Build Binary and fix docs (#10)

* add main.rs and CLAP parser to create a binary

* rename

* update docs by fixing the redirect

.github/workflows/docs.yaml

@@ -1,7 +1,7 @@
 name: Docs
 on:
   push:
-    branches: [main]
+    branches: [main, 20240719-view]
 permissions:
   contents: read
   pages: write
@@ -28,7 +28,7 @@ jobs:
       - name: Build docs
         run: cargo doc --no-deps
       - name: Add redirect
-        run: echo '<meta http-equiv="refresh" content="0;url=aoc/index.html">' > target/doc/index.html
+        run: echo '<meta http-equiv="refresh" content="0;url=pseutils/index.html">' > target/doc/index.html
       - name: Remove lock file
         run: rm target/doc/.lock
       - name: Upload artifact

.gitignore

@@ -1 +1,3 @@
 /target
+/binary_test
+/test_temporary

Cargo.toml

@@ -1,9 +1,10 @@
 [package]
-name = "pymol_session_utils"
+name = "pseutils"
 version = "0.1.0"
 edition = "2021"
 
 [dependencies]
+clap = { version = "4.5.9", features = ["derive"] }
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
 serde-pickle = "1.1"
@@ -13,6 +14,4 @@ validator = { version = "0.18", features = ["derive"] }
 pdbtbx = "0.11.0"
 itertools = "0.13.0"
 urlencoding = "2.1.3"
-num-traits = "0.2"
-num-derive = "0.3"
 serde_repr = "0.1.19"

Readme.md

@@ -1,6 +1,6 @@
 # pymol_session_utils
 
-**WIP: Currently not working**
+**Note: Work In Progress. Feature Incomplete**
 
 
 ## Goal
@@ -21,6 +21,23 @@ cargo clean --doc && cargo doc --no-deps --open
 # to look at results
 cargo test # generate an example
 cd test_temporary && python -m http.server
+
+# build the binary and test
+cargo build --release
+./target/release/pseutils  --psefile tests/data/example.pse --outputdir binary_test
+
+# outputs a complete directory
+> tree binary_test
+binary_test
+├── index.html
+├── molstar.css
+├── molstar.js
+├── pdb
+│   └── 1pdb.pdb
+├── pdb_contents.txt
+└── state.mvsj
+
+
 ```
 
 ## Status

src/lib.rs

@@ -2,9 +2,6 @@
 //!
 //! it is currently a work in progress.
 //!
-#[macro_use]
-extern crate num_derive;
-
 pub mod molviewspec;
 pub mod pymolparsing;
 

src/main.rs

@@ -0,0 +1,24 @@
+use clap::Parser;
+use pseutils::pymolparsing::psedata::PSEData;
+
+#[derive(Parser)]
+#[command(author, version, about, long_about = None)]
+struct Args {
+    /// Path to the PSE file
+    #[arg(short, long)]
+    psefile: String,
+
+    /// Output directory
+    #[arg(short, long)]
+    outputdir: String,
+}
+
+fn main() {
+    let args = Args::parse();
+
+    println!("PSE file: {}", args.psefile);
+    println!("Output directory: {}", args.outputdir);
+
+    let psedata: PSEData = PSEData::load(&args.psefile).expect("Reachable PSE file");
+    let _ = psedata.to_disk_full(&args.outputdir);
+}

src/pymolparsing/mod.rs

@@ -2,6 +2,3 @@
 // it may be advisable down the line to split these out
 pub mod parsing;
 pub mod psedata;
-pub mod settings;
-
-use crate::molviewspec;

src/pymolparsing/psedata.rs

@@ -30,8 +30,8 @@
 
 use crate::molviewspec::nodes::{self as mvsnodes, CameraParams, ColorNamesT, State};
 use crate::pymolparsing::parsing::{
-    CustomValue, PyObjectMolecule, PymolSessionObjectData, SceneView, SessionName,
-    SessionSelectorList, Settings, SettingsEnum,
+    PyObjectMolecule, PymolSessionObjectData, SceneView, SessionName, SessionSelectorList,
+    Settings, SettingsEnum,
 };
 use pdbtbx::PDB;
 use serde::{Deserialize, Serialize};
@@ -161,7 +161,7 @@ impl PSEData {
         let pdb_folder = path.join("pdb");
         std::fs::create_dir_all(&pdb_folder)?;
         let mut file_list = Vec::new();
-        for (index, molecule) in self.get_molecule_data().iter().enumerate() {
+        for molecule in self.get_molecule_data().iter() {
             let pdb = molecule.to_pdb();
             let filename = format!("{}.pdb", molecule.get_name());
             let file_path = pdb_folder.join(&filename);

tests/test_pse_parsing.rs

@@ -1,4 +1,4 @@
-use pymol_session_utils::pymolparsing::parsing::{CustomValue, Settings, SettingsEnum};
+use pymol_session_utils::pymolparsing::parsing::{CustomValue, SettingsEnum};
 use pymol_session_utils::PSEData;
 const TEST_OUTPUT_DIR: &str = "./test_temporary";