Merge pull request #197 from benjeffery/fix-codecov-again

Fix codecov

.circleci/config.yml

@@ -6,7 +6,7 @@ orbs:
 jobs:
   build:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     steps:
       - checkout
       - run:

.codecov.yml

@@ -3,9 +3,11 @@ coverage:
     project:
       python:
         target: 95%
-        flags: python
+        flags:
+          - python
 
     patch:
       python:
         target: 90%
-        flags: python
+        flags:
+          - python

.github/workflows/tests.yml

@@ -27,7 +27,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.7, 3.11 ]
+        python: [ 3.8, 3.11 ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:

.github/workflows/wheels.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -58,7 +58,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, "3.10", 3.11]
+        python: [3.8, 3.9, "3.10", 3.11]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
@@ -180,22 +180,6 @@ jobs:
           pip install -r python/requirements/CI/tests/requirements.txt
           python -m pytest -v python
 
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.7
-
-      - name: Run tests (3.7)
-        run: |
-          python -VV
-          # We install in this odd way to make sure we get both deps and a local kastore
-          pip install kastore --only-binary kastore -f python/dist/wheelhouse
-          pip uninstall -y kastore
-          pip install -v kastore --only-binary kastore -f python/dist/wheelhouse --no-index
-          python -c "import kastore"
-          pip install -r python/requirements/CI/tests/requirements.txt
-          python -m pytest -v python
-
       - name: Upload Wheels
         uses: actions/upload-artifact@v2
         with:

.mergify.yml

@@ -4,11 +4,11 @@ queue_rules:
       - "#approved-reviews-by>=1"
       - "#changes-requested-reviews-by=0"
       - status-success=Lint
-      - status-success=Python (3.7, macos-latest)
+      - status-success=Python (3.8, macos-latest)
       - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.7, ubuntu-latest)
+      - status-success=Python (3.8, ubuntu-latest)
       - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.7, windows-latest)
+      - status-success=Python (3.8, windows-latest)
       - status-success=Python (3.11, windows-latest)
       - "status-success=ci/circleci: build"
 
@@ -21,11 +21,11 @@ pull_request_rules:
       - base=main
       - label=AUTOMERGE-REQUESTED
       - status-success=Lint
-      - status-success=Python (3.7, macos-latest)
+      - status-success=Python (3.8, macos-latest)
       - status-success=Python (3.11, macos-latest)
-      - status-success=Python (3.7, ubuntu-latest)
+      - status-success=Python (3.8, ubuntu-latest)
       - status-success=Python (3.11, ubuntu-latest)
-      - status-success=Python (3.7, windows-latest)
+      - status-success=Python (3.8, windows-latest)
       - status-success=Python (3.11, windows-latest)
       - "status-success=ci/circleci: build"
     actions:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
@@ -13,29 +13,29 @@ repos:
     - id: clang-format
       verbose: true
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
+    rev: v3.12.0
     hooks:
       - id: reorder-python-imports
         args: [--application-directories=python,
                --unclassifiable-application-module=_kastore]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
-        args: [--py3-plus, --py37-plus]
+        args: [--py3-plus, --py38-plus]
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.3.0
     hooks:
       - id: black
         language_version: python3
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: [--config=python/.flake8]
         additional_dependencies: ["flake8-bugbear==20.1.4", "flake8-builtins==1.5.2"]
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.16.0
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==23.3.0]

docs/conf.py

@@ -76,7 +76,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

python/CHANGELOG.rst

@@ -1,3 +1,10 @@
+--------------------
+[0.3.X] - 202X-XX-XX
+--------------------
+
+kastore now requires Python 3.8 or later.
+
+
 --------------------
 [0.3.2] - 2022-07-12
 --------------------

python/kastore/cli.py

@@ -1,6 +1,3 @@
-"""
-The CLI for kastore. Provides utilities for examining kastore files.
-"""
 import argparse
 import logging
 import os
@@ -10,6 +7,9 @@
 
 import kastore
 
+"""
+The CLI for kastore. Provides utilities for examining kastore files.
+"""
 
 logger = logging.getLogger(__name__)
 

python/kastore/exceptions.py

@@ -1,11 +1,12 @@
-"""
-Exception definitions for kastore.
-"""
 from _kastore import FileFormatError
 from _kastore import KastoreException
 from _kastore import VersionTooNewError
 from _kastore import VersionTooOldError
 
+"""
+Exception definitions for kastore.
+"""
+
 # Some exceptions are defined in the low-level module. In particular, the
 # superclass of all exceptions for kastore is defined here. We define the
 # docstrings here to avoid difficulties with compiling C code on

python/kastore/store.py

@@ -1,3 +1,12 @@
+import logging
+import os
+import struct
+from collections.abc import Mapping
+
+import numpy as np
+
+import kastore.exceptions as exceptions
+
 """
 The Python engine for kastore.
 
