refactor!: flatten crate organization to use workspace properly (#321)

* refactor!: flatten crate organization to use workspace properly

* fix: update code to build using common deps versions

some subcrates were using outdated deps, which required code updates
to build. `cargo build --all-targets` now works, with many warnings

* fix: format `toml` file

* fix: fix clippy lints

* fix: format

Author: imrn99

Cargo.lock

@@ -1,70 +1,63 @@
 [workspace]
-members = [
-    ".",
-    "ffi",
-    "tools",
-    "tools/mesh-io",
-    "tools/mesh-io/ffi",
-    "tools/num-part",
-]
+members  = ["coupe", "coupe-ffi", "mesh-io", "mesh-io-ffi", "tools"]
+resolver = "3"
 
-[package]
+[workspace.package]
 authors = [
     "Armand Touminet <armand.touminet@protonmail.com>",
     "Hubert Hirtz <hubert@hirtz.pm>",
     "Cédric Chevalier",
     "Sébastien Morais",
 ]
-autobenches = false
 categories = ["algorithms", "mathematics"]
-description = """
-Coupe is a mesh partitioning library. It implements composable
-geometric and topologic algorithms.  
-"""
+description = "coupe, a parallel mesh partitioning library"
 edition = "2024"
 keywords = ["mesh", "partitioning"]
 license = "MIT OR Apache-2.0"
-name = "coupe"
 readme = "README.md"
 repository = "https://github.com/LIHPC-Computational-Geometry/coupe"
 version = "0.1.0"
 
-[features]
-default = ["sprs"]
 
-# Enable the nightly `stdsimd` feature and AVX512-accelerated algorithms.
-# Requires rust nightly.
-avx512 = []
+[workspace.dependencies]
+# members
+coupe       = { version = "0.1.0", path = "./coupe" }
+coupe-ffi   = { version = "0.1.0", path = "./coupe-ffi" }
+mesh-io     = { version = "0.1.0", path = "./mesh-io" }
+mesh-io-ffi = { version = "0.1.0", path = "./mesh-io-ffi" }
+tools       = { version = "0.1.0", path = "./tools" }
 
-[dependencies]
+# deps
+anyhow = { version = "1", default-features = false, features = ["std"] }
 approx = "0.5.1"
-itertools = "0.14.0"
+core_affinity = "0.8.3"
+criterion = { version = "0.8.0", default-features = false }
+getopts = { version = "0.2", default-features = false }
+itertools = { version = "0.14.0", default-features = false }
 ittapi = "0.5.0"
+metis = "0.2"
 nalgebra = { version = "0.34.1", default-features = false, features = [
     "rand",
     "std",
 ] }
 num-traits = "0.2.19"
-rand = "0.9.2"
-rayon = "1.11.0"
-sprs = { version = "0.11.4", optional = true, default-features = false, features = [
-    "multi_thread",
-] }
-tracing = { version = "0.1.43", default-features = false, features = ["std"] }
-
-[dev-dependencies]
-core_affinity = "0.8.3"
-criterion = "0.8.0"
 num_cpus = "1.17.0"
+once_cell = "1.21"
 proptest = { version = "1.9.0", default-features = false, features = [
     "std",
     "timeout",
 ] }
-tracing-chrome = "0.7.2"
-tracing-subscriber = "0.3.22"
-tracing-tree = "0.4.1"
-
-
-[[bench]]
-harness = false
-name    = "rcb_cartesian"
+rand = { version = "0.9.2", default-features = false }
+rand_distr = { version = "0.5.1", default-features = false }
+rand_pcg = { version = "0.9.0", default-features = false }
+rayon = "1.11.0"
+rusqlite = { version = "0.38.0", default-features = false }
+scotch = "0.2.1"
+sprs = { version = "0.11.4", default-features = false, features = [
+    "multi_thread",
+] }
+tracing = { version = "0.1.43", default-features = false, features = ["std"] }
+tracing-chrome = { version = "0.7.2", default-features = false }
+tracing-subscriber = { version = "0.3.22", default-features = false }
+tracing-tree = { version = "0.4.1", default-features = false }
+vtkio = { version = "0.6", default-features = false }

