MesserLab · petrelharp · Sep 2, 2026 · Sep 3, 2026
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -62,44 +62,32 @@ jobs:
     steps:
       - name: Check out repository code
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-      - name: Setup Miniforge
-        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
         with:
-          miniforge-version: latest
-          activate-environment: anaconda-client-env
-          python-version: ${{ matrix.python }}
+          python-version: ${{ inputs.python-version }}
+          version: "0.10.0"
+
       - name: Get Date
         id: get-date
         run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
         shell: bash
-      - name: Cache Conda env
-        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
-        with:
-          path: ${{ env.CONDA }}/envs
-          key:
-            conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{
-            steps.get-date.outputs.today }}-${{
-            hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}}
-        env:
-          # Increase this value to reset cache if
-          # treerec/tests/environment.yml has not changed
-          CACHE_NUMBER: 0
-        id: cache
-      - name: Update environment
-        run: conda env update -n anaconda-client-env -f treerec/tests/environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
+
       - name: Workaround for gcc-11
         if: startsWith(matrix.os, 'ubuntu') && matrix.gcc == 11
         run: |
           sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y && \
           sudo apt-get update -y
+
       - name: Set up default GCC (in Ubuntu)
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }} && \
           sudo update-alternatives \
             --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc }} 100 \
             --slave /usr/bin/g++ g++ /usr/bin/g++-${{ matrix.gcc }}
+
       - name: Build and test (Debug)
         run: |
           mkdir Debug && \
@@ -108,6 +96,7 @@ jobs:
           make -j 2 && \
           # Show any output from the test program whenever the test fails
           env CTEST_OUTPUT_ON_FAILURE=1 make test
+
       - name: Build and test (Release)
         run: |
           mkdir Release && \
@@ -116,13 +105,13 @@ jobs:
           make -j 2 && \
           # Show any output from the test program whenever the test fails
           env CTEST_OUTPUT_ON_FAILURE=1 make test
+
       - name: Treesequence tests
         shell: bash -el {0}
         run: |
-          conda activate anaconda-client-env && \
           export PATH=$PATH:$PWD/Release && \
           echo $PATH && \
-          cd treerec/tests && python -m pytest -xv
+          cd treerec/tests && uv run pytest -xv
 
   tests-Windows-CLI:
     if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')
@@ -137,8 +126,10 @@ jobs:
       run:
         shell: msys2 {0}
     steps:
+
       - name: Check out repository code
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
       - name: Setup MSYS2 ${{matrix.sys}}
         uses: msys2/setup-msys2@66cd2cce69caa17b53920067426061ca1de3a884 # v2.32.0
         with:
@@ -150,40 +141,19 @@ jobs:
             msys2-devel
             mingw-w64-${{matrix.env}}-toolchain
             mingw-w64-${{matrix.env}}-cmake
-      - name: Setup Miniforge
-        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1
-        with:
-          miniforge-version: latest
-          activate-environment: anaconda-client-env
-          auto-update-conda: true
-          python-version: ${{ matrix.python }}
+
       - name: Get Date
         id: get-date
         run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
         shell: bash
-      - name: Cache Conda env
-        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
-        env:
-          # Increase this value to reset cache if treerec/tests/environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          # Use faster GNU tar
-          enableCrossOsArchive: true
-          path: D:\conda_pkgs_dir
-          key:
-            conda-${{ runner.os }}--python-${{ matrix.python }}--${{ runner.arch }}--${{
-            steps.get-date.outputs.today }}-${{
-            hashFiles('treerec/tests/environment.yml') }}-${{ env.CACHE_NUMBER}}
-        id: cache
-      - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1
-        with:
-          activate-environment: anaconda-client-env
-          environment-file: treerec/tests/environment.yml
-          pkgs-dirs: D:\conda_pkgs_dir
-      - name: Update environment
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
         shell: bash -el {0}
-        run: conda env update -n anaconda-client-env -f treerec/tests/environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
+        with:
+          python-version: ${{ inputs.python-version }}
+          version: "0.10.0"
+
       - name: Build and test (Debug)
         run: |
           cd windows_compat/gnulib && \
@@ -195,6 +165,7 @@ jobs:
           make -j 2 && \
           # Show any output from the test program whenever the test fails
           env CTEST_OUTPUT_ON_FAILURE=1 make test
+
       - name: Build and test (Release)
         run: |
           cd windows_compat/gnulib && \
@@ -206,13 +177,13 @@ jobs:
           make -j 2 && \
           # Show any output from the test program whenever the test fails
           env CTEST_OUTPUT_ON_FAILURE=1 make test
+
       - name: Treesequence tests
         shell: bash -el {0}
         run: |
-          conda activate anaconda-client-env && \
           export PATH=$PATH:$PWD/Release && \
           echo $PATH && \
-          cd treerec/tests && python -m pytest -xv
+          cd treerec/tests && uv run pytest -xv
 
   tests-Unix-GUI:
     if: github.event_name != 'schedule' || (github.event_name == 'schedule' && github.repository == 'messerlab/slim')

diff --git a/treerec/tests/README.md b/treerec/tests/README.md
@@ -72,5 +72,8 @@ To add a new test:
       add individuals to the saved list by calling `addIndividuals(individuals)` at any point
       in the simulation.
 
