Add Provenance trait as optional feature (#98).

Author: molpopgen

.github/workflows/tests.yml

@@ -6,12 +6,13 @@ on:
 name: CI
 
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  run-tests:
+    runs-on: ${{ matrix.os }}
     #container:
     #  image: ubuntu:20.10
     strategy:
       matrix:
+        os: [ubuntu-latest, macos-latest]
         rust:
           - stable
           - beta
@@ -26,43 +27,27 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           submodules: recursive
       - run: sudo apt-get update -y
+        if: matrix.os == 'ubuntu-latest'
       - uses: actions-rs/toolchain@v1
         with:
           toolchain: ${{ matrix.rust }}
           override: true
       - name: cargo check
-        run: cargo check
+        run: cargo check 
       - name: cargo check examples
         run: cargo check --examples
+      - name: cargo check all features
+        run: cargo check --all-features
+      - name: cargo check examples w/all featurse
+        run: cargo check --examples --all-features
       - name: run tests
         run: |
             cargo test
             cargo test --examples
-
-  build-osx:
-    runs-on: macos-latest
-    strategy:
-      matrix:
-        rust:
-          - stable
-          - beta
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          submodules: recursive
-      - uses: actions-rs/toolchain@v1
-        with:
-          toolchain: ${{ matrix.rust }}
-          override: true
-      - name: cargo check
-        run: cargo check
-      - name: cargo check examples
-        run: cargo check --examples
-      - name: run tests
+      - name: run tests (all featurss)
         run: |
-            cargo test
-            cargo test --examples
+            cargo test --all-features
+            cargo test --all-features --examples
 
   fmt:
     name: rust fmt
@@ -93,4 +78,6 @@ jobs:
           override: true
       - run: rustup component add clippy
       - name: clippy (all targets)
+        run: cargo clippy --all-targets --all-features -- -D warnings
+      - name: clippy (all targets, all features)
         run: cargo clippy --all-targets -- -D warnings

Cargo.toml

@@ -16,6 +16,7 @@ thiserror = "1.0"
 libc = "0.2.81"
 streaming-iterator = "0.1.5"
 bitflags = "1.2.1"
+chrono = {version = "0.4.19", optional = true}
 
 [dev-dependencies]
 clap = "~2.27.0"
@@ -29,6 +30,12 @@ bindgen = "0.57.0"
 cc = { version = "1.0", features = ["parallel"] }
 pkg-config = "0.3"
 
+[features]
+provenance = ["chrono"]
+
+[package.metadata.docs.rs]
+all-features = true
+
 [[example]]
 name = "mutation_metadata_bincode"
 

src/_macros.rs

@@ -63,6 +63,35 @@ macro_rules! unsafe_tsk_ragged_column_access {
     }};
 }
 
+// Allow this to be unused for default features
+// to pass clippy checks
+#[allow(unused_macros)]
+macro_rules! unsafe_tsk_ragged_char_column_access {
+    ($i: expr, $lo: expr, $hi: expr, $array: expr, $offset_array: expr, $offset_array_len: expr) => {{
+        if $i < $lo || $i >= ($hi as tsk_id_t) {
+            Err(TskitError::IndexError {})
+        } else if $offset_array_len == 0 {
+            Ok(None)
+        } else {
+            let start = unsafe { *$offset_array.offset($i as isize) };
+            let stop = if $i < ($hi as tsk_id_t) {
+                unsafe { *$offset_array.offset(($i + 1) as isize) }
+            } else {
+                $offset_array_len as tsk_size_t
+            };
+            if start == stop {
+                Ok(None)
+            } else {
+                let mut buffer = String::new();
+                for i in start..stop {
+                    buffer.push(unsafe { *$array.offset(i as isize) as u8 as char });
+                }
+                Ok(Some(buffer))
+            }
+        }
+    }};
+}
+
 macro_rules! drop_for_tskit_type {
     ($name: ident, $drop: ident) => {
         impl Drop for $name {

src/lib.rs

@@ -10,9 +10,9 @@
 //!
 //! * [`TableCollection`] wraps `tsk_table_collection_t`.
 //! * [`TreeSequence`] wraps `tsk_treeseq_t`.
-//! * [`Tree`] wraps `tsk_tree_t`. 
+//! * [`Tree`] wraps `tsk_tree_t`.
 //! * Tree iteration occurs via traits from [streaming_iterator](https://docs.rs/streaming-iterator/).
-//! * Errors returned from C map to [`TskitError::ErrorCode`]. 
+//! * Errors returned from C map to [`TskitError::ErrorCode`].
 //!   Their string messages can be obtained by printing the error type.
 //!
 //! ## Safety
@@ -24,10 +24,23 @@
 //!     * Tree lifetimes are tied to that of the parent tree sequence.
 //!     * Table objects ([`NodeTable`], etc..) are only represented by non-owning, immutable types.
 //!
+//! # Optional features
+//!
+//! Some features are optional, and are activated by requesting them in your `Cargo.toml` file.
+//!
+//! * `provenance`
+//!     * Enables [`provenance`]
+//!
+//! To add features to your `Cargo.toml` file:
+//!
+//! ```toml
+//! [dependencies]
+//! tskit = {version = "0.2.0", features=["feature0", "feature1"]}
+//! ```
+//!
 //! # What is missing?
 //!
 //! * A lot of wrappers to the C functions.
-//! * Support for provenance tables.
 //! * Tree sequence statistics!
 
 #![allow(non_upper_case_globals)]
@@ -86,6 +99,10 @@ pub use traits::TableAccess;
 pub use traits::TskitTypeAccess;
 pub use trees::{NodeTraversalOrder, Tree, TreeSequence};
 
+// Optional features
+#[cfg(any(doc, feature = "provenance"))]
+pub mod provenance;
+
 /// Handles return codes from low-level tskit functions.
 ///
 /// When an error from the tskit C API is detected,