From f1a6abb301b1155954a30ecde72711c4d1af45f3 Mon Sep 17 00:00:00 2001
From: Vince Buffalo <vsbuffalo@gmail.com>
Date: Wed, 6 Sep 2023 11:33:06 -0700
Subject: [PATCH] removed unneeded dependencies, got rid of structopt

---
 .gitignore         |    1 +
 Cargo.lock         | 2974 ++++++++++++++++++++++++++++++++++++++++++++
 Cargo.toml         |   16 +-
 README.md          |    5 +-
 src/lib/project.rs |    1 +
 src/lib/utils.rs   |    2 +-
 src/main.rs        |   68 +-
 7 files changed, 3010 insertions(+), 57 deletions(-)
 create mode 100644 Cargo.lock

diff --git a/.gitignore b/.gitignore
index ea8c4bf..5b878fa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 /target
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diff --git a/Cargo.lock b/Cargo.lock
new file mode 100644
index 0000000..0a22362
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diff --git a/Cargo.toml b/Cargo.toml
index f4e83a9..d8c9e31 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,8 +1,13 @@
 [package]
 name = "scidataflow"
-version = "0.1.0"
+version = "0.8.0"
 edition = "2021"
 include = ["src/**/*", "tests/test_data/**/*"]
+exclude = ["logo.png"]
+license = "MIT"
+keywords = ["science", "reproducibility", "bioinformatics", "data"]
+categories = ["command-line-utilities", "science"]
+repository = "https://github.com/vsbuffalo/scidataflow"
 
 [lib]
 name = "scidataflow"
@@ -12,8 +17,6 @@ path = "src/lib.rs"
 name = "sdf"
 path = "src/main.rs"
 
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
-
 [dependencies]
 clap = { version = "4.3.19", features = ["derive", "cargo"] }
 colored = "2.0.4"
@@ -26,26 +29,19 @@ serde_derive = "1.0.180"
 md5 = "0.7.0"
 timeago = "0.4.1"
 reqwest = { version = "0.11.18", features = ["json", "stream"] }
-unicode-width = "0.1.10"
 tokio = { version = "*", features = ["full"] }
-structopt = "0.3.26"
-async-trait = "0.1"
 serde_json = "1.0.104"
 anyhow = "1.0.72"
 url = "2.4.0"
 futures = "0.3.28"
 futures-util = "0.3.28"
-pbr = "1.1.1"
 trauma = "2.2.3"
-console = "0.15.7"
 dirs = "5.0.1"
 tempfile = "3.8.0"
 rand = "0.8.5"
 flate2 = "1.0.27"
 lazy_static = "1.4.0"
 httpmock = "0.6.8"
-cd = "0.2.1"
 indicatif = { version = "0.17.6", features = ["futures"] }
 tokio-util = { version = "0.7.8", features = ["codec"] }
 csv = "1.2.2"
-
diff --git a/README.md b/README.md
index a447a5b..5d4ca15 100644
--- a/README.md
+++ b/README.md
@@ -392,7 +392,7 @@ to
 ## Contributing to SciDataFlow
 
 If you are a Rust developer, **please** contribute! Here are some great ways to
-get started:
+get started (also check the TODO list below, or for TODOs in code!):
 
  - Write some API tests. See some of the tests in `src/lib/api/zenodo.api` as
    an example.
@@ -405,3 +405,6 @@ get started:
 
  - Improve the documentation!
 
+## Todo
+
+ - [] `sdf mv` tests, within different directories.
diff --git a/src/lib/project.rs b/src/lib/project.rs
index 9875bc9..d12f0d7 100644
--- a/src/lib/project.rs
+++ b/src/lib/project.rs
@@ -431,6 +431,7 @@ impl Project {
             // convert to relative path (based on where we are)
             let filepath = self.relative_path_string(Path::new(&filepath))?;
 
+            // TODO: should compare MD5s!
             if !self.data.contains(&filepath).await? {
                 let data_file = DataFile::new(filepath.clone(), Some(url), &self.path_context()).await?;
 
diff --git a/src/lib/utils.rs b/src/lib/utils.rs
index d76a334..31221c1 100644
--- a/src/lib/utils.rs
+++ b/src/lib/utils.rs
@@ -151,7 +151,7 @@ pub fn print_fixed_width_status(rows: BTreeMap<String, Vec<StatusEntry>>, nspace
     dir_keys.sort();
     for key in dir_keys {
         let statuses = &rows[key];
-        let pretty_key = if key.len() == 0 { "." } else { &key };
+        let pretty_key = if key.is_empty() { "." } else { key };
         let prettier_key = if color { pretty_key.bold().to_string() } else { pretty_key.clone().to_string() };
         println!("[{}]", prettier_key);
 
diff --git a/src/main.rs b/src/main.rs
index 4aa9e4e..be7564e 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,6 +1,5 @@
 use clap::{Parser, Subcommand};
 use anyhow::Result;
-use structopt::StructOpt;
 #[allow(unused_imports)]
 use log::{info, trace, debug};
 use tokio::runtime::Builder;
@@ -57,7 +56,8 @@ https://github.com/vsbuffalo/scidataflow/issues.
 
