fix: bump version to 3.0.0-alpha.0 and fix compatibility checks

packages_rs/nextclade-cli/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nextclade-cli"
-version = "2.14.0"
+version = "3.0.0-alpha.0"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. CLI module."
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
@@ -34,7 +34,7 @@ rayon = "=1.7.0"
 regex = "=1.8.4"
 reqwest = { version = "=0.11.18", default-features = false, features = ["blocking", "deflate", "gzip", "brotli", "socks", "rustls-tls"] }
 schemars = { version = "=0.8.12", features = ["chrono", "either", "enumset", "indexmap1"] }
-semver = "=1.0.17"
+semver = { version = "=1.0.17", features = ["serde"] }
 serde = { version = "=1.0.164", features = ["derive"] }
 serde_json = { version = "=1.0.99", features = ["preserve_order", "indexmap", "unbounded_depth"] }
 strum = "=0.25.0"

packages_rs/nextclade-cli/src/cli/nextclade_dataset_get.rs

@@ -5,10 +5,9 @@ use eyre::{Report, WrapErr};
 use itertools::Itertools;
 use log::{warn, LevelFilter};
 use nextclade::io::dataset::{Dataset, DatasetsIndexJson};
+use nextclade::utils::info::{this_package_version, this_package_version_str};
 use nextclade::utils::string::find_similar_strings;
-use nextclade::{getenv, make_error, make_internal_error};
-
-const THIS_VERSION: &str = getenv!("CARGO_PKG_VERSION");
+use nextclade::{make_error, make_internal_error};
 
 pub struct DatasetHttpGetParams<'s> {
   pub name: &'s str,
@@ -93,12 +92,12 @@ pub fn dataset_http_get(http: &mut HttpClient, name: impl AsRef<str>, tag: &Opti
     }
   }?;
 
-  if !dataset.is_cli_compatible(THIS_VERSION) {
+  if !dataset.is_cli_compatible(&this_package_version()) {
     warn!(
       "The requested dataset '{}' with version tag '{}' is not compatible with this version of Nextclade ({}). This may cause errors and unexpected results. Please try to upgrade your Nextclade version and/or report this to dataset authors.",
       dataset.path,
       dataset.tag(),
-      THIS_VERSION
+      this_package_version_str()
     );
   }
 

packages_rs/nextclade-cli/src/cli/nextclade_dataset_list.rs

@@ -7,9 +7,8 @@ use itertools::Itertools;
 use log::LevelFilter;
 use nextclade::io::dataset::{Dataset, DatasetsIndexJson};
 use nextclade::io::json::{json_stringify, JsonPretty};
-use nextclade::{getenv, make_error};
-
-const THIS_VERSION: &str = getenv!("CARGO_PKG_VERSION");
+use nextclade::make_error;
+use nextclade::utils::info::this_package_version;
 
 pub fn nextclade_dataset_list(
   NextcladeDatasetListArgs {
@@ -50,7 +49,7 @@ pub fn nextclade_dataset_list(
       if let Some(tag) = tag.as_ref() {
         dataset.is_tag(tag)
       } else {
-        let is_compatible = include_incompatible || dataset.is_cli_compatible(THIS_VERSION);
+        let is_compatible = include_incompatible || dataset.is_cli_compatible(&this_package_version());
         let is_not_deprecated = include_deprecated || !dataset.is_deprecated();
         let is_not_experimental = include_experimental || !dataset.is_experimental();
         let is_not_community = include_community || !dataset.is_community();

packages_rs/nextclade-cli/src/io/http_client.rs

@@ -1,7 +1,8 @@
 use clap::{Parser, ValueHint};
 use eyre::Report;
 use log::info;
-use nextclade::{getenv, make_internal_error};
+use nextclade::make_internal_error;
+use nextclade::utils::info::{this_package_name, this_package_version_str};
 use reqwest::blocking::Client;
 use reqwest::{Method, Proxy};
 use std::str::FromStr;
@@ -57,7 +58,7 @@ impl HttpClient {
       client_builder
     };
 
-    let user_agent = format!("{} {}", getenv!("CARGO_PKG_NAME"), getenv!("CARGO_PKG_VERSION"));
+    let user_agent = format!("{} {}", this_package_name(), this_package_version_str());
 
     let client = client_builder
       .connection_verbose(verbose)

packages_rs/nextclade-web/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nextclade-web"
-version = "2.14.0"
+version = "3.0.0-alpha.0"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. WebAssembly module."
 edition = "2021"
 license = "MIT"

packages_rs/nextclade-web/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nextstrain/nextclade-web",
-  "version": "2.14.1",
+  "version": "3.0.0-alpha.0",
   "description": "Clade assignment, mutation calling, and sequence quality checks",
   "homepage": "https://clades.nextstrain.org",
   "repository": {

packages_rs/nextclade-web/src/io/fetchDatasetsIndex.ts

@@ -13,7 +13,7 @@ export function isEnabled(dataset: Dataset) {
 
 export function isCompatible(dataset: Dataset): boolean {
   const minVersion = dataset.version?.compatibility?.web ?? thisVersion
-  return semver.gte(thisVersion, minVersion) && semver.lte(thisVersion, minVersion)
+  return semver.gte(thisVersion, minVersion)
 }
 
