Update supported Python versions

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
       - published
 
 env:
-  MINIMUM_PYTHON_VERSION: "3.7"
+  MINIMUM_PYTHON_VERSION: "3.8"
 
 concurrency:
   group: ${{ github.head_ref || github.run_id }}
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Python ${{ env.MINIMUM_PYTHON_VERSION }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
       - uses: actions/checkout@v3
@@ -36,29 +36,25 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v3
       - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install Tox and any other packages
         run: |
           python -m pip install --upgrade pip
           python -m pip install tox-gh-actions poetry
-      - name: Run quick tests (Not Python ${{ env.MINIMUM_PYTHON_VERSION }})
-        if: ${{ matrix.python-version != env.MINIMUM_PYTHON_VERSION }}
-        run: tox -- -m "not slow"
-      - name: Run all tests (Python ${{ env.MINIMUM_PYTHON_VERSION }} only)
-        if: ${{ matrix.python-version == env.MINIMUM_PYTHON_VERSION }}
+      - name: Run all tests
         run: tox
 
   docs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Python ${{ env.MINIMUM_PYTHON_VERSION }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
       - uses: actions/checkout@v3
@@ -81,7 +77,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Python ${{ env.MINIMUM_PYTHON_VERSION }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ env.MINIMUM_PYTHON_VERSION }}
       - uses: actions/checkout@v3

.gitignore

@@ -107,3 +107,6 @@ ENV/
 
 # Poetry
 poetry.lock
+
+# vscode
+.vscode/

.pre-commit-config.yaml

@@ -1,29 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.4.0
     hooks:
       - id: check-docstring-first
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.0
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         language: python
-        args: [--py37-plus]
+        args: [--py38-plus]
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
   - repo: https://github.com/ambv/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
       - id: black
         language: python
-  - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
     hooks:
       - id: flake8
         language: python
@@ -35,8 +35,6 @@ repos:
           - mccabe
           - yesqa
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.931'
+    rev: 'v1.0.1'
     hooks:
       - id: mypy
-        additional_dependencies:
-          - types-setuptools  # Required for versioning on py37

HISTORY.md

@@ -1,5 +1,10 @@
 # History
 
+## 0.3.2 (UNRELEASED)
+
+ - Removed support for Python 3.7
+ - Added support for Python 3.10 and Python 3.11
+
 ## 0.3.1 (2022-01-24)
 
   - Added parameters to docker run commands to better reflect how

README.md

@@ -25,7 +25,7 @@ containers for grand-challenge.org.
 
 ## Getting Started
 
-[evalutils](https://github.com/comic/evalutils) requires Python 3.7 or
+[evalutils](https://github.com/comic/evalutils) requires Python 3.8 or
 above, and can be installed from `pip`.
 Please see the [Getting Started](https://comic.github.io/evalutils/usage.html)
 documentation for more details.

docs/conf.py

@@ -19,17 +19,10 @@
 #
 import os
 import sys
+from importlib.metadata import version as _get_version
 from typing import Dict, List
 
-try:
-    from importlib.metadata import version
-
-    evalutils_version = version("evalutils")
-except ImportError:
-    # py <= py37
-    from pkg_resources import get_distribution
-
-    evalutils_version = get_distribution("evalutils").version
+evalutils_version = _get_version("evalutils")
 
 sys.path.insert(0, os.path.abspath(".."))
 

docs/contributing.rst

@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python 3.7, 3.8 and 3.9. Check
+3. The pull request should work for Python 3.8, 3.9, 3.10 and 3.11. Check
    https://travis-ci.org/comic/evalutils/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

docs/usage.rst

@@ -67,7 +67,7 @@ The different challenge types that you can select are:
     For this sort of challenge, you may have many candidate points and many ground truth points per case.
     By default, the results per case are also reported.
 
-If you do not have a local python 3.7+ environment you can also
+If you do not have a local python 3.8+ environment you can also
 generate your project with docker by running a container and sharing your current user id:
 
 .. code-block:: console
@@ -396,7 +396,7 @@ The different algorithm types that you can select are:
     For instance, this evaluation could be used for detection of tumours in images.
     By default, the algorithm outputs a single `/output/results.json` which lists the results per case.
 
