Merge branch 'main' into pytorch

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.4.0'
+    rev: 'v4.5.0'
     hooks:
       - id: end-of-file-fixer
         exclude: 'setup.cfg'
@@ -16,19 +16,19 @@ repos:
       - id: debug-statements
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v3.13.0'
+    rev: 'v3.15.0'
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
   - repo: https://github.com/PyCQA/isort
-    rev: '5.12.0'
+    rev: '5.13.2'
     hooks:
       - id: isort
         args:
           - --profile=black
   - repo: https://github.com/psf/black
-    rev: '23.9.1'
+    rev: '23.12.1'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
@@ -38,7 +38,7 @@ repos:
         args:
           - --max-line-length=100
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+    rev: 1.7.1
     hooks:
       - id: nbqa-pyupgrade
         args:

notebooks/signac_301_Aggregation_Tutorial.ipynb

@@ -36,7 +36,7 @@
     "\n",
     "Aggregation allows a **signac-flow** operation to act on multiple jobs, rather than one job at a time.\n",
     "\n",
-    "An aggregate is defined as a subset of the jobs in a **signac** project. Aggregates are generated when the `@flow.aggregator` decorator is applied to an operation.\n",
+    "An aggregate is defined as a subset of the jobs in a **signac** project. Aggregates are generated when a `flow.aggregator` object is provided to the `FlowProject.operation` decorator.\n",
     "\n",
     "Please refer to the [documentation](https://docs.signac.io/en/latest/aggregation.html) for detailed instructions on how to use aggregation."
    ]

projects/flow.2D-random-walk/src/init.py

@@ -14,9 +14,9 @@
 logger.setLevel(logging.ERROR)
 
 # The standard deviations to use for generating random walk moves
-STANDARD_DEVIATIONS = np.linspace(start=0.1, stop=1, num=20)
+STANDARD_DEVIATIONS = np.linspace(start=0.1, stop=1, num=5)
 NUMBER_REPLICAS = 100
-RUN_STEPS = 5_000
+RUN_STEPS = 10_000
 MAX_SEED = 2**32 - 1
 
 

projects/flow.2D-random-walk/src/project.py

@@ -125,7 +125,8 @@ def plot_mean_squared_displacement(job):
 
 @agg_analyze_and_plot
 @RandomWalkProject.pre(all_simulated)
-@RandomWalkProject.post.true("msd_analyzed")
+@RandomWalkProject.pre(lambda *jobs: "squared_displacement" in jobs[0].data)
+@RandomWalkProject.post(lambda *jobs: jobs[0].doc.get("msd_analyzed"))
 @RandomWalkProject.operation(aggregator=std_aggregator)
 def compute_mean_squared_displacement(*jobs):
     """Compute and store the mean squared displacement for all std."""

projects/flow.gmx-lysozyme-in-water/project.py

@@ -3,7 +3,6 @@
 from flow import FlowProject
 
 gmx_exec = "gmx"  # or use gmx_mpi if available
-mpi_exec = "mpirun"
 
 """Define file level constants."""
 
@@ -84,16 +83,10 @@ def _grompp_str(op_name, gro_name, checkpoint_file=None):
     return cmd
 
 
-def _mdrun_str(op_name, np=1, nt=None, verbose=False):
+def _mdrun_str(op_name, nt=None, verbose=False):
     """Helper function, returns mdrun command string for operation."""
     num_threads = 1 if nt is None else nt
-    num_nodes = np // num_threads
-    cmd = (
-        "OMP_NUM_THREADS={num_threads} {mpi_exec} -n {np} {gmx} "
-        "mdrun -ntomp {num_threads} {verbose} -deffnm {op}"
-    ).format(
-        np=num_nodes,
-        mpi_exec=mpi_exec,
+    cmd = ("{gmx} mdrun -ntomp {num_threads} {verbose} -deffnm {op}").format(
         gmx=gmx_exec,
         num_threads=num_threads,
         op=op_name,
@@ -165,7 +158,7 @@ def solvate(job):
 @MyProject.post.isfile(ionization_config)
 @MyProject.operation(cmd=True, with_job=True)
 def grompp_add_ions(job):
-    return _grompp_str("ions", solvated_file)
+    return _grompp_str("ions", solvated_file).format(job)
 
