Merge pull request #369 from duncan-brown/cleanup

Merging so I can work on some other dependencies for 1.2.0 release.
gwastro · Sep 27, 2015 · c790a8a · c790a8a
2 parents 1d5e9e6 + b55adcb
commit c790a8a
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diff --git a/bin/hdfcoinc/pycbc_coinc_mergetrigs b/bin/hdfcoinc/pycbc_coinc_mergetrigs
diff --git a/bin/hdfcoinc/pycbc_distribute_background_bins b/bin/hdfcoinc/pycbc_distribute_background_bins
diff --git a/bin/hdfcoinc/pycbc_make_hdf_coinc_workflow → ...hdfcoinc/pycbc_make_coinc_search_workflow b/bin/hdfcoinc/pycbc_make_hdf_coinc_workflow → ...hdfcoinc/pycbc_make_coinc_search_workflow
diff --git a/bin/hdfcoinc/pycbc_page_recovery b/bin/hdfcoinc/pycbc_page_recovery
diff --git a/bin/hdfcoinc/pycbc_page_segments b/bin/hdfcoinc/pycbc_page_segments
diff --git a/bin/hdfcoinc/pycbc_page_segplot b/bin/hdfcoinc/pycbc_page_segplot
diff --git a/bin/hdfcoinc/pycbc_plot_hist b/bin/hdfcoinc/pycbc_plot_hist
diff --git a/bin/hdfcoinc/pycbc_strip_injections b/bin/hdfcoinc/pycbc_strip_injections
diff --git a/bin/hwinj/pycbc_generate_hwinj b/bin/hwinj/pycbc_generate_hwinj
diff --git a/bin/hwinj/pycbc_generate_hwinj_from_xml b/bin/hwinj/pycbc_generate_hwinj_from_xml
diff --git a/bin/hwinj/pycbc_plot_hwinj b/bin/hwinj/pycbc_plot_hwinj
diff --git a/bin/minifollowups/pycbc_page_coincinfo b/bin/minifollowups/pycbc_page_coincinfo
diff --git a/bin/minifollowups/pycbc_plot_trigger_timeseries b/bin/minifollowups/pycbc_plot_trigger_timeseries
diff --git a/bin/mvsc/pycbc_mvsc_dag b/bin/mvsc/pycbc_mvsc_dag
diff --git a/bin/mvsc/pycbc_mvsc_get_features b/bin/mvsc/pycbc_mvsc_get_features
diff --git a/bin/mvsc/pycbc_mvsc_update_sql b/bin/mvsc/pycbc_mvsc_update_sql
diff --git a/bin/pycbc_fit_sngl_trigs b/bin/pycbc_fit_sngl_trigs
diff --git a/bin/pycbc_make_coinc_workflow → bin/pycbc_make_coinc_pipedown_workflow b/bin/pycbc_make_coinc_workflow → bin/pycbc_make_coinc_pipedown_workflow
diff --git a/bin/pycbc_make_html_page b/bin/pycbc_make_html_page
diff --git a/bin/pycbc_optimal_snr b/bin/pycbc_optimal_snr
diff --git a/bin/pygrb/pygrb_make_summary_page → bin/pygrb/pycbc_make_grb_summary_page b/bin/pygrb/pygrb_make_summary_page → bin/pygrb/pycbc_make_grb_summary_page
diff --git a/bin/pygrb/pygrb_make_offline_workflow → bin/pygrb/pycbc_make_offline_grb_workflow b/bin/pygrb/pygrb_make_offline_workflow → bin/pygrb/pycbc_make_offline_grb_workflow
@@ -25,7 +25,7 @@ import pycbc.version
 __author__ = "Andrew Williamson <andrew.williamson@ligo.org>"
 __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
diff --git a/bin/sngl/pycbc_plot_bank b/bin/sngl/pycbc_plot_bank
diff --git a/bin/sngl/pycbc_plot_glitchgram b/bin/sngl/pycbc_plot_glitchgram
diff --git a/bin/sngl/pycbc_plot_histogram b/bin/sngl/pycbc_plot_histogram
diff --git a/bin/sngl/pycbc_plot_params b/bin/sngl/pycbc_plot_params
diff --git a/bin/sngl/pycbc_plot_rates b/bin/sngl/pycbc_plot_rates
diff --git a/bin/sngl/pycbc_plot_timeseries b/bin/sngl/pycbc_plot_timeseries
diff --git 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
@@ -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
@@ -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 → ...ow/pycbc_make_coinc_pipedown_workflow.rst b/docs/workflow/pycbc_make_coinc_workflow.rst → ...ow/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
@@ -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 <https://github.com/a-r-williamson/pycbc/tree/pygrb_dev>`_
-
-    **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
@@ -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
@@ -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']