Remove in-memory temporary files on task completion, fixes #40

algbio · Mar 9, 2024 · ec68afe · ec68afe
1 parent 3c5b0fa
commit ec68afe
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Showing 17 changed files with 17 additions and 16 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/crates/api/Cargo.toml b/crates/api/Cargo.toml
@@ -24,7 +24,7 @@ colors = { package = "ggcat_colors", path = "../colors" }
 utils = { package = "ggcat_utils", path = "../utils" }
 
 fdlimit = "0.3.0"
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 rayon = "1.7.0"
 dynamic-dispatch = "0.5.4"
 parking_lot = "0.12.1"

diff --git a/crates/api/src/lib.rs b/crates/api/src/lib.rs
@@ -105,6 +105,7 @@ fn create_tempdir(base_path: Option<PathBuf>) -> Option<PathBuf> {
 
 fn remove_tempdir(temp_dir: Option<PathBuf>) {
     if let Some(temp_dir) = temp_dir {
+        MemoryFs::remove_directory(&temp_dir, true);
         let _ = std::fs::remove_dir_all(temp_dir);
     }
 }

diff --git a/crates/assembler/Cargo.toml b/crates/assembler/Cargo.toml
@@ -15,7 +15,7 @@ utils = { package = "ggcat_utils", path = "../utils" }
 dynamic-dispatch = "0.5.4"
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/assembler_kmers_merge/Cargo.toml b/crates/assembler_kmers_merge/Cargo.toml
@@ -9,7 +9,7 @@ config = { package = "ggcat_config", path = "../config" }
 utils = { package = "ggcat_utils", path = "../utils" }
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/assembler_minimizer_bucketing/Cargo.toml b/crates/assembler_minimizer_bucketing/Cargo.toml
@@ -8,7 +8,7 @@ edition = "2021"
 config = { package = "ggcat_config", path = "../config" }
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 
 # Static dispatch

diff --git a/crates/cmdline/Cargo.toml b/crates/cmdline/Cargo.toml
@@ -48,7 +48,7 @@ dynamic-dispatch = "0.5.4"
 
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 io = { package = "ggcat_io", path = "../io" }
 colors = { package = "ggcat_colors", path = "../colors" }
 

diff --git a/crates/colors/Cargo.toml b/crates/colors/Cargo.toml
@@ -11,7 +11,7 @@ config = { package = "ggcat_config", path = "../config" }
 dynamic-dispatch = "0.5.4"
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/config/Cargo.toml b/crates/config/Cargo.toml
@@ -6,4 +6,4 @@ edition = "2021"
 
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
diff --git a/crates/dumper/Cargo.toml b/crates/dumper/Cargo.toml
@@ -11,7 +11,7 @@ config = { package = "ggcat_config", path = "../config" }
 utils = { package = "ggcat_utils", path = "../utils" }
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/io/Cargo.toml b/crates/io/Cargo.toml
@@ -16,7 +16,7 @@ utils = { package = "ggcat_utils", path = "../utils" }
 
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/kmers_transform/Cargo.toml b/crates/kmers_transform/Cargo.toml
@@ -9,7 +9,7 @@ config = { package = "ggcat_config",  path = "../config" }
 utils = { package = "ggcat_utils",  path = "../utils" }
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 hashes = { package = "ggcat_hashes",  path = "../hashes" }

diff --git a/crates/minimizer_bucketing/Cargo.toml b/crates/minimizer_bucketing/Cargo.toml
@@ -8,7 +8,7 @@ edition = "2021"
 config = { package = "ggcat_config", path = "../config" }
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/querier/Cargo.toml b/crates/querier/Cargo.toml
@@ -15,7 +15,7 @@ utils = { package = "ggcat_utils", path = "../utils" }
 dynamic-dispatch = "0.5.4"
 
 # Common libraries
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 streaming-libdeflate-rs = "0.1.5"
 nightly-quirks = "0.1.2"
 

diff --git a/crates/structs/Cargo.toml b/crates/structs/Cargo.toml
@@ -7,7 +7,7 @@ bincode = "1.3.3"
 byteorder = "1.4.3"
 config = { package = "ggcat_config", path = "../config" }
 io = { package = "ggcat_io", path = "../io" }
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
 serde = { version = "1.0.163", features = ["derive"] }
 
 

diff --git a/crates/utils/Cargo.toml b/crates/utils/Cargo.toml
@@ -6,4 +6,4 @@ edition = "2021"
 parking_lot = "0.12.1"
 rand = "0.8.5"
 
-parallel-processor = "0.1.13"
+parallel-processor = "0.1.14"
diff --git a/libs-crates/parallel-processor-rs b/libs-crates/parallel-processor-rs