Update copier template to v1.4.4 (#10)

* Temp remove readme.

* Update copier to 1.4.4

* Address odd merges in pre-commit

.copier-answers.yml

@@ -1,15 +1,17 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.1
+_commit: v1.4.4
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: LINCC Frameworks Team
 create_example_module: false
 custom_install: true
+include_benchmarks: false
 include_docs: false
 mypy_type_checking: none
 package_name: lf_asv_formatter
 preferred_linter: pylint
 project_license: MIT
 project_name: lf-asv-formatter
+project_organization: lincc-frameworks
 use_gitlfs: none
 use_isort: true

.github/workflows/linting.yml

@@ -9,19 +9,19 @@ on:
   pull_request:
     branches: [ main ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10']
-
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         sudo apt-get update
@@ -30,6 +30,6 @@ jobs:
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Analyze code with linter
-
       run: |
         pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc
+        pylint -rn -sn --recursive=y ./tests --rcfile=./tests/.pylintrc

.github/workflows/pre-commit-ci.yml

@@ -0,0 +1,34 @@
+# This workflow runs pre-commit hooks on pull requests to enforce coding style.
+# To ensure correct configuration, please refer to:
+#   https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
+
+name: Run pre-commit hooks
+
+on:
+  pull_request:
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    env: 
+      SKIP: "check-lincc-frameworks-template-version,pytest-check,no-commit-to-branch,validate-pyproject,check-added-large-files,sphinx-build"
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
+    - uses: pre-commit-ci/[email protected]
+      if: always()

.github/workflows/publish-to-pypi.yml

@@ -1,5 +1,5 @@
 # This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+# For more information see: https://github.com/pypa/gh-action-pypi-publish#trusted-publishing
 
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by

.github/workflows/smoke-test.yml

@@ -8,6 +8,9 @@ name: Unit test smoke test
 on:
   schedule:
     - cron: 45 6 * * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 jobs:
   build:

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+fail_fast: true
 repos:
 
     # Compare the local template version to the latest remote template version
@@ -22,22 +23,7 @@ repos:
         language: system
         entry: jupyter nbconvert --clear-output
 
-    # Run unit tests, verify that they pass. Note that coverage is run against
-    # the ./src directory here because that is what will be committed. In the 
-    # github workflow script, the coverage is run against the installed package
-    # and uploaded to Codecov by calling pytest like so:
-    # `python -m pytest --cov=<package_name> --cov-report=xml`
-  - repo: local
-    hooks:
-      - id: pytest-check
-        name: Run unit tests
-        description: Run unit tests with pytest.
-        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
-        language: system
-        pass_filenames: false
-        always_run: true
-
-    # prevents committing directly branches named 'main' and 'master'.
+    # Prevents committing directly branches named 'main' and 'master'.
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -49,23 +35,24 @@ repos:
         description: Prevent the user from committing very large files.
         args: ['--maxkb=500']
 
-    # verify that pyproject.toml is well formed
+    # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: v0.12.1
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
         description: Verify that pyproject.toml adheres to the established schema.
 
+
     # Automatically sort the imports used in .py files
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
       - id: isort
-        name: isort (python files in src/ and tests/)
-        description: Sort and organize imports in .py files.
-        types: [python]
-        files: ^(src|tests)/
+        name: Run isort
+        description: Sort and organize imports in .py and .pyi files.
+        types_or: [python, pyi]
+
 
 
     # Analyze the src code style and report code that doesn't adhere.
@@ -76,33 +63,41 @@ repos:
         entry: pylint
         language: system
         types: [python]
-        files: ^(src|tests)/
-        # It is recommended to specify the latest version of Python
-        # supported by your project here, or alternatively use
-        # pre-commit's default_language_version, see
-        # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.10
         files: ^src/
         args:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
             "--rcfile=src/.pylintrc",
           ]
+
     # Analyze the tests code style and report code that doesn't adhere.
   - repo: local
     hooks:
       - id: pylint
-        name: pylint (python files in tests/)
+        name: pylint (python files in tests/ and benchmarks/)
         entry: pylint
         language: system
         types: [python]
-        files: ^tests/
+        files: ^(tests|benchmarks)/
         args:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
             "--rcfile=tests/.pylintrc",
           ]
 