+    * Ensure that tree sequences are written to subdirectories! If there are no subdirectories
+      then nothing will happen.
+
 
 To temporarily turn off a test just comment out the appropriate line in `recipe_specs.py`
diff --git a/treerec/tests/conftest.py b/treerec/tests/conftest.py
@@ -40,12 +40,11 @@ def get_ts(self):
         # binary
         print("******** Binary input.")
         bin_ts = load_file_or_dir(os.path.join(self.dir, "test_output.trees"))
-        yield bin_ts
         # and nonsimplified binary
         print("******** Unsimplified binary.")
         bin_nonsimp_ts = load_file_or_dir(
             os.path.join(self.dir, "test_output.unsimplified.trees"))
-        yield bin_nonsimp_ts
+        return (bin_ts, bin_nonsimp_ts)
 
     @staticmethod
     def get_slim_ids(ts):
@@ -154,11 +153,13 @@ def make_result(run_dir):
     SLiM recipes are expected to output their results into a set of directories
     within the run_dir: return a list of results, one for each subdirectory
     """
-    return [
+    out = [
         OutputResult(os.path.join(run_dir, f.name))
         for f in os.scandir(run_dir)
         if f.is_dir()
     ]
+    assert len(out) > 0
+    return out
 
 def run_slim(recipe, run_dir, recipe_dir="test_recipes"):
     """

diff --git a/treerec/tests/init.slim b/treerec/tests/init.slim
@@ -30,6 +30,19 @@ function (void)initializeMarks(i$ num_marks)
    return;
 }
 
+function (void)saveTreeSeqTraits(void) {
+	 MD = Dictionary();
+	 for (mt in sim.mutationTypes) {
+	 	MD.setValue("m" + mt.id, Dictionary(
+	 		"convertToSubstitution", mt.convertToSubstitution
+	 	));
+	 }
+    sim.demandPhenotype(sim.subpopulations);
+   setwdForGen();
+   sim.treeSeqOutput("test_output.trees", metadata=Dictionary("mutation_types", MD));
+   sim.treeSeqOutput("test_output.unsimplified.trees", simplify=F);
+}
+
 function (void)saveTreeSeq(void) {
    // create tree seq representation in various formats: this could overwrite any
    // existing ones output in the same cycle, but they should be identical

diff --git a/treerec/tests/pyproject.toml b/treerec/tests/pyproject.toml
@@ -4,9 +4,9 @@ version = "0.1.0"
 requires-python = ">=3.13"
 dependencies = [
     "filelock>=3.32.4",
-    "msprime>=1.2.0",
+    "msprime>=1.4.4",
     "numpy>=2.5.2",
-    "pyslim>=1.0.4",
+    "pyslim @ git+https://github.com/tskit-dev/pyslim@main",
     "pytest>=9.1.1",
     "pytest-xdist>=3.8.0",
     "setuptools>=84.0.0",

diff --git a/treerec/tests/recipe_specs.py b/treerec/tests/recipe_specs.py
@@ -50,6 +50,21 @@
     "test_836_output from multiple-chromosome models.slim": {"mutations": True, "individuals": True},
     "test_169_complex multi-chromosome inheritance.slim": {"mutations": True, "individuals": True},
     "test_1610_modeling pseudo-autosomal regions.slim": {"mutations": True, "individuals": True},
+    "recipe_WF.slim":                               {"traits": True},
+    "recipe_WF_adds.slim":                          {"traits": True},
+    "recipe_WF_no_substitutions.slim":              {"traits": True},
+    "recipe_WF_H.slim":                             {"traits": True},
+    "recipe_WF_HF.slim":                            {"traits": True},
+    "recipe_WF_HM.slim":                            {"traits": True},
+    "recipe_WF_W.slim":                             {"traits": True},
+    "recipe_WF_X.slim":                             {"traits": True},
+    "recipe_WF_Y.slim":                             {"traits": True},
+    "recipe_WF_Z.slim":                             {"traits": True},
+    "recipe_nonWF.slim":                            {"traits": True},
+    "recipe_nonWF_substitutions.slim":              {"traits": True},
+    "recipe_nonWF_H.slim":                          {"traits": True},
+    "recipe_nonWF_X.slim":                          {"traits": True},
+    "recipe_nonWF_Y.slim":                          {"traits": True},
 }
 
