Merge branch 'tardis-sn:master' into gsoc

tardis-sn · Apr 12, 2024 · ac783bd · ac783bd
2 parents d3fb7c1 + 28caa4e
commit ac783bd
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diff --git a/.zenodo.json b/.zenodo.json
@@ -173,13 +173,13 @@
       "orcid": "0000-0002-2328-8030"
     },
     {
-      "name": "Bartnik, Matthew"
+      "name": "Kumar, Ansh"
     },
     {
-      "name": "Alam, Arib"
+      "name": "Bartnik, Matthew"
     },
     {
-      "name": "Kumar, Ansh"
+      "name": "Alam, Arib"
     },
     {
       "name": "Varma Buddaraju, Rohith"
@@ -191,54 +191,57 @@
       "name": "Livneh, Ran"
     },
     {
-      "name": "Kambham, Satwik"
+      "name": "Dutta, Anirban"
     },
     {
-      "name": "Dutta, Anirban"
+      "name": "Kambham, Satwik"
     },
     {
-      "name": "Lu, Jing"
+      "name": "Rajagopalan, Srinath"
     },
     {
-      "name": "Daksh, Ayushi"
+      "name": "Lu, Jing"
     },
     {
       "name": "Mishra, Sashank",
       "orcid": "0000-0001-8302-1584"
     },
     {
-      "name": "Rajagopalan, Srinath"
+      "name": "Daksh, Ayushi"
     },
     {
-      "name": "Jain, Rinkle"
+      "name": "Visser, Erin"
     },
     {
-      "name": "Floers, Andreas"
+      "name": "Jain, Rinkle"
     },
     {
       "name": "Reichenbach, John"
     },
     {
-      "name": "Actions, GitHub"
+      "name": "Floers, Andreas"
     },
     {
       "name": "Bhakar, Jayant"
     },
     {
-      "name": "Brar, Antreev"
+      "name": "Actions, GitHub"
     },
     {
-      "name": "Singh, Sourav"
+      "name": "Brar, Antreev"
     },
     {
       "name": "Chaumal, Aarya"
     },
     {
-      "name": "Matsumura, Yuki"
+      "name": "Singh, Sourav"
     },
     {
       "name": "Kumar, Aman"
     },
+    {
+      "name": "Matsumura, Yuki"
+    },
     {
       "name": "Patidar, Abhishek"
     },
@@ -248,60 +251,60 @@
     {
       "name": "Srivastava, Sarthak"
     },
-    {
-      "name": "Sofiatti, Caroline"
-    },
     {
       "name": "Talegaonkar, Chinmay"
     },
     {
-      "name": "Gupta, Harshul"
+      "name": "Selsing, Jonatan"
     },
     {
-      "name": "Visser, Erin"
+      "name": "Gupta, Harshul"
     },
     {
-      "name": "Selsing, Jonatan"
+      "name": "Sofiatti, Caroline"
     },
     {
-      "name": "Patra, Nilesh"
+      "name": "Gupta, Sumit"
     },
     {
-      "name": "Venkat, Shashank"
+      "name": "Yap, Kevin"
     },
     {
-      "name": "Patel, Pratik"
+      "name": "Truong, Le"
     },
     {
-      "name": "Volodin, Dmitry"
+      "name": "Sandler, Morgan"
     },
     {
-      "name": "Singh Rathore, Parikshit"
+      "name": "Zaheer, Musabbiha"
     },
     {
-      "name": "Sandler, Morgan"
+      "name": "Sarafina, Nance"
     },
     {
-      "name": "Sarafina, Nance"
+      "name": "Patra, Nilesh"
     },
     {
-      "name": "Zaheer, Musabbiha"
+      "name": "Singh Rathore, Parikshit"
     },
     {
-      "name": "Truong, Le"
+      "name": "Patel, Pratik"
     },
     {
-      "name": "Yap, Kevin"
+      "name": "Sharma, Sampark"
     },
     {
-      "name": "Gupta, Suyash"
+      "name": "Venkat, Shashank"
     },
     {
       "name": "Prasad, Shilpi"
     },
     {
       "name": "Buchner, Johannes"
     },
+    {
+      "name": "Gupta, Suyash"
+    },
     {
       "name": "Lemoine, Thom"
     },
@@ -312,7 +315,7 @@
       "name": "Aggarwal, Yash"
     },
     {
-      "name": "Sharma, Sampark"
+      "name": "Volodin, Dmitry"
     },
     {
       "name": "Dasgupta, Debajyoti"

diff --git a/docs/conf.py b/docs/conf.py
@@ -350,7 +350,7 @@ def generate_tutorials_page(app):
 
     for root, dirs, fnames in os.walk("io/"):
         for fname in fnames:
-            if fname.endswith(".ipynb") and "checkpoint" not in fname:
+            if fname.startswith("tutorial_") and fname.endswith(".ipynb") and "checkpoint" not in fname:
                 notebooks += f"\n* :doc:`{root}/{fname[:-6]}`"
 
     title = "Tutorials\n*********\n"
@@ -359,6 +359,21 @@ def generate_tutorials_page(app):
     with open("tutorials.rst", mode="wt", encoding="utf-8") as f:
         f.write(f"{title}\n{description}\n{notebooks}")
 