-If you do not have a local python 3.7+ environment you can also
+If you do not have a local python 3.8+ environment you can also
 generate your project with docker by running a container and sharing your current user id:
 
 .. code-block:: console

evalutils/cli.py

@@ -1,20 +1,14 @@
 import re
+import sys
+from importlib.metadata import version
 from pathlib import Path
 from typing import List
 
 import click
 from cookiecutter.exceptions import FailedHookException
 from cookiecutter.main import cookiecutter
 
-try:
-    from importlib.metadata import version
-
-    evalutils_version = version("evalutils")
-except ImportError:
-    # py <= py37
-    from pkg_resources import get_distribution
-
-    evalutils_version = get_distribution("evalutils").version
+evalutils_version = version("evalutils")
 
 EVALUATION_CHOICES = ["Classification", "Segmentation", "Detection"]
 ALGORITHM_CHOICES = EVALUATION_CHOICES
@@ -40,7 +34,7 @@ def validate_python_module_name_string(ctx, param, arg):
             exit(1)
 
         if not re.match(MODULE_REGEX, arg) or arg in FORBIDDEN_NAMES:
-            click.echo(f"ERROR: '{arg}' is not a valid Python module name!")
+            click.echo(f"ERROR: {arg!r} is not a valid Python module name!")
             exit(1)
 
         return arg
@@ -96,6 +90,8 @@ def init_evaluation(challenge_name, kind, dev):
                 "evalutils_version": evalutils_version,
                 "challenge_kind": kind,
                 "dev_build": 1 if dev else 0,
+                "python_major_version": sys.version_info.major,
+                "python_minor_version": sys.version_info.minor,
             },
         )
         click.echo(f"Created project {challenge_name}")
@@ -186,6 +182,8 @@ def init_algorithm(algorithm_name, kind, dev):
                 "evalutils_name": __name__.split(".")[0],
                 "evalutils_version": evalutils_version,
                 "dev_build": 1 if dev else 0,
+                "python_major_version": sys.version_info.major,
+                "python_minor_version": sys.version_info.minor,
             },
         )
         click.echo(f"Created project {algorithm_name}")

evalutils/evalutils.py

@@ -131,7 +131,7 @@ def _load_cases(
         *,
         folder: Path,
         file_loader: ImageLoader,
-        file_filter: Pattern[str] = None,
+        file_filter: Optional[Pattern[str]] = None,
     ) -> DataFrame:
         cases = None
 
@@ -183,7 +183,7 @@ def process(self):
         self.process_cases()
         self.save()
 
-    def process_cases(self, file_loader_key: str = None):
+    def process_cases(self, file_loader_key: Optional[str] = None):
         if file_loader_key is None:
             file_loader_key = self._index_key
         self._case_results = []
@@ -329,8 +329,8 @@ def __init__(
         file_sorter_key: Callable = first_int_in_filename_key,
         file_loader: FileLoader,
         validators: Tuple[DataFrameValidator, ...],
-        join_key: str = None,
-        aggregates: Set[str] = None,
+        join_key: Optional[str] = None,
+        aggregates: Optional[Set[str]] = None,
         output_file: PathLike = DEFAULT_EVALUATION_OUTPUT_FILE_PATH,
     ):
         """

evalutils/io.py

@@ -46,7 +46,7 @@ def first_int_in_filename_key(fname: Path) -> str:
     try:
         return f"{get_first_int_in(fname.stem):>64}"
     except AttributeError:
-        logger.warning(f"Could not find an int in the string '{fname.stem}'.")
+        logger.warning(f"Could not find an int in the string {fname.stem!r}.")
         return fname.stem
 
 

evalutils/templates/algorithm/cookiecutter.json

@@ -8,9 +8,7 @@
     "package_name": "{{ cookiecutter.algorithm_name|replace(' ', '') }}",
     "evalutils_name": "",
     "evalutils_version": "",
-    "docker_base_container": "python:3.9-slim",
     "dev_build": 0,
-    "_copy_without_render": [
-        "*.github"
-    ]
+    "python_major_version": "",
+    "python_minor_version": ""
 }

evalutils/templates/algorithm/hooks/pre_gen_project.py

@@ -7,5 +7,5 @@
 package_name = "{{ cookiecutter.package_name }}"
 
 if not re.match(MODULE_REGEX, package_name) or package_name in FORBIDDEN_NAMES:
-    print(f"ERROR: '{package_name}' is not a valid Python module name!")
+    print(f"ERROR: {package_name!r} is not a valid Python module name!")
     exit(1)

evalutils/templates/algorithm/{{ cookiecutter.package_name }}/.github/workflows/ci.yml

