update the intro, and getting-started.md -> quick-start.md; plus seve…

…ral pre-PR updates

_files/template.md

@@ -13,7 +13,7 @@ jupyter:
 ---
 
 # Descriptive Title of the Content of the Notebook
----
+<hr style="border: 2px solid #fadbac" />
 Header Section: include the following information.
 
 - **Description:** A template on how to write a notebook tutorial on sciserver.
@@ -24,7 +24,7 @@ Header Section: include the following information.
 - **Support:** How to get help.
 - **Last verified to run:** (00/00/000) When was this last tested.
 
----
+<hr style="border: 2px solid #fadbac" />
 
 
 ## 1. Introduction
@@ -45,7 +45,7 @@ When running this notebook inside Sciserver, make sure the HEASARC data drive is
 <b>Running Outside Sciserver:</b><br>
 This notebook runs in the heasoftpy conda environment on Sciserver.
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft are correctly installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure heasoftpy and heasoft are correctly installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 

analysis-ixpe-example.md

@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** `heasoftpy`, `xspec`, `matplotlib`
 - **Credit:** Kavitha Arur (Jun 2023).
 - **Support:** Contact the [IXPE Guest Observer Facility (GOF)](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback?selected=ixpe) or the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024.
+- **Last verified to run:** 02/28/2024.
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -40,7 +40,7 @@ Also, this notebook requires <code>heasoftpy</code>, which is available in the (
 
 <b>Running Outside Sciserver:</b><br>
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft are installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure heasoftpy and heasoft are installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 

analysis-nicer-example.md

@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** `heasoftpy`, `xspec`, `astropy`, `matplotlib`
 - **Credit:** Mike Corcoran / Abdu Zoghbi (May 2022).
 - **Support:** Contact the [HEASARC helpdesk or NICER Guest Observer Facility (GOF)](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024.
+- **Last verified to run:** 02/28/2024.
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -43,7 +43,7 @@ Heasoft higher than v6.31 is required in order to be able to run <code>nicerl3</
 
 <b>Running Outside Sciserver:</b><br>
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft (higher than v6.31) are installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure heasoftpy and heasoft (higher than v6.31) are installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 <!-- #endregion -->
@@ -52,7 +52,7 @@ If running outside Sciserver, some changes will be needed, including:<br>
 We need the following python modules:
 
 <div style='color: #333; background: #ffffdf; padding:20px; border: 4px solid #fadbac'>
-Note that for heasoftpy < 1.4, <code>nicerl2</code> is accessed via <code>heasoftpy.nicerl2</code>. For heasoftpy >= 1.4, it is available under a separate module called <code>nicer</code> that needs to be imported explicitly with <code>from heasoftpy import nicer</code>
+Note that for heasoftpy < 1.4, <code>nicerl2</code> is accessed via <code>heasoftpy.nicerl2</code>. For heasoftpy >= 1.4, it is available under a separate module called <code>nicer</code> that needs to be imported explicitly.
 </div>
 
 ```python
@@ -67,11 +67,13 @@ import matplotlib.pylab as plt
 import heasoftpy as hsp
 import xspec as xs
 
-from packaging import version
-if version.parse(hsp.__version__) < version.parse('1.4'):
-    nicer = hsp
-else:
-    from heasoftpy import nicer
+# import nicer tools from heasoftpy
+# for heasoftpy version >= 1.4, they are under heasoftpy.nicer.*
+# for heasoftpy version < 1.4, they are under heasoftpy.*
+try:
+    from heasoftpy.nicer import nicerl2, nicerl3_lc, nicerl3_spect
+except (ModuleNotFoundError, ImportError):
+    from heasoftpy import nicerl2, nicerl3_lc, nicerl3_spect
 ```
 
