Rust phylo compatibility fix

.github/workflows/clippy.yml

@@ -0,0 +1,65 @@
+name: rustfmt and clippy with annotations
+
+on:
+  push:
+    branches:    
+      - "**"
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  fmt_lib:
+    name: rustfmt on parsimony lib
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - run: rustup component add rustfmt
+      - uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --manifest-path ./parsimony/Cargo.toml --all -- --check
+
+  clippy_check_lib:
+    name: clippy on parsimony lib
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: rustup component add clippy
+      - uses: actions-rs/clippy-check@v1.0.7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          args: --manifest-path ./parsimony/Cargo.toml --all-features -- -D warnings
+
+  fmt_bin:
+    name: rustfmt on indelMaP bin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - run: rustup component add rustfmt
+      - uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --manifest-path ./indelMaP/Cargo.toml --all -- --check
+
+  clippy_check_bin:
+    name: clippy on indelMaP bin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: rustup component add clippy
+      - uses: actions-rs/clippy-check@v1.0.7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          args: --manifest-path ./indelMaP/Cargo.toml --all-features -- -D warnings

.github/workflows/test_coverage.yml

@@ -0,0 +1,40 @@
+name: library tests with coverage
+
+on:
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  test:
+    name: tests with coverage
+    runs-on: ubuntu-latest
+    env:
+      CARGO_INCREMENTAL: 0
+      RUSTFLAGS: -Cinstrument-coverage -Zprofile -Ccodegen-units=1 -Copt-level=0 -Clink-dead-code -Coverflow-checks=off -Zpanic_abort_tests -Cpanic=abort
+      RUSTDOCFLAGS: -Cinstrument-coverage -Zprofile -Ccodegen-units=1 -Copt-level=0 -Clink-dead-code -Coverflow-checks=off -Zpanic_abort_tests -Cpanic=abort
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions-rs/toolchain@v1.0.6
+      with:
+        toolchain: nightly
+        override: true
+    - name: Generate test results and coverage report
+      run: |
+          cargo install cargo2junit grcov;
+          rustup component add llvm-tools-preview;
+          cargo test --manifest-path ./parsimony/Cargo.toml -- -Z unstable-options --format json | cargo2junit > results.xml;
+          grcov . -s . --binary-path ./parsimony/target/debug/deps -t lcov --branch --ignore "**/*tests.rs" -o lcov.info;
+    - name: publish test results to github
+      uses: EnricoMi/publish-unit-test-result-action@v2
+      if: always()
+      with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          files: results.xml
+    - name: upload coverage report to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+          files: lcov.info

.github/workflows/tests.yml

@@ -0,0 +1,85 @@
+name: tests on stable
+
+on:
+  push:
+    branches:    
+      - "**"
+  workflow_dispatch:
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  check_lib:
+    name: cargo check lib
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - uses: actions-rs/cargo@v1
+        with:
+          command: check
+          args: --manifest-path ./parsimony/Cargo.toml
+
+  test_lib:
+    name: cargo test lib
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions-rs/toolchain@v1.0.6
+      with:
+        toolchain: nightly
+        override: true
+    - name: install cargo2junit
+      run: |
+          cargo install cargo2junit
+    - name: tests with cargo2junit
+      run: |
+        cargo test --manifest-path ./parsimony/Cargo.toml -- -Z unstable-options --format json --report-time | cargo2junit > results.xml 
+    - name: Publish test results
+      uses: EnricoMi/publish-unit-test-result-action@v2
+      if: always()
+      with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          files: results.xml
+
+  check_bin:
+    name: cargo check bin
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions-rs/toolchain@v1.0.6
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - uses: actions-rs/cargo@v1
+        with:
+          command: check
+          args: --manifest-path ./indelMaP/Cargo.toml
+
+  test_bin:
+    name: cargo test bin
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions-rs/toolchain@v1.0.6
+      with:
+        toolchain: nightly
+        override: true
+    - name: install cargo2junit
+      run: |
+          cargo install cargo2junit
+    - name: tests with cargo2junit
+      run: |
+        cargo test --manifest-path ./indelMaP/Cargo.toml -- -Z unstable-options --format json --report-time | cargo2junit > results.xml 
+    - name: Publish test results
+      uses: EnricoMi/publish-unit-test-result-action@v2
+      if: always()
+      with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          files: results.xml

