay:
     """Upgrade spec to current version."""
     UPGRADE = {
-        "0.0.0": upgrade_0_0_0_to_0_3_0,
-        "0.1.0": upgrade_0_1_0_to_0_3_0,
-        "0.1.1": upgrade_0_1_1_to_0_3_0,
-        "0.2.0": upgrade_0_2_0_to_0_3_0,
-        "0.3.0": upgrade_0_3_0_to_0_3_0,
+        "0.0.0": upgrade_0_0_0_to_0_4_0,
+        "0.1.0": upgrade_0_1_0_to_0_4_0,
+        "0.1.1": upgrade_0_1_1_to_0_4_0,
+        "0.2.0": upgrade_0_2_0_to_0_4_0,
+        "0.3.0": upgrade_0_3_0_to_0_4_0,
+        "0.4.0": upgrade_0_4_0_to_0_4_0,
     }
 
     if version not in UPGRADE:
@@ -80,13 +81,19 @@ def seqspec_upgrade(spec: Assay, version: str) -> Assay:
     return UPGRADE[version](spec)
 
 
-def upgrade_0_3_0_to_0_3_0(spec: Assay) -> Assay:
+def upgrade_0_4_0_to_0_4_0(spec: Assay) -> Assay:
     """No upgrade needed for current version."""
     return spec
 
 
-def upgrade_0_2_0_to_0_3_0(spec: Assay) -> Assay:
-    """Upgrade spec from version 0.2.0 to 0.3.0."""
+def upgrade_0_3_0_to_0_4_0(spec: Assay) -> Assay:
+    """Upgrade spec from version 0.3.0 to 0.4.0."""
+    spec.seqspec_version = "0.4.0"
+    return spec
+
+
+def upgrade_0_2_0_to_0_4_0(spec: Assay) -> Assay:
+    """Upgrade spec from version 0.2.0 to 0.4.0."""
     # Set files to empty for specs < v0.3.0
     for r in spec.sequence_spec:
         r.set_files(
@@ -117,21 +124,21 @@ def upgrade_0_2_0_to_0_3_0(spec: Assay) -> Assay:
                     url="",
                     urltype="",
                     md5=md5,
-                )
+                    )
     spec.seqspec_version = "0.3.0"
-    return spec
+    return upgrade_0_3_0_to_0_4_0(spec)
 
 
-def upgrade_0_1_1_to_0_3_0(spec: Assay) -> Assay:
-    """Upgrade spec from version 0.1.1 to 0.3.0."""
-    return upgrade_0_2_0_to_0_3_0(spec)
+def upgrade_0_1_1_to_0_4_0(spec: Assay) -> Assay:
+    """Upgrade spec from version 0.1.1 to 0.4.0."""
+    return upgrade_0_2_0_to_0_4_0(spec)
 
 
-def upgrade_0_1_0_to_0_3_0(spec: Assay) -> Assay:
-    """Upgrade spec from version 0.1.0 to 0.3.0."""
-    return upgrade_0_2_0_to_0_3_0(spec)
+def upgrade_0_1_0_to_0_4_0(spec: Assay) -> Assay:
+    """Upgrade spec from version 0.1.0 to 0.4.0."""
+    return upgrade_0_2_0_to_0_4_0(spec)
 
 
-def upgrade_0_0_0_to_0_3_0(spec: Assay) -> Assay:
-    """Upgrade spec from version 0.0.0 to 0.3.0."""
-    return upgrade_0_2_0_to_0_3_0(spec)
+def upgrade_0_0_0_to_0_4_0(spec: Assay) -> Assay:
+    """Upgrade spec from version 0.0.0 to 0.4.0."""
+    return upgrade_0_2_0_to_0_4_0(spec)

src/main.rs

@@ -22,7 +22,7 @@ use seqspec::utils;
 use clap::{Parser, Subcommand};
 
 #[derive(Parser, Debug)]
-#[clap(name = "seqspec", version = "0.X.0", author = "Your Name")]
+#[command(name = "seqspec", version)]
 struct Args {
     #[command(subcommand)]
     subcmd: Commands,
@@ -65,4 +65,4 @@ fn main() {
         ,Commands::Check(args) => { seqspec_check::run_check(&args); }
         ,Commands::Onlist(args) => seqspec_onlist::run_onlist(&args)
     }
-}
+}

tests/test_seqspec_upgrade.py

@@ -0,0 +1,25 @@
+from pathlib import Path
+
+from seqspec.seqspec_upgrade import seqspec_upgrade
+from seqspec.utils import load_spec
+
+
+def test_seqspec_upgrade_promotes_0_3_to_0_4():
+    spec = load_spec(Path("tests/fixtures/legacy_0_3_scalar_protocols.yaml"), strict=False)
+    assert spec.seqspec_version == "0.3.0"
+
+    upgraded = seqspec_upgrade(spec, spec.seqspec_version)
+
+    assert upgraded.seqspec_version == "0.4.0"
+
+
+def test_seqspec_upgrade_promotes_0_2_to_0_4_and_adds_files():
+    spec = load_spec(Path("tests/fixtures/legacy_0_2_missing_fields.yaml"), strict=False)
+    assert spec.seqspec_version == "0.2.0"
+    assert spec.sequence_spec[0].files == []
+
+    upgraded = seqspec_upgrade(spec, spec.seqspec_version)
+
+    assert upgraded.seqspec_version == "0.4.0"
+    assert len(upgraded.sequence_spec[0].files) == 1
+    assert upgraded.sequence_spec[0].files[0].file_id == upgraded.sequence_spec[0].read_id