 ## 3. Set up the NICER obsid directory
@@ -108,7 +110,7 @@ inPars = {
 }
 
 # run the task
-out = nicer.nicerl2(inPars)
+out = nicerl2(inPars)
 
 # check that everything run correctly
 if out.returncode == 0: 
@@ -160,7 +162,7 @@ inPars = {
 }
 
 # run the spectral extraction task
-out = nicer.nicerl3_spect(inPars)
+out = nicerl3_spect(inPars)
 
 # check that the task run correctly
 if out.returncode == 0: 
@@ -202,7 +204,7 @@ inPars = {
 }
 
 # run the light curve task
-out = nicer.nicerl3_lc(inPars)
+out = nicerl3_lc(inPars)
 
 # check the task runs correctly
 if out.returncode == 0: 

analysis-nustar-lightcurve.md

@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** `heasoftpy`, `numpy`, `matplotlib`
 - **Credit:** Abdu Zoghbi (Jan 2023).
 - **Support:** Contact the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024.
+- **Last verified to run:** 02/28/2024.
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -42,7 +42,7 @@ Also, this notebook requires <code>heasoftpy</code>, which is available in the (
 
 <b>Running Outside Sciserver:</b><br>
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft are installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure heasoftpy and heasoft are installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 
@@ -51,7 +51,7 @@ If running outside Sciserver, some changes will be needed, including:<br>
 We need the following python modules:
 
 <div style='color: #333; background: #ffffdf; padding:20px; border: 4px solid #fadbac'>
-Note that for heasoftpy < 1.4, <code>nupipeline</code> is accessed via <code>heasoftpy.nupipeline</code>. For heasoftpy >= 1.4, it is available under a separate module called <code>nustar</code> that needs to be imported explicitly with <code>from heasoftpy import nustar</code>
+Note that for heasoftpy < 1.4, <code>nupipeline</code> is accessed via <code>heasoftpy.nupipeline</code>. For heasoftpy >= 1.4, it is available under a separate module called <code>nustar</code> that needs to be imported explicitly.
 </div>
 
 ```python
@@ -62,11 +62,14 @@ import matplotlib.pyplot as plt
 
 import heasoftpy as hsp
 
-from packaging import version
-if version.parse(hsp.__version__) < version.parse('1.4'):
-    nustar = hsp
-else:
-    from heasoftpy import nustar
+# import nupipeline from heasoftpy
+# for heasoftpy version >= 1.4, it is under heasoftpy.nustar.nupipeline
+# for heasoftpy version < 1.4, it is under heasoftpy.nupipeline
+try:
+    from heasoftpy.nustar import nupipeline
+except ModuleNotFoundError:
+    from heasoftpy import nupipeline
+
 ```
 
