diff --git a/bin/hdfcoinc/pycbc_coinc_mergetrigs b/bin/hdfcoinc/pycbc_coinc_mergetrigs old mode 100755 new mode 100644 diff --git a/bin/hdfcoinc/pycbc_distribute_background_bins b/bin/hdfcoinc/pycbc_distribute_background_bins old mode 100755 new mode 100644 diff --git a/bin/hdfcoinc/pycbc_make_hdf_coinc_workflow b/bin/hdfcoinc/pycbc_make_coinc_search_workflow similarity index 100% rename from bin/hdfcoinc/pycbc_make_hdf_coinc_workflow rename to bin/hdfcoinc/pycbc_make_coinc_search_workflow diff --git a/bin/hdfcoinc/pycbc_page_recovery b/bin/hdfcoinc/pycbc_page_recovery old mode 100755 new mode 100644 diff --git a/bin/hdfcoinc/pycbc_page_segments b/bin/hdfcoinc/pycbc_page_segments old mode 100755 new mode 100644 diff --git a/bin/hdfcoinc/pycbc_page_segplot b/bin/hdfcoinc/pycbc_page_segplot old mode 100755 new mode 100644 diff --git a/bin/hdfcoinc/pycbc_plot_hist b/bin/hdfcoinc/pycbc_plot_hist old mode 100755 new mode 100644 diff --git a/bin/hdfcoinc/pycbc_strip_injections b/bin/hdfcoinc/pycbc_strip_injections old mode 100755 new mode 100644 diff --git a/bin/hwinj/pycbc_generate_hwinj b/bin/hwinj/pycbc_generate_hwinj old mode 100755 new mode 100644 diff --git a/bin/hwinj/pycbc_generate_hwinj_from_xml b/bin/hwinj/pycbc_generate_hwinj_from_xml old mode 100755 new mode 100644 diff --git a/bin/hwinj/pycbc_plot_hwinj b/bin/hwinj/pycbc_plot_hwinj old mode 100755 new mode 100644 diff --git a/bin/minifollowups/pycbc_page_coincinfo b/bin/minifollowups/pycbc_page_coincinfo old mode 100755 new mode 100644 diff --git a/bin/minifollowups/pycbc_plot_trigger_timeseries b/bin/minifollowups/pycbc_plot_trigger_timeseries old mode 100755 new mode 100644 diff --git a/bin/mvsc/pycbc_mvsc_dag b/bin/mvsc/pycbc_mvsc_dag old mode 100755 new mode 100644 diff --git a/bin/mvsc/pycbc_mvsc_get_features b/bin/mvsc/pycbc_mvsc_get_features old mode 100755 new mode 100644 diff --git a/bin/mvsc/pycbc_mvsc_update_sql b/bin/mvsc/pycbc_mvsc_update_sql old mode 100755 new mode 100644 diff --git a/bin/pycbc_fit_sngl_trigs b/bin/pycbc_fit_sngl_trigs old mode 100755 new mode 100644 diff --git a/bin/pycbc_make_coinc_workflow b/bin/pycbc_make_coinc_pipedown_workflow similarity index 100% rename from bin/pycbc_make_coinc_workflow rename to bin/pycbc_make_coinc_pipedown_workflow diff --git a/bin/pycbc_make_html_page b/bin/pycbc_make_html_page old mode 100755 new mode 100644 diff --git a/bin/pycbc_optimal_snr b/bin/pycbc_optimal_snr old mode 100755 new mode 100644 diff --git a/bin/pygrb/pygrb_make_summary_page b/bin/pygrb/pycbc_make_grb_summary_page old mode 100755 new mode 100644 similarity index 100% rename from bin/pygrb/pygrb_make_summary_page rename to bin/pygrb/pycbc_make_grb_summary_page diff --git a/bin/pygrb/pygrb_make_offline_workflow b/bin/pygrb/pycbc_make_offline_grb_workflow old mode 100755 new mode 100644 similarity index 99% rename from bin/pygrb/pygrb_make_offline_workflow rename to bin/pygrb/pycbc_make_offline_grb_workflow index eb9ff9d4743..4ac063de6bb --- a/bin/pygrb/pygrb_make_offline_workflow +++ b/bin/pygrb/pycbc_make_offline_grb_workflow @@ -25,7 +25,7 @@ import pycbc.version __author__ = "Andrew Williamson " __version__ = pycbc.version.git_verbose_msg __date__ = pycbc.version.date -__program__ = "pygrb_make_offline_workflow" +__program__ = "pycbc_make_offline_grb_workflow" import shutil import os diff --git a/bin/sngl/pycbc_ligolw_cluster b/bin/sngl/pycbc_ligolw_cluster old mode 100755 new mode 100644 diff --git a/bin/sngl/pycbc_plot_bank b/bin/sngl/pycbc_plot_bank old mode 100755 new mode 100644 diff --git a/bin/sngl/pycbc_plot_glitchgram b/bin/sngl/pycbc_plot_glitchgram old mode 100755 new mode 100644 