+def generate_how_to_guides_page(app):
+    """Create how_to_guides.rst"""
+    notebooks = ""
+
+    for root, dirs, fnames in os.walk("io/"):
+        for fname in fnames:
+            if fname.startswith("how_to_") and fname.endswith(".ipynb") and "checkpoint" not in fname:
+                notebooks += f"\n* :doc:`{root}/{fname[:-6]}`"
+
+    title = "How-To Guides\n*********\n"
+    description = "The following pages contain the TARDIS how-to guides:"
+
+    with open("how_to_guides.rst", mode="wt", encoding="utf-8") as f:
+        f.write(f"{title}\n{description}\n{notebooks}")
+
 
 def autodoc_skip_member(app, what, name, obj, skip, options):
     """Exclude specific functions/methods from the documentation"""
@@ -397,5 +412,6 @@ def create_redirect_files(app, docname):
 
 def setup(app):
     app.connect("builder-inited", generate_tutorials_page)
+    app.connect("builder-inited", generate_how_to_guides_page)
     app.connect("autodoc-skip-member", autodoc_skip_member)
     app.connect("build-finished", create_redirect_files)
diff --git a/docs/index.rst b/docs/index.rst
@@ -54,6 +54,7 @@ Mission Statement
     installation
     quickstart
     tutorials
+    how_to_guides
     faq
     API <api/modules>
 

diff --git a/...io/configuration/read_configuration.ipynb → ...uration/tutorial_read_configuration.ipynb b/...io/configuration/read_configuration.ipynb → ...uration/tutorial_read_configuration.ipynb
diff --git a/docs/io/grid/TardisGridTutorial.ipynb → docs/io/grid/how_to_TardisGridTutorial.ipynb b/docs/io/grid/TardisGridTutorial.ipynb → docs/io/grid/how_to_TardisGridTutorial.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Running TARDIS Model Grids\n",
+    "# How to Run TARDIS Model Grids\n",
     "\n",
     "This notebook demonstrates the capabilities of the TARDIS grid. The grid facilitates users running large numbers of TARDIS simulations."
    ]

diff --git a/docs/io/images/energy_level_widget_demo.gif b/docs/io/images/energy_level_widget_demo.gif
diff --git a/docs/io/images/energy_level_widget_options.gif b/docs/io/images/energy_level_widget_options.gif
diff --git a/docs/io/model/read_cmfgen_model.ipynb → docs/io/model/how_to_read_cmfgen_model.ipynb b/docs/io/model/read_cmfgen_model.ipynb → docs/io/model/how_to_read_cmfgen_model.ipynb
@@ -1,12 +1,10 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "# Reading CMFGEN models with TARDIS"
+    "# How to Read CMFGEN models with TARDIS"
    ]
   },
   {

diff --git a/docs/io/model/read_stella_model.ipynb → docs/io/model/how_to_read_stella_model.ipynb b/docs/io/model/read_stella_model.ipynb → docs/io/model/how_to_read_stella_model.ipynb
@@ -5,7 +5,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Reading STELLA models with TARDIS"
+    "# How to Read STELLA models with TARDIS"
    ]
   },
   {

diff --git a/docs/io/optional/custom_source.ipynb → docs/io/optional/how_to_custom_source.ipynb b/docs/io/optional/custom_source.ipynb → docs/io/optional/how_to_custom_source.ipynb
@@ -5,7 +5,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Running TARDIS with a Custom Packet Source\n"
+    "# How to Run TARDIS with a Custom Packet Source\n"
    ]
   },
   {

diff --git a/docs/io/optional/callback_example.ipynb → .../optional/tutorial_callback_example.ipynb b/docs/io/optional/callback_example.ipynb → .../optional/tutorial_callback_example.ipynb
diff --git a/docs/io/optional/logging_configuration.ipynb → ...onal/tutorial_logging_configuration.ipynb b/docs/io/optional/logging_configuration.ipynb → ...onal/tutorial_logging_configuration.ipynb
diff --git a/docs/io/output/physical_quantities.ipynb → ...o/output/how_to_physical_quantities.ipynb b/docs/io/output/physical_quantities.ipynb → ...o/output/how_to_physical_quantities.ipynb
@@ -6,7 +6,7 @@
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    "# Accessing Physical Quantities"
+    "# How to Access Physical Quantities"
    ]
   },
   {
@@ -24,7 +24,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Runing in interactive Python session"
+    "### Running an interactive Python session"
    ]
   },
   {

diff --git a/docs/io/output/plasma_graph.ipynb → docs/io/output/how_to_plasma_graph.ipynb b/docs/io/output/plasma_graph.ipynb → docs/io/output/how_to_plasma_graph.ipynb
@@ -5,7 +5,7 @@
    "id": "c7835cf9",
    "metadata": {},
    "source": [
-    "# Generating the Plasma Graph"
+    "# How to Generate the Plasma Graph"
    ]
   },
   {

diff --git a/docs/io/output/rpacket_tracking.ipynb → docs/io/output/how_to_rpacket_tracking.ipynb b/docs/io/output/rpacket_tracking.ipynb → docs/io/output/how_to_rpacket_tracking.ipynb
@@ -6,7 +6,7 @@
    "id": "f57cd4fe",
    "metadata": {},
    "source": [
-    "# Tracking the Properties of Real Packets"
+    "# How to Track the Properties of Real Packets"
    ]
   },
   {

diff --git a/docs/io/output/to_hdf.ipynb → docs/io/output/how_to_to_hdf.ipynb b/docs/io/output/to_hdf.ipynb → docs/io/output/how_to_to_hdf.ipynb
@@ -7,7 +7,7 @@
     "raw_mimetype": "text/restructuredtext"
    },
    "source": [
-    "# Storing Simulations to HDF\n",
+    "# How to Store Simulations to HDF\n",
     "\n",
     "You can ask TARDIS to store the state of each iteration of the simulation you are running. We show examples of how this is done:"
    ]

diff --git a/docs/io/visualization/abundance_widget.ipynb → ...sualization/how_to_abundance_widget.ipynb b/docs/io/visualization/abundance_widget.ipynb → ...sualization/how_to_abundance_widget.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Generating Custom Abundance Widget"
+    "# How to Generate Custom Abundance Widget"
    ]
   },
   {