Merge pull request #39 from j-andrews7/0.4.1

v0.4.1 changes

Author: j-andrews7

Diff for: README.md

@@ -253,7 +253,7 @@ The database file uses same format as for the standard `strprofiler` command.
 Then create a requirements.txt file in the same directory with `strprofiler` listed:
 
 ```
-strprofiler>=0.4.0
+strprofiler>=0.4.1
 ```
 
 This app can then be deployed to any of the above endpoints as [one would with any other Shiny app](https://shiny.posit.co/py/docs/deploy.html), e.g.:
@@ -279,7 +279,7 @@ It is released with zero warranty for any purpose and the authors retain no liab
 
 If you use **STRprofiler** in your research, please cite the DOI:
 
-Jared Andrews, Mike Lloyd, & Sam Culley. (2024). j-andrews7/strprofiler: v0.4.0 (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.7348386
+Jared Andrews, Mike Lloyd, & Sam Culley. (2024). j-andrews7/strprofiler: v0.4.1 (v0.4.1). Zenodo. https://doi.org/10.5281/zenodo.7348386
 
 If you use the `clastr` command or functionality from the Shiny application, please cite the Cellosaurus and CLASTR publications:
 

Diff for: app.py

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "strprofiler"
-version = "0.4.0"
+version = "0.4.1"
 description = "A python package, CLI tool, and Shiny application to compare short tandem repeat (STR) profiles."
 authors = ["Jared Andrews <[email protected]>",
            "Mike Lloyd <[email protected]>"]

Diff for: pyproject.toml

@@ -487,10 +487,31 @@ def create_app(db=None):
                 ),
             ),
             ui.nav_spacer(),
+            ui.nav_control(
+                ui.a(
+                    ui.p("Docs"),
+                    href="https://strprofiler.readthedocs.io/en/latest/",
+                    target="_blank",
+                ),
+            ),
+            ui.nav_control(
+                ui.a(
+                    ui.p("Package & CLI"),
+                    href="https://pypi.org/project/strprofiler/",
+                    target="_blank",
+                ),
+            ),
+            ui.nav_control(
+                ui.a(
+                    ui.span(ui.p("Bug Reports")),
+                    href="https://github.com/j-andrews7/strprofiler/issues/",
+                    target="_blank",
+                ),
+            ),
             ui.nav_control(
                 ui.a(
                     icon_svg("github", width="30px"),
-                    href="https://github.com/j-andrews7/strprofiler",
+                    href="https://github.com/j-andrews7/strprofiler/",
                     target="_blank",
                 ),
             ),

Diff for: strprofiler/shiny_app/shiny_app.py

@@ -1775,13 +1775,20 @@ <h2>Batch Query Specific</h2>
 <hr />
 </div>
 </div>
+<div id="python-package-cli" class="section level1">
+<h1>Python Package &amp; CLI</h1>
+<p><strong>STRprofiler</strong> also has a command line interface
+through a python package available from <a href="https://pypi.org/project/strprofiler/">PyPI</a>. The full docs are
+available on <a href="https://strprofiler.readthedocs.io/en/latest/">ReadTheDocs</a>.</p>
+<hr />
+</div>
 <div id="references" class="section level1">
 <h1>References</h1>
 <p><code>STRprofiler</code> is provided under the MIT license. If you
 use this app in your research please cite:<br />
 Jared Andrews, Mike Lloyd, &amp; Sam Culley. (2024).
 <a href="https://github.com/j-andrews7/strprofiler" target="_blank">j-andrews7/strprofiler</a>:
-v0.4.0. Zenodo.
+v0.4.1. Zenodo.
 <a href="https://doi.org/10.5281/zenodo.10544686" target="_blank">https://doi.org/10.5281/zenodo.10544686</a></p>
 <p>Bairoch A. (2018) The Cellosaurus, a cell line knowledge resource.
 Journal of Biomolecular Techniques. 29:25-38. DOI:

Diff for: strprofiler/shiny_app/www/help.html

@@ -134,10 +134,17 @@ Users can upload custom database files. The files must be in CSV format. A 'Samp
 
 ---
 
+# Python Package & CLI
+
+**STRprofiler** also has a command line interface through a python package available from [PyPI](https://pypi.org/project/strprofiler/).
+The full docs are available on [ReadTheDocs](https://strprofiler.readthedocs.io/en/latest/).
+
+---
+
 # References
 
 `STRprofiler` is provided under the MIT license. If you use this app in your research please cite:    
-Jared Andrews, Mike Lloyd, & Sam Culley. (2024). <a href="https://github.com/j-andrews7/strprofiler" target="_blank">j-andrews7/strprofiler</a>: v0.4.0. Zenodo. <a href="https://doi.org/10.5281/zenodo.10544686" target="_blank">https://doi.org/10.5281/zenodo.10544686</a>
+Jared Andrews, Mike Lloyd, & Sam Culley. (2024). <a href="https://github.com/j-andrews7/strprofiler" target="_blank">j-andrews7/strprofiler</a>: v0.4.1. Zenodo. <a href="https://doi.org/10.5281/zenodo.10544686" target="_blank">https://doi.org/10.5281/zenodo.10544686</a>
 
 Bairoch A. (2018) The Cellosaurus, a cell line knowledge resource. Journal of Biomolecular Techniques. 29:25-38. DOI: 10.7171/jbt.18-2902-002; PMID: 29805321 
 

Diff for: strprofiler/shiny_app/www/help.md

@@ -406,11 +406,16 @@ def make_summary(
         + ": "
         + samp_df["tanabe_score"].round(decimals=2).astype(str).iloc[1]
     )
-    next_hit = (
-        samp_df["Sample"].iloc[2]
-        + ": "
-        + samp_df["tanabe_score"].round(decimals=2).astype(str).iloc[2]
-    )
+    
+    # Check if there is a next hit and include it if so.
+    if len(samp_df) > 2:
+        next_hit = (
+            samp_df["Sample"].iloc[2]
+            + ": "
+            + samp_df["tanabe_score"].round(decimals=2).astype(str).iloc[2]
+        )
+    else:
+        next_hit = ""
 
     masters_q_match = samp_df[samp_df["masters_query_score"] >= mas_q_threshold]
     masters_q_out = (