@@ -14,14 +23,7 @@
 + 8 byte bounaries.
 +===================================+
 """
-import logging
-import os
-import struct
-from collections.abc import Mapping
-
-import numpy as np
 
-import kastore.exceptions as exceptions
 
 logger = logging.getLogger(__name__)
 

python/make_standard_files.py

@@ -1,6 +1,3 @@
-"""
-Makes the files in the test-data directory.
-"""
 import os.path
 import struct
 import tempfile
@@ -10,6 +7,10 @@
 import kastore as kas
 import kastore.store as store
 
+"""
+Makes the files in the test-data directory.
+"""
+
 
 class MalformedFilesBuilder:
     """

python/requirements/development.txt

@@ -1,4 +1,5 @@
 attrs
+breathe==4.35.0
 coverage
 flake8
 hypothesis
@@ -9,5 +10,6 @@ numpy
 mock
 pre-commit
 breathe
+Sphinx==5.3.0
 sphinx_rtd_theme
 sphinx-issues

python/setup.cfg

@@ -19,7 +19,6 @@ classifiers =
         Topic :: Scientific/Engineering :: Bio-Informatics
         License :: OSI Approved :: MIT License
         Programming Language :: Python :: 3
-        Programming Language :: Python :: 3.7
         Programming Language :: Python :: 3.8
         Programming Language :: Python :: 3.9
         Programming Language :: Python :: 3.10
@@ -36,7 +35,7 @@ platforms =
 
 [options]
 packages = kastore
-python_requires = >=3.7
+python_requires = >=3.8
 include_package_data = True
 install_requires =
     numpy>=1.7

python/stress_lowlevel.py

@@ -1,7 +1,3 @@
-"""
-Code to stress the low-level API as much as possible to expose
-any memory leaks or error handling issues.
-"""
 import argparse
 import os
 import random
@@ -16,6 +12,12 @@
 import tests.test_storage as test_storage
 
 
+"""
+Code to stress the low-level API as much as possible to expose
+any memory leaks or error handling issues.
+"""
+
+
 def main():
     modules = {
         "errors": test_errors,

python/tests/test_cli.py

@@ -1,6 +1,3 @@
-"""
-Test cases for the kastore CLI.
-"""
 import io
 import logging
 import os
@@ -16,6 +13,10 @@
 import kastore.__main__ as main
 import kastore.cli as cli
 
+"""
+Test cases for the kastore CLI.
+"""
+
 
 def capture_output(func, *args, **kwargs):
     """

python/tests/test_errors.py

@@ -1,6 +1,3 @@
-"""
-Tests for error conditions.
-"""
 import os
 import platform
 import struct
@@ -12,6 +9,10 @@
 import kastore as kas
 import kastore.store as store
 
+"""
+Tests for error conditions.
+"""
+
 IS_WINDOWS = platform.system() == "Windows"
 
 

python/tests/test_file_format.py

@@ -1,6 +1,3 @@
-"""
-Tests checking that the file format is as it should be.
-"""
 import os
 import pathlib
 import struct
@@ -14,10 +11,20 @@
 import kastore as kas
 import kastore.store as store
 
+"""
+Tests checking that the file format is as it should be.
+"""
+
 # Set the deadline to None to avoid weird behaviour on CI.
-hypothesis.settings.register_profile("kastore_defaults", deadline=None)
+hypothesis.settings.register_profile(
+    "kastore_defaults",
+    deadline=None,
+    # Supress warnings resultsing from inheritance
+    suppress_health_check=(hypothesis.HealthCheck.differing_executors,),
+)
 hypothesis.settings.load_profile("kastore_defaults")
 
+
 # Exclude any 'other' unicode categories:
 # http://www.unicode.org/reports/tr44/#General_Category_Values
 key_alphabet = hst.characters(blacklist_categories=("C",))

python/tests/test_fileobj.py

@@ -1,6 +1,3 @@
-"""
-Tests for load()ing and dump()ing with file-like objects.
-"""
 import multiprocessing
 import os
 import pathlib
@@ -17,6 +14,10 @@
 
 import kastore as kas
 
+"""
+Tests for load()ing and dump()ing with file-like objects.
+"""
+
 
 IS_WINDOWS = platform.system() == "Windows"
 

python/tests/test_interface.py

@@ -1,6 +1,3 @@
-"""
-Basic tests for the information API.
-"""
 import io
 import os
 import pathlib
@@ -12,6 +9,10 @@
 import kastore as kas
 import kastore.exceptions as exceptions
 
+"""
+Basic tests for the information API.
+"""
+
 
 class InterfaceTest(unittest.TestCase):
     """