Cargo.toml

@@ -0,0 +1,21 @@
+[package]
+categories.workspace = true
+edition.workspace    = true
+keywords.workspace   = true
+license.workspace    = true
+readme.workspace     = true
+repository.workspace = true
+version.workspace    = true
+
+description = "C bindings to coupe"
+name        = "coupe-ffi"
+
+
+[lib]
+crate-type = ["cdylib", "staticlib"]
+doc        = false                   # name conflicts with the rust lib
+name       = "coupe"
+
+
+[dependencies]
+coupe.workspace = true

coupe-ffi/Cargo.toml

@@ -33,24 +33,24 @@ impl Constant {
     {
         let mut v = Vec::new();
         v.try_reserve_exact(self.len)?;
-        let value = *(self.value as *const T);
+        let value = unsafe { *(self.value as *const T) };
         v.resize(self.len, value);
         Ok(v)
     }
 
-    pub unsafe fn iter<'a, T>(&'a self) -> impl Iterator<Item = T> + ExactSizeIterator + 'a
+    pub unsafe fn iter<'a, T>(&'a self) -> impl ExactSizeIterator<Item = T> + 'a
     where
         T: 'a + Copy,
     {
-        let value = *(self.value as *const T);
+        let value = unsafe { *(self.value as *const T) };
         (0..self.len).map(move |_| value)
     }
 
     pub unsafe fn par_iter<'a, T>(&'a self) -> impl IndexedParallelIterator<Item = T> + Clone + 'a
     where
         T: 'a + Copy + Send + Sync,
     {
-        let value = *(self.value as *const T);
+        let value = unsafe { *(self.value as *const T) };
         coupe::rayon::iter::repeat_n(value, self.len)
     }
 }
@@ -70,14 +70,14 @@ impl Array {
     where
         T: 'a,
     {
-        slice::from_raw_parts(self.array as *const T, self.len)
+        unsafe { slice::from_raw_parts(self.array as *const T, self.len) }
     }
 
-    pub unsafe fn iter<'a, T>(&'a self) -> impl Iterator<Item = T> + ExactSizeIterator + 'a
+    pub unsafe fn iter<'a, T>(&'a self) -> impl ExactSizeIterator<Item = T> + 'a
     where
         T: 'a + Copy,
     {
-        slice::from_raw_parts(self.array as *const T, self.len)
+        unsafe { slice::from_raw_parts(self.array as *const T, self.len) }
             .iter()
             .cloned()
     }
@@ -86,7 +86,7 @@ impl Array {
     where
         T: 'a + Copy + Send + Sync,
     {
-        slice::from_raw_parts(self.array as *const T, self.len)
+        unsafe { slice::from_raw_parts(self.array as *const T, self.len) }
             .par_iter()
             .cloned()
     }
@@ -113,15 +113,15 @@ impl Fn {
     {
         let mut v = Vec::new();
         v.try_reserve_exact(self.len)?;
-        v.par_extend(self.par_iter::<T>());
+        v.par_extend(unsafe { self.par_iter::<T>() });
         Ok(v)
     }
 
-    pub unsafe fn iter<'a, T>(&'a self) -> impl Iterator<Item = T> + ExactSizeIterator + 'a
+    pub unsafe fn iter<'a, T>(&'a self) -> impl ExactSizeIterator<Item = T> + 'a
     where
         T: 'a + Copy,
     {
-        (0..self.len).map(|i| {
+        (0..self.len).map(|i| unsafe {
             let ptr = (self.i_th)(self.context, i) as *const T;
             *ptr
         })
@@ -131,7 +131,7 @@ impl Fn {
     where
         T: 'a + Copy + Send,
     {
-        (0..self.len).into_par_iter().map(|i| {
+        (0..self.len).into_par_iter().map(|i| unsafe {
             let ptr = (self.i_th)(self.context, i) as *const T;
             *ptr
         })
@@ -158,9 +158,9 @@ impl Data {
         T: Copy + Send,
     {
         Ok(match self {
-            Self::Array(iter) => Cow::from(iter.to_slice()),
-            Self::Constant(iter) => Cow::from(iter.to_slice()?),
-            Self::Fn(iter) => Cow::from(iter.to_slice()?),
+            Self::Array(iter) => Cow::from(unsafe { iter.to_slice() }),
+            Self::Constant(iter) => Cow::from(unsafe { iter.to_slice()? }),
+            Self::Fn(iter) => Cow::from(unsafe { iter.to_slice()? }),
         })
     }