Replace Makefile with justfile

.github/workflows/build_and_publish.yaml

@@ -84,7 +84,7 @@ jobs:
     - name: Generate correct value for VERSION file
       run: echo "$VERSION" > cohortextractor/VERSION
     - name: Build docker
-      run: make docker-build ENV=prod VERSION=$VERSION
+      run: just docker-build prod
     - name: Basic docker test
       run: docker run cohortextractor --help
     - name: Log into GitHub Container Registry

.github/workflows/test_runner.yaml

@@ -15,16 +15,15 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: "3.8"
+      - uses: opensafely-core/setup-action@v1
+        with:
+          install-just: true
       - name: Install deps
         run: |
-            # ensure requirements .txt files are timestamped later than .in
-            # files so we don't re-compile them
-            touch requirements.*.txt
-            make devenv
-      - name: Run all pre-commit checks
+            just devenv
+      - name: Check files
         run: |
-          source ${{ github.workspace }}/venv/bin/activate
-          pre-commit run --all-files
+            just check
 
   test:
     name: Run test suite
@@ -35,26 +34,28 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: "3.8"
+      - uses: opensafely-core/setup-action@v1
+        with:
+          install-just: true
       - name: Install deps
         run: |
-            # ensure requirements .txt files are timestamped later than .in
-            # files so we don't re-compile them
-            touch requirements.*.txt
-            make devenv
+            just devenv
       - name: Start SQL Server and Trino instances for the tests
         run: docker-compose up -d mssql trino
       - name: Run tests
         run: |
-          source ${{ github.workspace }}/venv/bin/activate
-          PYTHONPATH=. pytest -vvv tests/
+          PYTHONPATH=. just test -vvv tests/
 
   docker-tests:
     name: Test docker build
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v3
+      - uses: opensafely-core/setup-action@v1
+        with:
+          install-just: true
       - name: Build docker
-        run: make docker-build ENV=dev
+        run: just docker-build dev
       - name: Basic docker test
         run: docker-compose run --rm -v $PWD:/workspace dev cohortextractor
       - name: Run unit tests in docker

.pre-commit-config.yaml

@@ -1,18 +1,15 @@
-repos:
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-    - id: black
+default_language_version:
+  python: python3.8
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    - id: flake8
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+repos:
+  - repo: local
     hooks:
-    - id: isort
+    - id: check
+      name: check
+      entry: just check
+      language: system
+      types: [python]
+      require_serial: true
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0

