docs - mostly asimov

MonteCarloMarginalizeCode/Code/RIFT/integrators/multivariate_truncnorm.py

@@ -44,8 +44,8 @@ def _get_new_bounds(bounds, q):
         index += 1
     new_bounds = np.empty((d, 2))
     for dim in range(d):
-        new_bounds[dim][0] = min(new_points[:,[dim]])
-        new_bounds[dim][1] = max(new_points[:,[dim]])
+        new_bounds[dim][0] = min(new_points[:, dim])
+        new_bounds[dim][1] = max(new_points[:, dim])
     return new_bounds
 
 

MonteCarloMarginalizeCode/Code/RIFT/simulation_manager/PBSManager.py

@@ -0,0 +1,136 @@
+import sys, os
+import subprocess
+import re
+import logging
+import RIFT.simulation_manager.BaseManager as bm
+
+logger = logging.getLogger(__name__)
+
+def default_pbs_build_job(tag='job_tag_default_pbs', exe=None, arg_str=None, sim_path=None, pbs_args=None, array_range=None, **kwargs):
+    """
+    Builds a PBS submit script.
+    pbs_args: dict of PBS options, e.g., {'queue': 'workq', 'walltime': '01:00:00', 'nodes': '1:ppn=1'}
+    array_range: PBS array job specification, e.g., '1-10' or '1-10:2' (step size)
+    """
+    if pbs_args is None:
+        pbs_args = {}
+
+    # Standard PBS headers
+    script_lines = ["#!/bin/bash", "#PBS -N " + tag]
+
+    # Add array job directive if specified
+    if array_range:
+        script_lines.append(f"#PBS -J {array_range}")
+
+    # Add custom PBS arguments
+    if 'queue' in pbs_args:
+        script_lines.append(f"#PBS -q {pbs_args['queue']}")
+    if 'walltime' in pbs_args:
+        script_lines.append(f"#PBS -l walltime={pbs_args['walltime']}")
+    if 'nodes' in pbs_args:
+        script_lines.append(f"#PBS -l {pbs_args['nodes']}")
+    if 'mem' in pbs_args:
+        script_lines.append(f"#PBS -l mem={pbs_args['mem']}")
+
+    script_lines.append("")  # newline
+    script_lines.append(f"cd $PBS_O_WORKDIR")
+    script_lines.append(f"{exe} {arg_str}")
+
+    script_content = "\n".join(script_lines)
+    return script_content, tag + ".pbs_sub"
+
+class SimulationArchiveOnLocalDiskIntegratedPBSQueue(bm.SimulationArchiveOnLocalDiskExternalQueue):
+    """
+    Simulation archive whose entries are queued and run via PBS/Larus.
+    """
+    def __init__(self, **kwargs):
+        self._internal_build_submit = default_pbs_build_job
+        self._internal_exe = 'echo'
+        self._internal_job_id = None 
+        self._internal_simulations_have_sub_directories = True
+        super().__init__(**kwargs)
+
+        if not os.path.exists(self.base_location + "/logs"):
+            os.mkdir(self.base_location + "/logs")
+        if not os.path.exists(self.base_location + "/pbs_submit_files/"):
+            os.mkdir(self.base_location + "/pbs_submit_files/")
+
+    def generate_simulation(self, sim_params, **kwargs):
+        return self.register_simulation(sim_params, **kwargs)
+
+    def build_single_job(self, tag=None, **kwargs):
+        """Builds and writes a single PBS submit script."""
+        build_args = {}
+        build_args.update(kwargs)
+
+        script_content, script_name = self._internal_build_submit(tag=tag, **build_args)
+
+        full_path = os.path.join(self.base_location, "pbs_submit_files", script_name)
+        with open(full_path, 'w') as f:
+            f.write(script_content)
+
+        self._internal_job_id = script_name  # Temporary reference
+        return full_path
+
+    def build_array_job(self, tag=None, array_range='1-10', **kwargs):
+        """
+        Builds and writes a PBS array job submit script.
+        array_range: PBS array job specification, e.g., '1-10' or '1-10:2'
+        """
+        build_args = dict(kwargs)
+        build_args['array_range'] = array_range
+
+        script_content, script_name = self._internal_build_submit(tag=tag, **build_args)
+
+        full_path = os.path.join(self.base_location, "pbs_submit_files", script_name)
+        with open(full_path, 'w') as f:
+            f.write(script_content)
+
+        self._internal_job_id = script_name
+        return full_path
+
+    def submit_job(self, script_path):
+        """Submits a PBS script via qsub and captures the job ID."""
+        try:
+            result = subprocess.run(['qsub', script_path], 
+                                   capture_output=True, text=True, check=True)
+            # qsub usually returns the job ID directly to stdout
+            job_id = result.stdout.strip()
+            logger.info(" PBS job submitted successfully: %s ", job_id)
+            return job_id
+        except subprocess.CalledProcessError as e:
+            logger.error(" Failed to submit PBS job %s: %s ", script_path, e.stderr)
+            return None
+        except FileNotFoundError:
+            logger.error(" qsub not found on PATH ")
+            return None
+
+    def refresh_status_from_pbs(self, job_id):
+        """
+        Checks the status of a PBS job using qstat.
+        Returns 'running' if job is in queue/running, 'complete' if gone (and output exists).
+        """
+        try:
+            # qstat -f provides full details; -n for numeric IDs
+            result = subprocess.run(['qstat', '-n', job_id], 
+                                   capture_output=True, text=True)
+
+            if result.returncode == 0:
+                # Job is still in the system
+                return 'running'
+            else:
+                # Job is no longer in qstat; check if output exists via _internal_check_complete
+                return 'complete'
+        except Exception as exc:
+            logger.warning(" refresh_status_from_pbs failed for %s: %s ", job_id, exc)
+            return None
+
+if __name__ == "__main__":
+    # Simple smoke test
+    archive = SimulationArchiveOnLocalDiskIntegratedPBSQueue(name="pbs_test", base_location="pbs_test_dir")
+    archive.generator = lambda k: k*2
+    archive.generate_simulation(0.5)
+
+    # Test build
+    path = archive.build_single_job(tag="smoke_test", exe="echo", arg_str="hello world")
+    print(f"PBS script built at: {path}")