-
+    # Run unit tests, verify that they pass. Note that coverage is run against
+    # the ./src directory here because that is what will be committed. In the 
+    # github workflow script, the coverage is run against the installed package
+    # and uploaded to Codecov by calling pytest like so:
+    # `python -m pytest --cov=<package_name> --cov-report=xml`
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: Run unit tests
+        description: Run unit tests with pytest.
+        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
+        language: system
+        pass_filenames: false
+        always_run: true

README.md

@@ -2,5 +2,15 @@
 
 [![Template](https://img.shields.io/badge/Template-LINCC%20Frameworks%20Python%20Project%20Template-brightgreen)](https://lincc-ppt.readthedocs.io/en/latest/)
 
+[![PyPI](https://img.shields.io/pypi/v/lf-asv-formatter?color=blue&logo=pypi&logoColor=white)](https://pypi.org/project/lf-asv-formatter/)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/lincc-frameworks/lf-asv-formatter/smoke-test.yml)](https://github.com/lincc-frameworks/lf-asv-formatter/actions/workflows/smoke-test.yml)
+[![codecov](https://codecov.io/gh/lincc-frameworks/lf-asv-formatter/branch/main/graph/badge.svg)](https://codecov.io/gh/lincc-frameworks/lf-asv-formatter)
+
 Simple script to re-format the output of ASV (air-speed-velocity) benchmarking
-outputs for use in github messages.
+outputs for use in github messages.
+
+## Acknowledgements
+
+LINCC Frameworks is supported by Schmidt Futures, a philanthropic initiative
+founded by Eric and Wendy Schmidt, as part of the Virtual Institute of 
+Astrophysics (VIA).

pyproject.toml

@@ -27,6 +27,10 @@ dev = [
     "pylint", # Used for static linting of files
 ]
 
+[metadata]
+long_description = { file = "README.md" }
+url = "https://github.com/lincc-frameworks/lf-asv-formatter"
+
 [build-system]
 requires = [
     "setuptools>=62", # Used to build and package the Python project

src/.pylintrc

@@ -183,6 +183,7 @@ good-names=i,
            k,
            ex,
            Run,
+           ra,
            _
 
 # Good variable names regexes, separated by a comma. If names match any regex,
@@ -277,19 +278,19 @@ exclude-too-few-public-methods=
 ignored-parents=
 
 # Maximum number of arguments for function / method.
-max-args=5
+max-args=10
 
 # Maximum number of attributes for a class (see R0902).
-max-attributes=7
+max-attributes=20
 
 # Maximum number of boolean expressions in an if statement (see R0916).
 max-bool-expr=5
 
 # Maximum number of branch for function / method body.
-max-branches=12
+max-branches=20
 
 # Maximum number of locals for function / method body.
-max-locals=15
+max-locals=20
 
 # Maximum number of parents for a class (see R0901).
 max-parents=7
@@ -329,7 +330,7 @@ indent-after-paren=4
 indent-string='    '
 
 # Maximum number of characters on a single line.
-max-line-length=100
+max-line-length=110
 
 # Maximum number of lines in a module.
 max-module-lines=1000
@@ -502,7 +503,7 @@ ignore-imports=yes
 ignore-signatures=yes
 
 # Minimum lines number of a similarity.
-min-similarity-lines=4
+min-similarity-lines=6
 
 
 [SPELLING]

tests/.pylintrc

@@ -183,6 +183,7 @@ good-names=i,
            k,
            ex,
            Run,
+           ra,
            _
 
 # Good variable names regexes, separated by a comma. If names match any regex,
@@ -277,19 +278,19 @@ exclude-too-few-public-methods=
 ignored-parents=
 
 # Maximum number of arguments for function / method.
-max-args=5
+max-args=10
 
 # Maximum number of attributes for a class (see R0902).
-max-attributes=7
+max-attributes=20
 
 # Maximum number of boolean expressions in an if statement (see R0916).
 max-bool-expr=5
 
 # Maximum number of branch for function / method body.
-max-branches=12
+max-branches=20
 
 # Maximum number of locals for function / method body.
-max-locals=15
+max-locals=30
 
 # Maximum number of parents for a class (see R0901).
 max-parents=7
@@ -329,7 +330,7 @@ indent-after-paren=4
 indent-string='    '
 
 # Maximum number of characters on a single line.
-max-line-length=100
+max-line-length=110
 
 # Maximum number of lines in a module.
 max-module-lines=1000
@@ -503,7 +504,7 @@ ignore-imports=yes
 ignore-signatures=yes
 
 # Minimum lines number of a similarity.
-min-similarity-lines=4
+min-similarity-lines=6
 
 
 [SPELLING]