DEVELOPERS.md

@@ -37,7 +37,7 @@ apt-get install -y gnupg && \
 export PATH=$PATH:/opt/mssql-tools/bin
 
 ```
-* Set up virtual env: `make devenv` - Note: if not on linux, you may need to install ctds manually
+* Set up virtual env: `just devenv` - Note: if not on linux, you may need to install ctds manually
 * `py.test tests/`
 
 Note: if you change the database schema

cohortextractor/__init__.py

@@ -11,6 +11,7 @@
 from .measure import Measure
 from .study_definition import StudyDefinition
 
+
 init_logging()
 
 with open(os.path.join(os.path.dirname(__file__), "VERSION")) as version_file:

cohortextractor/codelistlib.py

@@ -10,7 +10,7 @@ class Codelist(list):
 
 def codelist_from_csv(filename, system, column="code", category_column=None):
     codes = []
-    with open(filename, "r") as f:
+    with open(filename) as f:
         for row in csv.DictReader(f):
             # We strip whitespace below. Longer term we expect this to be done
             # automatically by OpenCodelists but for now we want to avoid the

cohortextractor/cohortextractor.py

@@ -39,6 +39,7 @@
 
 from .log_utils import log_execution_time, log_stats
 
+
 logger = structlog.get_logger()
 
 notebook_tag = "opencorona-research"

cohortextractor/emis_backend.py

@@ -14,6 +14,7 @@
 from .pandas_utils import dataframe_from_rows, dataframe_to_file
 from .trino_utils import trino_connection_from_url
 
+
 logger = structlog.get_logger()
 sql_logger = structlog.get_logger("cohortextractor.sql")
 
@@ -1105,7 +1106,7 @@ def _number_of_episodes_by_medication(
             match = re.match(pattern, episode_defined_as)
             if not match:
                 raise ValueError(
-                    f"Argument `episode_defined_as` must match " f"pattern: {pattern}"
+                    f"Argument `episode_defined_as` must match pattern: {pattern}"
                 )
             washout_period = int(match.group(1))
         else:
@@ -1169,7 +1170,7 @@ def _number_of_episodes_by_clinical_event(
             match = re.match(pattern, episode_defined_as)
             if not match:
                 raise ValueError(
-                    f"Argument `episode_defined_as` must match " f"pattern: {pattern}"
+                    f"Argument `episode_defined_as` must match pattern: {pattern}"
                 )
             washout_period = int(match.group(1))
         else:

cohortextractor/expressions.py

@@ -4,6 +4,7 @@
 import sqlparse
 from sqlparse import tokens as ttypes
 
+
 IGNORE = object()
 
 # As well as alphanumeric, underscore, and space characters, which are generally used

cohortextractor/measure.py

@@ -1,5 +1,6 @@
 import numpy
 
+
 SMALL_NUMBER_THRESHOLD = 5
 
 

cohortextractor/mssql_utils.py

@@ -7,6 +7,7 @@
 
 from .log_utils import log_execution_time, timing_log_counter
 
+
 # Some drivers warn about the use of features marked "optional" in the DB-ABI
 # spec, using a standardised set of warnings. See:
 # https://www.python.org/dev/peps/pep-0249/#optional-db-api-extensions

cohortextractor/pandas_utils.py

@@ -5,6 +5,7 @@
 import pandas
 import structlog
 
+
 logger = structlog.get_logger()
 
 

cohortextractor/process_covariate_definitions.py

@@ -2,6 +2,7 @@
 import datetime
 import re
 
+
 # ISARIC data has a lot of columns that are all varchar in the db.
 ISARIC_COLUMN_MAPPINGS = {
     "abdopain_ceoccur_v2": "str",

cohortextractor/study_definition.py

@@ -22,6 +22,7 @@
 from .process_covariate_definitions import process_covariate_definitions
 from .validate_dummy_data import validate_dummy_data
 
+
 logger = structlog.get_logger()
 
 

cohortextractor/tpp_backend.py

@@ -24,6 +24,7 @@
 from .process_covariate_definitions import ISARIC_COLUMN_MAPPINGS
 from .therapeutics_utils import ALLOWED_RISK_GROUPS
 
+
 logger = structlog.get_logger()
 
 
@@ -1401,7 +1402,7 @@ def _number_of_episodes_by_medication(
             match = re.match(pattern, episode_defined_as)
             if not match:
                 raise ValueError(
-                    f"Argument `episode_defined_as` must match " f"pattern: {pattern}"
+                    f"Argument `episode_defined_as` must match pattern: {pattern}"
                 )
             washout_period = int(match.group(1))
         else:
@@ -1467,7 +1468,7 @@ def _number_of_episodes_by_clinical_event(
             match = re.match(pattern, episode_defined_as)
             if not match:
                 raise ValueError(
-                    f"Argument `episode_defined_as` must match " f"pattern: {pattern}"
+                    f"Argument `episode_defined_as` must match pattern: {pattern}"
                 )
             washout_period = int(match.group(1))
         else:
@@ -3211,7 +3212,7 @@ def _number_of_episodes_by_covid_therapeutics(
             match = re.match(pattern, episode_defined_as)
             if not match:
                 raise ValueError(
-                    f"Argument `episode_defined_as` must match " f"pattern: {pattern}"
+                    f"Argument `episode_defined_as` must match pattern: {pattern}"
                 )
             washout_period = int(match.group(1))
         else:

cohortextractor/trino_utils.py

@@ -9,6 +9,7 @@
 import requests
 import structlog
 
+
 # The Trino client ought to be close to a drop-in replacement for the Presto
 # but it isn't: despite the tests passing we get 500s from Presto in production
 # whenever we try to query it. As a quick fix we want to revert to using the
@@ -29,6 +30,7 @@
 from retry import retry
 from tabulate import tabulate
 
+
 urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
 
 sql_logger = structlog.get_logger("cohortextractor.sql")

cohortextractor/update_custom_medication_dictionary.py

@@ -4,6 +4,7 @@
 
 from .mssql_utils import mssql_dbapi_connection_from_url
 
+
 CUSTOM_MEDICATION_DICTIONARY_CSV = pathlib.Path(__file__).with_name(
     "custom_medication_dictionary.csv"
 )