 ## 3. Run the Reprocessing Pipeline
@@ -107,7 +110,7 @@ outdir = obsid + '_p/event_cl'
 stem   = 'nu' + obsid
 
 # call the tasks
-out = nustar.nupipeline(indir=indir, outdir=outdir, steminputs=stem, instrument='FPMA',
+out = nupipeline(indir=indir, outdir=outdir, steminputs=stem, instrument='FPMA',
                         clobber='yes', noprompt=True, verbose=True)
 ```
 

analysis-rxte-lightcurve.md

@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** `heasoftpy`, `pyvo`, `matplotlib`, `tqdm`
 - **Credit:** Tess Jaffe (Sep 2021). Parallelization by Abdu Zoghbi (Jan 2024)
 - **Support:** Contact the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024.
+- **Last verified to run:** 02/28/2024.
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -44,7 +44,7 @@ Also, this notebook requires <code>heasoftpy</code>, which is available in the (
 
 <b>Running Outside Sciserver:</b><br>
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft are installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure heasoftpy and heasoft are installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 

analysis-rxte-ml.md

@@ -39,7 +39,7 @@ Also, the required python modules are available in the (heasoft) conda environme
 
 <b>Running Outside Sciserver:</b><br>
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft are installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure <code>pyxspec</code> and heasoft are installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 

analysis-rxte-spectra.md

@@ -18,7 +18,7 @@ jupyter:
 - **Description:** Finding standard spectral products from RXTE.
 - **Level:** Intermediate.
 - **Data:** RXTE observations of **eta car** taken over 16 years.
-- **Requirements:** `heasoftpy`, `pyvo`, `matplotlib`, `pyxspec`
+- **Requirements:** `pyvo`, `matplotlib`, `pyxspec`
 - **Credit:** Tess Jaffe (Sep 2021).
 - **Support:** Contact the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
 - **Last verified to run:** 01/26/2024.
@@ -37,11 +37,10 @@ We first find all of the standard spectra, then use `pyxspec` to do some basic a
 <b>Running On Sciserver:</b><br>
 When running this notebook inside Sciserver, make sure the HEASARC data drive is mounted when initializing the Sciserver compute container. <a href='https://heasarc.gsfc.nasa.gov/docs/sciserver/'>See details here</a>.
 <br>
-Also, this notebook requires <code>heasoftpy</code>, which is available in the (heasoft) conda environment. You should see (heasoft) at the top right of the notebook. If not, click there and select it.
 
 <b>Running Outside Sciserver:</b><br>
 If running outside Sciserver, some changes will be needed, including:<br>
-&bull; Make sure heasoftpy and heasoft are installed (<a herf='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
+&bull; Make sure <code>pyxspec</code> and heasoft are installed (<a href='https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/'>Download and Install heasoft</a>).<br>
 &bull; Unlike on Sciserver, where the data is available locally, you will need to download the data to your machine.<br>
 </div>
 

data-access.md

@@ -12,7 +12,7 @@ jupyter:
     name: heasoft
 ---
 
-# HEASARC data access on SciServer
+# HEASARC Data Access on SciServer
 <hr style="border: 2px solid #fadbac" />
 
 - **Description:** A general overview on accessing data on Sciserver.
@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** `pyvo`.
 - **Credit:** Tess Jaffe (Sep 2021).
 - **Support:** Contact the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024.
+- **Last verified to run:** 02/28/2024.
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -30,14 +30,14 @@ jupyter:
 ## 1. Introduction
 This notebook presents a tutorial of how to access HEASARC data using the virtual observatory (VO) python client `pyvo`.
 
-We handle the general case of using the Tabel Access Protocol (TAP) to query any information about the HEASARC tables. A more specific data access tutorial when the table is known is give in the [Finding and Downloading Data notebook](data-find-download.md).
+We handle the general case of using the Tabel Access Protocol (TAP) to query any information about the HEASARC tables. A more specific data access tutorial when the table is known, is given in the [notebook on Finding and Downloading Data](data-find-download.md).
 
 The case will be illustrated by querying for XTE observations of **Eta Car** .
 
 
 <div style='color: #333; background: #ffffdf; padding:20px; border: 4px solid #fadbac'>
 <b>Running On Sciserver:</b><br>
-The notebook requires `pyvo`, and on Sciserver, it is available on the `heasoft` conda kernel. Make sure you run the notbeook using that kernel by selecting it in the top right.