indelMaP/src/main.rs

@@ -10,7 +10,7 @@ use parsimony::parsimony_alignment::parsimony_costs::parsimony_costs_model::{
 };
 use phylo::alignment::{compile_alignment_representation, Alignment};
 use phylo::io;
-use phylo::phylo_info::{setup_phylogenetic_info, PhyloInfo};
+use phylo::phylo_info::{phyloinfo_from_files, PhyloInfo};
 use phylo::sequences::{get_sequence_type, SequenceType};
 use phylo::tree::{get_percentiles_rounded, NodeIdx};
 use phylo::Rounding;
@@ -98,7 +98,7 @@ fn main() -> Result<()> {
     info!("IndelMaP run started");
     let cli = Cli::try_parse()?;
     info!("Successfully parsed the command line parameters");
-    let info = setup_phylogenetic_info(cli.seq_file, cli.tree_file);
+    let info = phyloinfo_from_files(cli.seq_file, cli.tree_file);
     match info {
         Ok(info) => {
             let (alignment, scores) = match get_sequence_type(&info.sequences) {

indelMaP/src/real_data_tests.rs

@@ -1,12 +1,12 @@
 use crate::indel_map_align_protein_rounded;
 use parsimony::parsimony_alignment::parsimony_costs::parsimony_costs_model::GapMultipliers;
-use phylo::phylo_info::setup_phylogenetic_info;
+use phylo::phylo_info::phyloinfo_from_files;
 use phylo::Rounding;
 use std::path::PathBuf;
 
 #[test]
 fn align_HIV_example_wag() {
-    let info = setup_phylogenetic_info(
+    let info = phyloinfo_from_files(
         PathBuf::from("./data/HIV_subset.fas"),
         PathBuf::from("./data/HIV_subset.nwk"),
     )

parsimony/src/parsimony_alignment/parsimony_alignment_tests.rs

@@ -7,7 +7,7 @@ use crate::parsimony_alignment::{
     parsimony_sets::get_parsimony_sets,
 };
 use bio::io::fasta::Record;
-use phylo::phylo_info::PhyloInfo;
+use phylo::phylo_info::phyloinfo_from_sequences_tree;
 use phylo::sequences::SequenceType;
 use phylo::tree::{NodeIdx::Internal as I, NodeIdx::Leaf as L, Tree};
 
@@ -92,11 +92,11 @@ pub(crate) fn align_two_on_tree() {
         Record::with_attrs("A", None, b"AACT"),
         Record::with_attrs("A", None, b"AC"),
     ];
-    let mut tree = Tree::new(&sequences.to_vec());
+    let mut tree = Tree::new(&sequences).unwrap();
     tree.add_parent(0, L(0), L(1), 1.0, 1.0);
     tree.complete = true;
     tree.create_postorder();
-    let info = PhyloInfo::new(tree, sequences.to_vec());
+    let info = phyloinfo_from_sequences_tree(&sequences, tree).unwrap();
 
     let scoring = ParsimonyCostsSimple::new(mismatch_cost, gap_open_cost, gap_ext_cost);
 
@@ -214,14 +214,14 @@ pub(crate) fn align_four_on_tree() {
         Record::with_attrs("D", None, b"GA"),
     ];
 
-    let mut tree = Tree::new(&sequences.to_vec());
+    let mut tree = Tree::new(&sequences).unwrap();
     tree.add_parent(0, L(0), L(1), 1.0, 1.0);
     tree.add_parent(1, L(2), L(3), 1.0, 1.0);
     tree.add_parent(2, I(0), I(1), 1.0, 1.0);
     tree.complete = true;
     tree.create_postorder();
 
-    let info = PhyloInfo::new(tree, sequences.to_vec());
+    let info = phyloinfo_from_sequences_tree(&sequences, tree).unwrap();
 
     let scoring = ParsimonyCostsSimple::new(c, a, b);