Merge pull request #119 from ax3l/pre-commit-setup

Install pre-commit
optimas-org · Oct 10, 2023 · afda164 · afda164
2 parents 94042f8 + 2baa6d3
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diff --git a/.github/workflows/unix.yml b/.github/workflows/unix.yml
@@ -39,11 +39,6 @@ jobs:
         conda install numpy pandas pytorch cpuonly -c pytorch
         conda install -c conda-forge mpi4py mpich
         pip install .[test]
-    - shell: bash -l {0}
-      name: Lint with flake8
-      run: |
-        flake8 ./optimas
-        flake8 ./examples --extend-ignore F821 --exclude custom_fld_diags.py,custom_ptcl_diags.py
     - shell: bash -l {0}
       name: Run unit tests with MPICH
       run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,136 @@
+# To use:
+#
+#     pre-commit run -a
+#
+# Or:
+#
+#     pre-commit install  # (runs every time you commit in git)
+#
+# To update this file:
+#
+#     pre-commit autoupdate
+#
+# See https://pre-commit.com for more information
+
+# Do not check/format anything from third party directories
+#exclude: '^share/openPMD/thirdParty'
+
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    - id: trailing-whitespace
+      args: [--markdown-linebreak-ext=md]
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+    - id: check-json
+    - id: check-toml
+    - id: check-yaml
+      args: [--allow-multiple-documents]
+    - id: check-added-large-files
+      args: ['--maxkb=40']
+    - id: requirements-txt-fixer
+#  - id: fix-encoding-pragma
+#    exclude: ^noxfile.py$
+
+# documentation files: .rst
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+    - id: rst-backticks
+    - id: rst-directive-colons
+    - id: rst-inline-touching-normal
+
+#- repo: https://github.com/asottile/pyupgrade
+#  rev: v2.29.0
+#  hooks:
+#  - id: pyupgrade
+
+# Changes tabs to spaces
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.4
+  hooks:
+  - id: remove-tabs
+
+# CMake formatting
+#- repo: https://github.com/cheshirekow/cmake-format-precommit
+#  rev: v0.6.13
+#  hooks:
+#  - id: cmake-format
+#    additional_dependencies: [pyyaml]
+#    types: [file]
+#    files: (\.cmake|CMakeLists.txt)(.in)?$
+
+# Autoremoves unused Python imports
+- repo: https://github.com/hadialqattan/pycln
+  rev: v2.2.2
+  hooks:
+  - id: pycln
+    name: pycln (python)
+
+# Sorts Python imports according to PEP8
+# https://www.python.org/dev/peps/pep-0008/#imports
+#- repo: https://github.com/pycqa/isort
+#  rev: 5.12.0
+#  hooks:
+#  - id: isort
+#    name: isort (python)
+
+# Python: Flake8 (checks only, does this support auto-fixes?)
+#- repo: https://github.com/PyCQA/flake8
+#  rev: 4.0.1
+#  hooks:
+#  - id: flake8
+#    additional_dependencies: &flake8_dependencies
+#      - flake8-bugbear
+#      - pep8-naming
+#    exclude: ^(docs/.*|tools/.*)$
+# Alternatively: use autopep8?
+
+# Docstring formatting according to numpy style
+- repo: https://github.com/pycqa/pydocstyle
+  rev: 6.3.0
+  hooks:
+  - id: pydocstyle
+    additional_dependencies:
+    - tomli
+    exclude: |
+        (?x)(
+            ^examples/multitask_lpa_fbpic_waket/custom_*|
+            ^setup.py|
+            ^doc/source/conf.py
+        )
+
+# Python Formatting
+- repo: https://github.com/psf/black
+  rev: 23.9.1  # Keep in sync with blacken-docs
+  hooks:
+  - id: black
+- repo: https://github.com/asottile/blacken-docs
+  rev: 1.16.0
+  hooks:
+  - id: blacken-docs
+    args: [--line-length=80]
+    additional_dependencies:
+    - black==23.9.1  # keep in sync with black hook
+  # TODO: black-jupyter
+
+# Jupyter Notebooks: clean up all cell outputs
+# - repo: https://github.com/roy-ht/pre-commit-jupyter
+#   rev: v1.2.1
+#   hooks:
+#   - id: jupyter-notebook-cleanup
+#     args:
+#       - --pin-patterns
+#       - "[pin];[donotremove]"
+#       # - --remove-kernel-metadata
+
+# Checks the manifest for missing files (native support)
+- repo: https://github.com/mgedmin/check-manifest
+  rev: "0.49"
+  hooks:
+  - id: check-manifest
+    # This is a slow hook, so only run this if --hook-stage manual is passed
+    stages: [manual]
+    additional_dependencies: [cmake, ninja]
diff --git a/.zenodo.json b/.zenodo.json
@@ -25,12 +25,12 @@
             "affiliation": "Deutsches Elektronen-Synchrotron, previously LBNL",
             "name": "Th\u00e9venet, Maxence",
             "orcid": "0000-0001-7216-2277"
-        },        
+        },
         {
             "affiliation": "Argonne National Laboratory",
             "name": "Larson, Jeffrey",
             "orcid": "0000-0001-9924-2082"
-        },        
+        },
         {
             "affiliation": "Argonne National Laboratory",
             "name": "Hudson, Stephen",
@@ -40,7 +40,7 @@
             "affiliation": "Lawrence Berkeley National Laboratory",
             "name": "Huebl, Axel",
             "orcid": "0000-0003-1943-7141"
-        },        
+        },
         {
             "affiliation": "Lawrence Berkeley National Laboratory",
             "name": "Vay, Jean-Luc",