+The notebook requires <code>pyvo</code>, and on Sciserver, it is available on the <code>heasoft</code> conda kernel. Make sure you run the notbeook using that kernel by selecting it in the top right.
 </div>
 
 <!-- #endregion -->
@@ -66,7 +66,7 @@ We start with the Registry of all VO services.  The HEASARC table service is usi
 
 
 ```python
-tap_services = pyvo.regsearch(servicetype='tap',keywords=['heasarc'])
+tap_services = pyvo.regsearch(servicetype='tap', keywords=['heasarc'])
 ```
 
 We then ask the service for all of the tables that are available at the HEASARC:
@@ -86,7 +86,7 @@ for tablename in heasarc_tables.keys():
 
 The `xtemaster` catalog is the one that we're interested in.  
 
-Let's see what this table has in it.  Alternatively, we can google it and find the same information here:
+Let's see what this table has in it.  The same information is availabe in the table description in the website:
 
 https://heasarc.gsfc.nasa.gov/W3Browse/all/xtemaster.html
 

data-catalog-cross-match.md

@@ -12,7 +12,7 @@ jupyter:
     name: heasoft
 ---
 
-# Searching a Large Catalog With a List of Sources
+# Query a List of Sources in a Large Catalog
 <hr style="border: 2px solid #fadbac" />
 
 - **Description:** An example of cross-matching a list of sources to data in the archive.
@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** [`pyvo`, `astropy`]".
 - **Credit:** Tess Jaffe (May 2023).
 - **Support:** Contact the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024.
+- **Last verified to run:** 02/28/2024.
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -37,7 +37,7 @@ This tutorial is a HEASARC-specific example of a more general workflow querying
 
 <div style='color: #333; background: #ffffdf; padding:20px; border: 4px solid #fadbac'>
 <b>Running On Sciserver:</b><br>
-The notebook requires `pyvo`, and on Sciserver, it is available on the `heasoft` conda kernel. Make sure you run the notbeook using that kernel by selecting it in the top right.
+The notebook requires <code>pyvo</code>, and on Sciserver, it is available on the <code>heasoft</code> conda kernel. Make sure you run the notbeook using that kernel by selecting it in the top right.
 </div>
 
 
@@ -79,7 +79,7 @@ heasarc.describe()
 
 To include our list of source with the query, VO protocols use the `VOTable`, which is both powerful and complicated.  But `astropy` has easy tools to handle it. 
 
-As we will show, when submitting that query that includes table data (the list of source coordinates in our case), these can be passed to `pyvo` as either an `astropy` table, or as a file name of the VO table in XML format.
+As we will show, when submitting a query that includes table data (the list of source coordinates in our case), these can be passed to `pyvo` as either an `astropy` table, or as a file name of the VO table in XML format.
 
 
 Typically, you may start from a list of sources you want to query. In this tutorial, we first create this list in comma-separated value (CSV) format to be used as our input. The file `source_list.csv` contains a list of 10000 RA and DEC values.

data-find-download.md

@@ -12,7 +12,7 @@ jupyter:
     name: heasoft
 ---
 
-# Finding and Downloading Data From a Source Using Python
+# Finding and Downloading Data For an Object Using Python
 <hr style="border: 2px solid #fadbac" />
 
 - **Description:** Tutorial on how to access HEASARC data using the Virtual Observatory client `pyvo`.
@@ -21,7 +21,7 @@ jupyter:
 - **Requirements:** `pyvo`.
 - **Credit:** Abdu Zoghbi (May 2022).
 - **Support:** Contact the [HEASARC helpdesk](https://heasarc.gsfc.nasa.gov/cgi-bin/Feedback).
-- **Last verified to run:** 01/26/2024
+- **Last verified to run:** 02/28/2024
 
 <hr style="border: 2px solid #fadbac" />
 
@@ -39,7 +39,7 @@ This notebook searches the NuSTAR master catalog `numaster` using pyvo. We speci
 
 <div style='color: #333; background: #ffffdf; padding:20px; border: 4px solid #fadbac'>
 <b>Running On Sciserver:</b><br>
-The notebook requires `pyvo`, and on Sciserver, it is available on the `heasoft` conda kernel. Make sure you run the notbeook using that kernel by selecting it in the top right.
+The notebook requires <code>pyvo</code>, and on Sciserver, it is available on the <code>heasoft</code> conda kernel. Make sure you run the notbeook using that kernel by selecting it in the top right.
 </div>
 
 <!-- #endregion -->
@@ -62,6 +62,8 @@ from astropy.coordinates import SkyCoord
 ## 3. Finding and Downloading the data
 This part assumes we know the ID of the VO service. Generally these are of the form: `ivo://nasa.heasarc/{table_name}`.
 
+If you don't know the name of the table, you can search the VO registry, as illustrated in the [data access notebook](data-access.md).
+
 ### 3.1 The Search Serivce
 First, we create a cone search service: