Added report execution scripts

reports/annual_category_location_heatmap.ipynb

@@ -162,7 +162,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "venv",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -180,7 +180,7 @@
   },
   "vscode": {
    "interpreter": {
-    "hash": "f085c86085609b1ab2f295d8cd5b519618e19fd591a6919f4ec2f9290a6745f6"
+    "hash": "7a792fcb311f9eb9f3c1b942a8c87ada8484712b89b670347c16a1088e0a1f69"
    }
   }
  },

reports/category_life_list.ipynb

@@ -115,7 +115,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "venv",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -133,7 +133,7 @@
   },
   "vscode": {
    "interpreter": {
-    "hash": "f085c86085609b1ab2f295d8cd5b519618e19fd591a6919f4ec2f9290a6745f6"
+    "hash": "7a792fcb311f9eb9f3c1b942a8c87ada8484712b89b670347c16a1088e0a1f69"
    }
   }
  },

reports/location_richness_map.ipynb

@@ -170,7 +170,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "venv",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -189,7 +189,7 @@
   "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
-    "hash": "f085c86085609b1ab2f295d8cd5b519618e19fd591a6919f4ec2f9290a6745f6"
+    "hash": "7a792fcb311f9eb9f3c1b942a8c87ada8484712b89b670347c16a1088e0a1f69"
    }
   }
  },

reports/requirements.txt

@@ -1,3 +1,4 @@
+ansicolors==1.1.8
 anyio==4.9.0
 appnope==0.1.4
 argon2-cffi==23.1.0
@@ -13,12 +14,14 @@ branca==0.8.1
 certifi==2025.1.31
 cffi==1.17.1
 charset-normalizer==3.4.1
+click==8.1.8
 comm==0.2.2
 contourpy==1.3.2
 cycler==0.12.1
 debugpy==1.8.14
 decorator==5.2.1
 defusedxml==0.7.1
+entrypoints==0.4
 et_xmlfile==2.0.0
 executing==2.2.0
 fastjsonschema==2.21.1
@@ -69,6 +72,7 @@ overrides==7.7.0
 packaging==24.2
 pandas==2.2.3
 pandocfilters==1.5.1
+papermill==2.6.0
 parso==0.8.4
 pexpect==4.9.0
 pillow==11.2.1
@@ -94,14 +98,17 @@ rpds-py==0.24.0
 scipy==1.15.2
 seaborn==0.13.2
 Send2Trash==1.8.3
+setuptools==80.3.1
 six==1.17.0
 sniffio==1.3.1
 soupsieve==2.6
 sqlparse==0.5.3
 stack-data==0.6.3
+tenacity==9.1.2
 terminado==0.18.1
 tinycss2==1.4.0
 tornado==6.4.2
+tqdm==4.67.1
 traitlets==5.14.3
 types-python-dateutil==2.9.0.20241206
 typing_extensions==4.13.2

reports/run_all.sh

@@ -0,0 +1,31 @@
+#!/bin/bash -f
+
+# Activate the virtual environment
+export REPORTS_ROOT=$( cd "$( dirname "$0" )" && pwd )
+. $REPORTS_ROOT/venv/bin/activate
+
+# Suppress warnings about the output file extension
+export PYTHONWARNINGS="ignore"
+
+# Define a list of notebooks to skip
+declare -a exclusions=(
+)
+
+# Get a list of Jupyter Notebooks and iterate over them
+files=$(find `pwd` -name '*.ipynb')
+while IFS= read -r file; do
+    # Get the notebook file name and extension without the path
+    filename=$(basename -- "$file")
+
+    # See if the notebook is in the exclusions list
+    found=0
+    if [[ " ${exclusions[@]} " =~ " $filename " ]]; then
+        found=1
+    fi
+
+    # If this notebook isn't in the exclusions list, run it
+    if [[ found -eq 0 ]]; then
+    echo $file
+        papermill "$file" /dev/null
+    fi
+done <<< "$files"

reports/run_notebook.sh

@@ -0,0 +1,13 @@
+#!/bin/bash -f
+
+if [[ $# -ne 1 ]]; then
+    echo Usage: run_notebook.sh NOTEBOOK
+    exit 1
+fi
+
+# Activate the virtual environment
+export REPORTS_ROOT=$( cd "$( dirname "$0" )" && pwd )
+. $REPORTS_ROOT/venv/bin/activate
+
+export PYTHONWARNINGS="ignore"
+papermill "$1" /dev/null

reports/sql/species_location.sql

@@ -0,0 +1,7 @@
+SELECT l.Name AS 'Location', sp.Name AS 'Species', c.Name AS 'Category', DATE( s.Date ) AS 'Date', IFNULL( s.Number, 1 ) AS 'Count'
+FROM SIGHTINGS s
+INNER JOIN SPECIES sp ON sp.Id = s.SpeciesId
+INNER JOIN CATEGORIES c ON c.Id = sp.CategoryId
+INNER JOIN LOCATIONS l ON l.Id = s.LocationId
+WHERE l.Name IN ( $LOCATIONS )
+AND sp.Name = "$SPECIES";