Update project yaml to v5, python to v2, sqlrunner to v1

.github/workflows/main.yml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v7
       - uses: "opensafely-core/setup-action@v1"
         with:
-          python-version: "3.8"
+          python-version: "3.10"
           install-just: true
       - name: Check formatting, linting and import sorting
         run: just check
@@ -24,7 +24,7 @@ jobs:
       - uses: actions/checkout@v7
       - uses: "opensafely-core/setup-action@v1"
         with:
-          python-version: "3.8"
+          python-version: "3.10"
           install-just: true
       - name: Run tests
         run: |

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3.8
+  python: python3.10
 
 repos:
   - repo: local
@@ -24,7 +24,7 @@ repos:
       require_serial: true
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v6.0.0
     hooks:
     - id: trailing-whitespace
     - id: end-of-file-fixer

.python-version

@@ -1 +1 @@
-3.8.10
+3.10

analysis/query.sql

@@ -5,7 +5,7 @@ SELECT
     TableName,
     ColumnName,
     ColumnType,
-    Precision,
+    [Precision],
     Scale,
     MaxLength,
     IsNullable,

analysis/report.ipynb

@@ -6,11 +6,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import dateutil\n",
-    "from IPython.display import Markdown\n",
     "import json\n",
+    "import pathlib\n",
+    "\n",
+    "import dateutil\n",
     "import pandas\n",
-    "import pathlib"
+    "from IPython.display import Markdown"
    ]
   },
   {
@@ -127,12 +128,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Markdown(\n",
-    "    f\"\"\"\n",
+    "Markdown(f\"\"\"\n",
     "This report was run on {report_run_date:%-d %B %Y}.\n",
     "It reflects the state of the database on this date.\n",
-    "\"\"\"\n",
-    ")"
+    "\"\"\")"
    ]
   },
   {

analysis/vaccination_reference_report.ipynb

@@ -2,15 +2,16 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import dateutil\n",
-    "from IPython.display import Markdown\n",
     "import json\n",
+    "import pathlib\n",
+    "\n",
+    "import dateutil\n",
     "import pandas\n",
-    "import pathlib"
+    "from IPython.display import Markdown"
    ]
   },
   {
@@ -123,12 +124,10 @@
     }
    ],
    "source": [
-    "Markdown(\n",
-    "    f\"\"\"\n",
+    "Markdown(f\"\"\"\n",
     "This report was run on {report_run_date:%-d %B %Y}.\n",
     "It reflects the state of the database on this date.\n",
-    "\"\"\"\n",
-    ")"
+    "\"\"\")"
    ]
   },
   {

justfile

@@ -3,7 +3,7 @@ export VIRTUAL_ENV  := env_var_or_default("VIRTUAL_ENV", ".venv")
 export BIN := VIRTUAL_ENV + if os_family() == "unix" { "/bin" } else { "/Scripts" }
 export PIP := BIN + if os_family() == "unix" { "/python -m pip" } else { "/python.exe -m pip" }
 
-export DEFAULT_PYTHON := if os_family() == "unix" { "python3.8" } else { "python" }
+export DEFAULT_PYTHON := if os_family() == "unix" { "python3.10" } else { "python" }
 
 
 # list available commands
@@ -91,7 +91,7 @@ upgrade env package="": virtualenv
     #!/usr/bin/env bash
     set -euo pipefail
 
-    opts="--upgrade"
+    opts="--upgrade --strip-extras --pip-args uploaded-prior-to=P7D"
     test -z "{{ package }}" || opts="--upgrade-package {{ package }}"
     FORCE=true "{{ just_executable() }}" requirements-{{ env }} $opts
 

project.yaml

@@ -1,12 +1,9 @@
-version: "3.0"
-
-expectations:
-  population_size: 1000
+version: "5.0"
 
 actions:
   query:
     run: >
-      sqlrunner:latest
+      sqlrunner:v1
         --output output/files_for_release/rows.csv
         --log-file logs/log.json
         analysis/query.sql
@@ -17,7 +14,7 @@ actions:
 
   data_dictionary_query:
     run: >
-      sqlrunner:latest
+      sqlrunner:v1
         --output output/files_for_release/data_dictionary.csv
         --log-file logs/data_dictionary_log.json
         analysis/data_dictionary_query.sql
@@ -28,7 +25,7 @@ actions:
 
   decision_support_value_reference_query:
     run: >
-      sqlrunner:latest
+      sqlrunner:v1
         --output output/files_for_release/decision_support_value_reference.csv
         --log-file logs/decision_support_value_reference_log.json
         analysis/decision_support_value_reference_query.sql
@@ -39,7 +36,7 @@ actions:
 
   vaccination_reference_query:
     run: >
-      sqlrunner:latest
+      sqlrunner:v1
         --output output/files_for_release/vaccination_reference.csv
         --log-file logs/vaccination_reference_log.json
         analysis/vaccination_reference_query.sql
@@ -60,7 +57,7 @@ actions:
     # --output-dir=output
     #   write HTML reports to the `output` directory
     run: >
-      python:latest jupyter nbconvert
+      python:v2 jupyter nbconvert
         --execute
         --no-input
         --to=html
@@ -76,7 +73,7 @@ actions:
 
   categorical_columns:
     run: >
-      sqlrunner:latest
+      sqlrunner:v1
         --output output/files_for_release/results_categorical_columns.csv
         --dummy-data-file analysis/dummy_results.csv
         analysis/query_tpp_categorical_columns.sql

requirements.dev.in

@@ -1,4 +1,4 @@
---constraint requirements.prod.txt
+-c requirements.prod.txt
 
 # Additional dev requirements
 # To generate a requirements file that includes both prod and dev requirements, run: