Merge branch 'trunk' of https://github.com/glotzerlab/hoomd-validation …

…into add_kT_to_validation
glotzerlab · Nov 8, 2024 · fbb57e2 · fbb57e2
2 parents 8bb0126 + 8c7250c
commit fbb57e2
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diff --git a/.github/workflows/stale.yaml b/.github/workflows/stale.yaml
@@ -8,4 +8,4 @@ on:
 
 jobs:
   stale:
-    uses: glotzerlab/workflows/.github/workflows/stale.yaml@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+    uses: glotzerlab/workflows/.github/workflows/stale.yaml@1747bc5c994ec280440dd051f2928791407692c8 # 0.5.1
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -19,20 +19,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
     - name: Set up Python
-      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
       with:
         python-version: "3.12"
     - name: Set up Python environment
-      uses: glotzerlab/workflows/setup-uv@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+      uses: glotzerlab/workflows/setup-uv@1747bc5c994ec280440dd051f2928791407692c8 # 0.5.1
       with:
         lockfile: ".github/workflows/requirements-test.txt"
     - name: Initialize workspace
       run: python3 hoomd_validation/project.py init
     - name: Show workflow
       run: cat --number workflow.toml
     - name: Set up row
-      uses: glotzerlab/workflows/setup-row@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+      uses: glotzerlab/workflows/setup-row@1747bc5c994ec280440dd051f2928791407692c8 # 0.5.1
     - name: Show project status
       run: row show status
diff --git a/documentation/delta.md b/documentation/delta.md
@@ -4,7 +4,7 @@
 
 ```
 max_cores_sim = 64
-max_cores_submission = 512
-max_gpus_submission = 8
+max_cores_submission = 128
+max_gpus_submission = 1
 max_walltime = "2 days, 00:00:00"
 ```
diff --git a/hoomd_validation/alj_2d.py b/hoomd_validation/alj_2d.py
@@ -6,6 +6,7 @@
 import itertools
 import math
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -450,13 +451,18 @@ def plot(*, ax, data, quantity_name, legend=False):
 
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the job complete
+    for job in jobs:
+        Path(job.fn('conservation_analyze_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.conservation_analyze',
     Action(
         method=conservation_analyze,
         configuration={
             'previous_actions': nve_md_sampling_jobs,
+            'products': ['conservation_analyze_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/hard_disk.py b/hoomd_validation/hard_disk.py
@@ -6,6 +6,7 @@
 import itertools
 import json
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -795,13 +796,18 @@ def compare_modes(*jobs):
     filename = f'hard_disk_compare_density{round(set_density, 2)}.svg'
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('compare_modes_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.compare_modes',
     Action(
         method=compare_modes,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['compare_modes_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/hard_sphere.py b/hoomd_validation/hard_sphere.py
@@ -5,6 +5,7 @@
 
 import itertools
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -651,13 +652,18 @@ def compare_modes(*jobs):
     filename = f'hard_sphere_compare_density{round(set_density, 2)}.svg'
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('compare_modes_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.compare_modes',
     Action(
         method=compare_modes,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['compare_modes_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/lj_fluid.py b/hoomd_validation/lj_fluid.py
@@ -8,6 +8,7 @@
 import json
 import math
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -1075,13 +1076,18 @@ def compare_modes(*jobs):
 
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('compare_modes_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.compare_modes',
     Action(
         method=compare_modes,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['compare_modes_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},
@@ -1239,13 +1245,18 @@ def distribution_analyze(*jobs):
     )
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('distribution_analyze_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.distribution_analyze',
     Action(
         method=distribution_analyze,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['distribution_analyze_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},
@@ -1470,13 +1481,18 @@ def plot(*, ax, data, quantity_name, legend=False):
 
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('conservation_analyze_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.conservation_analyze',
     Action(
         method=conservation_analyze,
         configuration={
             'previous_actions': nve_md_sampling_jobs,
+            'products': ['conservation_analyze_complete'],
             'group': _group_compare | _include_nve,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/lj_union.py b/hoomd_validation/lj_union.py
@@ -8,6 +8,7 @@
 import json
 import math
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -1094,13 +1095,18 @@ def compare_modes(*jobs):
     filename = f'lj_union_compare_kT{kT}_density{round(set_density, 2)}.svg'
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('compare_modes_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.compare_modes',
     Action(
         method=compare_modes,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['compare_modes_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},
@@ -1299,13 +1305,18 @@ def distribution_analyze(*jobs):
     )
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('distribution_analyze_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.distribution_analyze',
     Action(
         method=distribution_analyze,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['distribution_analyze_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},
@@ -1526,13 +1537,18 @@ def plot(*, ax, data, quantity_name, legend=False):
 
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('conservation_analyze_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.conservation_analyze',
     Action(
         method=conservation_analyze,
         configuration={
             'previous_actions': nve_md_sampling_jobs,
+            'products': ['conservation_analyze_complete'],
             'group': _group_compare | _include_nve,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/patchy_particle_pressure.py b/hoomd_validation/patchy_particle_pressure.py
@@ -6,6 +6,7 @@
 import itertools
 import json
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -805,13 +806,18 @@ def compare_modes(*jobs):
         transparent=False,
     )
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('compare_modes_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.compare_modes',
     Action(
         method=compare_modes,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['compare_modes_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/simple_polygon.py b/hoomd_validation/simple_polygon.py
@@ -6,6 +6,7 @@
 import itertools
 import json
 import os
+from pathlib import Path
 
 try:
     import hoomd
@@ -659,13 +660,18 @@ def compare_modes(*jobs):
     filename = f'simple_polygon_compare_density{round(set_density, 2)}.svg'
     fig.savefig(os.path.join(jobs[0]._project.path, filename), bbox_inches='tight')
 
+    # mark the action complete
+    for job in jobs:
+        Path(job.fn('compare_modes_complete')).touch()
+
 
 ValidationWorkflow.add_action(
     f'{__name__}.compare_modes',
     Action(
         method=compare_modes,
         configuration={
             'previous_actions': [f'{__name__}.analyze'],
+            'products': ['compare_modes_complete'],
             'group': _group_compare,
             'resources': {
                 'processes': {'per_submission': 1},

diff --git a/hoomd_validation/workflow.py b/hoomd_validation/workflow.py
@@ -13,6 +13,7 @@
 
 import argparse
 import subprocess
+import warnings
 from pathlib import Path
 
 import rtoml
@@ -77,6 +78,9 @@ def add_action(cls, name, action):
             message = f'Action {name} cannot be added twice.'
             raise ValueError(message)
 
+        if 'products' not in action._configuration:
+            warnings.warn(f'Action {name} is missing products.', stacklevel=2)
+
         cls._actions[name] = action
 
     @classmethod
@@ -138,10 +142,10 @@ def main(cls, init=None, init_args=None, **kwargs):
         as options to the ``init`` subparser with ``add_argument``.
 
         Args:
-            init(callable): User-provided initializaiton routine. Must take one
+            init(callable): User-provided initialization routine. Must take one
                 argument: ``args`` - the ``argparse`` parsed arguments.
             init_args(list[str]): List of args to add to the ``init`` subparser.
-            **kwargs: Fowarded to `make_workflow`.
+            **kwargs: Forwarded to `make_workflow`.
         """
         parser = argparse.ArgumentParser()
         command = parser.add_subparsers(dest='command', required=True)
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,4 +8,4 @@ on: @@
     jobs:
       stale:
-        uses: glotzerlab/workflows/.github/workflows/stale.yaml@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+        uses: glotzerlab/workflows/.github/workflows/stale.yaml@1747bc5c994ec280440dd051f2928791407692c8 # 0.5.1