From 51977e921c07c5ef4e04aaec9358208a0bf97241 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Fri, 15 Jul 2022 10:59:28 +0200
Subject: [PATCH] Address referee comments

---
 README.md              | 53 ++++++++++++++++++++++++++++++++++++++++++
 setup.py               |  9 ++++++-
 tests/test_metadata.py |  4 ++++
 3 files changed, 65 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 666da20..fd041cd 100644
--- a/README.md
+++ b/README.md
@@ -4,3 +4,56 @@
 The Scintillation Pipeline produces from LOFAR scintillation dataproducts a set of previews and metadata
 able to describe the observation characteristics.
 
+
+## Install the tool locally
+To use the tool to inspect a Dynspec dataset locally you can install it
+by executing the following command
+
+```bash
+python setup.py install 
+```
+
+It is suggested to run it in a virtualenv 
+
+## How to run the command
+Once installed you can find the help of the command by typing:
+```bash
+$ scintillation_utils.py --help
+usage: scintillation_utils.py [-h] [--samples_size SAMPLES_SIZE] [--averaging_window AVERAGING_WINDOW] [--export_only_station EXPORT_ONLY_STATION] scintillation_dataset output_directory
+
+Scintillation averaging script
+
+positional arguments:
+  scintillation_dataset
+                        Scintillation dataset [e.g. Dynspec_rebinned_L271905_SAP000.h5]
+  output_directory      Output directory
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --samples_size SAMPLES_SIZE
+                        Samples size in seconds
+  --averaging_window AVERAGING_WINDOW
+                        Averaging window in seconds
+  --export_only_station EXPORT_ONLY_STATION
+```
+
+For example if you want to process the dataset **dynspec.h5** and save the result in a directory named 
+**out_dynspect** you can just run the command
+```bash
+$ scintillation_utils.py dynspec.h5 out_dynspect
+```
+
+## How to run the pipeline
+
+If you want to run the CWL pipeline to dowload and process the dataset this is the command to execute
+
+```bash
+cwltool cwl/scintillation_preview_generation.cwl --surls srm://lta_site_url/path/filename.tar 
+```
+Other optional parameters can be specified a description is printed by executing the command
+
+```bash
+cwltool cwl/scintillation_preview_generation.cwl --help 
+```
+_Note that to download the data from srm url you use a GRID proxy.
+Check this [link](https://drupal.star.bnl.gov/STAR/book/export/html/3182) for reference._
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 32c1890..917e157 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,11 @@
 import setuptools
 from setuptools import setup
+import os
+
+requirements_file_path = os.path.join(os.path.dirname(__file__), 'requirements.txt')
+install_requires = []
+with open(requirements_file_path, 'r') as f_in:
+    install_requires = f_in.read().split('\n')
 
 setup(
     name='scintillation_tools',
@@ -11,5 +17,6 @@ setup(
     author_email='mancini@astron.nl',
     description='Utils to process scintillation h5 files',
     test_suite='tests',
-    scripts=['bin/scintillation_utils.py']
+    scripts=['bin/scintillation_utils.py'],
+    install_requires=install_requires
 )
diff --git a/tests/test_metadata.py b/tests/test_metadata.py
index 77c0064..9a61b5c 100644
--- a/tests/test_metadata.py
+++ b/tests/test_metadata.py
@@ -20,6 +20,10 @@ class TestMetadata(unittest.TestCase):
         metadata_per_dynspec = extract_metadata(dataset)
         metadata, *_ = metadata_per_dynspec.values()
         compute_start_end_azimuth_elevation(metadata)
+        self.assertIn('point_start_azimuth', metadata)
+        self.assertIn('point_start_elevation', metadata)
+        self.assertIn('point_end_azimuth', metadata)
+        self.assertIn('point_end_elevation', metadata)
 
     @unittest.skipUnless(is_test_data_present(), 'test data is missing')
     def test_fields_name(self):
-- 
GitLab