From 40846fb38f5abe471bdebdd40193ed2b5e545826 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Fri, 19 May 2023 08:06:23 -0700 Subject: [PATCH] feat: allow AlignmentMode to be used on the command line (#44) * Allow AlignmentMode to be used on the command line --- Cargo.lock | 166 +++++++++++++++++++++++++++++++++++++++++++++++ Cargo.toml | 2 +- src/alignment.rs | 3 + 3 files changed, 170 insertions(+), 1 deletion(-) diff --git a/Cargo.lock b/Cargo.lock index 8765bb0..fc57007 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -11,6 +11,17 @@ dependencies = [ "memchr", ] +[[package]] +name = "atty" +version = "0.2.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8" +dependencies = [ + "hermit-abi", + "libc", + "winapi", +] + [[package]] name = "autocfg" version = "1.0.1" @@ -21,6 +32,7 @@ checksum = "cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a" name = "bio-types" version = "0.13.0" dependencies = [ + "clap", "derive-new", "lazy_static", "petgraph", @@ -30,6 +42,51 @@ dependencies = [ "thiserror", ] +[[package]] +name = "bitflags" +version = "1.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" + +[[package]] +name = "clap" +version = "3.2.25" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4ea181bf566f71cb9a5d17a59e1871af638180a18fb0035c92ae62b705207123" +dependencies = [ + "atty", + "bitflags", + "clap_derive", + "clap_lex", + "indexmap", + "once_cell", + "strsim", + "termcolor", + "textwrap", +] + +[[package]] +name = "clap_derive" +version = "3.2.25" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ae6371b8bdc8b7d3959e9cf7b22d4435ef3e79e138688421ec654acf8c81b008" +dependencies = [ + "heck", + "proc-macro-error", + "proc-macro2", + "quote", + "syn", +] + +[[package]] +name = "clap_lex" +version = "0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2850f2f5a82cbf437dd5af4d49848fbdfc27c157c3d010345776f952765261c5" +dependencies = [ + "os_str_bytes", +] + [[package]] name = "derive-new" version = "0.5.9" @@ -59,6 +116,15 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2540771e65fc8cb83cd6e8a237f70c319bd5c29f78ed1084ba5d50eeac86f7f9" +[[package]] +name = "hermit-abi" +version = "0.1.19" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33" +dependencies = [ + "libc", +] + [[package]] name = "indexmap" version = "1.7.0" @@ -75,12 +141,30 @@ version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" +[[package]] +name = "libc" +version = "0.2.144" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1" + [[package]] name = "memchr" version = "2.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "308cc39be01b73d0d18f82a0e7b2a3df85245f84af96fdddc5d202d27e47b86a" +[[package]] +name = "once_cell" +version = "1.17.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b7e5500299e16ebb147ae15a00a942af264cf3688f47923b8fc2cd5858f23ad3" + +[[package]] +name = "os_str_bytes" +version = "6.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ceedf44fb00f2d1984b0bc98102627ce622e083e49a5bacdb3e514fa4238e267" + [[package]] name = "petgraph" version = "0.6.0" @@ -91,6 +175,30 @@ dependencies = [ "indexmap", ] +[[package]] +name = "proc-macro-error" +version = "1.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c" +dependencies = [ + "proc-macro-error-attr", + "proc-macro2", + "quote", + "syn", + "version_check", +] + +[[package]] +name = "proc-macro-error-attr" +version = "1.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869" +dependencies = [ + "proc-macro2", + "quote", + "version_check", +] + [[package]] name = "proc-macro2" version = "1.0.29" @@ -152,6 +260,12 @@ dependencies = [ "syn", ] +[[package]] +name = "strsim" +version = "0.10.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623" + [[package]] name = "strum_macros" version = "0.24.0" @@ -176,6 +290,21 @@ dependencies = [ "unicode-xid", ] +[[package]] +name = "termcolor" +version = "1.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "be55cf8942feac5c765c2c993422806843c9a9a45d4d5c407ad6dd2ea95eb9b6" +dependencies = [ + "winapi-util", +] + +[[package]] +name = "textwrap" +version = "0.16.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "222a222a5bfe1bba4a77b45ec488a741b3cb8872e5e499451fd7d0129c9c7c3d" + [[package]] name = "thiserror" version = "1.0.29" @@ -201,3 +330,40 @@ name = "unicode-xid" version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3" + +[[package]] +name = "version_check" +version = "0.9.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f" + +[[package]] +name = "winapi" +version = "0.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419" +dependencies = [ + "winapi-i686-pc-windows-gnu", + "winapi-x86_64-pc-windows-gnu", +] + +[[package]] +name = "winapi-i686-pc-windows-gnu" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" + +[[package]] +name = "winapi-util" +version = "0.1.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178" +dependencies = [ + "winapi", +] + +[[package]] +name = "winapi-x86_64-pc-windows-gnu" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" diff --git a/Cargo.toml b/Cargo.toml index 1d52d28..1e9f079 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -15,9 +15,9 @@ exclude = [".gitignore", ".github"] [features] phylogeny = ["petgraph"] - [dependencies] serde = { version = "^1", optional = true, features=["derive"] } +clap = { version = ">=3.2.0", optional = true, features = ["derive"] } thiserror = "1" regex = "1.0" lazy_static = "1.1" diff --git a/src/alignment.rs b/src/alignment.rs index bdb5c68..cf31fc6 100644 --- a/src/alignment.rs +++ b/src/alignment.rs @@ -5,6 +5,8 @@ //! Types for representing pairwise sequence alignments +#[cfg(feature = "clap")] +use clap::ValueEnum; #[cfg(feature = "serde")] use serde::{Deserialize, Serialize}; @@ -38,6 +40,7 @@ pub enum AlignmentOperation { /// /// The default alignment mode is Global. #[cfg_attr(feature = "serde", derive(Serialize, Deserialize))] +#[cfg_attr(feature = "clap", derive(ValueEnum))] #[derive(Debug, PartialEq, Eq, Copy, Clone)] pub enum AlignmentMode { Local,