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
   </a>
 
   <h3 align="center">
-    Optimization at scale, powered by 
+    Optimization at scale, powered by
     <a href="https://libensemble.readthedocs.io/"><strong>libEnsemble</strong></a>
   </h3>
 

diff --git a/doc/make.bat b/doc/make.bat
@@ -5,7 +5,7 @@ pushd %~dp0
 REM Command file for Sphinx documentation
 
 if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
+    set SPHINXBUILD=sphinx-build
 )
 set SOURCEDIR=source
 set BUILDDIR=build
@@ -14,15 +14,15 @@ if "%1" == "" goto help
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
+    echo.
+    echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+    echo.installed, then set the SPHINXBUILD environment variable to point
+    echo.to the full path of the 'sphinx-build' executable. Alternatively you
+    echo.may add the Sphinx directory to PATH.
+    echo.
+    echo.If you don't have Sphinx installed, grab it from
+    echo.https://www.sphinx-doc.org/
+    exit /b 1
 )
 
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%

diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -1,7 +1,7 @@
+ax-platform >= 0.2.9
+libensemble >= 0.9.2
+matplotlib
+numpydoc
 pydata-sphinx-theme
 sphinx-design
 sphinx-gallery
-numpydoc
-matplotlib
-libensemble >= 0.9.2
-ax-platform >= 0.2.9
diff --git a/doc/source/_templates/autosummary/base.rst b/doc/source/_templates/autosummary/base.rst
@@ -2,4 +2,4 @@
 
 .. currentmodule:: {{ module }}
 
-.. auto{{ objtype }}:: {{ objname }}
+.. auto{{ objtype }}:: {{ objname }}
diff --git a/doc/source/_templates/autosummary/class.rst b/doc/source/_templates/autosummary/class.rst
@@ -31,4 +31,4 @@
       {% endif %}
    {%- endfor %}
    {% endif %}
-   {% endblock %}
+   {% endblock %}
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -13,17 +13,18 @@
 import os
 import sys
 from datetime import date
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Import version ----------------------------------------------------------
 from optimas import __version__  # noqa: E402
 
 
 # -- Project information -----------------------------------------------------
-project = 'optimas'
-project_copyright = '2023-%s, the optimas collaborators' % date.today().year
-author = 'The optimas collaborators'
+project = "optimas"
+project_copyright = "2023-%s, the optimas collaborators" % date.today().year
+author = "The optimas collaborators"
 
