Merge branch 'trunk' into fix-deadlock

.github/dependabot.yml

@@ -2,7 +2,7 @@ version: 2
 updates:
   - package-ecosystem: "github-actions"
     directory: "/"
-    target-branch: main
+    target-branch: trunk
     schedule:
       interval: "monthly"
     pull-request-branch-name:
@@ -11,7 +11,7 @@ updates:
 
   - package-ecosystem: "pip"
     directory: ".github/workflows"
-    target-branch: main
+    target-branch: trunk
     schedule:
       interval: "monthly"
     pull-request-branch-name:

.github/workflows/CI.yml

@@ -22,12 +22,12 @@ jobs:
     name: flow-status
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.5.2
+      - uses: actions/checkout@v4.1.0
       - name: Set up Python
-        uses: actions/setup-python@v4.6.1
+        uses: actions/setup-python@v4.7.0
         with:
-          python-version: '3.10'
-      - uses: actions/[email protected].1
+          python-version: '3.11'
+      - uses: actions/[email protected].2
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('.github/workflows/requirements-test.txt') }}

.github/workflows/requirements-test.txt

@@ -1,5 +1,5 @@
-signac==2.0.0
-signac-flow==0.25.1
-numpy==1.24.3
-PyYAML==6.0
-gsd==2.9.0
+signac==2.1.0
+signac-flow==0.26.1
+numpy==1.26.0
+PyYAML==6.0.1
+gsd==3.2.0

.gitignore

@@ -9,3 +9,4 @@ signac_project_document.json
 .signac_sp_cache.json.gz
 __pycache__
 .signac
+*.code-workspace

.mailmap

@@ -0,0 +1,3 @@
+Tim Moore <[email protected]> Tim Moore <[email protected]>
+Tommy Waltmann <[email protected]> Tommy Waltmann <[email protected]>
+Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]>

CONTRIBUTING.md

@@ -6,7 +6,7 @@ the project.
 
 ## Base your work off the correct branch
 
-All new work should be based on `main`.
+All new work should be based on `trunk`.
 
 ## Propose a minimal set of related changes
 

CONTRIBUTORS.md

@@ -0,0 +1,8 @@
+# Contributors
+
+The following people have contributed to hoomd-validation:
+
+* Joshua A. Anderson, University of Michigan
+* Tommy Waltmann, University of Michigan
+* Tim Moore, University of Michigan
+* Brandon Butler, University of Michigan

dashboard.py

@@ -32,11 +32,25 @@ def job_title(self, job):
                    f"rho={job.statepoint.density}"
         elif (job.statepoint.subproject == 'hard_disk'
               or job.statepoint.subproject == 'hard_sphere'
-              or job.statepoint.subproject == 'simple_polygon'):
+              or job.statepoint.subproject == 'simple_polygon'
+              or job.statepoint.subproject == 'patchy_particle_pressure'):
             return f"{job.statepoint.subproject}: rho={job.statepoint.density}"
         else:
             raise RuntimeError("Unexpected job")
 
+    def job_sorter(self, job):
+        """Sort jobs."""
+        if job.statepoint.subproject == 'patchy_particle_pressure':
+            return (
+                job.sp.density,
+                job.sp.pressure,
+                job.sp.temperature,
+                job.sp.chi,
+                job.sp.replicate_idx,
+            )
+        else:
+            return job.statepoint.num_particles
+
 
 if __name__ == "__main__":
     ValidationDashboard(modules=modules).main()

hoomd_validation/config_parser.py

@@ -33,8 +33,8 @@ def __init__(self, config_file_path=DEFAULT_CONFIG_PATH):
         self["max_cores_submission"] = int(
             config.get("max_cores_submission", 16))
         self["max_gpus_submission"] = int(config.get("max_gpus_submission", 1))
-        self["max_walltime"] = int(config.get("max_walltime", 24))
-        self["short_walltime"] = int(config.get("short_walltime", 2))
+        self["max_walltime"] = float(config.get("max_walltime", 24))
+        self["short_walltime"] = float(config.get("short_walltime", 2))
         self["replicates"] = int(config.get("replicates", 32))
         self["enable_llvm"] = bool(config.get("enable_llvm", True))
         self["enable_gpu"] = bool(config.get("enable_gpu", True))

hoomd_validation/init.py

@@ -14,6 +14,7 @@
 import hard_disk
 import hard_sphere
 import simple_polygon
+import patchy_particle_pressure
 
 subprojects = [
     alj_2d,
@@ -22,6 +23,7 @@
     hard_disk,
     hard_sphere,
     simple_polygon,
+    patchy_particle_pressure,
 ]
 
 project = signac.init_project(path=config.project_root)