 
 @MyProject.pre.after(grompp_add_ions)
@@ -197,58 +190,60 @@ def ionize(job):
 @MyProject.post.isfile(em_op + ".tpr")
 @MyProject.operation(cmd=True, with_job=True)
 def grompp_minim(job):
-    return _grompp_str("minim", ionized_file)
+    return _grompp_str("minim", ionized_file).format(job)
 
 
 @MyProject.pre.after(grompp_minim)
 @MyProject.post.isfile(em_file)
 @MyProject.operation(cmd=True, with_job=True)
 def minim(job):
-    return _mdrun_str("minim")
+    return _mdrun_str("minim").format(job)
 
 
 # Equilibration: NVT then NPT
 @MyProject.pre.after(minim)
 @MyProject.post.isfile(nvt_op + ".tpr")
 @MyProject.operation(cmd=True, with_job=True)
 def grompp_nvt(job):
-    return _grompp_str("nvt", em_file)
+    return _grompp_str("nvt", em_file).format(job)
 
 
 @MyProject.pre.after(grompp_nvt)
 @MyProject.post.isfile(nvt_file)
 @MyProject.operation(cmd=True, directives={"np": 16}, with_job=True)
 def nvt(job):
-    return _mdrun_str("nvt")
+    return _mdrun_str("nvt").format(job)
 
 
 @MyProject.pre.after(nvt)
 @MyProject.post.isfile(npt_op + ".tpr")
 @MyProject.operation(cmd=True, with_job=True)
 def grompp_npt(job):
-    return _grompp_str("npt", nvt_file)
+    return _grompp_str("npt", nvt_file).format(job)
 
 
 @MyProject.pre.isfile(npt_op + ".tpr")
 @MyProject.post.isfile(npt_file)
 @MyProject.operation(cmd=True, directives={"np": 16}, with_job=True)
 def npt(job):
-    return _mdrun_str("npt")
+    return _mdrun_str("npt").format(job)
 
 
 # Final run
 @MyProject.pre.isfile(npt_file)
 @MyProject.post.isfile(production_op + ".tpr")
 @MyProject.operation(cmd=True, with_job=True)
 def grompp_md(job):
-    return _grompp_str("md", npt_file)
+    return _grompp_str("md", npt_file).format(job)
 
 
 @MyProject.pre.after(grompp_md)
 @MyProject.post(finished)
-@MyProject.operation(cmd=True, directives={"np": 16}, with_job=True)
+@MyProject.operation(
+    cmd=True, directives={"nranks": 4, "omp_num_threads": 4}, with_job=True
+)
 def md(job):
-    return _mdrun_str("md")
+    return _mdrun_str("md", nt=4).format(job)
 
 
 if __name__ == "__main__":

projects/flow.gmx-mtools/src/project.py

@@ -69,21 +69,21 @@ def initialize(job):
 @MyProject.post(minimized)
 @MyProject.operation(cmd=True, with_job=True)
 def em(job):
-    return gromacs_command(name="em", gro="init", sys="init")
+    return gromacs_command(name="em", gro="init", sys="init").format(job)
 
 
 @MyProject.pre(minimized)
 @MyProject.post(equilibrated)
 @MyProject.operation(cmd=True, with_job=True)
 def equil(job):
-    return gromacs_command(name="equil", gro="em", sys="init")
+    return gromacs_command(name="equil", gro="em", sys="init").format(job)
 
 
 @MyProject.pre(equilibrated)
 @MyProject.post(sampled)
 @MyProject.operation(cmd=True, with_job=True)
 def sample(job):
-    return gromacs_command(name="sample", gro="equil", sys="init")
+    return gromacs_command(name="sample", gro="equil", sys="init").format(job)
 
 
 if __name__ == "__main__":

projects/run-tests.sh

@@ -18,7 +18,7 @@ for PROJECT in `ls -d */`; do
         cat ${REQUIREMENTS_FILE}
         mamba install --yes --file ${REQUIREMENTS_FILE} --quiet
     fi
-    python flow-test.py ${PROJECT} -vv --timeout=600 $@
+    python flow-test.py ${PROJECT} -v --timeout=600 $@
     if [[ "$CI" ]]; then
         echo "::endgroup::"
     fi