 # The full version, including alpha/beta/rc tags
 release = __version__
@@ -35,18 +36,18 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.coverage',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
     # 'sphinx.ext.intersphinx',
-    'sphinx_design',
+    "sphinx_design",
     # 'sphinx_gallery.gen_gallery',
-    'numpydoc',
+    "numpydoc",
     "matplotlib.sphinxext.plot_directive",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -59,12 +60,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'  # "sphinx_rtd_theme"
+html_theme = "pydata_sphinx_theme"  # "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Logo
 html_logo = "_static/logo.png"
@@ -87,7 +88,7 @@
     "pygment_light_style": "default",
     "pygment_dark_style": "monokai",
     "use_edit_page_button": True,
-    "navigation_depth": 2
+    "navigation_depth": 2,
 }
 
 html_context = {
@@ -98,7 +99,7 @@
 }
 
 # Do not show type hints.
-autodoc_typehints = 'none'
+autodoc_typehints = "none"
 
 # Do  not use numpydoc to generate autosummary.
 numpydoc_show_class_members = False

diff --git a/doc/source/examples/bo_basic.rst b/doc/source/examples/bo_basic.rst
@@ -10,7 +10,7 @@ Description
 This example illustrates how to run a generic Bayesian optimization with
 simulations. This typically requires:
 
-- An `optimas` script for defining and running the optimization.
+- An *optimas* script for defining and running the optimization.
 - A template simulation script.
 - A function to analyze the simulation output.
 

diff --git a/doc/source/examples/bo_multitask_fbpic_waket.rst b/doc/source/examples/bo_multitask_fbpic_waket.rst
@@ -30,9 +30,9 @@ Scripts
 Files included:
 
 - :download:`run_opt.py <../../../examples/multitask_lpa_fbpic_waket/run_opt.py>`:
-  defines and launches the optimization with `optimas`.
+  defines and launches the optimization with *optimas*.
 - :download:`template_simulation_script.py <../../../examples/multitask_lpa_fbpic_waket/template_simulation_script.py>`:
-  template used by `optimas` to generate the FBPIC and Wake-T simulation
+  template used by *optimas* to generate the FBPIC and Wake-T simulation
   scripts.
 - :download:`analysis_script.py <../../../examples/multitask_lpa_fbpic_waket/analysis_script.py>`:
   defines how the simulation data is analyzed to yield the value of the

diff --git a/doc/source/examples/ps_grid_sampling.rst b/doc/source/examples/ps_grid_sampling.rst
@@ -50,12 +50,12 @@ where :math:`l_b=0` and :math:`u_b=15`, the grid of sample looks like:
            break
    x0 = np.zeros(len(all_trials))
    x1 = np.zeros(len(all_trials))
-   
+
    for i, trial in enumerate(all_trials):
        trial_params = trial.parameters_as_dict()
        x0[i] = trial_params['x0']
        x1[i] = trial_params['x1']
-       
+
    fig, ax = plt.subplots()
    ax.scatter(x0, x1, s=3, label='generated evaluations')
    ax.set(
@@ -89,4 +89,4 @@ The example is executed by running
 
 .. literalinclude:: ../../../examples/dummy_grid_sampling/template_simulation_script.py
    :language: python
-   :caption: template_simulation_script.py (:download:`download <../../../examples/dummy_grid_sampling/template_simulation_script.py>`)
+   :caption: template_simulation_script.py (:download:`download <../../../examples/dummy_grid_sampling/template_simulation_script.py>`)
diff --git a/doc/source/examples/ps_line_sampling.rst b/doc/source/examples/ps_line_sampling.rst
@@ -53,12 +53,12 @@ where :math:`x_0` and :math:`x_1` have a default values of :math:`5` and
            break
    x0 = np.zeros(len(all_trials))
    x1 = np.zeros(len(all_trials))
-   
+
    for i, trial in enumerate(all_trials):
        trial_params = trial.parameters_as_dict()
        x0[i] = trial_params['x0']
        x1[i] = trial_params['x1']
-       
+
    fig, ax = plt.subplots()
    ax.scatter(x0, x1, s=3, label='generated evaluations')
    ax.set(
@@ -94,4 +94,4 @@ You can find both example scripts below.
 
 .. literalinclude:: ../../../examples/dummy_line_sampling/template_simulation_script.py
    :language: python
-   :caption: template_simulation_script.py (:download:`download <../../../examples/dummy_line_sampling/template_simulation_script.py>`)
+   :caption: template_simulation_script.py (:download:`download <../../../examples/dummy_line_sampling/template_simulation_script.py>`)