 

diff --git a/treerec/tests/test_recipes/recipe_WF.slim b/treerec/tests/test_recipes/recipe_WF.slim
@@ -0,0 +1,24 @@
+initialize()
+{
+    setSeed(23);
+    initializeSLiMOptions(keepPedigrees=T);
+    initializeTreeSeq(timeUnit="generations");
+	source("init.slim");
+	 initializeSex();
+    initializeChromosome(1, 100, "A", "A");
+    initializeMutationRate(1e-2);
+    initializeMutationType("m1", 0.5, "f", -0.1);
+    initializeGenomicElementType("g1", m1, 1.0);
+    initializeGenomicElement(g1, 0, 99);
+    initializeRecombinationRate(1e-2);
+}
+
+1 early() { 
+    sim.addSubpop("p1", 10);
+}
+
+30 late() {
+    saveTreeSeqTraits();
+    catn("Done.");
+    sim.simulationFinished();
+}
diff --git a/treerec/tests/test_recipes/recipe_WF_H.slim b/treerec/tests/test_recipes/recipe_WF_H.slim
@@ -0,0 +1,23 @@
+initialize()
+{
+    setSeed(23);
+    initializeSLiMOptions(keepPedigrees=T);
+    initializeTreeSeq(timeUnit="generations");
+	source("init.slim");
+    initializeChromosome(1, 100, "A", "A");
+    initializeMutationRate(1e-2);
+    initializeMutationType("m1", 0.5, "f", -0.1);
+    initializeGenomicElementType("g1", m1, 1.0);
+    initializeGenomicElement(g1, 0, 99);
+    initializeRecombinationRate(1e-2);
+}
+
+1 early() { 
+    sim.addSubpop("p1", 10);
+}
+
+30 late() {
+    saveTreeSeqTraits();
+    catn("Done.");
+    sim.simulationFinished();
+}
diff --git a/treerec/tests/test_recipes/recipe_WF_HF.slim b/treerec/tests/test_recipes/recipe_WF_HF.slim
@@ -0,0 +1,24 @@
+initialize()
+{
+    setSeed(23);
+    initializeSLiMOptions(keepPedigrees=T);
+    initializeTreeSeq(timeUnit="generations");
+	source("init.slim");
+	 initializeSex();
+    initializeChromosome(1, 100, "A", "A");
+    initializeMutationRate(1e-2);
+    initializeMutationType("m1", 0.5, "f", -0.1);
+    initializeGenomicElementType("g1", m1, 1.0);
+    initializeGenomicElement(g1, 0, 99);
+    initializeRecombinationRate(1e-2);
+}
+
+1 early() { 
+    sim.addSubpop("p1", 10);
+}
+
+30 late() {
+    saveTreeSeqTraits();
+    catn("Done.");
+    sim.simulationFinished();
+}
diff --git a/treerec/tests/test_recipes/recipe_WF_HM.slim b/treerec/tests/test_recipes/recipe_WF_HM.slim
@@ -0,0 +1,24 @@
+initialize()
+{
+    setSeed(23);
+    initializeSLiMOptions(keepPedigrees=T);
+    initializeTreeSeq(timeUnit="generations");
+	source("init.slim");
+	 initializeSex();
+    initializeChromosome(1, 100, "A", "A");
+    initializeMutationRate(1e-2);
+    initializeMutationType("m1", 0.5, "f", -0.1);
+    initializeGenomicElementType("g1", m1, 1.0);
+    initializeGenomicElement(g1, 0, 99);
+    initializeRecombinationRate(1e-2);
+}
+
+1 early() { 
+    sim.addSubpop("p1", 10);
+}
+
+30 late() {
+    saveTreeSeqTraits();
+    catn("Done.");
+    sim.simulationFinished();
+}
diff --git a/treerec/tests/test_recipes/recipe_WF_W.slim b/treerec/tests/test_recipes/recipe_WF_W.slim
@@ -0,0 +1,24 @@
+initialize()
+{
+    setSeed(23);
+    initializeSLiMOptions(keepPedigrees=T);
+    initializeTreeSeq(timeUnit="generations");
+	source("init.slim");
+	 initializeSex();
+    initializeChromosome(1, 100, "A", "A");
+    initializeMutationRate(1e-2);
+    initializeMutationType("m1", 0.5, "f", -0.1);
+    initializeGenomicElementType("g1", m1, 1.0);
+    initializeGenomicElement(g1, 0, 99);
+    initializeRecombinationRate(1e-2);
+}
+
+1 early() { 
+    sim.addSubpop("p1", 10);
+}
+
+30 late() {
+    saveTreeSeqTraits();
+    catn("Done.");
+    sim.simulationFinished();
+}