diff --git a/bin/sngl/pycbc_plot_histogram b/bin/sngl/pycbc_plot_histogram old mode 100755 new mode 100644 diff --git a/bin/sngl/pycbc_plot_params b/bin/sngl/pycbc_plot_params old mode 100755 new mode 100644 diff --git a/bin/sngl/pycbc_plot_rates b/bin/sngl/pycbc_plot_rates old mode 100755 new mode 100644 diff --git a/bin/sngl/pycbc_plot_timeseries b/bin/sngl/pycbc_plot_timeseries old mode 100755 new mode 100644 diff --git a/docs/workflow.rst b/docs/workflow.rst index 0d784ffdb53..6f4bd3a81f1 100644 --- a/docs/workflow.rst +++ b/docs/workflow.rst @@ -39,9 +39,9 @@ in the source tree under:: These examples are described in each section below ------------------------------ -``pycbc_make_coinc_workflow`` ------------------------------ +-------------------------------------- +``pycbc_make_coinc_pipedown_workflow`` +-------------------------------------- This is an example of how to run a coincidence workflow, mimicking standard ihope coincidence analysis as closely as possible. It calls into pipedown to do the post-processing and using `lalapps_write_ihope_page` to make an output html page. In total this will: @@ -63,7 +63,7 @@ More details of how to run this is found in the following link: .. toctree:: :maxdepth: 1 - workflow/pycbc_make_coinc_workflow + workflow/pycbc_make_coinc_pipedown_workflow ---------------------------- ``pycbc_make_sngl_workflow`` diff --git a/docs/workflow/hdf_coincidence.rst b/docs/workflow/hdf_coincidence.rst index 8bb12df899a..597fc809715 100644 --- a/docs/workflow/hdf_coincidence.rst +++ b/docs/workflow/hdf_coincidence.rst @@ -153,19 +153,6 @@ Additional plots can be made by adding a tag. This works similary to the system example you can add [plot_sensitivity-mchirp], [plot_sensitivity-mtotal], and [plot_sensitivity-spin] sections to make three versions of the plot. -===================================== -Workflow Generation an Planning -===================================== - -Configure a two-detector search using a single fixed template bank for all ifos -and the entire analysis. Follow the standard module configurations up through -the inspiral stage of the workflow. - -Add '--enable-hdf-post-processing' to the 'pycbc_make_coinc_workflow' invocation and proceed with the standard instructions.:: - - pycbc_make_coinc_workflow \ - --enable-hdf-post-processing - =============================================================== Reusing data from workflow that uses some other post-processing =============================================================== diff --git a/docs/workflow/pycbc_bns_hdf_config_walkthrough.rst b/docs/workflow/pycbc_bns_hdf_config_walkthrough.rst index 672957b93c6..0062608b734 100644 --- a/docs/workflow/pycbc_bns_hdf_config_walkthrough.rst +++ b/docs/workflow/pycbc_bns_hdf_config_walkthrough.rst @@ -4,7 +4,7 @@ Walkthrough of running the PyCBC BNS focused pipeline on SUGAR First install PyCBC by following the instructions for installing PyCBC. -Now if you have a script (which includes your start/end time, the parameters you need for pycbc_make_hdf_coinc_workflow) and a config file you are ready to set up the dax and submit it. See an example of both and explanations below: +Now if you have a script (which includes your start/end time, the parameters you need for pycbc_make_coinc_search_workflow) and a config file you are ready to set up the dax and submit it. See an example of both and explanations below: :: @@ -20,7 +20,7 @@ start time of your analysis - this does not not need to be a time when the detec ``GPS_END_TIME=1102489216`` end time of your analysis -``pycbc_make_hdf_coinc_workflow \`` +``pycbc_make_coinc_search_workflow\`` executable