@@ -3,17 +3,17 @@ name: CI
 on: [push, pull_request]
 
 env:
-  PYTHON_VERSION: '3.9'
+  PYTHON_VERSION: '{{ cookiecutter.python_major_version }}.{{ cookiecutter.python_minor_version }}'
 
 jobs:
 
   algorithm-tests:
     runs-on: ubuntu-latest
     steps:
-      - name: Install Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v3
+      - name: Install Python ${{ "{{" }} env.PYTHON_VERSION {{ "}}" }}
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version: ${{ "{{" }} env.PYTHON_VERSION {{ "}}" }}
       - uses: actions/checkout@v3
       - name: Build the containers
         run: |

evalutils/templates/algorithm/{{ cookiecutter.package_name }}/Dockerfile

@@ -1,4 +1,4 @@
-FROM {{ cookiecutter.docker_base_container }}
+FROM python:{{ cookiecutter.python_major_version }}.{{ cookiecutter.python_minor_version }}-slim
 
 {% if cookiecutter.dev_build|int -%}
 RUN apt-get update && apt-get install -y git
@@ -28,4 +28,4 @@ RUN python -m pip install --user -rrequirements.txt
 
 COPY --chown=algorithm:algorithm process.py /opt/algorithm/
 
-ENTRYPOINT python -m process $0 $@
+ENTRYPOINT [ "python", "-m", "process" ]

evalutils/templates/algorithm/{{ cookiecutter.package_name }}/requirements.txt

@@ -1,5 +1,3 @@
 {% if not cookiecutter.dev_build|int %}
 {{ cookiecutter.evalutils_name }}=={{ cookiecutter.evalutils_version }}
 {% endif %}
-scikit-learn==0.24.2
-scipy==1.6.3

evalutils/templates/algorithm/{{ cookiecutter.package_name }}/test.sh

@@ -24,12 +24,12 @@ docker run --rm \
 
 docker run --rm \
         -v {{ cookiecutter.package_name|lower }}-output-$VOLUME_SUFFIX:/output/ \
-        {{ cookiecutter.docker_base_container }} cat /output/results.json | python -m json.tool
+        python:{{ cookiecutter.python_major_version }}.{{ cookiecutter.python_minor_version }}-slim cat /output/results.json | python -m json.tool
 
 docker run --rm \
         -v {{ cookiecutter.package_name|lower }}-output-$VOLUME_SUFFIX:/output/ \
         -v $SCRIPTPATH/test/:/input/ \
-        {{ cookiecutter.docker_base_container }} python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
+        python:{{ cookiecutter.python_major_version }}.{{ cookiecutter.python_minor_version }}-slim python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
 
 if [ $? -eq 0 ]; then
     echo "Tests successfully passed..."

evalutils/templates/evaluation/cookiecutter.json

@@ -8,9 +8,7 @@
     ],
     "evalutils_name": "",
     "evalutils_version": "",
-    "docker_base_container": "python:3.9-slim",
     "dev_build": 0,
-    "_copy_without_render": [
-        "*.github"
-    ]
+    "python_major_version": "",
+    "python_minor_version": ""
 }

evalutils/templates/evaluation/hooks/pre_gen_project.py

@@ -7,5 +7,5 @@
 package_name = "{{ cookiecutter.package_name }}"
 
 if not re.match(MODULE_REGEX, package_name) or package_name in FORBIDDEN_NAMES:
-    print(f"ERROR: '{package_name}' is not a valid Python module name!")
+    print(f"ERROR: {package_name!r} is not a valid Python module name!")
     exit(1)

evalutils/templates/evaluation/{{ cookiecutter.package_name }}/.github/workflows/ci.yml

@@ -3,17 +3,17 @@ name: CI
 on: [push, pull_request]
 
 env:
-  PYTHON_VERSION: '3.9'
+  PYTHON_VERSION: '{{ cookiecutter.python_major_version }}.{{ cookiecutter.python_minor_version }}'
 
 jobs:
 
   evaluation-tests:
     runs-on: ubuntu-latest
     steps:
-      - name: Install Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v3
+      - name: Install Python ${{ "{{" }} env.PYTHON_VERSION {{ "}}" }}
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version: ${{ "{{" }} env.PYTHON_VERSION {{ "}}" }}
       - uses: actions/checkout@v3
       - name: Build the containers
         run: |