Merge 467acc8 into da10c3a

Author: delucchi-cmu

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.2
+_commit: v1.4.3
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: lincc-frameworks-team@lists.lsst.org
 author_name: LINCC Frameworks

.github/workflows/asv-pr.yml

@@ -12,6 +12,10 @@ env:
   PYTHON_VERSION: "3.10"
   WORKING_DIR: ${{ github.workspace }}/benchmarks
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
 
   setup-python:

.github/workflows/build-documentation.yml

@@ -9,6 +9,10 @@ on:
   pull_request:
     branches: [ main ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 

.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

.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/action@v3.0.0
+      with:
+        extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
+    - uses: pre-commit-ci/lite-action@v1.0.1
+      if: always()

.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.
@@ -83,15 +70,16 @@ repos:
             "-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
@@ -100,6 +88,22 @@ repos:
           ]
 
 
+
+
+    # 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
     # Make sure Sphinx can build the documentation while explicitly omitting 
     # notebooks from the docs, so users don't have to wait through the execution 
     # of each notebook or each commit. By default, these will be checked in the 

docs/guide/contributing.rst

@@ -23,13 +23,38 @@ branches and tickets, but it's nice when it's in the name.
 Set up a development environment
 -------------------------------------------------------------------------------
 
-Most folks use conda for virtual environments. You may want to as well.
+Before installing any dependencies or writing code, it's a great idea to create a
+virtual environment. LINCC-Frameworks engineers primarily use `conda` to manage virtual
+environments. If you have conda installed locally, you can run the following to
+create and activate a new environment.
 
 .. code-block:: bash
 
-    $ git clone https://github.com/astronomy-commons/hipscat
-    $ cd hipscat
-    $ pip install -e .
+   >> conda create env -n <env_name> python=3.10
+   >> conda activate <env_name>
+
+
+Once you have created a new environment, you can install this project for local
+development using the following commands:
+
+.. code-block:: bash
+
+   >> pip install -e .'[dev]'
+   >> pre-commit install
+   >> conda install pandoc
+
+
+Notes:
+
+1) The single quotes around ``'[dev]'`` may not be required for your operating system.
+2) ``pre-commit install`` will initialize pre-commit for this local repository, so
+   that a set of tests will be run prior to completing a local commit. For more
+   information, see the Python Project Template documentation on
+   `pre-commit <https://lincc-ppt.readthedocs.io/en/latest/practices/precommit.html>`_.
+3) Install ``pandoc`` allows you to verify that automatic rendering of Jupyter notebooks
+   into documentation for ReadTheDocs works as expected. For more information, see
+   the Python Project Template documentation on
+   `Sphinx and Python Notebooks <https://lincc-ppt.readthedocs.io/en/latest/practices/sphinx.html#python-notebooks>`_.
 
 .. tip::
     Installing on Mac

pyproject.toml

@@ -17,42 +17,39 @@ dynamic = ["version"]
 
 requires-python = ">=3.8"
 dependencies = [
+    "astropy",
+    "fsspec", # Used for abstract filesystems
     "healpy",
+    "numba",
     "pandas",
-    "setuptools_scm",
     "pyarrow>=10.0.0",
-    "astropy",
-    "typing-extensions>=4.3.0",
-    "numba",
-    "fsspec", # Used for abstract filesystems
-    "ipykernel", # Support for Jupyter notebooks
+    "setuptools_scm",
+    "typing-extensions>=4.3.0"
 ]
 
 # On a mac, install optional dependencies with `pip install '.[dev]'` (include the single quotes)
 [project.optional-dependencies]
 dev = [
+    "adlfs", # abfs filesytem support
+    "asv==0.5.1", # Used to compute performance benchmarks
+    "ipykernel", # Support for Jupyter notebooks
+    "ipython", # Also used in building notebooks into Sphinx
+    "matplotlib", # Used in sample notebook intro_notebook.ipynb
     "mypy", # Used for static type checking of files
-    "pylint", # Used for static linting of files
+    "myst_parser", # Renders markdown alongside RST
+    "nbconvert", # Needed for pre-commit check to clear output from Python notebooks
+    "nbsphinx", # Used to integrate Python notebooks into Sphinx documentation
+    "numpy", # Used in sample notebook intro_notebook.ipynb
     "pre-commit", # Used to run checks before finalizing a git commit
+    "pylint", # Used for static linting of files
     "pytest",
     "pytest-cov", # Used to report total code coverage
     "pytest-timeout", # Used to test for code efficiency
+    "s3fs", # s3 filesystem support
     "sphinx", # Used to automatically generate documentation
-    "sphinx-rtd-theme", # Used to render documentation
     "sphinx-autoapi", # Used to automatically generate api documentation
-    # if you add dependencies here while experimenting in a notebook and you
-    # want that notebook to render in your documentation, please add the
-    # dependencies to ./docs/requirements.txt as well.
-    "nbconvert", # Needed for pre-commit check to clear output from Python notebooks
-    "nbsphinx", # Used to integrate Python notebooks into Sphinx documentation
-    "ipykernel", # Also used in building notebooks into Sphinx
-    "ipython", # Also used in building notebooks into Sphinx
-    "myst_parser", # Renders markdown alongside RST
-    "asv", # Used to compute performance benchmarks
-    "adlfs", # abfs filesytem support
-    "s3fs", # s3 filesystem support
+    "sphinx-rtd-theme" # Used to render documentation
 ]
-
 [build-system]
 requires = [
     "setuptools>=62", # Used to build and package the Python project

src/.pylintrc

@@ -290,7 +290,7 @@ max-bool-expr=5
 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
@@ -503,7 +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,
@@ -277,10 +278,10 @@ 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