 export function isLatest(dataset: Dataset): boolean {

packages_rs/nextclade/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nextclade"
-version = "2.14.0"
+version = "3.0.0-alpha.0"
 description = "Alignment, mutation calling, phylogenetic placement, clade assignment and quality control checks for viral genetic sequences. Library module."
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
@@ -49,7 +49,7 @@ pretty_assertions = "=1.3.0"
 rayon = "=1.7.0"
 regex = "=1.8.4"
 schemars = { version = "=0.8.12", features = ["chrono", "either", "enumset", "indexmap"] }
-semver = "=1.0.17"
+semver = { version = "=1.0.17", features = ["serde"] }
 serde = { version = "=1.0.164", features = ["derive"] }
 serde_json = { version = "=1.0.99", features = ["preserve_order", "indexmap", "unbounded_depth"] }
 serde_repr = "=0.1.12"

packages_rs/nextclade/src/analyze/virus_properties.rs

@@ -14,6 +14,7 @@ use crate::run::params_general::NextcladeGeneralParamsOptional;
 use crate::tree::params::TreeBuilderParamsOptional;
 use crate::utils::boolean::{bool_false, bool_true};
 use eyre::{Report, WrapErr};
+use semver::Version;
 use serde::{Deserialize, Serialize};
 use std::collections::BTreeMap;
 use std::path::Path;
@@ -199,4 +200,11 @@ impl VirusProperties {
 
     json_parse::<VirusProperties>(s).wrap_err("When parsing pathogen.json file")
   }
+
+  pub fn is_cli_compatible(&self, current_cli_version: &Version) -> bool {
+    self
+      .compatibility
+      .as_ref()
+      .map_or(true, |compat| compat.is_cli_compatible(current_cli_version))
+  }
 }

packages_rs/nextclade/src/io/dataset.rs

@@ -4,6 +4,7 @@ use crate::o;
 use eyre::Report;
 use itertools::Itertools;
 use schemars::JsonSchema;
+use semver::Version;
 use serde::{Deserialize, Serialize};
 use std::cmp::Ordering;
 use std::collections::BTreeMap;
@@ -96,7 +97,7 @@ impl Dataset {
     [&self.root_path(), filename.as_ref()].iter().join("/")
   }
 
-  pub fn is_cli_compatible(&self, cli_version: impl AsRef<str>) -> bool {
+  pub fn is_cli_compatible(&self, cli_version: &Version) -> bool {
     self
       .version
       .compatibility
@@ -191,15 +192,20 @@ impl Default for DatasetVersion {
 #[serde(rename_all = "camelCase")]
 pub struct DatasetCompatibility {
   #[serde(default, skip_serializing_if = "Option::is_none")]
-  cli: Option<String>,
+  #[schemars(with = "String")]
+  pub cli: Option<Version>,
 
   #[serde(default, skip_serializing_if = "Option::is_none")]
-  web: Option<String>,
+  #[schemars(with = "String")]
+  pub web: Option<Version>,
 }
 
 impl DatasetCompatibility {
-  pub fn is_cli_compatible(&self, cli_version: impl AsRef<str>) -> bool {
-    self.cli.as_ref().map_or(true, |cli| cli_version.as_ref() >= cli)
+  pub fn is_cli_compatible(&self, cli_version: &Version) -> bool {
+    self
+      .cli
+      .as_ref()
+      .map_or(true, |min_cli_version| cli_version >= min_cli_version)
   }
 }
 

packages_rs/nextclade/src/io/results_json.rs

@@ -9,6 +9,7 @@ use crate::utils::datetime::date_iso_now;
 use eyre::Report;
 use serde::{Deserialize, Serialize};
 use std::path::{Path, PathBuf};
+use crate::utils::info::this_package_version_str;
 
 #[derive(Serialize, Deserialize, schemars::JsonSchema)]
 #[serde(rename_all = "camelCase")]
@@ -33,11 +34,9 @@ pub struct ResultsJson {
 
 impl ResultsJson {
   pub fn new(clade_node_attrs: &[CladeNodeAttrKeyDesc], phenotype_attr_keys: &[PhenotypeAttrDesc]) -> Self {
-    const VERSION: &str = env!("CARGO_PKG_VERSION");
-
     Self {
-      schema_version: "1.0.0".to_owned(),
-      nextclade_algo_version: VERSION.to_owned(),
+      schema_version: "3.0.0".to_owned(),
+      nextclade_algo_version: this_package_version_str().to_owned(),
       nextclade_web_version: None,
       created_at: date_iso_now(),
       clade_node_attr_keys: clade_node_attrs.to_vec(),

packages_rs/nextclade/src/utils/getenv.rs

@@ -1,4 +1,4 @@
-#[macro_export(local_inner_macros)]
+#[macro_export]
 macro_rules! getenv {
   ($arg:tt) => {{
     match core::option_env!($arg) {

packages_rs/nextclade/src/utils/info.rs

@@ -0,0 +1,26 @@
+use lazy_static::lazy_static;
+use semver::Version;
+
+pub fn this_package_name() -> &'static str {
+  lazy_static! {
+    pub static ref PKG_NAME: &'static str = env!("CARGO_PKG_NAME");
+  }
+  &PKG_NAME
+}
+
+pub fn this_package_version() -> &'static Version {
+  lazy_static! {
+    pub static ref VERSION: Version = Version::parse(env!("CARGO_PKG_VERSION")).expect(
+      "Unable to parse env var `CARGO_PKG_VERSION` in semantic version format. \
+        In most cases it comes from `version` field in `Cargo.toml` file."
+    );
+  }
+  &VERSION
+}
+
+pub fn this_package_version_str() -> &'static str {
+  lazy_static! {
+    pub static ref VERSION_STR: String = this_package_version().to_string();
+  }
+  &VERSION_STR
+}

packages_rs/nextclade/src/utils/mod.rs

@@ -4,6 +4,7 @@ pub mod datetime;
 pub mod error;
 pub mod getenv;
 pub mod global_init;
+pub mod info;
 pub mod num;
 pub mod option;
 pub mod string;