 
 #[derive(Parser)]
-#[command(author, version, about, long_about = None)]
+#[clap(name = "sdf")]
+#[clap(about = INFO)]
 struct Cli {
     #[arg(short, long, action = clap::ArgAction::Count)]
     debug: u8,
@@ -66,88 +66,76 @@ struct Cli {
     command: Option<Commands>,
 }
 
-#[derive(Subcommand,StructOpt)]
+#[derive(Subcommand)]
 enum Commands {
-     #[structopt(name = "add")]
     /// Add a data file to the manifest.
     Add {
         /// the file to begin tracking.
-        #[structopt(name = "filenames", required = true)]
+        #[arg(required = true)]
         filenames: Vec<String>,
     },
-     #[structopt(name = "config")]
     /// Set local system-wide metadata (e.g. your name, email, etc.), which 
     /// can be propagated to some APIs.
     Config {
         /// Your name.
-        #[structopt(long)]
+        #[arg(long)]
         name: Option<String>,
         // Your email.
-        #[structopt(long)]
+        #[arg(long)]
         email: Option<String>,
         // Your affiliation.
-        #[structopt(long)]
+        #[arg(long)]
         affiliation: Option<String>,
     },
-    #[structopt(name = "init")]
     /// Initialize a new project.
     Init {
         /// Project name (default: the name of the directory).
-        #[structopt(long)]
+        #[arg(long)]
         name: Option<String>
     },
-    #[structopt(name = "get")]
     /// Download a file from a URL.
     Get {
         /// Download filename (default: based on URL).
         url: String,
-        #[structopt(long)]
+        #[arg(long)]
         name: Option<String>,
         /// Overwrite local files if they exit.
-        #[structopt(long)]
+        #[arg(long)]
         overwrite: bool
     },
-    #[structopt(name = "bulk")]
     /// Download a bunch of files from links stored in a file.
     Bulk {
         /// A TSV or CSV file containing a column of URLs. Type inferred from suffix.
         filename: String,
         /// Which column contains links (default: first).
-        #[structopt(long)]
+        #[arg(long)]
         column: Option<u64>,
         /// The TSV or CSV starts with a header (i.e. skip first line).
-        #[structopt(long)]
+        #[arg(long)]
         header: bool,
         /// Overwrite local files if they exit.
-        #[structopt(long)]
+        #[arg(long)]
         overwrite: bool,
     },
-    #[structopt(name = "status")]
     /// Show status of data.
     Status {
         /// Show remotes status (requires network).
-        #[structopt(long)]
+        #[arg(long)]
         remotes: bool, 
 
         /// Show statuses of all files, including those on remote(s) but not in the manifest.
-        #[structopt(long)]
+        #[arg(long)]
         all: bool
 
     },
-
-    #[structopt(name = "stats")]
     /// Show file size statistics.
     Stats {
     },
-
-    #[structopt(name = "update")]
     /// Update MD5s
     Update {
         /// Which file to update (if not set, all tracked files are update).
         filename: Option<String>,
     },
-
-    #[structopt(name = "link")]
     /// Link a directory to a remote storage solution.
     Link {
         /// Directory to link to remote storage.
@@ -158,25 +146,21 @@ enum Commands {
         key: String,
         /// Project name for remote (default: the metadata title in the data 
         /// manifest, or if that's not set, the directory name).
-        #[structopt(long)]
+        #[arg(long)]
         name: Option<String>,
 
         /// Don't initialize remote, only add to manifest. This will retrieve
         /// the remote information (i.e. the FigShare Article ID or Zenodo
         /// Depository ID) to add to the manifest. Requires network.
-        #[structopt(long)]
+        #[arg(long)]
         link_only: bool
 
     },
-
-    #[structopt(name = "untrack")]
     /// No longer keep track of this file on the remote.
     Untrack {
         /// The file to untrack with remote.
         filename: String
     },
-
-    #[structopt(name = "track")]
     /// Keep track of this file on the remote.
     Track {
         /// The file to track with remote.
@@ -187,46 +171,40 @@ enum Commands {
         source: String,
         destination: String
     },
-    #[structopt(name = "push")]
     /// Push all tracked files to remote.
     Push {
         /// Overwrite remote files if they exit.
-        #[structopt(long)]
+        #[arg(long)]
         overwrite: bool,
     },
-
-    #[structopt(name = "pull")]
     /// Pull in all tracked files from the remote. If --urls is set,
     /// this will (re)-download all files (tracked or not) in that manifest
     /// from their URLs.
     Pull {
         /// Overwrite local files if they exit.
-        #[structopt(long)]
+        #[arg(long)]
         overwrite: bool,
 
         /// Pull in files from the URLs, not remotes.
-        #[structopt(long)]
+        #[arg(long)]
         urls: bool,
 
         /// Pull in files from remotes and URLs.
-        #[structopt(long)]
+        #[arg(long)]
         all: bool,
 
         // multiple optional directories
         //directories: Vec<PathBuf>,
     },
-
-     #[structopt(name = "metadata")]
     /// Update the project metadata.
     Metadata {
         /// The project name.
-        #[structopt(long)]
+        #[arg(long)]
         title: Option<String>,
         // A description of the project.
-        #[structopt(long)]
+        #[arg(long)]
         description: Option<String>,
     },
- 
 }
 
 pub fn print_errors(response: Result<()>) {