MonteCarloMarginalizeCode/Code/RIFT/simulation_manager/__init__.py

@@ -1 +1 @@
-__all__ = ['BaseManager', 'CondorManager', 'SlurmManager']
+__all__ = ['BaseManager', 'CondorManager', 'PBSManager', 'SlurmManager']

MonteCarloMarginalizeCode/Code/bin/cepp_basic_htcondor

@@ -1,6 +1,6 @@
 #! /usr/bin/env python
 import htcondor2 as htcondor
-from htcondor2.dags import DAG, Node
+from htcondor2.dags import DAG
 #
 #  GOAL
 #    Simple pipeline: just ILE+fitting iteration jobs

docs/source/api_reference/asimov/asimov_production.rst

@@ -114,15 +114,14 @@ Apply the base infrastructure configuration. These define the cluster, accountin
    - Base Singularity image
 
 2. **cbcflow/testing.yaml**: cbcflow configuration
-   - Workflow manager settings
 
 3. **production-pe-priors.yaml**: Prior distributions
    - Default prior settings for mass, spin, etc.
 
 Stage 4: cbcflow Integration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-cbcflow manages the overall workflow for production PE. It coordinates multiple pipelines and handles result aggregation:
+cbcflow provides metadata about identified event candidates and internal understanding of them, recording state about previous investigations:
 
 .. code-block:: bash
 
@@ -135,10 +134,10 @@ cbcflow manages the overall workflow for production PE. It coordinates multiple
 
 **What cbcflow does:**
 
-- Coordinates data retrieval (graceDB)
-- Manages multiple PE pipelines
-- Handles result merging and aggregation
-- Generates summary pages
+`cbcflow documentation <https://cbc.docs.ligo.org/projects/cbcflow/index.html>`_ provides:
+
+- **Metadata for superevents**, stored in a standardized format.
+- **A Python API** for interacting with that metadata.
 
 Stage 5: Output Configuration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -193,12 +192,12 @@ Define a function to add events. This is the core of the multi-event pattern:
 
