REL: release 0.4.0

.github/workflows/release.yml

@@ -3,7 +3,7 @@ name: Release
 on: [workflow_dispatch]
 
 jobs:
-  build_wheels:
+  build-wheels:
     name: Build Wheels for ${{matrix.platform_id}} on ${{matrix.os}}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -34,6 +34,15 @@ jobs:
         with:
           platforms: arm64
 
+      - name: Set macOS Deployment Target
+        if: ${{startsWith(matrix.os, 'macos')}}
+        run: |
+          if [[ "${{ matrix.os }}" == "macos-13" ]]; then
+            echo "MACOSX_DEPLOYMENT_TARGET=13.0" >> $GITHUB_ENV
+          elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
+            echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
+          fi
+
       - name: Build wheels
         uses: pypa/[email protected]
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
@@ -51,9 +60,57 @@ jobs:
           name: cibw-wheels-${{ matrix.platform_id }}
           path: ./wheelhouse/*.whl
 
-  release_test:
+  build-iqtree:
+    name: Fetch or Build IQ-TREE 2 Static Library
+    runs-on: ubuntu-latest
+    steps:
+      - uses: "actions/checkout@v4"
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - id: build
+        uses: ./.github/actions/build-iqtree
+        with:
+          os: ubuntu-latest
+
+    outputs:
+      iqtree2-sha: ${{steps.build.outputs.iqtree2-sha}}
+
+  build-docs:
+    runs-on: ubuntu-latest
+    needs: build-iqtree
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - uses: ./.github/actions/setup-piqtree
+        with:
+          python-version: "3.12"
+          cache-key: libiqtree-ubuntu-latest-${{ needs.build-iqtree.outputs.iqtree2-sha }}
+
+      - name: Install Docs Dependencies
+        run: |
+          pip install .[doc]
+
+      - name: Build documentation
+        run: |
+          echo `pwd`
+          mkdocs build
+        working-directory: ${{ github.workspace }}
+
+      - name: Upload documentation artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: piqtree-docs-html
+          path: site
+
+  release-test:
     name: Release to Test PyPI
-    needs: build_wheels
+    needs: [build-wheels, build-docs]
     environment: release
     runs-on: ubuntu-latest
     permissions:
@@ -74,7 +131,7 @@ jobs:
 
   release:
     name: Release to PyPI
-    needs: release_test
+    needs: release-test
     environment: release
     runs-on: ubuntu-latest
     permissions:

changelog.md

@@ -1,4 +1,35 @@
 
+<a id='changelog-0.4.0'></a>
+# Changes in release "0.4.0"
+
+## Contributors
+
+- @rmcar17 integrated new functions from IQ-TREE in Python, added multithreading support, and wrote the API refererence and quickstart.
+- @thomaskf exposed all new functions from IQ-TREE to be available from Python, and worked on multithreading support.
+- @GavinHuttley worked on setting up and writing the documentation and associated devtools, ModelFinder, and integration with `cogent3` apps.
+- @YapengLang worked on bootstrapping support and extracting model parameters
+- @KatherineCaley worked on processing the ModelFinder results.
+
+## ENH
+
+- piqtree2 renamed piqtree to support future major releases of IQ-TREE.
+- piqtree now supports multithreading!
+- New function `nj_tree` constructs a rapid neighbour-joining tree from a pairwise distance matrix.
+- New function `model_finder` finds the best model for a given alignment.
+- New function `jc_distances` constructs a pairwise JC distance matrix from an alignment.
+- New function `make_model` allows converting an IQ-TREE string representation of a model to a `Model` class.
+- API for `random_trees` has changed - new order (`num_trees`, `num_taxa`, `tree_mode`, then `rand_seed`).
+- API for `robinson_foulds` has changed - now accepts a Sequence of trees.
+- Model parameters are now extracted from IQ-TREE where for now possible.
+- `build_tree` now supports ultrafast bootstrapping.
+- `Model` creation is now more robust.
+- Use `piqtree.__iqtree_version__` to see what version of piqtree is being used.
+- See what can now be done in our [new documentation](https://piqtree.readthedocs.io)!
+
+## DOC
+
+- [Documentation](https://piqtree.readthedocs.io) is now on readthedocs!
+
 <a id='changelog-0.3.1'></a>
 # Changes in release "0.3.1"
 

src/piqtree/__init__.py

@@ -22,7 +22,7 @@
     make_model,
 )
 
-__version__ = "0.3.2"
+__version__ = "0.4.0"
 
 __all__ = [
     "Model",