diff --git a/docs/workflow/pycbc_make_coinc_workflow.rst b/docs/workflow/pycbc_make_coinc_pipedown_workflow.rst similarity index 96% rename from docs/workflow/pycbc_make_coinc_workflow.rst rename to docs/workflow/pycbc_make_coinc_pipedown_workflow.rst index 7770a72e6e8..7abb9b21709 100644 --- a/docs/workflow/pycbc_make_coinc_workflow.rst +++ b/docs/workflow/pycbc_make_coinc_pipedown_workflow.rst @@ -1,12 +1,12 @@ -################################################################ -``pycbc_make_coinc_workflow``: A CBC analysis workflow generator -################################################################ +######################################################################### +``pycbc_make_coinc_pipedown_workflow``: A CBC analysis workflow generator +######################################################################### =============== Introduction =============== -The executable ``pycbc_make_coinc_workflow`` is a tool used to analyse data from multiple detectors independently and then perform a coincidence test and various signal-based veto cuts and data quality cuts to determine whether or not a compact binary coalescence is present in the given data. +The executable ``pycbc_make_coinc_pipedown_workflow`` is a tool used to analyse data from multiple detectors independently and then perform a coincidence test and various signal-based veto cuts and data quality cuts to determine whether or not a compact binary coalescence is present in the given data. The output is a webpage containing the plots that can be used to understand the results of the analysis @@ -16,7 +16,7 @@ The output is a webpage containing the plots that can be used to understand the How to run ======================= -Here we document the stages needed to run ``pycbc_make_coinc_workflow`` to generate an offline matched filtered CBC search. +Here we document the stages needed to run ``pycbc_make_coinc_pipedown_workflow`` to generate an offline matched filtered CBC search. ---------------------------------------------------------------------------- The configuration file - Do you already have configuration (.ini) file(s)? @@ -57,7 +57,7 @@ An example configuration file set is found in three parts:: /src/dir/pycbc/workflow/ini_files/example_pipedown.ini /src/dir/pycbc/workflow/ini_files/example_inj.ini -These files contain all the details needed to run ``pycbc_make_coinc_workflow`` +These files contain all the details needed to run ``pycbc_make_coinc_pipedown_workflow`` .. note:: @@ -166,7 +166,7 @@ You also need to choose where the html page will be generated. For example:: If you are using locally editted or custom configuration files then you can create the workflow using:: - pycbc_make_coinc_workflow --config-files ${LOCAL_CONFIG_FILES} \ + pycbc_make_coinc_pipedown_workflow --config-files ${LOCAL_CONFIG_FILES} \ --config-overrides workflow:start-time:${GPS_START_TIME} \ workflow:end-time:${GPS_END_TIME} \ workflow:workflow-html-basedir:${HTMLDIR} \ diff --git a/docs/workflow/pygrb.rst b/docs/workflow/pygrb.rst index 2b81a9eaa00..b69d8486cd6 100644 --- a/docs/workflow/pygrb.rst +++ b/docs/workflow/pygrb.rst @@ -20,22 +20,6 @@ gamma-ray burst. The output will be a webpage containing plots and other data files that can be used to understand the results of the analysis. -.. note:: - These instructions refer to code that currently resides only in the GitHub - repository at the following link: - - `PyGRB on GitHub `_ - - **These instructions do not apply to the version of PyGRB currently on PyCBC - master branch!