Merge branch 'mod-permits' into skipmer

Cargo.toml

@@ -9,23 +9,22 @@ name = "sourmash_plugin_directsketch"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = "0.23.3", features = ["extension-module","anyhow"], default = ["extension-module"] }
+pyo3 = { version = "0.23.3", features = ["extension-module","anyhow"]}
 rayon = "1.10.0"
 serde = { version = "1.0.204", features = ["derive"] }
-#sourmash = { version = "0.18.0"}
-sourmash = {git = "https://github.com/sourmash-bio/sourmash/", branch = "try-skipmers"}
-serde_json = "1.0.132"
+sourmash = { version = "0.18.0"}
+serde_json = "1.0.134"
 niffler = "2.4.0"
 needletail = "0.5.1"
 async_zip={version="0.0.17", features=["full"]}
 simple-error = "0.3.1"
-anyhow = "1.0.90"
+anyhow = "1.0.95"
 camino = "1.1.7"
 csv = "1.3.1"
-reqwest = { version = "0.12.8", features = ["json", "stream"] }
+reqwest = { version = "0.12.9", features = ["json", "stream"] }
 tokio = { version = "1.42.0", features = ["full"] }
-tokio-util = "0.7.11"
-regex = "1.11.0"
+tokio-util = "0.7.13"
+regex = "1.11.1"
 chrono = "0.4.32"
 lazy_static = "1.5.0"
 md5 = "0.7.0"

README.md

@@ -146,6 +146,8 @@ options:
                         number of cores to use (default is all available)
   -r RETRY_TIMES, --retry-times RETRY_TIMES
                         number of times to retry failed downloads
+  -n {1,2,3}, --n-simultaneous-downloads {1,2,3}
+                        number of accessions to download simultaneously (default=1)
   -g, --genomes-only    just download and sketch genome (DNA) files
   -m, --proteomes-only  just download and sketch proteome (protein) files
 ```
@@ -211,6 +213,8 @@ options:
                         number of cores to use (default is all available)
   -r RETRY_TIMES, --retry-times RETRY_TIMES
                         number of times to retry failed downloads
+  -n {1,2,3}, --n-simultaneous-downloads {1,2,3}
+                        number of simultaneous downloads (default=3)
 ```
 
 ## Code of Conduct

environment.yml

@@ -6,7 +6,7 @@ channels:
 dependencies:
   - sourmash>=4.8,<5
   - pip
-  - rust=1.75
+  - rust==1.75
   - maturin>=1,<2
   - pytest
   - pandas

pyproject.toml

@@ -25,7 +25,7 @@ urlsketch = "sourmash_plugin_directsketch:Download_and_Sketch_Url"
 [project.optional-dependencies]
 test = [
   "pytest>=6.2.4,<8.4.0",
-  "pytest-cov>=2.12,<6.0",
+  "pytest-cov>=2.12,<7.0",
   "pytest-xdist",
 ]