 **What each blueprint provides:**
 
-- **o4b-production.yaml**: Data retrieval from graceDB
-- **standard.yaml**: PE configurator settings
-- **standard-settings.yaml**: Bayeswave PSD settings
-- **analysis_rift_SEOBNRv5PHM.yaml**: RIFT with SEOBNRv5PHM waveform
-- **analysis_rift_NRSur7dq4.yaml**: RIFT with NRSur7dq4 waveform
-- **bilby analyses**: Bilby with various waveforms (for cross-validation)
+* `o4b-production.yaml <https://git.ligo.org/asimov/data/-/blob/main/analyses/get-data/o4b-production.yaml?ref_type=heads>`_: This blueprint provides analyses to retrieve calibration and the online PE results (needed to set priors)
+* `pe-configurator/standard.yaml <https://git.ligo.org/asimov/data/-/blob/main/analyses/pe-configurator/standard.yaml>`_: PE configurator settings needed to set the priors
+* `bayeswave-psd/standard-settings.yaml <https://git.ligo.org/asimov/data/-/blob/main/analyses/bayeswave-psd/standard-settings.yaml>`_: Bayeswave PSD settings
+* `analysis_rift_SEOBNRv5PHM.yaml`: RIFT with SEOBNRv5PHM waveform
+* `analysis_rift_NRSur7dq4.yaml`: RIFT with NRSur7dq4 waveform
+* `bilby analyses`: Bilby with various waveforms (for cross-validation)
 
 Stage 8: Event Loop
 ^^^^^^^^^^^^^^^^^^

docs/source/api_reference/asimov/asimov_simple.rst

@@ -138,7 +138,7 @@ Label to Argument Mapping (rift.ini)
 
 The authoritative ``rift.ini`` template is located at:
 
-`MonteCarloMarginalizeCode/Code/RIFT/asimov/rift.ini <https://github.com/oshaughnessy-junior/research-projects-rit/blob/main/MonteCarloMarginalizeCode/Code/RIFT/asimov/rift.ini>`_ in this repository.
+`MonteCarloMarginalizeCode/Code/RIFT/asimov/rift.ini <https://github.com/oshaughnessy-junior/research-projects-rit/blob/rift_O4d_junior/MonteCarloMarginalizeCode/Code/RIFT/asimov/rift.ini>`_ in this repository.
 
 .. _asimov-rift-example:
 

docs/source/api_reference/calmarg.rst

@@ -0,0 +1,19 @@
+Calibration Marginalization API Reference
+===========================================
+
+This module provides tools for performing calibration marginalization in RIFT, allowing for the estimation of parameters while accounting for uncertainty in the calibration.
+
+.. automodule:: RIFT.calmarg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: RIFT.calmarg.generate_realizations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. automodule:: RIFT.calmarg.rift_source
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/calmarg/index.rst

@@ -1,7 +1 @@
-Calibration Marginalization
-===========================
-
-.. automodule:: RIFT.calmarg
-   :members:
-   :undoc-members:
-   :show-inheritance:
+.. include:: ../calmarg.rst

docs/source/api_reference/index.rst

@@ -14,7 +14,7 @@ Core RIFT Modules
    plot_utilities/index
    simulation_manager/index
    asimov/index
-   calmarg/index
+   calmarg
    misc/index
    lalsimutils
 

docs/source/api_reference/physics/EOBTidalExternal.rst

@@ -0,0 +1,7 @@
+EOBTidalExternal API Reference
+==============================
+
+.. automodule:: RIFT.physics.EOBTidalExternal
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/EOBTidalExternalC.rst

@@ -0,0 +1,7 @@
+EOBTidalExternalC API Reference
+================================
+
+.. automodule:: RIFT.physics.EOBTidalExternalC
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/EOSManager.rst

@@ -0,0 +1,7 @@
+EOSManager API Reference
+==========================
+
+.. automodule:: RIFT.physics.EOSManager
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/MonotonicSpline.rst

@@ -0,0 +1,7 @@
+MonotonicSpline API Reference
+===============================
+
+.. automodule:: RIFT.physics.MonotonicSpline
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/PrecessingFisherMatrix.rst

@@ -0,0 +1,7 @@
+PrecessingFisherMatrix API Reference
+======================================
+
+.. automodule:: RIFT.physics.PrecessingFisherMatrix
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/ROMWaveformManager.rst

@@ -0,0 +1,7 @@
+ROMWaveformManager API Reference
+==================================
+
+.. automodule:: RIFT.physics.ROMWaveformManager
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/effectiveFisher.rst

@@ -0,0 +1,7 @@
+Effective Fisher API Reference
+================================
+
+.. automodule:: RIFT.physics.effectiveFisher
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/api_reference/physics/index.rst

@@ -1,7 +1,14 @@
-Physics Utilities
-==================
+Physics API Reference
+=====================
 
-.. automodule:: RIFT.physics
-   :members:
-   :undoc-members:
-   :show-inheritance:
+.. toctree::
+   :maxdepth: 1
+
+   EOBTidalExternal
+   EOBTidalExternalC
+   EOSManager
+   GWSignal
+   MonotonicSpline
+   PrecessingFisherMatrix
+   ROMWaveformManager
+   effectiveFisher