** - -This may be retreived by cloning the repository, for example using https:: - - git clone https://github.com/a-r-williamson/pycbc.git - cd pycbc - git checkout pygrb_dev - python setup.py install --prefix=/path/to/install/directory - .. _howtorunpygrb: ======================= @@ -47,33 +31,11 @@ Here we document the stages needed to run the triggered coherent GRB search. Once PyCBC is installed, you should be able to run the following help command for the workflow generation script:: - pygrb_make_offline_workflow --help - -This should produce a help message like the following:: - - usage: pygrb_make_offline_workflow [-h] [--version] [-d OUTPUT_DIR] - [--config-files CONFIGFILE [CONFIGFILE ...]] - [--config-overrides [SECTION:OPTION:VALUE [SECTION:OPTION:VALUE ...]]] - - optional arguments: - -h, --help show this help message and exit - --version show program's version number and exit - -d OUTPUT_DIR, --output-dir OUTPUT_DIR - Path to output directory. + pycbc_make_offline_grb_workflow --help - workflow: - Options needed for workflow setup. +This should produce a help message like the following - --config-files CONFIGFILE [CONFIGFILE ...] - List of localconfig files to be used in analysis. - --config-overrides [SECTION:OPTION:VALUE [SECTION:OPTION:VALUE ...]] - List of section,option,value combinations to add into - the configuration file. Normally the gps start and end - times might be provided this way, and user specific - locations (ie. output directories). This can also be - provided as SECTION:OPTION or SECTION:OPTION: both of - which indicate that the corresponding value is left - blank. +.. command-output:: pycbc_make_offline_grb_workflow --help This outlines the command line arguments that may be passed to the executable. The majority of options passed to the workflow will come from configuration @@ -323,7 +285,7 @@ provide this too:: If you are using locally editted or custom configuration files then you can create the workflow from within the run directory using:: - pygrb_make_offline_workflow \ + pycbc_make_offline_grb_workflow \ --config-files ${LOCAL_CONFIG_FILES} \ --config-overrides workflow:ra:${RA} \ workflow:dec:${DEC} \ diff --git a/setup.py b/setup.py index bddcfd0a77a..26a8987a6c5 100644 --- a/setup.py +++ b/setup.py @@ -386,10 +386,10 @@ def run(self): 'bin/gstlal/pycbc_compute_far_from_snr_chisq_histograms', 'bin/gstlal/pycbc_gen_ranking_data', 'bin/gstlal/pycbc_pickle_horizon_distances', - 'bin/pycbc_make_coinc_workflow', + 'bin/pycbc_make_coinc_pipedown_workflow', 'bin/pycbc_make_html_page', 'bin/pycbc_ligolw_find_playground', - 'bin/hdfcoinc/pycbc_make_hdf_coinc_workflow', + 'bin/hdfcoinc/pycbc_make_coinc_search_workflow', 'bin/hdfcoinc/pycbc_make_psd_estimation_workflow', 'bin/hdfcoinc/pycbc_calculate_psd', 'bin/hdfcoinc/pycbc_average_psd', @@ -443,8 +443,8 @@ def run(self): 'bin/pycbc_coinc_time', 'bin/hdfcoinc/pycbc_plot_background_coincs', 'bin/hdfcoinc/pycbc_plot_bank_bins', - 'bin/pygrb/pygrb_make_offline_workflow', - 'bin/pygrb/pygrb_make_summary_page', + 'bin/pygrb/pycbc_make_offline_grb_workflow', + 'bin/pygrb/pycbc_make_grb_summary_page', ], packages = [ 'pycbc', diff --git a/tools/static/hooks/hook-pycbc.py b/tools/static/hooks/hook-pycbc.py index a74ac46ec7b..48377260b8f 100644 --- a/tools/static/hooks/hook-pycbc.py +++ b/tools/static/hooks/hook-pycbc.py @@ -11,7 +11,7 @@ from PyInstaller.hooks.hookutils import (collect_data_files, collect_submodules) # Executables that need the html assets -needs_assets = ['pycbc_make_html_page', 'pycbc_make_hdf_coinc_workflow'] +needs_assets = ['pycbc_make_html_page', 'pycbc_make_coinc_search_workflow'] # Executables that need MKL needs_mkl = ['pycbc_inspiral','pycbc_single_template']